Patent Application
20230027270
This invention generally relates to chemoinformatics, i.e., data processing methods or systems for the retrieval, analysis, visualization, or storage of data, and specifically storage of data within molecules or chemicals.
Biology provides a robust model for molecular memory. RNA and DNA molecules are information-dense, stable over long periods of time, and energy efficient. Reading information from RNA or DNA is cumbersome using stochastic methods, for example by polymerase chain reaction (PCR) and shotgun sequencing, or by using sequential methods, for example, nanopores.
Biomolecular information systems offer many potential advantages over conventional semiconductor technologies. Researchers used DNA for long-term archival information storage. See, U.S. Pat. No. 9,384,320 (Church); Church, Gao & Kosuri, Science 337(6102), 1628 (September 2012); De Silva & Ganegoda, Biomed. Res. Int. 8072463 (2016). One advantage of molecular storage over silicon-based devices is density; DNA achieves about 214 petabytes per gram. Erlich & Zielinski, Science 355, 950-954 (2017).
The metabolome is an information-rich molecular system with diverse chemical dimensions that could be harnessed for information storage and manipulation. The metabolome has an amplified and dynamic relationship to the genome, the transcriptome, the proteome, and the environment. Kell & Oliver, Metabolomics 12(9), 148 (Sep. 2, 2016). This relationship makes the metabolome an information-rich system, with diverse chemical, structural and biological dimensions, and properties. The molecular computing art is formalizing methods for mitigating errors arising from metabolic chemical and structural diversity. Gowda & Djukovic, Methods Mol. Biol. 1198, 3{12 (2014); Matsuda, Mass Spectrom. (Tokyo) 5(2), S0052 (2016).
The molecular computing art has recently made progress in proteomic and metabolic profiling. Cox & Mann, Ann. Rev. Biochem. 80, 273-299 (2011); Nagaraj et al., Molecular Systems Biology 7(1), 548 (2011); Roumpeka et al., Front. Genet. 8, 23 (2017). Thus, it is timely to test the use of metabolites for more dynamic postgenomic information representations, and whether to make use of the higher dimensions of complexity inherent in metabolism to improve data storage in fundamental ways.
Therefore, there is a need for molecular and chemical information storage with high information density, and parallel speedy memory interrogation.
The invention provides, in the first embodiment, a method for computing with chemicals, including the steps of encoding an abstract digital data into a plurality of liquid volumes of a plurality of chemicals to obtain a dataset; translating the dataset into a chemical form; reading the data set using spectrometry, spectroscopy, or both analytical methods; querying the dataset by performing a volumetric operation to obtain a perceptron; and analyzing the perceptron for identifying chemical structure, concentration, or both characteristics, of at least one of the chemicals, thereby developing a chemical computational language.
In the second embodiment, the abstract digital data includes a binary computer language. The computer language is selected from the group consisting of programming language, command language, general-purpose language, machine language, markup language, style sheet language, configuration language, construction language, query language, modeling language and simulation language. In the third embodiment, the translating step further includes assembling a library of chemicals in the dataset.
In the fourth embodiment, the volumetric operation is performed robotically. In the fifth embodiment, the volumetric operation further includes a programmed standard volumetric transfer. In the sixth embodiment, the plurality of liquid volumes of the plurality of chemicals is a mixture of different chemical molecules. In the seventh embodiment, the abstract digital data corresponds to the presence or the absence of chemical molecules in the mixture.
In the eighth embodiment, the spectrometry is mass spectrometry. In the ninth embodiment, the spectroscopy is selected from ultraviolet-visible spectroscopy, Rydberg spectroscopy, infrared spectroscopy, fluorescence spectroscopy, and absorption spectroscopy.
The invention also provides, in the tenth embodiment, a method for molecular computing using a chemical perceptron, including the steps of preparing a plurality of distinct mixtures of molecules to obtain a chemical data set, such that the mixtures of molecules are an input unit of the perceptron; writing the data set on an array; applying an operation to the data set for transduction of the input unit; combining the input unit by an operation to obtain an operation product; and detecting a threshold of the operation product, thereby obtaining a product of the chemical perceptron.
In the eleventh embodiment, the array is a micro-well plate or a Matrix-Assisted Laser Desorption/lonization (MALDI) plate. The array is located in or is arrayed in a micro-well plate or a MALDI plate. In the twelfth embodiment, the method further includes the step of applying a chemical multiply accumulate (MAC) operation to obtain the mathematical equivalent of the perceptron. In the thirteenth embodiment, the chemical multiply accumulate operation is z=Liwi·xi+b, such that z is the output of the multiply accumulate operation, wi is the weight of a species, X is the initial amount of the species, and b is the bias.
The invention further provides, in the fourteenth embodiment, a chemical perceptron including a plurality of analytes; an array spectrum; a fluid handling robot; a computer; and a molecule quantifier or a molecule identifier.
In the fifteenth embodiment, the molecule quantifier or molecule identifier is a high performance liquid chromatography (HPLC) machine, a mass spectrometer, or both assay machines. In the sixteenth embodiment, the array spectrum is at least one selected from a micro-well plate or a MALDI plate.
The invention provides, in a seventeenth embodiment, a method for obtaining an output of a linear classification operation, including the steps of encoding binary data into a chemical composition of a plurality of liquid samples; receiving an input of binary data; performing multiplication operation by a plurality of fractional volume transfers of the liquid samples into a plurality of micro-wells corresponding to the input and pooling the liquid samples to obtain an output; and analyzing the concentration of the chemicals in the output by HPLC, thereby obtaining the output for the linear classification operation.
In the eighteenth embodiment, the method further including scaling a classifier weight corresponding to maximum available volume in each of the micro-wells. In the nineteenth embodiment, the classifier weight corresponds to amount of the plurality of fractional volume transfers of the liquid samples.
In the twentieth embodiment, the method further includes performing the plurality of fractional volume transfers by a robot (i.e., a robot performs the transfers). In the twenty-first embodiment, the liquid samples are nonreactive. In the twenty-second embodiment, the liquid samples are reactive. In the twenty-third embodiment, the method further includes performing parallel computing to obtain the output for the linear classification operation.
The invention provides, in the twenty-fourth embodiment, a method for coding information with a mixture of product molecules, including the steps of mapping of a plurality of each pixels on an array corresponding to a plurality of known organic chemical entity molecules each in a known location within the array to obtain a pixel map; reacting a selected subset of the molecules corresponding to the pixel map thereby synthesizing the mixture of product molecules; and analyzing the mixture of product molecules to identify the product molecules.
In the twenty-fifth embodiment, reacting further includes performing an Ugi reaction to obtain an Ugi product molecule or a first Ugi molecules, or at least one product molecule. In the twenty-sixth embodiment, the method further includes creating a new Ugi product molecule or a second product molecule. In the twenty-seventh embodiment, the plurality of known organic chemical entity molecules includes a chemical scaffold.
In the twenty-eighth embodiment, the plurality of known organic chemical entity molecules include reaction groups. In the twenty-ninth embodiment, the groups are selected from carboxylic acid, ester, acid chloride, amide, nitrile, aldehyde, ketone, alcohol, thiol, amine, alkene, alkyne, alkane, ether, alkyl halide, and nitro. In the twenty-ninth embodiment, reacting further includes substituting the reaction groups. In the thirtieth, the reacting step further includes changing pH of at least one of the plurality of known organic chemical entity molecules.
The invention provides, in the thirty-first embodiment, a method for computing with chemicals, including the steps of encoding digital data into a plurality of chemicals to obtain a dataset and translating the dataset into a chemical form; reading the data set using spectrometry, spectroscopy, or both assay methods; querying the dataset by performing an operation to obtain a perceptron; and analyzing the perceptron for identifying the chemical structure, concentration, or both characteristics of at least one of the chemicals, thereby developing a chemical computational language.
In the thirty-second embodiment, the operation further includes at least one of a volumetric transfer or a chemical reaction. In the thirty-third embodiment, the operation further includes measuring a rate constant, an equilibrium constant of the chemical reaction, or both characteristics. In the thirty-fourth embodiment, the chemical reaction further includes an Ugi reaction to obtain at least one Ugi product molecule.
In the thirty-fifth embodiment, the method further includes synthesizing a new chemical entity. In the thirty-sixth embodiment, digital data includes a computer language. In the thirty-seventh embodiment, the plurality of chemicals further includes a plurality of liquid volumes. In the thirty-eighth embodiment, the plurality of chemicals is a mixture of different chemical molecules.
In the thirty-ninth embodiment, the digital data includes presence or absence of chemical molecules in the mixture. In the fortieth embodiment, spectrometry includes mass spectrometry. In the forty-first embodiment, the spectroscopy method is selected from ultraviolet-visible spectroscopy, Rydberg spectroscopy, Infrared spectroscopy, fluorescence spectroscopy, and absorption spectroscopy. In the forty-second embodiment, the plurality of chemicals includes reaction groups.
In the forty-third embodiment, reacting further includes substituting the reaction groups. In certain embodiments of the method, reacting further includes changing a pH of at least one of the plurality of chemicals.
The invention provides, in a forty-fourth embodiment, for the purposeful encoding of information in a metabolome or another mixture of chemicals. The invention provides an implementation using encoded synthetic metabolome. The invention thus provides post-genomic data storage and demonstrates a workflow for representing abstract data in metabolomes, synthetic metabolomes, and molecular mixtures. The invention can use robotic liquid handling for producing chemical data mixtures and mass spectrometry for inherently parallel data readout. Also presented are several demonstrations of kilobyte-scale image data sets stored in synthetic metabolomes, recovered at >99% accuracy.
In the forty-fifth embodiment, embodiment, the invention provides an information storage system, comprising a solid surface with a plurality of addressable locations, wherein each addressable location comprises a mixture of small molecules, and each mixture contains one set of small molecules per addressable location. In the forty-sixth embodiment, the small molecules are metabolomic elements. Each mixture of small molecules may be selected from a synthetic metabolome. In the forty-seventh embodiment, the solid surface is a MALDI plate.
In the forty-eighth embodiment, the addressable locations comprise at least 1024 independent mixture spots. The inventors wrote more than 100 kbits of image data into synthetic metabolomes; this number is conservative and can be expanded. In the forty-ninth embodiment, the addressable locations comprise thousands of spatially arrayed nanoliter spots. In the fiftieth embodiment, the storage system comprises more than 100 kbits of data. In the fifty-first embodiment, the storage system comprises a gigabyte of data. Diversified small-molecule approaches have intrinsic capacities for gigabyte-scale data storage. The invention thus provides increased storage density. Increased diversity of chemical information systems has uses where sensitive information should be physically encoded, transported, and easily overwritten in small, zero-power devices.
In the fifty-second embodiment, the invention provides a method of storing information in a plurality of metabolomic elements. The steps of the method are (a) converting a format of information into a plurality of digital sequences; (b) converting the plurality of digital sequences into a plurality of corresponding metabolomic elements using one bit per metabolomic element, and (c) storing the plurality of corresponding metabolomic elements on a solid surface, where the location of a metabolomic element is an addressable location. In the fifty-third embodiment, The converting the plurality of digital sequences into a plurality of corresponding metabolomic elements Is performed using robotic liquid handling.
In the fifty-fourth embodiment, the invention provides a method of retrieving a format of information from a plurality of metabolomic elements encoding digital sequences of the format of information. The steps of the method are (a) assaying a solid surface comprising a set of metabolomic elements, where the location of a metabolomic element is an addressable location; (b) converting the metabolomic elements to digital sequences; and (c) converting the digital sequences to a format of information. Molecular information can be ‘read’ using a variety of analysis techniques including mass spectrometry, sequencing, chromatography, or spectroscopy, as in
In the fifty-seventh embodiment, retrieving a format of information from a plurality of metabolomic elements results in an information recovery at >99% accuracy. The inventors demonstrated kilobyte-scale image data sets stored in synthetic metabolomes, recovered at >99% accuracy.
In the fifty-eighth embodiment, the method has a further step of visualizing the format of information.
In the fifty-ninth embodiment, the method has a further step of mitigating errors in the converting of the metabolomic elements to digital sequences. In a sixteenth embodiment, mitigating the errors includes a logistic regression analysis.
In the sixty-first embodiment, converting the digital sequences to a format of information is performed using one m/z peak selected per metabolomic element. In the sixty-second embodiment, converting the digital sequences to a format of information is performed using multiple m/z peaks selected per metabolomic element.
In the sixty-third embodiment, the invention provides a chemical perceptron, comprising the mathematical framework described for quantifying chemical memory. In a sixty-fourth embodiment, the chemical perceptron has autocatalytic thresholding.
In one aspect, the invention provides a path to quantifying the information capacity available from the exponentially larger non-genomic chemical space.
In another aspect, the invention provides a general mathematical framework for quantifying chemical memory, which extends to mixtures of molecules of all types. The theoretical limit for molecular information storage is two orders of magnitude denser by mass than DNA memory storage.
In yet another aspect, the invention provides a general theory of information storage in molecules and in mixtures of molecules. This theory provides a unified description of mixtures of molecules, e.g., small molecules.
As a proof-of-principle of chemical data storage, the inventors chemically encoded several MNIST images of handwritten digits and demonstrate successful chemical-domain classification of the digits using volumetric perceptrons. LeCun et al., Gradient-based learning applied to document recognition. Proceedings of the IEEE, 86(11), 2278-2324 (1998). The inventors quantified the performance of the method with a larger dataset of binary vectors and compare the assay measurements against predicted results.
As a proof-of-principle of postgenomic data storage, the inventors encoded abstract binary data into the chemical composition of thousands of spatially arrayed nanoliter volumes. See, EXAMPLE 6 and
In a sixty-fifth embodiment, the invention provides a technique that enables users to store vast amounts of information in the small volumes occupied by molecules using small molecules in disordered mixtures. These small molecules are more stable to enzymatic and thermal degradation than DNA. These small molecules are also less expensive because they do not rely on synthesizing phosphodiester bonds, which are needed to stitch DNA together. This invention enables information storage in a space-efficient and energy-efficient way, which answers the growing call for small, cheaper storage technologies when the need for storage is rapidly outpacing storage capacity.
In a sixty-sixth embodiment, the invention provides a product that enables the storage of vast amounts of information in small volumes. This product is useful for health care companies and institutions, which must store large amounts of patient data, often on the premises, to store data on and within objects. This technique is useful for tracing the history of different products in the supply chain. Molecular storage is inherently much more compact than current two-dimensional (2D) digital media. Molecular storage is three-dimensional (3D), so more can be stored in a more compact space, which is important when more media are being developed that require more memory.
In another advantage, molecular storage using species already existent is much harder to destroy than magnetic storage.
In another advantage, molecular storage can be performed in vivo and in materio since the body and materials are made from molecules. One need not interface CMOS with the body or materials to store information.
In another advantage, small molecule storage can be cheaper than DNA, particularly if the libraries used for storage are pre-made out of easy-to-synthesize molecules. The invention can use any molecules if they differ stable.
An ever-increasing worldwide demand for digital data storage, alongside a looming slowdown of semiconductor technology scaling, has led to growing interest in molecular-scale platforms for information storage and computing. Molecular data systems have the potential to store information at a dramatically higher density than existing electronic media. Some of the first assay demonstrations of this idea used DNA, but nucleic acids are only one of the ways to use chemicals to preserve, process, and transmit information.
Chemical computation can be useful in ultra-low-power systems, extreme environments, and as complements to electronic computing systems. Adleman, Molecular computation of solutions to combinatorial problems, Science, 266(5187), 1021-1024 (1994). Similarly to how DNA archival data storage may complement traditional electronic media and neural-inspired computing has revolutionized how to process large datasets, chemical-domain computations may provide entirely new ways of leveraging the information processing capabilities of the natural world.
Modern information technology is moving towards a more unified vision of computation and memory, and fluid molecular mixtures offer an intriguing space for future generations of computing systems that take advantage of the natural complexity and intrinsic statistics of chemical systems. Arcadia et al., Proceedings of the IEEE Conference on Rebooting Computing (ICRC) (2018) [EXAMPLE 2]; Chen et al., Natural Computing, 13(4), 517-534 (2014); Jiang et al., IEEE Design and Test of Computers 21-31 (May/June 2012); Kennedy et al., Applied Physics Letters, 112(26), 264103 (June 2018); Rose et al., 2018 IEEE International Symposium on Information Theory (ISIT) (Vail, CO, June 2018), pp. 2236-2240 [EXAMPLE 1]; and Soloveichik et al., Proceedings of the National Academy of Sciences, U.S.A., 107(12), 5393-5398 (2010). Quantifying the information capacity of chemical mixtures is an advance in this direction.
A molecule contains enough molecular information to be a secret input to a chemical hash function. Boukis et al., Nature Communications, 9(1), 1439 (2018); Sarkar et al., Nature Communications, 7:11374 (May 2016). Two-dimensional arrays containing single compounds per grid position can encode digital data by photochemical or electrochemical means. Green et al., Nature, 445:414 (January 2007); Malinakova, Reports in Organic Chemistry, pages 75-90 (2015); Thomas et al., Proceedings of the National Academy of Sciences, U.S.A., 106(23), 9147-9150 (June 2009).
DNA sequences have previously been useful for storing abstract digital data. Church, Gao & Kosuri, Science 337(6102), 1628 (September 2012); Zhirnov et al., Nature Materials, 15:366 (March 2016). DNA can be an information carrier because of the combinatorial complexity that can exist within one molecule. Cartwright et al., Phil. Trans. Roy. Soc. of London A: M., Phys. and Eng. Sci. 374(2064) (2016). Scientists synthesized complex pools of DNA oligomers representing hundreds of megabytes of text, images, videos, and other media files and retrieved the data using commercial high-throughput sequencing instruments. Blawat et al., Procedia Computer Science, 80:1011-1022 (2016); Erlich & Zielinski, Science, 355(6328), 950-954 (March 2017); Goldman et al., Nature, 494:77, (January 2013); Grass et al., Angewandte Chemie International Edition, 54(8), 2552-2555 (February 2015); Organick et al., Nature Biotechnology, 36:242 (February 2018).
DNA memory studies often offer net bits per nucleotide (nt) as a metric for comparison but reaching 2 bits/nt is not the final goal. Demonstrations of DNA data storage exceeded 200 megabytes or 3.2 million unique ≈110-nt sequences. Organick et al., Nature Biotechnology, 36:242 (February 2018). Although this amount stretches today's synthesis capabilities, it represents a tiny fraction of the potential of molecular data storage. This is a mixture with a sparsity (S) of only one out of every 1059 molecules from the library.
The metabolome is diverse and contains many coexisting molecules that can interact and react in complex ways. Sung et al., Nature Communications 8, 15393 (2017). DNA achieves about 214 petabytes/gram, while an encoded metabolome written using a large metabolic library could theoretically improve on this number by up to two orders of magnitude. See Erlich & Zielinski, Science 355, 950-954 (2017); Rosenstein et al., Theory of information storage in molecular mixtures; EXAMPLE 6. The intuition underlying this potential is similar to that which posits that information density can be increased by expanding beyond the four canonical DNA bases. The higher degrees of chemical diversity, afforded by large metabolic libraries, can increase information capacity. While a polymer is processed serially, a metabolome is an inherently parallel system, with many energetic dimensions (each of the independent reactions having their own free energy barriers) of varying coupling. While DNA and proteins are often large molecules which exist in relatively small numbers, metabolites are smaller in mass, higher in number, and more structurally diverse.
By developing a formal theory of the information capacity of mixtures of molecules, the inventors show how information can be represented by any chemical library. For new synthetic molecular information systems, the inventors show that long polymers are neither required nor necessarily desirable to maximize total information capacity. Mixtures of molecules offer far greater potential capacity, even when the constituent molecules are polymers themselves.
In non-genomic (or “post-genomic”) chemical space, working within the assumptions that led to an estimate of 1060 drug-like small molecules (see, Bohacek et al., Medicinal Research Reviews, 16(1), 3-50 (September 1996), the selection of one 500 Da molecule could represent as much as log21060≈200 bits. To represent the same amount of information in DNA requires a molecule with a mass of 65,000 Da. Thus, there are opportunities for chemical information systems with up to two orders of magnitude lower mass than DNA, and with far greater chemical diversity.
For convenience, the meaning of some terms and phrases used in the specification, examples, and appended claims, are listed below. Unless stated otherwise or implicit from context, these terms and phrases have the meanings below. These definitions are to aid in describing embodiments and are not intended to limit the claimed invention. Unless otherwise defined, all technical and scientific terms have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. For any apparent discrepancy between the meaning of a term in the art and a definition provided in this specification, the meaning provided in this specification shall prevail.
Abstract digital data or digital data is data that is represented using the binary number system of ones (1) and zeros (0), as opposed to analog representation. Abstract digital data can correspond to real objects.
Address has the computer art-recognized meaning. An address is a location for data. Each location has an address (a unique number) assigned to it. By specifying a memory address, those skilled in the molecular computing art can access particular data. An addressable location can be a location on a solid surface containing a mixture of molecules, e.g., small molecules.
Addressable locations have the computer art-recognized meaning. An addressable location is a location whose position in a storage medium is precisely defined and can be accessed.
Array spectrum has the computer art-recognized meaning. An array spectrum is an array of entities ordered in accordance with the magnitudes of a common physical property.
Binary code has the computer art-recognized meaning. Binary code represents text, computer processor instructions, or any other data using a two-symbol system. The two-symbol system used is often “0” and “1” from the binary number system. The binary code assigns a pattern of binary digits, also known as bits, to each character, instruction, etc. In computing and telecommunications, binary codes are used for various methods of encoding data, such as character strings, into bit strings. Those methods may use fixed-width or variable-width strings. In a fixed-width binary code, each letter, digit, or other character is represented by a bit string of the same length; that bit string, interpreted as a binary number, is usually displayed in code tables in octal, decimal or hexadecimal notation. There are many character sets and many character encodings for them.
Binary computer language is a computer language written in binary code. The computer language can be selected from the group consisting of programming language, command language, general-purpose language, machine language, markup language, style sheet language, configuration language, construction language, query language, modeling language and simulation language.
Binary data has the computer art-recognized meaning. Binary data is data whose unit can take on only two possible states, traditionally labeled as 0 and 1 in accordance with the binary numeral system and Boolean algebra. Binary data occurs in many different technical and scientific fields, where it can be called by different names: bit (binary digit) in computer science, truth value in mathematical logic and related domains, binary variable in statistics.
Chemical perceptron is the implementation of a perceptron in an artificial (simulated) chemistry. A perceptron is a machine learning algorithm that helps provide classified outcomes for computing. A perceptron is the simplest system capable of learning (inspired by the functioning of a biological neuron). See, Banda et al., Online Learning in a Chemical Perceptron. Artificial Life, 19(2), 195-219, (Spring 2013); Banda et al., Journal of the Royal Society Interface, 11(93) (April 2014). A perceptron algorithm is a supervised classification because the computer is aided by the human classification of data points. See, Arcadia et al., Proceedings of the IEEE Conference on Rebooting Computing (ICRC) (2018) [EXAMPLE 2] and Rose et al., 2018 IEEE International Symposium on Information Theory (ISIT) (Vail, CO, June 2018), pp. 2236-2240 [EXAMPLE 1].
Chemical scaffold has the chemical art-recognized meaning. A chemical scaffold is a molecular core to which functional groups are attached.
Dataset is, when working with machine learning methods, a collection of instances.
Ground truth has the computer art-recognized definition. In machine learning, the term refers to the accuracy of the training set's classification for supervised learning techniques. This is used in statistical models to prove or disprove. The related term ground truthing refers to the process of gathering the proper objective (provable) data for this test. A synthetic metabolome has ground truth. A metabolome from a living organism may obtain ground truth as a result of the progress of science and the useful arts.
HPLC is high-pressure liquid chromatography. In HPLC, a liquid sample is injected into a stream of solvents. Together, the sample and solvents are forced, at high pressure, through an analytical column. Depending on the type of column and solvents, some chemicals can exit the column at different times. At the end of the column is an ultraviolet (UV) light source and a photodetector. When an appropriate wavelength is selected, the analyte can be detected by a change in absorbance as it exits the column. The absorbance is plotted over time as a chromatogram. See, Karger, Journal of Chemical Education, 74(1), 45 (1997).
In-memory computing, also known as In-memory computation, has the computational art-recognized meaning of the technique of running computer calculations entirely in computer memory, e.g., in RAM.
In-situ processing, also known as in-storage processing (ISP), has the computational art-recognized meaning of processing data where it resides.
Linear classification is the identification to which class (or group) it belongs based upon an object's characteristics, where the classification decision is based upon on the value of a linear combination of the characteristics.
Logistic regression analyses are computer art-recognized algorithms to solve a classification problem, where the algorithm involves a linear discriminant separating the classes. A classification problem occurs when independent variables are continuous, and a dependent variable is in categorical form, i.e., in classes like positive class and negative class. To check the performance of logistic regression analyses, those skilled in the computing art can use a confusion matrix (see,
MALDI mass spectroscopy is described in U.S. Pat. No. 7,084,396 (Schneider). Mass spectrometry (MS) fundamentally consists of three components: ion sources, mass analyzers, and ion detectors. The three components are interrelated; some ion sources may be better suited to a particular type of mass analyzer or analyte. Certain ion detectors are better suited to specific mass analyzers. Electrospray (ESI) and matrix-assisted laser-induced desorption (MALDI) ionization sources are widely used for organic molecules, particularly biomolecules and are generally preferred for the ionization of non-volatile organic species. ESI is widely practiced because it can be readily coupled with liquid chromatography and capillary electrophoresis for added discrimination capability. MALDI techniques are widely practiced on large molecules (e.g., proteins) that can be difficult to solubilize and volatize in ESI. The principal advantage of MALDI is the small number of charge states that arise from molecules with a multiplicity of ionizable groups.
Mass spectrometry (MS) is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. Accordingly, a mass spectrum measures the masses within a sample. Mass spectrometry is useful for broad and high-throughput metabolic screening. Zampieri et al., Current Opinion in Chem. Bio. 36, 15-23 (2017). Advances in statistical tools and databases support mass spectrometry. Brown et al., Analyst. 134(7), 1322-32 (2009); Wishart et al., Nucleic Acids Res. 4(46), 608{617 (2018).
Metabolome is all the molecules (e.g., small molecules) present in each organism, including metabolites and the products of catabolism. See, U.S. Pat. No. 7,329,489 (Kaddurah-Daouk et al.). The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. Metabolites are biologically ubiquitous, and their primary pathways and processes are highly conserved across species and historical epoch. Peregrin-Alvarez et al., Genome Biol. 10(6), R63 (2009). The whole human metabolome has ˜125,000 elements. Wishartet al., HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 4(46), 608-617 (2018). By analogy, if DNA is the ‘hard drive’ of living systems, then the surrounding molecules are the logic and RAM. DNA represents only ≈1% of the mass of a cell. The remaining 99% also confers important information.
Metabolomic element is an element (e.g., a small molecule) in a metabolome.
Microwell plate is a flat plate with multiple “wells” used as small test tubes. A microplate is a standard tool in analytical research and clinical diagnostic testing laboratories. Robots have been developed specifically to handle microplates for high-throughput assays. Ultra-low attachment (ULA) plates that support 3D cell culture are commercially available, e.g., from ThermoFisher Scientific, Waltham, Mass., USA.
Molecular computing has the computational art-recognized meaning of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies.
Molecular memory has the computational art-recognized meaning of data storage technologies that use molecular species as the data storage element, rather than e.g., circuits, magnetics, inorganic materials, or physical shapes. In a perfect molecular memory device, each individual molecule contains a bit of data, leading to massive data capacity.
Multiply accumulate (MAC) operation is a common step in computing, especially digital signal processing, that computes the product of two numbers and adds that product to an accumulator.
Nanoscale refers to having dimensions measured in nanometers (10−9 meters). Nanomolar (nM) is 10−9 mol/L (10−6 mol/m3). Nanoliter is 10−9 L.
One-hit has the computer art-recognized definition. A one-hit has a single positive bit in a digital sequence. A one-hit is useful as a basis for further molecular computing.
Parallel computing is a type of computation in which many calculations or the execution of processes are carried out simultaneously. Large problems can often be divided into smaller ones, which can then be solved at the same time.
Perceptron is a flexible and universal pattern classification structure and a key element of neural network systems that handle large data sets. See, Courbariaux et al., arXiv:1602.02830 (Mar. 17, 2016). Mathematically, a perceptron is a dot product between a real input vector x and a real weight vector w, both of dimension J, followed by a nonlinearity ø(w·x) where ø(·) is a sigmoidal, non-decreasing thresholding function with a rapid transition between two discrete levels. Accordingly, a perceptron is a binary classifier which separates inputs into two groups.
Pixel map is a video display technique applicable to devices with native fixed pixels, such as LCD monitors and plasma displays. A monitor that has been set to 1:1 pixel mapping displays an input source without scaling it, such that each pixel received is mapped to a single native pixel on the monitor.
Reaction groups or functional groups has the chemical art-recognized meaning. Reaction groups are specific substituents or moieties within molecules that are responsible for characteristic chemical reactions of those molecules. The same functional group undergoes the same or similar chemical reaction regardless of the size of the molecule of which it is a part.
Small molecule has the biological art-recognized definition. The NCI Dictionary of Cancer Terms defines a small molecule as A substance that can enter cells easily because it has a low molecular weight. Inside the cells, it can affect other molecules, such as proteins. This characteristic is different from drugs that have a large molecular weight, such as monoclonal antibodies, which cannot get inside cells very easily.
Spectrometry is an instrumental method for identifying the chemical constitution of a substance by means of the separation of gaseous ions according to their differing mass and charge.
Spectroscopy is the branch of science concerned with the investigation and measurement of spectra produced when matter interacts with or emits electromagnetic radiation. The term spectroscopy includes ultraviolet-visible spectroscopy, Rydberg spectroscopy, Infrared spectroscopy, fluorescence spectroscopy, and absorption spectroscopy.
Zettabyte is 1021 bytes. See, Cisco, The Zettabyte Era: Trends and Analysis (2016).
The invention provides a method of computing using chemical manipulations to store and process abstract digital information. The invention provides methods for chemical encoding, computational processing and readout. The invention provides a method for encoding binary data into the chemical composition of liquid samples. The invention provides a method for storing multiple datasets in parallel by multiple co-existing chemicals. The inventors used programmable robotic liquid handling sequences to perform volumetric multiply accumulate (MAC) operations on parallelized chemical datasets. The inventors used high-performance liquid chromatography (HPLC) to read and verify the results of the chemical MAC calculations. Several images of handwritten digits from the MNIST database (LeCun et al., Proceedings of the IEEE, 86(11), 2278-2324 (1998)) were chemically encoded and successfully implemented on several single layer volumetric chemical perceptrons to classify the images. The inventors quantified the performance of the methods with a larger dataset of binary vectors. The inventors demonstrate herein the accurate linear classification of several MNIST images and Boolean data vectors.
A perceptron is a simple linear classifier which can be trained to determine whether or not an input belongs to a certain class. Rosenblatt, Psychological Review, 65(6), 386 (1958); Minsky et al., Perceptrons: An Introduction to Computational Geometry (MIT Press, 2017); Bishop, Pattern Recognition and Machine Learning (Springer, 2006). A perceptron uses a set of constant coefficients to compute a weighted sum of input features and thresholds the result to produce a Boolean label. The computation can be written as:
where N is the number of input features (e.g., pixels in an image or dimensions of a vector), xi and wi are the ith feature and its corresponding weight, and b is a scalar bias. When the bias is nonzero, it is common to fold b into w by introducing an additional input feature whose value is always 1. The summation result z determines the class label, l, of the input according to the following threshold:
For a linearly separable dataset, the training for a perceptron is guaranteed to converge such that a set of weight values is found that correctly classify all training points. While a perceptron is a simple classifier, it can be used as a building block for larger discriminative models, such as multilayer perceptrons [Gibson & Cowan, Proceedings of the IEEE, 78(10), 1590-1594, (1990)] and support vector machines [Fu et al., IEEE Transactions on Neural Networks, 21(12), 1963-1975, 2010] that can realize more complicated decision boundaries.
A perceptron can be designed to classify an MNIST handwritten digit image into one of two groups such as “zero” vs. “not a zero.” LeCun et al., Proceedings of the IEEE, 86(11), 2278-2324 (1998). By controlling the values of the weights, one can change the classification operation. One advantage of using perceptron-based computation is that the weights can be flexibly designed; another advantage is that the computations are error tolerant. For instance, the precision of the weights can be flexibly set in floating point, fixed point, or even binary (−1|1 or 0|1), but nevertheless, the classification outcome can still be accurate because the training process can compensate for the reduction in precision and “heal” the perceptron. See, Rastegari et al., CoRR, abs/1603.05279 (2016); Courbariaux et al., arXiv:1602.02830 (Mar. 17, 2016); Lin et al., CoRR, abs/1510.03009 (2015); Gupta et al., CoRR, abs/1502.02551 (2015). Such flexibility and error tolerance are useful given the underlying discrete nature of the input-coding disclosed here and the stochastic nature of chemical reactions.
A person of ordinary skill in the computational art can use these materials and methods as guidance to predictable results when making and using the invention:
Materials and reagents. The solvent dimethyl sulfoxide (DMSO, anhydrous, ≥99.9%, MilliporeSigma) was used to prepare all solutions in the library and data plates. Analytical grade α-cyano-4-hydroxycinnamic acid (HCCA, ≥99.0%, MilliporeSigma) was used as the matrix material for all MALDI samples. The library of 1500 Ugi products was constructed with the following five amines: benzylamine, 4-methylbenzylamine, p-methoxybenzylamine, 4-chlorobenzylamine, 4-tertbutylbenzylamine; five aldehydes: cyclohexanecarboxaldehyde, 3-cyclohexylpropanal, valeradlehyde, isovaleraldehyde, cyclopentanecarboxaldehyde; 12 carboxylic acids: Boc-glycine, Boc-proline, Boc-N-methyl-L-valine, Boc-L-asparagine, Boc-L-beta-homoleucine, Boc-L-methionine, Boc-L-beta-homoglutamine, Boc-L-betahomo-methionine, Boc-L-phenylalanine, Boc-N-alpha-N-epsilon-formyl-L-lysine, Boc-N-methyl-L-phenylalanine, Boc-O-methyl-L-tyrosine; and five isocyanides: cyclohexyl isocyanide, ethyl isocyanoacetate, benzyl isocyanide, 2-naphthyl isocyanide, methyl isocyanoacetate. These compounds were obtained at synthesis grade or higher and used as received from their vendors (Chem-Impex for the carboxylic acids and MilliporeSigma for the others).
Library preparation (I). Each reagent can be dissolved in dimethyl sulfoxide to a concentration of 500 mM and placed into a 384-well plate. Using an acoustic fluid handler, one dispenses the reagents, 200 nL per inclusion, into a 1536-well plate to enumerate all possible four-component Ugi reactions. The array of reagent mixtures was left to react at room temperature for one-two days. After reacting, dimethyl sulfoxide was added to each library well to reach a final volume of 4 μL.
Chemical library preparation (II). Reagent grade samples of thirty-six distinct metabolic compounds were diluted in dimethyl sulfoxide (anhydrous), each to a nominal concentration of 25 mM. Some metabolites were initially dissolved in an alternative solvent (deionized water with or without 0.5M or 1M hydrochloric acid) to facilitate solvation in dimethyl sulfoxide. 10 μL of each compound was aliquoted into a 384-well microplate (Labcyte 384LDV).
Ugi product library synthesis (Ill). To make a library, the reagents are manually prepared as 500 mM solutions in dimethyl sulfoxide and 60 μL of each is pipetted into a 384-well plate. To level the fluid menisci, one spins the plate in a centrifuge for five minutes at 2,500 rpm. The reagent plate is then placed into an Echo 550 acoustic liquid dispenser, surveyed to check volume levels, and finally used to prepare the reaction wells according to a pre-generated list of transfers. The reagents are added by class, in the following order: amines, aldehydes, carboxylic acids, and lastly isocyanides. The resulting reaction wells, filled with 200 nL of each reagent solution (800 nL in total), are left to react. After an incubation period of about 24-48 hours, dimethyl sulfoxide solvent is added to bring the final product volumes to 4 μL. The inventors generally use these library elements for data storage without further purification. Over the course of this EXAMPLE, the inventors ran over 10,000 Ugi reactions, up to 1,500 at a time.
Library validation. To identify successful reactions, a small volume (20 nL) from each library well was spotted to a unique location on a stainless steel plate (78 mm×120 mm) along with matrix (20 nL of 176.2 mM α-cyano-4-hydroxycinnamic acid in dimethyl sulfoxide). The plated samples were allowed to dry overnight (˜10 h) into round crystals (˜800 μm in diameter), before analysis via mass spectrometry. In the resulting mass spectra, one looks for peaks corresponding to expected Ugi product masses and used peak height as a coarse measure of reaction yield. Since the Ugi products have similar ionization profiles, the inventors performed a global statistical analysis of the library spectra, using the SNR of their sodiated peaks. A common threshold (τ) was found using receiver operator characteristic (ROC) curve analysis. To construct the ROC curve, one looks for the sodiated product peaks across all reaction wells, applies a given SNR threshold to assess the presence or absence of these peaks, tallies detected library peaks to estimate the true positive (TPR) and false positive (FPR) rates, and repeat this process for all candidate thresholds. Because there should be exactly one product per well, if the expected product is detected, the product is counted as a true positive (TP), and if not, then it is marked as a false negative (FN). Similarly, if other products are detected in the well, they are counted as false positives (FP) and otherwise as true negatives (TN). The products with masses that overlap with that of the expected product are counted as TPs or FNs. Error rates can be calculated as TPR=TP/(TP+FN) and FPR=FP/(FP+TN), and used to find an optimal SNR threshold, by minimizing the distance to the (0,1)-corner: [(0-FPR(SNR))2+(1-TPR(SNR))2]1/2. The Ugi products whose SNR exceeds this threshold (SNR≥τ) are declared present.
Library subset selection. The data storage examples described have all used a subset of the compound library, due in large part to the limited write speed. To select a subset, one begins with the list of library products having confirmed M+Na peaks. In the example below, 90% (1346=1500) were detected. One then sorts these compounds by sodiated peak intensity. Starting from the strongest peak, one includes each successive compound when its monoisotopic mass has a distance of at least 0.008 Da from any previously selected compounds. For an exemplary thirty-two products, the average mass separation was 3.970 Da and the average SNR was approximately 10,000. The inventors note that by using multi-peak detection, one can distinguish library elements with overlapping monoisotopic masses.
Data plate preparation. First, a digital file is converted into a one-dimensional binary vector. This vector is then encoded, either with a direct or sparse mapping, into an M×N compound-presence matrix, where M is the number of compounds to be used, and N is the number of independent mixtures to be made. The value of element pmn in this matrix indicates the presence (“1”) or absence (“0”) of the mth compound in the nth mixture. To physically generate the mixtures, 2.5 nL droplets are transferred from the 1536-well library plate to their appropriate locations on a MALDI plate. Finally, 30 nL of matrix solution (176.2 mM α-cyano-4-hydroxycinnamic acid in dimethyl sulfoxide) is added to each data mixture spot. The overall time to write a data plate ranged from 0.3 to 7.9 hours, varying with the encoding scheme and file size. Once all transfers are complete, the data plate is left to dry in a fume hood overnight or a vacuum chamber for about two hours. The resulting dried mixture spots are typically 1 mm in diameter. Currently, the number of compounds that can be included in each mixture is limited by the layout of samples on a MALDI plate. For a 1536-well grid, spots can contain up to 200 nL of solution before they begin to merge with adjacent samples. For more complex samples, mixing would have to be done in an intermediate well plate.
Data plate analysis. During plate preparation, the matrix solution is spiked with a reference Ugi molecule which is used to calibrate for small offsets in the recorded masses. After offset calibration, raw mass spectra are resampled to a common m/z grid to construct a single analysis-ready matrix containing the mass spectra of all spots on a plate. For single peak detection, the sodiated adduct intensities for a product are simply one row in the spectral matrix, and this vector can be thresholded to determine, which mixtures contain the compound. The detection threshold for each compound was found using ROC analysis of labeled training data, as previously described for library validation. Recovering the data file from the presence matrix depends on the encoding method. For direct mapping, the matrix is simply reshaped to obtain the stored data. For sparse mappings, each matrix row was matched to the nearest valid key and converted to the corresponding binary data value.
For multi-peak detection, a similar procedure was followed, except that the presence matrix was found by applying a regression model trained to identify each compound based on multiple spectral features. To reduce computational overhead, instead of building the models on the entire mass spectra matrix, masses whose average intensities were close to the noise floor were discarded, reducing the feature space to <1% of its original size, from four million initial points to at most 20,000 candidate masses. For logistic regression, these features were further refined based on AUROC scores. This additional filtering was not needed for random forest regression since it automatically performs feature selection. The Python library Scikit-learn5l was used to construct a regression model for each compound. Logistic regressions were configured to use 64 spectral peaks, while random forest regressions were configured to use 300 trees of unlimited depth and at most 20,000 spectral features. The regression models used a 30/70 train/test split.
Synthesis; Multicomponent Reactions: Data encoded in molecules produced via Ugi reactions are high-yielding, combinatorial, soluble in reaction solvents (acetonitrile, methanol; water), with yield stable, nonpolar products, readily characterized by NMR and mass spectrometry, and amenable to tandem reactions, like peptides.
Data storage. To write a dataset, compounds from a library plate are used to create mixtures corresponding to the data to be stored, by dispensing droplets with an acoustic liquid handler. The time required to write a dataset depends on the several factors, including the size of the data, the encoding scheme, the rate of droplet dispensing, and the time that the liquid handler takes to move between library wells.
Long-term storage. Usually, one measures data plates within two weeks of writing them. However, the datasets are stable for much longer than that. One of the earliest data plates (Ibex, see
Temperature. The melting points of the matrix and encoding compounds represent a limit to the temperature a data plate can be exposed to before crystal integrity becomes compromised. The matrix (α-cyano-4-hydroxycinnamic acid) melting point is 252° C. The Ugi products are highly stable, due to their peptide-like amide bonds and are reported to have melting points around 200° C. Simulations using OCHEM models predict the average melting and boiling points of the synthesized Ugi library to be around 113° C. and 810° C., respectively.
Humidity. Because both α-cyano-4-hydroxycinnamic acid and the Ugi products are soluble and stable in water, individual spots should take on water for a short period without affecting the data they store, though the samples should be dried before reading. The amide bonds in the Ugi products will slowly degrade by hydrolysis over time. This process can be drastically accelerated in the presence of certain enzymes. Keeping the samples in a dry and sterile environment is recommended.
Light and radiation. The Ugi products, specifically their amide bonds, are to some extent susceptible to dissociation under UV and X-ray radiation and should be stored in a dark or LED lit room, without direct sunlight.
Mass spectrometry. Mass spectra were acquired with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer in positive ion mode. Samples were crystallized in matrix, using an ˜100:1 ratio of matrix to Ugi product. Samples were ionized using matrix-assisted laser desorption ionization (MALDI). Spectra produced by FT-ICR are particularly high resolution, often reaching peak widths of 0.001 Da or smaller. To ensure the accuracy of peak assignment, a mass calibration is performed before each run using sodium trifluoroacetate as a reference. One typically acquires spectra for 1.5 seconds, which results in a resolving power of 1.3×105 at 600 Da. The instrument serially addresses each crystallized spot and takes about four hours to record all 1,536 spots on a plate. Each measurement is made by ionizing a portion of a sample with a laser configured to take 500 shots at 1000 Hz, over a scan area of 500-900 μm, with medium focus, and ×4 averaging. One converts the raw data files from the instrument into a custom HDF5 file, for more efficient querying and ease of access. To normalize signals across measurements, the inventors often convert the raw intensity values of a spectrum to signal-to-noise ratios (SNR) according to the following shift-and-scale relation: SNR=(I−μ)/σ, where I is an intensity and μ and σ are the mean and standard deviation of the spectrum's background.
One can assume molecule identification via mass spectrometry, a widespread and powerful analytical technique in which molecules are ionized and accelerated in an electromagnetic field, reaching speeds which depend on their masses. Typically, an instrument produces a “mass spectrum” identifying the abundance of molecules across a range of measured mass-to-charge ratios. Several types of mass spectrometers exist, with different tradeoffs between resolution, speed, and complexity. Analyzing a solution with exactly one pure Ugi product, one expects to see several identifiable peaks in the mass spectrum, corresponding to atomic isotopes and adducts of sodium ions present in the solution. The base mass of the Ugi molecule is approximately equal to the sum of the masses of its four reactants, and the multiple peaks appear at consistent offsets from this base mass, though their relative amplitudes may vary. For simplicity, each molecule has two isotopes and two possible adducts, allocated in a random fraction. Each peak appears with a finite width determined by the resolution of the instrument, having a standard deviation between 1 to 0.001 m/z. The total detected peak heights vary with chemical preparation and ionization yield, and for these purposes one assumes a log normal distribution.
1H NMR spectroscopy is a technique that probes hydrogen electron distributions. The inventors used this technique to predict chemical shifts and splittings using counter-propagation neural networks. MAE=0.25 ppm. This technique takes minutes to run, usually entirely online when rescripted to run on clusters. See Aires-de-Sousa, Hemmer, & Gastinger, Anal. Chem., 74(1), 80-90 (2002).
Infrared (IR) spectroscopy is a technique that probes molecules' vibrations, the characteristic infrared stretch frequencies in organic molecules. The inventors used this technique and modeled Using B3LYP/6-31G* Basis. Geometries were taken from RDKit, relaxed, and rescaled based upon fitting to the known dataset. The time used for this technique is measured in hours. See Werner et al., Molpro. WIRES Comput. Mol. Sci. (March/April 2012).
Mass spectrometry. Spectrum acquisition. To analyze the chemical makeup of many samples per day, one can use a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer with matrix assisted laser desorption ionization (MALDI). During a measurement, a small fraction of each spot's material is re-moved by a laser, and ions are excited into orbit in a high vacuum and a strong magnetic field. The orbital frequencies are a function of the mass and charge of each ion. The mass-to-charge ratio (m/z) of the ions can be found by taking the Fourier transform of the detected time-domain signal. Because the ions can be kept in orbit for several seconds, corresponding to millions of orbital cycles, FT-ICR mass spectra have exceptionally high resolution, often reaching peak widths of 0.001 Da or less. One typically acquires spectra for 1.5 seconds which results in a resolving power of 1.3×105 near 600 Da.
FT-ICR mass spectrometry. Fourier-Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometer for detection, determines mass based upon Lorentz's Law: F=qv x B. Mass resolution: 106. Mass range: 100-10000 Da. Loading: 106 to 107 charges. Minimum number of ions for detection: ˜100. ˜104 to 105 compounds per loading. See, e.g., Bruker Daltonics SolariX XR 7T FT-ICR.
Mass calibration. To ensure the mapping from cyclotron frequency to mass-to-charge ratio is done as accurately as possible, the mass spectrometer is calibrated with a sample having several known masses across the measurable range of 150-3000 Da. One can perform this calibration before each MALDI plate measurement, using a solution of sodium trifluoroacetate (NaTFA): 0.05 g L−1 NaTFA dissolved in a 1:1 water:methanol mixture. The solution is injected into the instrument via electrospray ionization (ESI) and peaks are observed across the spectra which correspond to Nax(CF3CO2)y. The measured positions of these peaks are then adjusted to their known values with a quadratic model, as are the rest of the m/z values.
Additionally, a small offset calibration is performed within each spectrum using a common known mass. One can spike the α-cyano-4-hydroxycinnamic acid matrix solution with a manually purified Ugi product (F13) at a concentration of about 8 mM. This peak, commonly referred to as a mass lock, appears in all measured spectra, and is used to correct for fine offsets in each measured spectra ±0.01 Da or less.
Repeated reads. Each read from a MALDI spot removes a portion of the original sample. To quantify how a spot degrades
after repeated measurement, one can perform a series of spot burnout tests at various laser powers. The Ugi product (purified H6) and matrix concentrations in these samples were 1.56 mM and 88 mM, respectively. Each measurement was performed with 500 shots of the laser which was at medium focus and set to fire at 1000 Hz, while the scan region width was set to 500 μm. For most of the tested laser powers, the product could still be detected after 100 repeated reads.
Using the burned out region, one can estimate the amount of matrix material ionized per spectral recording. From the Anubis data plate (see
Parametric sweeps. There are numerous experimental parameters that can be adjusted in these MALDI mass spectrometry measurements, such as acquisition duration and mass range, laser settings (power, diameter, frequency, shot count), scan settings (walk type, width, grid increment), and spot composition (sample and matrix concentrations, masses, spot size). Some of the tests were done to select key parameters are shown here. Fortunately, the Ugi products in our library tend to respond similarly, and most of these parameters can be kept constant once a satisfactory configuration is found. However, to account for run-to-run and plate-to-plate variability, and to ensure high signal-to-noise ratios, a few parameters, such as laser shot count and power, are often manually tuned before measuring an entire plate, by selecting a single spot on the plate and tuning its total ion current (TIC) to the 108-109 range. If the TIC is made much higher than this, spectra begin to degrade due to increased ion-ion interactions.
Data mixture preparation. The chemical data mixtures were prepared on a 76×120 mm2 stainless steel MALDI plate. An acoustic liquid handler (Labcyte Echo 550) was used to transfer the compounds from the library well-plate onto the MALDI plate. The nominal droplet transfer volume is 2.5 nL, but to reduce variability, one can use two droplets (5 nL) per compound. The destinations of the droplets are programmed to match a standard 2.25 mm pitch 1536-spot (32×48) target.
After spotting the compounds to the MALDI plate, a MALDI matrix material was added to each location. The inventors selected 9-aminoacridine for its compatibility with metabolite libraries, its low background in the small molecule regime, and its support for both positive and negative ion modes. The MALDI plate is left to dry and crystallize overnight (˜10 hours). After being dried, the plate can be stored in a humidity controlled cabinet or analyzed by MALDI-FT-ICR mass spectrometry.
Mass analysis of data plates. A Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer (SolariX 7T, Bruker) was used to analyze the crystallized metabolite data mixtures. The exact resolution is a function of the measurement time allocated per spectrum. For these assays, one can use 0.5−1 sec, for a resolution of <0.001 Da. The instrument is run in MALDI mode and is configured to serially measure the mass spectrum of each mixture on the 48×32 grid. Acquisition for a full plate takes less than two hours.
To read the encoded data from the mass spectra, one models the probability of a metabolite being present as a combination of multiple predictor masses. A multinomial logistic regression considers the natural exponent of an offset plus the sum of all identifying mass signal-to-noise ratios (SNRs), where each signal-to-noise ratio is multiplied by a trained weight coefficient. A limited-memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm was used to predict the logistic accuracy scores given an input of the n best peaks per metabolite. The inventors iterated this process for all metabolome constituents.
Encoding data in chemical mixtures. To carry out computation in the chemical mixture domain, one first creates a representation for the data. Because chemically expressed data is stored in microwell plates, one maps each well position to one bit in the input data. The value of the data at a given position is represented by a high concentration (‘1’) or low concentration (‘0’) of a designated chemical. This strategy can be extended to multi-bit concentration coding schemes, with the trade-off of reduced noise margin. To enable parallel data storage and processing, one uses the diversity of chemical compounds and overlay (concurrently encode) features from multiple input datasets in the same set of microplate wells. One can take many binary images and realize all pixels with the same position in a single well, by assigning a unique chemical species to each image.
Method for chemical computing. A high-level summary of the proposed computation scheme is shown in
Liquid-phase robotic synthesis. Robotics enables scaling with minimal labor by performing multicomponent reactions in wells and using robotics to form desired mixtures, e.g., Labcyte Echo Liquid Handling System with a 384-well plate.
Software, modeling tools, and comparisons. Molecular systems with many components have undesired or unintended cross-reactivity among the reactants, which introduces noise into the results. One can perform comprehensive simulations and assays to identify feasible cascades of basic reactions, accounting for cross-reactivity. The inventors develop “Molecular Simulation Link”—or “MolLink”—a software tool that compiles the different computational reactions into building blocks that can be combined to build robust larger computations. The tool automates the selection of appropriate reactions for target functions and algorithms; optimize the reagents to minimize cross-reactions; and minimize the number of steps required to achieve the target results. It also performs simulation and validation and provide visualization functions.
Computer-aided design (CAD) software can optimize synthesis, select optimal chemical encodings of datasets, and automate statistical data recovery from multi-dimensional datasets.
Data and metadata standards. Molecular data can be maintained in standard formats including those specified in METLIN Gen2. This data can be managed as Unix files and in SQL databases. The contextual details needed to make the data meaningful are visualizations and graphs. Graphs can be made using the “Matplotlib” python package. 3D visualizations of molecular interactions can be created using the package “3dMol.js.” When graphs are presented on the website, links can be provided for the raw plotting commands, as wells as for downloading the underlying data.
The following Examples are provided to illustrate the invention and should not be considered to limit its scope in any way.
Computing with Chemicals: Perceptrons Using Mixtures of Small Molecules
Introduction and summary. Computation that can use the Avogadrian numbers of molecules in heterogeneous solutions, and the even larger number of potential interactions among these molecules, is useful and beneficial. In principle, molecules can be used for realizing levels of parallelism orders of magnitude beyond what is achievable in silica, while requiring substantially less energy. See, Frank. IEEE Spectrum, 54(9), 32-37 (September 2017). However, the lack of precise specificity and control of chemical interactions has previously made computation that can use the Avogadrian numbers of molecules in heterogeneous solutions very difficult or impossible. Molecules in solution can react in a stochastic fashion because of diffusion, which depends both upon ambient conditions and also upon what other molecules and reagents are present. This inherent stochasticity has made chemistry a challenging field, but also makes chemical computation useful and beneficial. For more information, see Rose et al., 2018 IEEE International Symposium on Information Theory (ISIT) (Vail, CO, June 2018), pp. 2236-2240, which is incorporated by reference.
This EXAMPLE 1 provides computational systems that perform classification and signal processing on massive data sets by using the inherent parallelism of solution phase chemical reactions. The target architecture is the perceptron, which is a flexible and universal pattern classification structure and a key element of neural network systems that handle large data sets. See, Courbariaux et al., arXiv:1602.02830 (Mar. 17, 2016). In this EXAMPLE 1, the perceptron is a single multiply accumulate primitive followed by a nonlinearity, as shown in
This EXAMPLE 1 demonstrates how relatively simple chemistry can produce a ubiquitous computational primitive (the multiply accumulate (MAC) operation) that supports a single layer neural network called a perceptron. This perceptron is produced using distinct chemical mixtures whose inclusion/exclusion in a pool is controlled by a binary input vector, applying different reagents/processes to the pooled inputs, and reading the result through simple indicators such acidity, alkalinity, or fluorescence emission. Using distinct mixtures as inputs and different reagents as operations, this EXAMPLE 1 shows how to produce the perceptron MAC operation and read out the result using simple indicators such as pH or fluorescence. With a moderately large chemical library, the number of potential inputs can be Avogadrian, so that reagent addition implicitly performs a concomitantly large number of MAC operations in parallel. Because implementations may be noisy, due to stochastic reactions or weight quantization errors, this EXAMPLE derives a signal-to-noise-like figure of merit to predict expected perceptron performance under a weight uncertainty.
This EXAMPLE 1 first reviews perceptron structure. This EXAMPLE 1 then briefly describes the small molecules upon which the scheme is built. Based upon the presence or absence of small molecule mixtures as inputs, this EXAMPLE 1 next describes how, for a given desired perceptron weight set, mixture compositions can be found so their collective interaction with different reagents produces the desired perceptrons and the desired indicator outputs.
This EXAMPLE 1 shows how to implement chemical perceptrons using small molecules composed of reactive groups (R-groups), and reagents which act differentially (but without impractical exquisite specificity) upon them. Given multiple reagents with differing R-group reactivity, the inventors can realize multiple independent perceptrons (one per reagent) assuming there are no more reagents than R-groups. This EXAMPLE 1 has also characterized the effects weight quantization error and reaction uncertainty to perceptron performance by deriving a signal-to-noise-like figure of merit. From the quantization perspective, high fidelity representation of given perceptrons seems possible. To determine whether similarly high fidelity representation is possible under reaction uncertainty, work must be done to identify chemical systems and characterize their associated Γ and/or Γ and KΓ. Data for Γ can likely be gathered from the literature, but chemical system characteristics such as Γ and KΓ rarely are studied or reported. Chemical training (see, Banda et al., Artificial Life, 19(2), 195-219 (Spring 2013); Banda et al., Journal of the Royal Society Interface, 11(93), (April 2014)) and layering into larger networks are the subjects of ongoing work.
The number of possible inputs to the perceptron is combinatorically large. The ongoing Ugi synthesis work (see EXAMPLE 3 below) produces a library of about 3×104 different molecules, implying 230000-1 non-empty mixtures. The number of simultaneous multiply accumulate (MAC) operations (inputs×weights to produce an indicator product) implemented by reagent addition can also be extremely large, even after selecting only for mixtures which implement a set of weights. Because small molecules are used and operation relies upon the natural promiscuity of liquid phase chemical reactions, the physical size of these perceptrons is limited only by the amount of indicator product that can be reliably detected.
Larger libraries (2×106) are possible. Tan et al., Journal of the American Chemical Society, 120(33), 8565-8566 (1998). The number of simultaneous multiply accumulate (MAC) operations (inputs×weights to produce an indicator product) implemented by reagent addition can also be extremely large even after selecting only for mixtures which implement a given set of weights.
Perceptrons through differential reactivity. Concept overview. De novo design of exquisitely specific reactions that can select for (each of) one and only one molecule has remained an outstanding challenge for synthetic chemistry. Until now, selecting individual molecules from a mixture to react without affecting other molecules has been untenable, meaning that mapping individual molecules to inputs in the perceptron model has been untenable.
Instead of using the presence or absence of distinct molecules as perceptron inputs, this EXAMPLE 1 uses distinct mixtures of molecules as units of input, then combine these mixtures as dictated by the binary input vector x, resulting in a mixture of mixtures (a pool). The inventors then apply a reagent or process to the pool to perform the multiply accumulate (MAC) operations. Next, the inventors follow with a threshold detection of a detectable reaction product to produce the perceptron output.
The individual molecules comprise different “R-groups,” which are molecular species with different chemical properties that can be attached to some chemical backbone. The number of R-groups comprising a molecule is some fixed K. While the chemistry may allow for multiple copies of the same R-group per molecule, the inventors make some restrictions, so a R-group can appear only once per molecule. The multiplicity of potential R-groups and the size of K means that the number of different molecules is combinatorial and thus can be very large.
A specific reagent interacts differently with different R-group types. When a reagent Gi reacts with R-group n and replaces
n with a different detectable R-group (that may be a fluorophore or have a different acidity, polarity, or charge) with a given yield. Then, Gi is also assumed to affect other R-groups with varying degrees of specificity/affinity. When one assumes that the reagent is plentiful and accessible to all molecules in a mixture given sufficient mixing and/or diffusion, then one can define an operator Gi (⋅) where Gi (
n)=γin∈[0, 1] is the equilibrium proportion of R-group
n replaced by indicator Ti under application of reagent Gi. Given N different R-groups, any given reagent Gi has an associated R-group replacement “equilibrium/yield vector” γi defined as:
When the skilled artisan could design a reagent Gi that would react only with R-group n, always replacing it completely by Ti, then γi=en, then the canonical unit vector is
N. However, the lack of precise ligand/receptor specificity between R-groups and reagents makes such a scenario unlikely. So, the replacement vector associated with reagent Gi contains an assortment of non-negative numbers between zero and one. γ might be stochastic (with known statistics). γ is defined by assuming that all the related reactions achieved equilibrium. While γ varies with time as reactions proceed, one need only consider final γ values in this EXAMPLE 1.
When molecules {μm}, comprise K R-groups at m1,
m2, . . .
mK, each molecule μm is represented as an integer N-vector where nonzero entries in position l Indicates the number of
contained in μm. For molecules constructed of K R-groups, one must have
μm
1=K, but the structure of μm may be further constrained depending upon how molecules are constructed. For instance, perhaps a given R-group can appear only once per molecule so that μm is always a binary vector. Further, one might also have K distinct classes of R-groups where each class may be represented only once.
Reagent-Rich Reactions. One can assume throughout that reagent is plentiful relative reaction targets (R-groups). This assumption allows us to effectively decouple competition between R-groups for reagent. One can consider the reactions between R-groups A and Band reagent G, developing an approach to realizing perceptrons (and thence more complex neural networks) which does not depend on carefully matched ligand/receptor chemistry is desirable. Thus, instead of using the presence or absence of distinct molecules as perceptron inputs, the inventors use distinct mixtures of molecules as units of input and combine these mixtures as dictated by the binary input vector x resulting in a mixture of mixtures the inventors call a pool. The inventors then apply some reagent (or process) to the pool to perform the necessary multiply-accumulate operations and follow with threshold detection of a detectable reaction product to produce the perceptron output.
To demonstrate, consider the reactions between R-groups A and B and reagent G. See:
where the forward and backward reaction rates are specified above and below the =, respectively.
A “master equation” such as [Equation 1] implies a Markov chain with states A+G and X and the equilibrium yield value γx is the steady state probability of being in state X. For such two state Markov chains, one therefore has:
Owing to competition for reagent between A and B, the equilibrium constants for [Equation 5] can differ from the γx and γy obtained in isolated reactions. Such equilibrium yield constant coupling (or “interference”) would complicate the design problem owing to the combinatorial multiplicity of competing reactions which must be characterized.
So, consider the Markov chain of
{dot over (√)}=AΠ [Equation 6]
where Π is the 4-vector state probabilities and A is:
The steady state probability vector II* is then:
However, for large K, as befits a reagent-rich assumption, one has
One can then find:
The Mathematics of Mixture Composition. In this EXAMPLE 1, one assumes the entries are non-negative integers that sum to K. If reagent-rich R-group reactions are effectively independent, then consider molecules, {μm}, composed of L R-groups m1,
m2, . . .
mL. The inventors represent each molecule ∪m as an integer R-vector where nonzero entries in position r indicate the number of
r| contained in ∪m. For molecules constructed of L R-groups, one must have ∥μm∥1=L, but the structure of μm may be further constrained depending upon how molecules are constructed. For instance, perhaps a given R-group can appear only once per molecule so that μm is always a binary vector. Further, one might also have L distinct classes of R-groups where each class may be represented only once. However, for now assume the entries are non-negative integers that sum to L.
An N×M molecule matrix, ∪, is:
∪=[μ1,μ2, . . . μM] [Equation 1] [Equation 13],
which contains the “universe” of M distinguishable molecules, m1, . . . , mM.
Each component of a particular group of molecular mixtures, {Mj}, j=1, . . . , J, can be defined by a binary M-vector θj whose components are 0|1, corresponding to which molecules are absent|present in Mj (at presumed unit concentration). A matrix θ, each column of which specifies the molecules that comprise input j, can be defined as:
Θ=[θ1,θ2, . . . ,θJ] [Equation 2] [Equation 14],
where J≤2M is the number of inputs to the perceptron. Mixture j is present in the pool when perceptron input xj=1 and is not present when xj=0. Because M can be very large (libraries as large as 2×106 have been built in other contexts), the number of distinct mixtures (and therefore, potential inputs) is essentially limitless.
Because reagents act on R-groups, one obtains the results of reagent application by translating Θ into a corresponding collection of R-group mixtures, {rj}, upon whose components the γin can operate. The inventors define the N×J matrix as:
=∪Θ [Equation 3] [Equation 15],
Note that
=[r1, . . . θJ], and
where the integer rjn indicates the number of n's in mixture j. Because the action of reagent Gi on molecule μm is γiiTμm, applying reagent Gi to a given mixture Mj results in non-negative indicator “weight”:
w
ij=γiTUθj
Finally, when the presence or absence of Mj in the pool is defined by the binary variable xj, the indicator amount produced by applying reagent Gi to the pool is:
and each wij≥0. Then:
w
i=ΘT∪Tγi [Equation 5] [Equation 17].
To Summarize this as a Theorem:
Theorem 1 (Chemical Perceptron (Reagent-Rich Decoupling)): Assuming the presence or absence of each of an ensemble of molecular mixtures as binary inputs, xj, the scalar ∥Ti∥ as given in [Equation 4] [Equation 16] represents a chemical multiply accumulate operation on the xj using weights wij≥0. Applying a threshold operator ϕ( ) to ∥Ti∥ results in the mathematical equivalent of the perceptron structure in m is approximately equal to the sum of individual unmixed-
m yields with similarly plentiful reagent.]
Proof [Theorem 1]: See the mathematical development leading to the statement of Theorem 1.
Designing the input composition, Θ. Assuming R-groups, molecules, and reagents have been chosen, one is then presented with at least two mathematical problems:
Let weight set, wi, corresponding to application of reagent Gi:
γiTR=γiTUΘ=[wi1. . . wiJ]=wiT
First consider non-negative weight sets. Let wp correspond to application of reagent GP so that:
γpTR−γpTUΘ−[wp1. . . wpJ]−wpT
Now, let:
Γ=[β1 . . . γp]
where P is the number of different perceptrons required of a given data set corresponding to the set of input mixtures, M1, j=1, . . . , J. One then has:
ΘTUTΓ=RTΓ=[w1. . . wp]=W [Equation 6] [Equation 20]
and then solves for Θ.
However, before considering specific approaches, some useful general observations can be made from the structure of [Equation 6] [Equation 20]. When any column of Γ, γq depends linearly on another set of columns {γl}, set of constants {αl} exists so:
By [Equation 5] [Equation 17]:
so that at least one of the weight sets that comprises W cannot be chosen independently from others.
Note:
Theorem 2 (Independent Perceptron Limit): The number, P, of perceptrons that can be independently composed by choice of Θ is less than or equal to N, the number of R-groups.
Proof [Theorem 2]: By [Equation 7] [Equation 21], the number, P, of independent weight sets wp that can be composed by choice of Θ is upper-bounded by the number of independent γl which is identically the column rank of F. The number of independent {γl} is upper-bounded by the dimension, N, of the {γl} which completes the proof.
∪ is fixed and r is a deterministic or random (with known density) vector. In either case, solution of (or approximation to) [Equation 5] [Equation 17] can be approached as an optimization over binary matrices {Θ} using some norm such as component-wise mean square error between ΘTUTΓ (or RTΓ) and some target W. When the thresholding function ø(⋅) can be adjusted or when different thresholding functions −øi(•) can be used after application of reagent Gi then one can choose a set of nonzero constants {ap}, p=1, 2, . . . P to relax [Equation 5] and obtain:
ΘTUTΓ=RTΓ=[α1w1 . . . αpwp]=WA [Equation 8], where
Rewriting [Equation 8]:
ΘTUTΓ=RTΓ=WA [Equation 9]
Theorem 3 (Chemical Perceptron): Assuming the presence or absence of each of an ensemble of molecular mixtures as binary inputs, x J, the scalar Ti as given in Equation 5] [Equation 16] represents a chemical multiply accumulate operation on the x1 using weights WiJ 0. Applying a threshold operator ø( ) to Ti results in the mathematical equivalent of the perceptron structure in
Proof: [Theorem 3]: See the mathematical development leading to the statement of Theorem 2 and 3.
Accommodating positive and negative weights is straightforward because any weight vector w can be represented as:
w=w
+
−w
− [Equation 18]
where both w+ and w− are non-negative as required by the development. One can therefore imagine:
In both cases one obtains indicators T+=xTw+ and T−=xTw−. so that:
T=T
+
−T
−
=x
T(w+−w−)=xTw [Equation 19]
Before considering specific approaches, some useful general observations can be made from the structure of [Equation 6] [Equation 20]. When any column of Γ, γq depends linearly on another set of columns {}, set of constants {αl} exists so:
By [Equation 5]:
so that at least one of the weight sets that comprises W cannot be chosen independently from others.
Note:
By [Equation 17], one must then have:
so that at least one of the weight sets that comprises W cannot be chosen independently from others. To state the implication of [Equation 21] as a theorem:
Theorem 4 (Independent Perceptron (Weight Set) Limit): The number, P, of weight sets that can be independently composed by choice of e is less than or equal to R, the number of R-groups.
Proof [Theorem 4): By [Equation 21], the number, P, of independent weight sets wp that can be composed by choice of Θ is upper-bounded by the number of independent γl which is identically the column rank of r. The number of independent {γl} is in turn upper-bounded by the dimension, R, of the {γl} which completes the proof.
∪ is fixed and Γ is a deterministic or random (with known density) vector. In either case, the solution of (or approximation to) [Equation 5] [Equation 17] can be approached as an optimization over binary matrices {e} using some norm such as component-wise total square error between ΘT∪TΓ (or RTΓ) and some target W. When the thresholding function ø(•) can be adjusted or when different thresholding functions ø1(•) can be used after application of reagent G; then one can choose a set of nonzero constants {ap}, p=1, 2, P to relax [Equation 17] and obtain:
ΘTUTΓ=RTΓ=[α1w1 . . . αpwp]=WA [Equation 22), where
When only one threshold function ø(•) can be used, then one can choose arbitrary αp=αE+, p=1, 2, . . . P.
Rewriting [Equation 22] as:
ΘTUTΓ=RTΓ=WA [Equation 24]
so that the total square error, e2, between WA and its approximation ΘT∪TΓ can be written as:
e
2=Trace[(ΘT∪TΓ−WA)T(ΘT∪TΓ−WA)] [Equation 25]
which one can also write as
e
2=Trace[(ΘT∪TΓ−WA)(ΘT∪TΓ−WA)T] [Equation 26)
because Trace[zTzJ=Trace[zzTJ for any matrix Z. [Equation (25) and Equation (26) are definitions of the Frobenius norm I eTuTr−WA If2.) When one then defines W°=WA, the optimization is:
d
o=min(Θ,A)Trace[(ΘT∪TΓ−w)(ΘT∪T−w)T] [Equation 12] [Equation 27]
One can also pursue a less constrained optimization over R:
d
R=min(R,A)Trace[(RTΓ−w)(RTΓ−w)T] [Equation 13] [Equation 28]
because the possible R are constrained by the Θ, dθ≤dR.
While chemical realization constraints confine R and Θ to be non-negative matrices, nothing in the mathematical development precludes their having both positive and negative elements. Going forward, relax the non-negativity constraint and show how [Equation 18) can realize general weight sets with positive and negative elements.
Input composition optimization; optimization for fixed A. One first shows that for fixed A the minimizations [Equation 13] [Equation 28] and [Equation 12] Equation 27] are convex in continuous R and Θ, respectively, whether or not one restricts their component vectors to the non-negative orthant.
Theorem 5 (dR and dθ; convexity in R and Θ): When A is fixed, dR and dθ are convex optimizations in continuous R and Θ, respectively, over convex search spaces. dR and dΘ are strictly convex with unique solutions if there are R linearly independent yield vectors, γp.
Proof/Theorem 5): Let A∈(0,1). When one sets R=λR1+(1−λ)R2, convexity of dR requires
for any two different R1 and R2.
Strict convexity further requires equality if A=0 or A=1. Expansion and rearrangement of [Equation 29] produces the inequality:
−λ(1−λ)Trace[(R1−R2)TΓΓT(R1−R2)]≤0 [Equation 30]
which is satisfied because Trace[ZZT] 0 for any real matrix Z. Therefore, dR is convex. Furthermore, dR is strictly convex if ΓΓT has rank ′R, to preclude (R1−R2)TΓ=0 for some choice of R1≠R2. ΓΓT has rank if
linearly independent γp which comprise r. The structure of dθ is identical to that of dR. So, assuming continuous Θ, the same argument for convexity of dθ applies.
Finally, the rj and θj which comprise R and Θ, respectively, are confined to the non-negative orthant—a convex search space for R and Θ. When the positivity constraint on R and Θ is relaxed, the search space is still convex. Thus, dR and dθ are convex optimizations over convex spaces. Strict convexity implies unique solutions, thus completing the proof.
Because dR and dθ are convex, efficient numerical methods exist to find optimizing continuous R* and Θ*. Feasible solutions for [Equation 12] [Equation 27] and [Equation 13] [Equation 28] are integer matrices. But once continuous R* and Θ* are identified, the continuity of dR and dθ in their arguments allow us to examine feasible discrete solutions within the neighborhoods of R* and Θ*. The quality of these discrete solutions (essentially quantization) depends upon their coarseness regarding the metrics' variation in the continuous search space. Therefore, solutions can be improved through choice of A.
Choosing A. Consider R• a continuous solution to [Equation 13] [Equation 28] for an arbitrary A which produces minimum error:
(e*)2=Trace[(R*)TΓ−{tilde over (W)})((R*)TΓ−{tilde over (W)})T]
Then, the integer approximation Ř* to R* is obtained by rounding. Define Δ so R*=Ř+Δ and note that each element of Δ cannot have magnitude larger than 1. Then consider that when Ŵ is replaced by αŴ, the optimizing R* becomes α R* and the integer matrix solution obeys αR*=Ř+Δ. Applying Ř to [Equation 13] [Equation 28] produces:
As α→∞, e2→(e*)2. Thus, larger α produces better discrete approximation of R*. As [Equation 12] [Equation 27] is structurally equivalent to [Equation 13] [Equation 28], the same argument applies to integer approximations of Θ*. Therefore, one can seek continuous solutions to [Equation 12] [Equation 27] and [Equation 13] [Equation 28] for A=I and then scale its elements until performing the integer matrix approximation is sufficiently close to that of the optimal continuous solution, at least within practical limits of chemical mixture composition. The choice of the αp in [Equation 23] depends on the coarseness with which the corresponding RTγp and ΘT∪Tγp approximate wp. The choice of the αp depends upon the coarseness with which the corresponding rp and θp approximate wp.
Optimization with random Γ. For the case of random equilibrium vectors γp the optimizations are still convex, as stated in the following lemma:
Lemma 1 (Random Γ): When r is random with mean f′ and correlation E[ΓΓT]=KΓ, then the optimizations dR and dθ remain convex, and strictly convex if the Kr is positive definite.
Proof [Lemma 1]: When the equilibrium vectors γp are random, the optimizations dR and dθ are replaced with optimizations of E[dR] and E[de] respectively. The optimizations are still convex because ΓΓT in the proof of Theorem 5 is replaced by the positive semi-definite correlation matrix E[ΓΓT]=KΓ so that [Equation 30] is still satisfied. When KΓ is positive definite (full rank) then the optimizations are strictly convex.
The inventors again formulate the optimization problem because one must understand how r randomness can affect perceptron performance. [Equation 13] [Equation 28] becomes
Expanding and regrouping, one obtains
When one requires an unbiased W estimator, then the optimizing R* must obey:
E[(R*)TΓ−{tilde over (W)}]=(R*)T
The optimization of [Equation 32] then becomes:
Evaluating [Equation 32] with the optimum R* produces a minimum total squared weight error of:
E[dR]=Trace[(R*)TCΓR*] [Equation 34]
The optimization in Θ [Equation 27] can be similarly formulated and a similar expression for E[dΘ] derived.
Realization of Weight Sets With ±Values. While the chemistry precludes single-pot direct realization of W with negative weights (γ elements cannot be negative), the preceding mathematical development was general. When one allows two pots—one representing positive weights and the other representing negative weights as in [Equation 18] and [Equation 19]-one can realize general weight matrices by:
Because reaction characterization could be time-intensive, one considers only the second possibility of duplicate multiple input mixtures.
Thus, let R=R+−R− where the R± are non-negative. Substituting R=R+−R− into [Equation 28] produces:
Trace[(R+−R−)TΓ−{tilde over (W)})(R+−R−)TΓ−{tilde over (W)})T] [Equation 35]
Given the optimization of [Equation 28] is convex, the optimization in non-negative orthant R+ is convex for fixed R−, as is the optimization of non-negative orthant R− for fixed R. The joint optimization in R+ and R− is convex. The same argument applies to the optimization of [Equation 27] for Θ=Θ+−Θ−.
To implement W with positive and negative values one can either find an unconstrained R which minimizes [Equation 28] and decompose it directly into non-negative R+ and R− (as opposed to separately approximating W± with non-negative R± which in general could be suboptimal). Alternatively, one could:
Direct decomposition is efficient while iterative search can allow additional chemistry-related constraints to be applied to where the ± separately.
Noisy Weight Sets. Weight approximation can be coarse and chemical reactions are stochastic processes. Thus, RTr realization may not be identically equal to the target W owing to approximation error, yield randomness, or both causes. The weights can likely be noisy and such noise can cause misclassification of inputs.
Assuming a simple weight noise model and an equally simple binary classification problem, one can derive an expression for the excess error imposed by noisy weights.
To begin, consider that a perceptron distinguishes between two classes A and B by the decision rule:
Where β∈E is some threshold. With no loss of generality, assume β=0. Thus, the weight set vector w defines a plane:
x
T
w=0 [Equation 37]
above or below which one assign inputs to A and B, respectively. The {x} which satisfy [Equation 37] are orthogonal to w. Thus, the vector:
is exactly the unit normal to the decision plane, P, and a given input's distance to P is then:
d(x,P)=xT{circumflex over (p)}
When the training set inputs are drawn from the following simple i.i.d. Gaussian distributions centered on ±z as in:
where z=bp, b>0 being a measure of how distinguishable the hypotheses are.
When the hypotheses are equiprobable, the optimal decision rule for guessing A or B is exactly [Equation 3] and the irreducible probability of classification error is:
One defines the ratio b/σ as the classification signal-to-noise ratio, X.
For simplicity, the weight set is perturbed by a zero mean i.i.d. Gaussian noise vector n, each element of variance N0. Then the perturbed weight set w is:
The perturbation effectively rotates the nominal decision plane so given n, the probability of error becomes:
However, taking the decision plane perspective, one sees that noise rotates the antipodal points ±z regarding the decision plane. Symmetry (noise and point set) dictate that the probability of misclassification depends only on the distance between the points ±z and the noisy plane P′:
d(z,P′)=zT{circumflex over (p)}′, where
And such rotation can only increase the probability of misclassification.
Therefore, the probability of misclassification becomes above or below which one assigns inputs to A and B, respectively. The {x} which satisfy [Equation 37] are orthogonal to w. Thus, the vector is exactly the unit normal to the decision plane, P, and a given input's distance to P.
The probability of misclassification becomes:
Rewriting:
and then noting that because |{circumflex over (p)}Tn|≤|n|,
one can define:
as the excess error factor which multiplies the minimum error coefficient x so that:
P
e|n
=Q(Xδ(n))
Pe|n is minimized when δ(n)=1, maximized when δ(n)=−1, and for δ(n)=0, classification is random (Pe|n=0.5).
Because of noise symmetry, one can with no loss of generality set w=I w I e1 where ek is the kth canonical unit vector with 1 in the kth dimension and zero elsewhere. [For exquisite classification (x=8), weight imprecision much beyond 9% results in poor performance. However, when the perceptron is only 98% accurate to start (x=2), then only 25% weight precision is necessary.] One then has p=e1 so that:
where n1 is the first component of n. The magnitude term in the denominator of [Equation 45] can then be written as:
However, for very large J, the law of large numbers implies that:
so that when one defines:
so, the overall expected probability of error owing to weight approximation noise is roughly:
One can also apply [Equation 46] when weight uncertainty is owed to stochastic reactivity rather than quantization (or other estimation) error. When Γ is a random matrix, the total square error from [Equation 34] provides a measure of how well the perceptron implementation is likely to perform. When one equates E I dR I+PJN0, and define the average weight energy as:
then one can write
and use [Equation 46] as a performance predictor of chemical perceptron realizations with random yield matrices as well input composition construction imprecision.
Plots of [Equation 46] are provided in
Thus, [Equation 46] serves both as a guide for the choice of A to keep quantization noise within accept-able bounds, and as an indicator of achievable performance when reaction yields are uncertain.
Numerical example. For a two-perceptron system based on 8 available R-groups and two reagents G1 and G2 with reaction product matrix
The Γ is illustrative, but exact Γ values may be taken from the literature for different types of reactions. Then assume that molecules mm are 2-mers with distinct R-groups, so that the total number of different molecules is 28 (i.e., 28) and the total number of (non-zero) mixtures is 228−1.
A weight matrix for 4-input perceptrons with values chosen randomly between zero and one can be:
Numerically solving the implicit quadratic programming problem of [Equation 13] [Equation 28] with A=I yields:
so that:
Producing the integer matrix approximation to R* is then a matter of scaling. Scaling by 105 can produce the same precision as the original in this EXAMPLE, though scaling by a smaller number may also provide sufficient weight approximation given the robustness of neural networks.
When the number of R-groups is set at =10, the number of perceptron inputs J=10 and the number of perceptrons P=2. Then, for the following J×P weight matrix W, each element chosen i.i.d. N(0,1):
Reagent yield matrix Γ, each element chosen i.i.d. from a uniform distribution on (0,1):
Numerical calculation of the optimal continuous according to [Equation 35] (shown here to three decimal places) yields:
Note that:
differs from:
although there may exist some R± which separately provide good approximations to W± besides providing jointly good approximations to W.
Then, consider the weight estimation accuracy |RTΓ−W|f2 for different R precisions and the corresponding ζ2 as shown in TABLE 1. According to
Weight error and ξ2 for different precision approximations to the optimal continuous R.
Now consider Θ± which is produced by assuming each molecule is formed with 4 of 10 different R-groups for a total of 210 molecules. Then, compose the binary (10×210) matrix ∪ to obtain the least squares solution to [Equation 27].
TABLE 2 is the analog to TABLE 1 for different precision Θ± derived from the continuous Θ. Here, according to
Weight error and ξ2 for different precision approximations to the optimal continuous Θ.
Parallelized Linear Classification with Volumetric Chemical Perceptrons
Introduction and summary. This EXAMPLE 2 introduces a linear classifier that is implemented in a chemical form. This EXAMPLE 2 also discloses an encoding technique that simultaneously represents multiple datasets in an array of microliter-scale chemical mixtures. Parallel computations on these datasets are performed as robotic liquid handling sequences. These outputs are analyzed by high-performance liquid chromatography.
This invention combines aspects of chemical and electrical information systems. Paired with appropriate chemical analysis tools, this approach can operate with increasingly parallel datasets. This invention provides computational efficiency and massive parallelism comes with computing in chemical domains.
For more information, see Arcadia et al., Proceedings of the IEEE Conference on Rebooting Computing (ICRC) (2018), which is incorporated by reference.
This EXAMPLE 2 presents a method for implementing linear classification operations using chemical mixtures. Binary input data is encoded in the chemical composition of an array of liquid samples, and a robotic fluid handler is programmed to perform multiplications and additions as fractional volume transfers and pooling operations. The chemical coding enables parallel computation and allows for increased information density. The result of the volumetric operations is represented in the concentration of chemicals in output pools, which are analyzed using high performance liquid chromatography. The inventors used this system for parallel classification of several 16×16 binary MNIST images of handwritten digits (see, LeCun et al., Proceedings of the IEEE, 86(11), 2278-2324 (1998)), as well as a set of pseudo-random binary vectors. Thus, the inventors demonstrated the overall accuracy of the method, producing 55 correct classifications out of 57 tests.
This EXAMPLE 2 provides a class of chemical-domain computational engines which can operate on increasingly parallel datasets. Chemical computation can find applications in ultra-low-power systems, extreme environments, and as complements to electronic computing systems. Adleman, Science, 266(5187), 1021-1024 (1994). DNA archival data storage can complement traditional electronic media. See, Church, Gao, & Kosuri, Science, 337(6102), 1628 (September 2012); Bornholt et al., ACM SIGOPS Operating Systems Review, 50(2), 637-649, (2016); and Goldman et al., Nature, 494(7435), 77 (2013). Neural-inspired computing provided the ability for those skilled in the molecular computing art to process large datasets. See, Krizhevsky et al., Advances in Neural Information Processing systems, (2012), pp. 1097-1105; Graves et al., Acoustics, Speech and Signal Processing (ICASSP), 2013 IEEE International Conference on. IEEE (2013), pp. 6645-6649; Lawrence et al., IEEE Transactions on Neural Networks, 8(1), 98-113 (1997); Tann et al., Flexible deep neural network processing, arXiv, 2018. Chemical-domain computation thus provides an advantageous ways of leveraging the information processing capabilities of natural elements.
An electrical system cannot fully recreate the massive parallelism and emergent properties that come from the diversity of subtle molecular interactions and coexistence of thousands of unique chemical compounds. See, Rose et al., 2018 IEEE International Symposium on Information Theory (ISIT), (June 2018), pp. 2236-2240 [EXAMPLE 1]; Kennedy et al., Applied Physics Letters, 112(26), 264103 (2018); Huang et al., Sensors and Actuators B: Chemical, 239, 704-710 (2017); Salehi et al., IEEE Transactions on Molecular, Biological and Multi-Scale Communications, 1(3), 249-264 (2015). See also, Erlich & Zielinski, Science, 355(6328), 950-954 (2017); Shipman et al., Nature, 547(7663), 345 (2017). Organick et al., Nature Biotechnology, 36(3); 242 (2018).
Accordingly, this EXAMPLE 2 is directed toward develop a computational framework to concurrently process digital information represented in solutions of chemical compounds. This EXAMPLE 2 provides methods for chemical encoding, computation, and readout.
This EXAMPLE 2 also provides an approach to computing with chemical solutions. This EXAMPLE 2 provides a method to encode binary data into the chemical composition of liquid samples. This EXAMPLE 2 provides shows that multiple datasets can be stored in parallel with multiple coexisting chemicals.
This EXAMPLE 2 uses programmable robotic liquid handling sequences to perform volumetric multiply accumulate (MAC) operations on parallelized chemical datasets. This EXAMPLE 2 uses high-performance liquid chromatography to read and verify the results of the chemical calculations. This EXAMPLE 2 provides a description of the system developed to perform these functions.
This EXAMPLE 2 demonstrates linear classification of several MNIST images and Boolean test vectors. This EXAMPLE 2 demonstrates the chemically encoding of several images of handwritten digits from the MNIST database and implements several single layer volumetric chemical perceptrons which successfully classify the images. This EXAMPLE 2 additionally quantifies the performance of the method with a larger set of binary vectors.
This EXAMPLE 2 provides ways to scale and extend the chemical computation scheme.
This EXAMPLE 2 is intended as an advance towards realizing general-purpose chemical-domain computational tools. By demonstrating that the proposed method can reliably perform these operations, chemical mixtures are shown to provide an interesting basis for alternative computing.
Mass conservation in chemical mixtures. When working with well-mixed solutions and there are no chemical reactions in these solutions, then the simplest constraint is the conservation of mass. When two or more volumes containing the same chemical are combined, the final mixture can have a concentration that is a linear function of the concentrations of that chemical in each of the sources.
When a mixture of N sources, each containing a concentration Ci of a certain chemical, is formed by transferring a volume Vi from each source to a common destination, then the final concentration can be given as:
where Vi·Ci is the total mass of the chemical added to the destination and Vf is the final total volume in the destination. Compare this [Equation A] to [Equation I]. This [Equation A] can be extended through linear superposition to mixtures of different chemical species if they do not interact with each other. This simple relationship forms the basis for parallel chemical computation.
Analogies between electrical and chemical domains. In TABLE 3, ANALOGIES BETWEEN ELECRTICAL AND CHEMICAL DOMAINS, the parameters of a chemical mixture-based system relate to familiar electrical terms. An advantage of data storage and processing with chemicals is the parallelism that can be achieved by operating with multiple coexisting chemical species.
This potential is realized in many biological contexts, such as in bacterial communication [Taga & Bassler, Proceedings of the National Academy of Sciences, U.S.A., 100(suppl. 2), 14549-14554, (2003)] and neural signaling [Bloom, American Journal of Physiology-Cell Physiology, 246(3), C184-C194 (1984)]. Another benefit of chemical data storage is its potentially high information density, as has been noted for DNA [Church et al, Science, p. 1226355 (2012); Bornholt et al., ACM SIGOPS Operating Systems Review, 50(2), 637-649 (2016)].
The advantages of computing with chemical mixtures stem from the ability for many datasets to coexist in parallel. In the case of overlaid chemical images, any operation on a single well can simultaneously be applied to the corresponding pixel in all images. As such, this encoding scheme can support massively parallel storage and computation.
TABLE 4, COMPUTATIONAL COST OF CLASSIFYING M BINARY INPUTS, EACH CONTAINING N BITS, IN A TRADITIONAL VERSUS VOLUMETRIC PERCEPTRON shows a comparison of the number of operations for a perceptron with a traditional computer versus the proposed mixture-based technique. The number of operations to be performed with chemical mixtures scales only with the number of input features and is independent of the number of input instances.
Computing with chemical mixtures.
The total volume transferred from the ith well can be: Vi=|wi|·Vo. The scaling of the transfer volume represents a multiplication and the pooling of volumes into a common well represents an addition. Because bits from different datasets may be stored in the same well, these pooling operations allow for parallel multiply accumulate operations on all concurrently stored datasets. There is zero marginal computational cost to increasing parallelism, because, regardless of the complexity of the chemical mixtures, one can perform the pooling transfers once. To show that the system shown in
z
m
=ΔC
m
=C
m
+
−C
m
− [Equation B]
where Cm+ and Cm− are the concentrations of species m in the positive and negative weight pools, respectively. According to [Equation A] the concentration of molecule m at the output of each MAC can be expressed as:
where Vp+ and Vp− are the total volumes in each pool, i is the index of the data well, Vi=|wi|·Vo is the weighted volume transferred from the ith well, and Cmi is the concentration of molecule m in the ith well. One can then expand [Equation B] as:
If the pooled volumes are intentionally set to be equal after weighted pooling (V+=V−=Vp), by appropriately adding pure solvent, one can collect the summations as:
where the features have been defined to be the scaled data [pixel] concentrations: xmi=(V0/Vp)·cmi. This yields the original form of the pre-classification output.
Reading the Results of Chemical Mixture Computations. To verify the output of the computations, one can determine the amount of each component present in the liquid samples. The inventors used high performance liquid chromatography (HPLC). A liquid sample is injected into a stream of solvents known as the mobile phase. The mobile phase, now containing the sample to be analyzed, flows through a column containing a solid adsorbent, the stationary phase. Components in the sample interact with the adsorbent to varying degrees based on their chemical properties, causing different chemicals to leave the column (to ‘elute’), at different times. These retention times are used to identify individual components. When a compound that absorbs UV light elutes from the column and passes the detector, a peak in optical absorbance is observed, and the area of this peak is proportional to the relative abundance of the compound in the sample. The resulting absorbance time series, known as a chromatogram, can be used to both identify and quantify the chemicals in a mixture.
The laboratory setup and data flow used for the assays in this EXAMPLE 2. Weight matrices were trained in simulation and then converted, along with test data, into sequences of pipetting instructions for a robotic liquid handler. Analytes were dispensed into a 384-well microplate to form the chemical dataset and then collected in volume fractions corresponding to the classifier weight matrix. The outputs were analyzed by HPLC to produce class labels.
Operational setup. Binary input data and classifier weights are first trained through simulations on a desktop computer, in a Python environment. Before chemically encoding the input data, concentrated stock solutions are prepared of each analyte, at 62.5 mg/mL in dimethyl sulfoxide (DMSO, Macron Fine Chemicals 4948-02). To write the chemical data to a 384-well plate, the binary datasets are converted to pipetting instructions for a fluid handling robot (Andrew Alliance 1000G pipetting robot). For each input data bit whose value is ‘1’, the robot is instructed to transfer 20 μL of the corresponding analyte to the appropriate well. When the input data is ‘0’, it transfers 20 μL of dimethyl sulfoxide solvent instead. After the chemical datasets are created, the classifier weights are converted into additional pipetting instructions which the robot uses to perform the weighted-summation operations, placing the pooled outputs into an empty well plate.
Weighted pools. After the positive and negative weight pools are generated, each output is analyzed using high performance liquid chromatography (HPLC). The analytes representing each dataset exit the instrument at different times, allowing separate estimations of the output concentration of each component. For each paired output [analyte], the differential concentration ((ΔCm) is calculated. When the differential concentration is greater than zero, then the data contained in the well plate is classified as a match; otherwise, the data is classified as mismatch.
Chemical selection. The inventors selected three similar phenol compounds to encode the data: 2,4,6-tri-tert-butylphenol (analyte 1, 98%, Sigma Aldrich T49409), 2,6-dimethylphenol (analyte 2, ≥99.5%, Sigma Aldrich D174904), and 4-nitrophenol (analyte 3, ≥99%, Sigma Aldrich 241326). Phenols were selected due to their established UV absorbance and well-defined HPLC peak shapes. Mateos et al., Journal of Agricultural and Food Chemistry, 49(5), 2185-2192 (2001); Montedoro et al., Journal of Agricultural and Food Chemistry, 40(9), 1571-1576 (1992) The inventors initially also considered benzoates and other aromatics. However, phenol compounds also offer a range of chemical functionalization options through acylation [Murashige et al., Tetrahedron, 67(3), 641-649 (2011)], protection with benzyl [Kuwano & Kusano, Organic Letters, 10(10), 1979-1982 (2008)] or tert-butyloxycarbonyl [Cheraiet et al., Green Chemistry Letters and Re-views, 6(3), 211-216 (2013)], silylation [Sefkow & Kaatz, Tetrahedron Letters, 40(36), 6561-6562 (1999)], or even methylation [Ouk et al., Tetrahedron Letters, 43(14), 2661-2663 (2002)]. This introduces the possibility of increasing parallelism through simple chemical manipulations, which would generate numerous related com-pounds with similar UV sensitivity.
Measurement calibration. The HPLC used in this work was an Agilent 1260 infinity series model with a quaternary pump, a standard autosampler, a thermostatted column compartment, and a variable wavelength detector that was set at 204, 214, and 254 nm with bandwidths of 4 nm. To identify the characteristic elution time of each analyte, the three compounds were measured independently using a C18 reversed phase column (Agilent Poroshell 120 EC-C18, 699975-902, 4.5 mm×50 mm, 2.7 μm part|c|e size). A gradient flow program was run with a two-part mobile phase comprised of water (A) and acetonitrile (B), where the volume ratios at each gradient time endpoint were set to 95%-A & 5%-B at 0 min, 5%-A & 95%-B at 9 min, 5%-A & 95%-B at 10 min, 95%-A & 5%-B at 11 min, and 95%-A & 5%-B at 12.5 min. Chromatograms for the three analytes are shown in
MNIST image classification. For a demonstration, the inventors used images derived from the well-known MNIST database of handwritten digits [LeCun et al., Proceedings of the IEEE, 86(11), 2278-2324 (1998)]. The original images were grayscale at 28×28 pixel resolution, but for these assays, the inventors binarized and resized the images to 16×16. The inventors trained three one-versus-all classifiers on a computer a priori for three foreground classes, representing the digits ‘0’, ‘1’, and ‘2’. Each classifier was trained using 100 foreground class images and 100 background class images which were randomly selected from the MNIST training set. For example, the classifier with the digit ‘0’ foreground class was trained using 100 images of the digit ‘0’ and 100 images of other digits ‘1’ through ‘9’. Color maps of the trained weight matrices are shown in
The inventors constructed a dataset of three overlaid MNIST images (see, LeCun et al., Proceedings of the IEEE, 86(11), 2278-2324 (1998)), consisting of two distinct ‘0’ images and one image of ‘1’. These images were mapped onto a well plate and encoded with the three previously discussed analytes. The resulting microplate is shown in
While these perceptrons performed well, the aim is to reproduce the perceptron operations using chemical computations.
Performance evaluation. Chemical computation is not limited to images and is extensible to linear classification of any binary dataset. To evaluate the robustness of the computations, the inventors performed a set of assays using smaller pseudo-random binary vectors. Sixteen 16-element weight vectors (w∈[−1, 1]) were selected at random, as shown in
The expected and HPLC-measured concentrations of the positively and negatively weighted pools are shown in
The classification output is robust to moderate assay variations, but the exact output concentrations are affected by several sources of assay variability. Inconsistent pipetting volumes during the initial dataset creation, as well as the tolerance of the weighted summing volumes, cause variations in the pooled output. Additionally, the HPLC is sensitive to small changes in its sample injection volume, and the chromatogram calibration can drift slightly over time. In total, the inventors observed errors on the scale of 10% of the expected outputs, which naturally has a larger effect on decisions closer to the classifier boundary. The mean differential concentration error was close to zero (0.041 mg/mL), and the 3a spread was approximately 0.3 mg/mL. The overall chemical classifier accuracy was 96%, correctly classifying 46 out of 48 test vectors.
The utility of this method as a valuable alternative computing model is provided by its ability to scale up to operating in parallel on many datasets. In this EXAMPLE 2, the scale of the demonstrations is limited by the throughput of the automated liquid handler. Between assembling the dataset and performing the classifications, the MNIST demonstration required a total of 1,716 liquid transfers, used 697 disposable pipette tips, and took 24 hours to complete. While this is a considerable amount of time, it does not represent a physical limit, as higher throughput liquid handling systems are common in pharmaceutical laboratories. Moving forward, improved robotics can allow an increase in the computational throughput by several orders of magnitude.
The parallelism of the chemical analysis is another important avenue for improvement. The demonstrations used a set of only three compounds, but the current system could be readily scaled to several dozen. This would not impact the inference or readout time, but the time to prepare the input data wells would increase. Putting aside the dataset creation time, scaling up to hundreds or thousands of parallel computations would likely require supplementing HPLC with other analytical techniques such as mass spectrometry. Zeng & Kassel, Analytical Chemistry, 70(20), 4380-4388 (1998); Shockcor et al., Analytical Chemistry, 68(24), 4431-4435 (1996).
The finite volume of the chemical datasets implies a limit to the number of times that data can be sampled and processed. In the MNIST tests, each well began with a volume of 60 μL, and the classifier weights were scaled to transfer between 0-6.25 μL from each well. Thus, the current system can operate on each data well approximately twenty times. With improved liquid handling tools, the sample volumes can be reduced to make more efficient use of each chemical dataset. These current demonstrations require analyzing two chemical output pools and electronically calculating the differential concentrations of their analytes. To scale up the scope and complexity of the chemical computational system, one can implement methods approaches for cascading multiple computing stages and integrating other operations beyond linear volumetric additions and multiplications.
This EXAMPLE 2 presented a scheme for implementing linear classification operations using chemical mixtures. Binary data is encoded into the chemical composition of an array of liquid samples, and a robotic fluid handler is programmed to perform multiplications and additions as fractional volume transfers and pooling operations. The chemical encoding increases information density and enables parallel computation. The result of these operations is represented in the concentration of chemicals in pooled outputs, which are analyzed using high performance liquid chromatography (HPLC). This EXAMPLE 2 used this system to classify several 16×16 binary MNIST images of handwritten digits, as well as to classify a set of pseudo-random binary vectors. The method's accuracy was demonstrated, producing 55 correct classifications out of 57 operations.
THIS EXAMPLE 2 first step towards a new class of chemical-domain computational engines which can operate on increasingly parallel datasets.
Summary Molecular data systems can store information at dramatically higher density than existing electronic media. Molecular memory has previously been based upon custom-built long-chain oligomers (like RNA or DNA). The concomitant needs for readout using somewhat cumbersome processes like shotgun sequencing and the like, or even the more modern nanopore sequential readout method.
This EXAMPLE 3 presents a general framework for quantifying chemical memory, which is not limited to polymers and extends to mixtures of molecules of all types. This EXAMPLE 3 shows that the theoretical limit for molecular information is two orders of magnitude denser by mass than DNA. This EXAMPLE 3 demonstrates kilobyte-scale information storage in mixtures of small synthetic molecules and considers some of the new perspectives that are necessary to harness the information capacity available from the vast non-genomic chemical space.
This EXAMPLE 3 demonstrates the coding of information using mixtures of small molecules and subsequent en masse readout using combinations of spectrometry, chromatography, and spectroscopy. This EXAMPLE 3 used memory representation to formulate the readout problem as a multi-user signature specification/detection problem in suitable signal spaces. This EXAMPLE 3 shows how to detect mixtures of 106 molecules in one pass at relatively high speed.
Introduction. RNA and DNA are information-dense, stable over long periods of time, and energy efficient. Reading information from RNA and DNA is currently cumbersome, whether stochastic methods such as polymer chain reaction (PCR) and shotgun sequencing or emerging more elegant sequential methods using nanopores are used.
This EXAMPLE 3 instead considers the molecular information storage problem with an eye not only toward high information density, but also highly parallel, speedy memory interrogation. The inventors apply bulk probes such as mass spectrometry, spectroscopy, chromatography, and other methods to enable readout of megabits or more within seconds or less.
This EXAMPLE 3 first considers information storage using molecules and mixtures of molecules (specifically avoiding long oligomeric approaches such as RNA, DNA, or proteins) in a way that can be applied to any chemical system. This EXAMPLE 3 avoids long oligomers (or lattices), instead using natural intermolecular interaction promiscuity available in gas/solution phase mixtures of smaller molecules. This EXAMPLE 3 then considers readout of molecular mixtures as a classification problem in some high dimensional signal space, deriving empirical bounds on the rate at which information can be extracted from the system. This EXAMPLE 3 then applies this thinking to models of a particular chemical system (Ugi molecules) using mass spectrometry as the interrogation method.
Theoretical foundation of molecular information capacity. Where D is the total number of different distinguishable system states, then the memory capacity is upper-bounded by loge. Embedded in this statement is the readout problem (the notion of distinguishability) which is quantified for any given system, as discussed below.
By neglecting potentially resolvable differences in the conformational, vibrational, rotational, and electronic states of the molecules, the enumeration of system state is queried by three simple questions:
(1) Which marbles are present?
(2) How many of each marble is present?
(3) Where are the marbles?
This formulation is sufficiently robust and accurate for capturing the capacity of any molecular memory, even when the quantum states of the molecules are also considered.
Counting the states. The number of unique possible states that a system can realize (regardless of what parameters make the states unique) sets an upper bound on memory capacity. Where there are n distinguishable states overall, then the system can code at most log2n bits. Thus, establishing memory capacity is a question of counting the distinguishable states and the three questions enumerated above allow us to answer this question.
Linear oligomers, such as nucleic acids or proteins, are a well-known form of molecular information storage/representation. For RNA or DNA, there are four bases, so the number, M, of possible N-monomer strands is 4N. When those skilled in the molecular computing art ask which of the M molecules is present, a given strand represents 2N bits. For proteins, N bases drawn from an “alphabet” of twenty amino acids carry log2(20N)=4.3N bits.
These “beads on a necklace” representations are themselves an instance of “where are the marbles?” memory coding in that position, as well as base identity, provides information. Persons skilled in the molecular computing art understand two-dimensional or three-dimensional structures, where each position in a lattice represents information. These structures become necessarily large and their interiors less accessible to easy interrogation as memory size grows. Planar lattices could allow easier interrogation, but a subtext of the approach is a desire to utilize the natural promiscuity of molecule interactions in liquid/gas phase for computation. Thus, this EXAMPLE 3 focuses on small molecules (although persons skilled in the molecular computing art can use larger scale spatial ordering of molecular mixtures as an information dimension).
For a mixture of molecules where position information is inaccessible or inconsequential owing to molecular motion, but where those skilled in the molecular computing art can identify the presence or absence of different molecules in a mixture, then for given M molecule types, there are 2M possible system states. Thus, the system can store NI bits.
How many of each type of molecule is present? Persons skilled in the molecular computing art can use up to Q molecules for storage. That is, a given “bag” can contain any number between zero and Q marbles. This is a typical bin-packing problem [Papoulis, Probability, Random Variables, and Stochastic Processes (McGraw-Hill, New York, third edition, 1991); Feller, An Introduction to Probability Theory and Its Applications, Volume I. (Wiley, third edition, 1968)] that results in:
possibilities. For analytic clarity, let us assume that M»10 and that Q−M»10 so that Stirling's approximation is reasonably accurate and:
so that
Let us define Q=αM. This definition results in:
which reduces to
Storage Capacity and Density Comparisons. In TABLE 5, MOLECULAR STORAGE CAPACITY FOR UGI TRIM ERS (K=8) WITH 10, 30 AND 90 R-GROUPS PER SITE. C3(NK, m) IS CALCULATED FOR m=1, 10, 100, the inventors compare the storage capacities C2 and C3 (M,m) as a function of N with K=S sites, which corresponds an Ugi “trimer”, made from three conjoined Ugi monomers.
A mixture of Ugi trimers can store nearly a gigabit of information with just N=10 unique R-groups. This is much more than a mixture of comparable Ugi monomers (K=4 and N=10), which can store only tens of kilobits. Ugi trimers furthermore have a molecular space-filling volume on the order of 125A3. When the information storage density is 2 bits/molecule, then for Ugi trimer mixtures this implies a maximum storage density of approximately 2×1018 bytes/mm3. This tremendous information density led us to focus on Ugi trimers, sufficiently long, yet synthetically tractable Ugi oligomers, for the GB-scale molecular storage system.
Location: The position of each molecule: Theoretically, an infinite amount of information could be stored via position as it is, for all intents and purposes, a continuous variable. However, several practical concerns limit fine position as a chemical information storage mechanism including the need for a rigid supporting lattice, molecular vibration and the (relatively large) probe wavelengths which limit location resolution. Moreover, this project is concerned not only with memory but also with computation which implies a need to foster interactions between molecules. Thus, one focusses primarily on unordered mixtures of molecules as an information storage mechanism.
When two solutions are physically separated (or encapsulated), they can contain different sets of molecules so that the information capacity grows linearly with the number of separate mixtures, when one mixture in P separate mixtures represent P×C bits.
Memory capacity motifs and quantum issues. In quantifying molecular memory capacity, two important motifs emerged. First, memory capacity scales linearly in each degree of freedom. Each spatial dimension adds a degree of freedom. However, “tranche” properties of the constituents of molecules such as sensitivity to specific probe types (frequency, reactivity) could also be used as dimensions to increase memory capacity. Second, the numbers of identifiable molecules only increase capacity as the log of those numbers. While quantities like concentration can increase capacity, they do so less efficiently than through adding more degrees of freedom.
When one has M different molecule types, each of which can be stably put into S quantum states where typically S«1\1 because the combinatorial complexity of molecules which drives M can be high while the number of stable and accessible quantum states is generally much smaller. The memory capacity of such a system is log SM=log S+log M. So, whether the design (and probing) of those S stable quantum states should be pursued is a question of how difficult it is to increase S as compared to M.
Quantum entanglement can vastly increase the capacity of any system because the state is defined by the values of the entangled state probabilities. When each element can occupy one of two states, an N-element system has 2N states, each of which is specified by a complex constant. Even when one supposes those constants are constrained to either 0 or 1, the N-element system represents 22˜1 bits. So, quantum entanglement is a powerful method of memory storage. For the chemical systems here, controllable entanglement between constituent atoms beyond a single bond-length is unlikely, so that while N might be 2, the gain in distinguishable molecules (a factor of 8, or 3 bits) is minimal.
Comparing the various methods suggests that simple “presence/absence” coding wherein information is represented by the presence or absence of each of M molecule types in a mixture is a good first approach.
Memory and detection using Ugi chemistry. A specific chemical substrate can allow one to formulate the memory storage problem in concrete terms, from coding through detection using mass spectrometry. Because the synthesis of large numbers of different molecules is difficult, consider theoretical collections of small organic molecules that can be synthesized by multicomponent reactions, such as Ugi reactions. The Ugi reaction is a popular reaction in which four reactants combine to form a new molecule which condenses the four elements onto a peptide-like backbone, while retaining nearly all the atoms of the original inputs. Dömling & Ugi, Angewandte Chemie International Edition, 39(18), 3168-3210 (2000); Ugi et al., Endeavour, 18(3), 115 122, (1994); Ugi et al., Molecules, 8(1), 53-66 (2003).
Consider a set of Ugi molecules created from combinatorial sets of four appropriate reagents available from the Sigma-Aldrich catalog. Using thirty isocyanides, nineteen carboxylic acids, twelve amines, and seventeen ketones, one can create I 16,280 (30×19×12×17) theoretical Ugi products.
Technical approach. The program goals of this EXAMPLE 4 are (1) to store abstract digital data by taking advantage of small molecule chemical diversity; (2) to develop leading-edge synthesis and analysis techniques that can scale to billions of molecules/day; and (3) to establish scalable strategies for solution-phase information processing using small-molecule reactions.
Regarding combinatorial synthesis. Prior methods: Split pool synthesis of 2.18 million compounds (Schreiber group; see, Schreiber, Int. J. Mass. Spec. (2000)); fully-populated library only; and verification of 456 compounds (0.02%).
This EXAMPLE 4: Synthesis of 30,000 Unique Mixtures of 30,000 compounds via robotics and multicomponent reactions; 30K×30K=900 million synthesis features; create arbitrary library subsets; including 100% quality control (QC).
Regarding mass spectrometry. Prior methods: Identification of >120,000 compounds in 12 hours (Marshall group); amortized 3 compounds/second.
This EXAMPLE 4: Enumeration of 30,000 mixtures×30,000 compounds in 24 hours; >10,000 compounds/second.
Regarding molecular computing; storage. Prior methods (DNA): Stored 200 MB subdivided among DNA oligonucleotides (Strauss/Ceze/Seelig); Data+payload representation; Reed-Solomon codes for error correction; 13 million ˜150-base oligos carrying >100 bits of data per molecule.
This EXAMPLE 4: To store >1 billion bytes in unordered small molecules; not inherently sequence-based; 1-100 bits of data per Ugi-derived molecule
Regarding molecular computing; computing. Prior methods (DNA): Relies on hybridization interactions, optimized by evolution; solutions to several-destination Hamiltonian path and SAT problems (Adelman/Lipton); several-bit digital logic circuits based on strand displacement (Soloveichik/Bruck) See, Zielinski, Science (2017); Adelman, Scientific American (1998); Qian, Science (2011).
This EXAMPLE 4: Use 1-to-many reactions to perform highly parallel matrix algebra and pattern classification.
Mitigation of possible risks: (1) Use of heteroatoms to synthesize Ugi molecules to reduce a risk of too many isomers. (2) Smaller mixtures with non-mass dimensions to reduce a risk of too many isomers. (3) Direct storage of mixtures on MALDI plates to reduce risk from fluid handling speeds of 100 Mmb/day (the Labcyte Echo can handle >750,000 transfers/day). (4) Storage of pre-formed mixture libraries; parallel fluid transfers; specialized robotics to reduce risk from fluid handling speeds of 100 Mmb/day. (5) Careful preliminary studies of reaction networks; optical strategies, to reduce the risk of reaction-based computation.
Summary: This EXAMPLE 4 shows how to (1) store digital images, digital audio, and digital weather datasets in mixtures of synthetic small molecules; (2) synthesize data molecules by combinatorial multi-component Ugi reactions; (3) automate synthesis fluid handling can be automated with robotics and high density well plates; (4) use high-performance FT-ICR mass spectrometry for analysis; (5) use reactions targeting specific R-groups to compute on chemical datasets and build classifiers; and (6) optimize the data encoding, synthesis automation, and statistical analysis for error rates and time constraints using custom computer-aided design (CAD) software.
Technical approach. The program goals of this EXAMPLE 5 are (1) to store abstract digital data by taking advantage of small molecule chemical diversity; (2) to develop leading-edge synthesis and analysis techniques that can scale to billions of molecules/day; and (3) to establish scalable strategies for solution-phase information processing using small-molecule reactions.
Regarding storage: This EXAMPLE 5 shows that one can store and detect kilobits of information in hundreds of Ugi compounds.
Regarding computation: This EXAMPLE 5 shows that the inventors developed a parallel molecular perceptron for image recognition.
Regarding theory: This EXAMPLE 5 shows that the inventors developed new molecular computing algorithms and analyzed chemical space (see Rose et al., 2018 IEEE International Symposium on Information Theory (ISIT) (Vail, CO, June 2018), pp. 2236-2240 [EXAMPLE 1]; Arcadia et al., Proceedings of the IEEE Conference on Rebooting Computing (ICRC) (2018) [EXAMPLE 2]:
w
i=ΘTUTγi [Equation L]
Regarding multicomponent synthesis. Prior methods: Split pool synthesis of 2.18 million compounds (Schreiber group; see, Schreiber, Int. J. Mass. Spec. (2000)); sparse verification of 456 compounds (0.02%).
This EXAMPLE 5: Completed synthesis and characterization of 300 unique Ugi compounds using basic pipetting robot; roughly 1 kilobit of data; characterized nearly all compounds; established concept of using multicomponent reactions for chemical diversity. Continued improved scaling using advanced liquid handling robotics (Labcyte Echo).
Regarding mass spectrometry. Prior methods: Identification of >120,000 compounds in 12 hours (Marshall group); amortized 3 compounds/second.
This EXAMPLE 5: Completed measurements of hundreds of samples, up to 48 compounds in each mixture.
Regarding automation. This EXAMPLE 5: Performed CAD automation of synthesis; significant progress automating analysis of spectra; with improved reliability, repeatability, with 1000 steps/day with 200 nL resolution.
Prior methods (DNA): Stored 200 MB subdivided among DNA oligonucleotides (Strauss/Ceze/Seelig); millions of unique sequences of ˜150 base pair polymers.
This EXAMPLE 5: Performed >1 Kbit of data in a diversity of small compounds.
Regarding computing. Prior methods (DNA): Relies on hybridization interactions, optimized by evolution; solutions to several-destination Hamiltonian path and SAT problems (Adelman/Lipton); several-bit digital logic circuits based on strand displacement (Soloveichik/Bruck) See, Zielinski, Science (2017); Adelman, Scientific American (1998); Qian, Science (2011).
This EXAMPLE 5: First to perform small molecule computing based upon volumes/concentrations; developing reaction-based computation; inherently parallel chemical computation; CAD-directed robotic liquid handling.
FT-ICR mass spectrometry. Two liquid-handling systems (Labcyte Echo 550 acoustic droplet liquid handler and Andrew Alliance 1000G pipetting robot) were installed.
Optimized libraries of molecules for MS/LC detection; Currently growing the library.
Demonstration of perceptron. The demonstration was show in the EXAMPLES above.
Mitigation of possible risks: (1) Use of heteroatoms to synthesize Ugi molecules to reduce a risk of too many isomers. Completed computational study of mass and non-mass dimension capacities. (2) Smaller mixtures with non-mass dimensions to reduce a risk of too many isomers. Completed computational study of mass and non-mass dimension capacities. (3) Direct storage of mixtures on MALDI plates to reduce risk from fluid handling speeds of 100 Mmb/day (the Labcyte Echo can handle >750,000 transfers/day). Engaged in discussions with supplier about direct transfers to MS, parallelization. (4) Storage of pre-formed mixture libraries; parallel fluid transfers; specialized robotics to reduce risk from fluid handling speeds of 100 Mmb/day. Used volume/concentration-based computing strategies. (5) Careful preliminary studies of reaction networks; optical strategies, to reduce the risk of reaction-based computation. Used volume/concentration-based computing strategies.
Molecular data storage concept. Using a library of M molecules provides 2M possible un-ordered mixtures. When one creates N independent mixtures, there are (2M)N possible states (unique data values). This implies log2((2M)N)=MXN bits of information, with the presence/absence of each molecule in each mixture representing one bit of data.
Arrayed MALDI mass spectrometry. One MALDI plate can contain individual library elements, data mixtures, intermediate compounds, and calibration standards.
Data mixture generation. When data[i, j]==1, then mixture j should include library compound i. The digital data is mapped onto chemical mixtures, and the software produces an automation script for the robotic liquid handler. Benefits: (1) natural error tolerance; (2) spreads data across multiple compounds and multiple mixtures; and (3) only local data scrambling (not global).
Mass spectrometry mixture analysis. The inventors mapped a 640 bit dataset to N=14 mixtures using an M=48 compound library (a subset of “Library 2”). In the first of these mixtures (column 1), the inventors wrote 22 ones and 26 zeros. Monoisotopic masses of the 22 expected present molecules were calculated. When present, these molecules usually appear with multiple isotopes and ions. The inventors have another list of twenty-six expected absent molecules. Using some very simple criteria, this EXAMPLE 5 is at 70-80% accuracy in the first datasets. Improved software and more detailed statistics are in progress.
Summary. In this EXAMPLE 5, the inventors synthesized three combinatorial Ugi libraries, with 102, 140, and 140 molecules, respectively. (Total: 382). The inventors wrote two different datasets, each 640 bits, into mixtures of Ugi compounds. (Total: 1.28 Kb). Each dataset was diluted, copied, and its mass spectrum measured multiple times. Simple metrics indicate 70-80% raw readout accuracy. More detailed statistical analyses and software tools are continuing. With the Echo liquid handler, one can scale up storage capacities by two-three orders of magnitude.
Foundations of molecular information capacity. The invention provides a chemical perceptron, being the implementation of a perceptron in an artificial (simulated) chemistry. The invention provides a mathematical framework for quantifying chemical memory.
For more information, see Rosenstein et al, Principles of Information Storage in Small-Molecule Mixtures arXiv:1905.02187 (May 6, 2019), incorporated by reference.
When more potential states are available to a given system, it becomes less likely that one state can be realized. The information capacity of a system accounts for (i) the number of possible states and (ii) the likelihood of confusing one state for another. When a chemical system has Ω identifiable states, then its information capacity (C, in bits) has an upper bound of:
C≤log2Ω [Equation M]
Because each molecule can be defined only by its chemical identity, those skilled in the molecular computing art can quantify the amount of information represented in a chemical mixture by answering the three following questions:
(1) What is the set of unique molecules which could be present?
(2) Which of these unique molecules is present?
(3) How many copies of each unique molecule are present?
Compare to EXAMPLE 3, discussion of “marbles”. This formulation provides for the precise quantification of any type of molecular memory. This formulation is extensible to cases which include multiple rotational, vibrational, or electronic states of molecules within mixtures.
Nucleic acids have four canonical bases, so the number of possible N-monomer strands is M=4N. When only one of the M molecules may be present, then Ω=M and the identity of the molecule represents 2N bits.
Similarly, proteins with N monomers drawn from an alphabet of twenty amino acids carry log2 20N≈4.3N bits. The information capacity of a single polymer molecule is therefore expressed as:
C≤log2M=N log2B [Equation N]
where B is the number of different monomers.
Although information is often mapped independently onto substructures (monomers) within a molecule, it is the identity of the whole molecule that holds log2 M bits. Those skilled in the molecular computing art understands that when one nucleotide in a nucleic acid polymer changes, the resulting nucleic acid polymer is a different molecule with different genetic information. This understanding is important for generalizing theories of information storage to more diverse non-polymeric molecules.
Unordered Molecular Mixtures. For an unordered mixture of up to Q molecules, when exactly Q molecules are drawn from a library of size M (with potential duplication), then the total number of possible combinations is (M+Q−1)/(M−1). Feller, An Introduction to Probability Theory and Its Applications (John Wiley and Sons, Inc, 1960). When between 0 and Q molecules are selected, then:
The capacity of the system is, therefore:
When there is no duplication among the Q selections, then:
so that the capacity is:
When all molecules may be present (Q=M) without duplication, this capacity becomes:
which are simply M bits.
C1 is the larger of these capacities and provides an upper bound on all memory schemes in unordered mixtures. Making use of C1 requires that one knows the exact concentration (count) of each unique molecule. C2 represents the reduced capacity when duplication carries no information, which is also equivalent to classifying each unique molecule as absent or present above some concentration threshold. Representative curves in
In practice, many copies of each unique molecule are likely present in a mixture. Rather than counting molecules, one can specify that each of the M molecules may exist at one of L distinguishable concentrations. Thus, the capacity becomes:
C
3(M,L)≤C2(M,M)×log2L=M log2L [Equation T]
which reduces to [Equation S] when L=2.
[Equation T] also applies when there are L potential states of each of the M library molecules, which may include chemical modifications or electronic, vibrational, or rotational states. L is the number of states, not the number of dimensions. To reach this upper bound, each molecule's L states is independent. When the states only describe ensembles, the capacity multiplier is less than log2 L.
Molecular data addressing. There are practical advantages to re-introducing ordering and hierarchy to correspond to concepts of ‘addressing’ within the data. The choice of chemical addressing scheme can affect information density, the total capacity, and possibilities for random access.
Spatial addressing. Storing information across a set of independent chemical pools (such as in standard microwell plates) increases capacity linearly with the number of independent wells (W). Because the wells are physically separated, the same library of M potential molecules can be reused in each well. In the limit of very small Q, spatial addressing also describes existing chemical microarrays. Schena et al., Science 270(5235), 467-470 (October 1995); Schirwitz et al., Biointerphases, 7(1), 47 (2012). Also, in the limit of very small Q, spatial addressing describes two-dimensional molecular memory. Green et al., Nature, 445:414 (January 2007); Liu et al., Nature, 347:658 (October 1990).
Sparse data mixtures and address-payload coding. Another concept involves the subdivision of M library molecules into groups of size S, and production of sparse mixtures which contain exactly one molecule from each subgroup. A mixture with sparsity S thus contains M/S molecules. Because each molecule represents an exclusive choice among S possibilities, the total capacity is:
C
4(M,S)≤(M/S)log 2S [Equation U]
This C4 is less than both C1 and C2. This sparse mixture is identical to an address-payload DNA data representation. Bornholt et al., A DNA-Based archival storage system. In Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems, ASPLOS '16, pages 637-649 (New York, N.Y., USA, 2016). ACM. See,
Enforced sparsity reduces the number of valid mixture states (0), by disallowing mixtures which contain more than one molecule from the same address space. The information conveyed per molecule increases, but the overall mixture capacity is reduced.
Capacity. As shown in
In theory, a library consisting of short DNA oligomers of length N=40 could theoretically be used to either select one molecule conveying 80 bits or to create one unordered molecular mixture which represents 151 zettabytes (151×1021 bytes) of data, which is on the scale of all the digital information produced in the entire world per year. See,
Long DNA synthesis and long-read nucleotide sequencing are real bottlenecks for some biological applications. Jain et al., Nature Biotechnology, 36, 338 (January 2018); Kosuri & Church, Nature Methods 11(5), 499-507 (2014). By contrast, mixtures of short polymers can represent any fathomable amount of digital data.
Energy constraints of molecular memory. Any implementation of molecular memory faces constraints in both synthesizing the library and creating the data mixtures. Given library size (M), mixture size (Q), and the number of independent mixtures (W), what constitutes an optimal design? Consider the costs of representing the same information in different configurations. For a mixture of polymers, where the marginal energy per monomer incorporation is ε, then W mixtures of Q unique molecules with length N would require a total energy of:
E=εWQN [Equation V]
Accordingly, [Equation U] becomes:
C≤Q log2(M/S)=Q(log2M−log2(M/S)) [Equation W]
For very sparse mixtures (including single molecules), the second term is negligible. Substituting M=BN, the energy per bit (Eb) becomes:
E
b
=E/C≈ϵ/log28) [Equation X]
Accordingly, for very sparse mixtures of polymers, there are energy benefits from increasing monomer diversity (B), although the scaling is sublinear. For dense binary mixtures (large Q), which may contain many unique compounds, [Equation X] indicates that C≈M per well. In many datasets, one can also approximate Q≈M/2. Thus:
E
b
=E/C≈εN/2 [Equation Y]
This [Equation Y] implies that the optimal strategy is to produce mixtures using the simplest molecules (smallest N) capable of yielding mixtures with the desired capacity.
Across multiple dense mixtures, there can be many duplicated syntheses. When the entire library is synthesized ahead of time, the synthesis cost can be amortized, and the energy constraint may be better described by a physical mixing or fluid handling cost (γ):
M/2=γC/2 [Equation Z]
Thus, the energy per bit is a constant:
E
b
=E/C≈γN/2 [Equation AA]
This [Equation AA] reveals no clear opportunity for the optimization of writing dense molecular mixtures.
To minimize the sizes of both the pre-synthesized library and the array of mixtures, one can optimize for min(M+W) while maintaining C=MW. Geometrically this is a minimum perimeter problem, satisfied by:
W≈M≈√{square root over (C)} [Equation AB]
This [Equation AB] indicates that, for dense mixtures, one optimum occurs when the data mixtures' spatial diversity and molecular diversity are similar.
In summary, a library of M unique molecules can produce a binary mixture representing up to M bits of information. See, [Equation S]. Even among small organic molecules, there are potentially more than 1060 unique compounds. Bohacek et al., Medicinal Research Reviews 16(1), 3-50, (September 1996). Within this space, there are many potential targets for gigabyte-scale small-molecule libraries.
Diversified small-molecule memory. Combinatorial chemistries are regularly used in pharmaceutical pipelines to test the space of potential drug candidates [21, 44]. One of the most scalable strategies for generating functional group diversity is using multicomponent reactions (MCRs). Malinakova, Reports in Organic Chemistry, pages 75-90 (2015). Multicomponent reactions which include the Hantzsch, Biginelli, Passerini, and Ugi reactions, are chemical transformations in which three or more reactants combine, mostly independent of the order in which they are added, to form a single, multicomponent product. Because there are hundreds to thousands of different commercially-available possibilities for each reactant, Multicomponent reactions can generate extremely large libraries.
The readout options in unexplored chemical spaces are not as mature as those for DNA, but a single unambiguous measurement of each molecule need not necessarily be present. The goal is to recover the encoded information, which can be designed to tolerate some chemical ambiguity and errors.
Reading Molecular Memories; Detection Signal Spaces. Depending on the chemical library, mass spectrometry, optical spectroscopy, NMR, or chromatography may all be leveraged to analyze molecular mixtures, and thereby read the data. The detection signal space is typically larger than the chemical mixture space, but the critical goal is to uniquely identify each of the Q potential mixtures, as shown in
A one-to-one correspondence between detection signal space and the molecule in the library is not necessary. Users of the Oxford Nanopore platform showed that chemical structure can be reliably decoded from extremely complex signals when the signals are repeatable and training datasets are available. Rang et al., Genome Biology, 19(1), 90, (2018). Statistical approaches which identify correlated variables and reduce dimensionality can be used to disambiguate signals from data mixtures of non-genomic compounds. Aeron et al., IEEE Transactions on Information Theory 56(10), 5111-5130 (2010).
Capacity under detection limits. Detection errors that mistake one mixture for another are likely to occur, but when these errors are probabilistic, then there are many ways to encode data so that retrieval is asymptotically error-free. Cover & Thomas, Elements of Information Theory. 2nd edition (Wiley, 2012); Polyanskiy et al., IEEE Transactions on Information Theory 56(5), 2307-2359 (2010). The upper limit for the capacity of a memory system can be described by its ‘confusion matrix,’ which quantifies the probabilities of mistaking one of the Ω mixtures for another.
C′=log2Ω+Pc log2Pc+(1−Pc)log2(1−Pc/Ω-1) [Equation AC]
When there is never any confusion (Pc=1), the capacity reaches its maximum of log2 0 bits. When Ω is large, one can approximate:
C′≈P
c log2Ω−HB(Pc) [Equation AD]
where HB(⋅) is the binary entropy function. Cover & Thomas. Elements of information theory (Wiley, 2nd edition, 2012).
Thus, the information capacity scales linearly with the probability of correctly identifying the mixture (Pc).
Channel coding and error correction. From the capacity expression in [Equation AC], those skilled in the molecular computing art tolerate some errors in identifying mixtures while minimizing errors in the data assignments. It is well-known in the molecular computing art that by spreading data across digital sequences of binary inputs (‘codewords’) of length Nc, the probability of errors after decoding can be made vanishingly small when the number of valid codewords |c| satisfies:
(log2|c|)/Nc<C′ [Equation AE]
where C′ is the capacity of the system (in bits) which incorporates expected error rates.
To encode ten bits of information using a library of M=twenty molecules, one can designate only |c|=210 binary mixtures as ‘valid’ out of the Ω=220 mixtures which are possible. Because |c|<Ω, channel coding can be thought of as another form of strategic sparsity, although it constrains the valid states in more sophisticated ways than limiting the number of molecules present. When analysis noise and errors result in an invalid mixture state, the decoder can classify it as the ‘nearest’ valid codeword, by some metric. This workflow is shown in
Successful DNA memory demonstrations used Reed-Solomon codes and fountain codes, which are robust error correcting codes (ECC). Erlich & Zielinski, Science 355(6328), 950-954 (March 2017). Modern communications systems offer more practical methods for constructing near-capacity codes. Berrou et al., in, Proceedings of ICC '93 IEEE International Conference on Communications, vol. 2, pages 1064-1070 (May 1993). A recent system is “noise guessing,” where a codebook is constructed with random binary codewords, and upon detection, a finite series of maximum likelihood noise sequences are applied to the channel output sequentially. Duffy et al., arXiv, (2) (2018) This new “channel-centric” method is both efficient and capacity-achieving in the limit of large N.
The synthetic metabolome for this EXAMPLE is a diverse set of 36 components including vitamins, nucleosides, nucleotides, amino acids, sugars, and metabolic pathway intermediates.
diphosphate sodium
hydrate
indicates data missing or illegible when filed
Chemical preparation. Reagent grade samples of 36 distinct metabolic compounds shown in TABLE 6 were diluted in dimethyl sulfoxide (anhydrous), each to a nominal concentration of 25 mm. Several metabolites were initially dissolved in a small fraction (up to <25%) of alternative solvent (de-ionized water with or without 0.5M or 1M hydrochloric acid) to facilitate solvation in dimethyl sulfoxide. 10 μL of each compound was aliquoted into a 384-well low dead volume microplate from Labcyte Inc., San Jose, Calif., USA.
The read accuracy of each metabolite was found from a 50.4 kbit data plate written using combinatorial mixtures of all 36 metabolites, See,
Data mixture preparation. The inventors then proceeded to assay the spots using Matrix Assisted Laser Desorption Ionization (MALDI) mass spectrometry (MS).
The chemical mixtures were prepared on a 76×120 mm2 stainless steel MALDI plate. To write data with the synthetic metabolome, the inventors used an acoustic liquid handler (Echo 550, Labcyte) to transfer purified metabolic solutions in 2.5 nL increments from the library well-plate onto pre-defined locations on a steel MALDI plate. The nominal droplet transfer volume is 2.5 nL but to reduce variability one can use two droplets (5 nL) per compound. The destinations of the droplets are programmed to match a standard 2.25 mm pitch 1536-spot (32×48) target. This produces a spatial array of different mixtures of metabolites. The presence or absence of each compound in each mixture encodes one bit of information, and thus the total data capacity of a data plate is equal to the size of the metabolome library multiplied by the number of spots on the plate.
After evaporating the solvent, each data plate contains up to 1536 dried spots on a 2.25 mm pitch. See,
After spotting the compounds to the MALDI plate, a MALDI matrix material was added to each location. The inventors selected the matrix 9-Aminoacridine for its compatibility with metabolite libraries, its low background in the small molecule regime, and its support for both positive and negative ion modes. The MALDI plate, containing droplets with both matrix and metabolite mixtures, is left to dry and crystallize overnight (˜10 hours).
Once dried, the plate can be stored in a humidity controlled cabinet or analyzed by MALDI-FT-ICR mass spectrometry.
To prescreen each compound in the synthetic metabolome, a 50.4 kbit data plate was written using combinatorial mixtures of all thirty-six metabolites. See, the chart in
Ion cyclotron mass spectrometry of metabolite mixtures. The inventors used a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer (SolariX 7T, Bruker) to assay the array of crystallized mixtures. An FT-ICR mass spectrometer uses a strong magnetic field to excite ions into a periodic orbit, which enables a much finer mass resolution than time-of-flight (ToF) instruments. In these assays, the mass resolution was typically <0.001 Da. See
The inventors wrote more than 100 kbits of image data into synthetic metabolomes. This number is conservative.
The inventors selected a subset of 6 metabolites, which were used to encode a 6142-pixel binary image of a Nubian ibex into an array 1024 mixtures. See,
A Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer (SolariX 7T, Bruker) was used to analyze the crystallized metabolite data mixtures. The exact resolution is a function of the measurement time allocated per spectrum. For these assays, the inventors typically used 0.5-1 sec, yielding a resolution of <0.001 Da (see supplemental figure S2). The instrument is run in MALDI mode (laser power ˜22%) and is configured to serially measure the mass spectrum of each mixture on the 48×32 grid. Acquisition for a full plate takes <2 hours.
To decode the mass spectra into binary data, the inventors chose a threshold of 3a as the intensity required to declare the presence of a metabolite. For the tryptophan [2Mtp+K]+ mass shown in
This detection scheme can also be visualized by position on the plate, as shown in
Statistical analysis of data plates. The analysis in
Each high-resolution FT-ICR mass spectrum contains ˜2×106 m/z points. By calculating the ensemble average of all mass spectra from the entire plate, the inventors restricted the search to peaks present in this ensemble spectrum (as averaging over spots with exactly the contents), which yields 1444 candidate peaks.
Those skilled in the molecular computing art can test each of these candidate peaks against the encoded dataset, to determine how accurately its intensity predicts the encoded data. See,
Although the inventors identified these peaks without chemical bias, many features can be attributed to known adducts.
Decoding Data from Multiple Peaks Using Logistic Regression
Although multiple m/z features yield similar decoding accuracy, only one peak was selected per metabolite. By assuming that the errors are not correlated (see
After identifying the set of statistically discriminating peaks, the inventors performed a logistic regression using between 1 and 16 of the best-performing peaks. Those metabolites whose single-mass classification began at >99% showed minimal improvements with increasing numbers of features. Sorbitol (so) error rates fell more significantly from 20% to 4% with multi-peak regression. See,
Multi-mass linear regression achieved an accuracy of 97.7% for the whole cat image. See,
The inventors presented several kilobyte-scale data sets encoded into synthetic metabolomes using robotic liquid handling, followed by recovery of the data by mass spectrometry. Statistically discriminating m/z features were used to classify the metabolite mixtures and recover the data at 98-99.5% accuracy. Typical write speeds were 5 bits/sec, and aggregate read speeds were 11 bits/sec.
The inventors performed assays where the cumulative concentration of all metabolites was typically 25 mM per spot. When a similar concentration is spread across the whole human metabolome (˜125,000 elements, with half present on average), then each metabolite is present at 0.4 μM concentration.
The method of the invention can be performed by assaying with MALDI mass spectroscopy. Sub-zeptomole mass spectrometry and nanomolar concentration detection were available for nearly two decades. Belov et al., Anal. Chem. 72(10), 2271-2279 (2000); Tang et al., J. Bact. 189, 940-949 (2007). Therefore, μM detection of a whole metabolome can be demonstrated, and typical whole metabolome profiling identifies on the order of 10,000 ion peaks. Lu, Annu. Rev. Biochem. 86, 277{304 (2017).
Due consideration of interconversion of metabolites in the analysis will, therefore, reduce errors.
Small molecules have several compelling advantages for both storage and computation. They do not require polymerization or enzymatic steps. They can resist cellular digestion and extreme environmental conditions. Some are cheap to synthesize. Small molecules have higher information capacity than DNA. In principle, they could store information at densities greater than 4×1018 bytes/mm3. This exceeds the theoretical storage density of DNA by up to two orders of magnitude.
This EXAMPLE focuses on classes of small molecules that can: (1) store large amounts of information with little degradation over time; (2) realize computations that can be embedded in the target applications; and (3) be detected in time and space with high resolution.
Several classes of small molecule classes are being tested, including acids and bases, inorganic catalysts and redox operations, stereoisomers, and multicomponent mixtures. Molecular computing processes can thus be tested theoretically and computationally. These include computing on analog/fractional values; Boolean logic; thresholding and majority logic; and autocatalytic reactions.
This EXAMPLE spans end-to-end the tasks of encoding data with small molecules, computing, and reading out results. The diversity in form and function of small molecules opens new possibilities for computing. The research results can be validated by applying them to a variety of impactful applications. These include image and signal processing; parallel pattern recognition; neural computation and machine learning; and hyperdimensional computing.
An overarching goal of this EXAMPLE is to devise in situ computing capabilities, where sensing, computing, and actuating occur at the molecular level, with no interfacing with external electronics.
This EXAMPLE has three synergistic thrusts. The first emphasizes testing and analysis; the second algorithmic development; and the third validation.
Thrust I: Small molecules for information encoding to test a variety of small-molecule classes from different domains of chemistry. The inventors establish theoretically and experimentally the information density of these classes for molecular storage. The inventors identify the reaction mechanisms suitable for in situ computation. The classes of molecular compounds include:
Acids and bases: Ubiquitous and easy to work with, acids and bases are complementary, a useful property that the inventors use for digital logic.
Inorganic catalysts and redox operations: Inorganic molecules are key reactants in autocatalytic reactions, which one can use for their natural thresholding properties in classification tasks. See EXAMPLE 1 above.
Stereoisomers share the same chemical formula but differ in their atomic arrangement. Examples are enantiomers: pairs of molecules that are mirror images of each other. The invention uses the relative concentrations of the two forms for fractional encodings and analog computation. Enantiomers are pairs of stereoisomers that are mirror images of each other. Enantiomers can be created using molecules with chiral carbons, i.e., carbon atoms bonded with four different chemical groups and possess a tetrahedral structure. Two enantiomers of the molecule carvone exist in nature. The R conformation is found in spearmint. The S conformation is found in caraway seeds. The two forms have distinct odors.
Multicomponent molecular mixtures: By encoding information in the presence or absence of diverse libraries of small molecules, molecular mixtures can store far more information than pure samples of single polymer sequences. See Walker et al. (eds), From Matter to Life: Information and Causality (Cambridge University Press, 2017).
Thrust II: Robust computing with small molecules to devise computing processes using the small molecule classes outlined in Thrust I above. The inventors used chemical reaction networks (CRNs) as a formalism. See
Computing on analog/fractional values tests a paradigm for computing on molecular concentrations: a so-called fractional representation. See Soeken et al., IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 36(11), 1842-1855 (2017). Building on the theory of stochastic logic, one can implement complex math functions (polynomials, exponentials, logarithms, and hyperbolic tangents) with simple and efficient chemical reaction networks. See
Thresholding, majority logic, and neural computation applies the complementarity of chemical species to implement a variety of forms of computation: parity, majority, thresholding, and neural computation. A “dual-rail” representation with acid and bases, as well as with stereoisomers, is a key concept.
Autocatalytic reactions for nonlinear computation use the nonlinearity of autocatalytic reactions to implement thresholding operations for neural computation.
Spanning these themes is the software tool, MolLink, which enables interdomain compilation and synthesis. MolLink enables one to compile programs into target chemistries, minimizing their cross-reactivity. It also provides simulation, verification, and visualization functions.
Thrust III: In situ molecular processing: Building upon the first two thrusts, the inventors test uses of small molecule storage and computing. The goal is to devise in situ computing capabilities, where sensing, computing, and actuating occur at the molecular level, with no interfacing at all with external electronics, such as the following applications:
Image processing and classification to implement a full-scale molecular image classifier using neural network algorithms. Performing the requisite image processing in situ, in molecular form, eliminates data transfer bottlenecks. The inventors use conceptual topics from Thrust II: autocatalytic reactions for thresholding; complementarity for Boolean operations; and concentration-based molecular computation for arithmetic. One can quantify the accuracy of image processing in terms of the signal-to-noise ratio and the structural similarity index.
Machine learning to test a common data representation for integrating sensing, computing, and actuation in situ: hyperdimensional random vectors. Data is represented by long random vectors of integer or Boolean values. One can deploy this paradigm for machine learning, using the randomness of molecular mixtures for encoding, which can naturally map to large vector representations.
Rather than representing information in linear molecular sequences, one can store data in disordered mixtures of small molecules which can be identified by their molecular structures. To scale this approach to large amounts of data, the inventors created large libraries of unique compounds through automated multicomponent reactions.
Small molecule reactions often occur spontaneously, if they are exergonic reactions, or with single-digit kcal/mol energy input, if they are endergonic reactions at room temperature. In principle, this makes them up to seven orders of magnitude more energy-efficient than electronics.
The purpose of this is EXAMPLE is to provide updated results concerning the practice of the invention disclosed in the EXAMPLES above. The goal of the invention disclosed in the EXAMPLES above is to (1) to store abstract digital data by taking advantage of small molecule chemical diversity; (2) to develop leading-edge synthesis and analysis techniques that can scale to billions of molecules/day; and (3) to establish scalable strategies for solution-phase information processing using small-molecule reactions. Using small molecules, information can be represented by combinations of chemical identity/formula/structure, chemical concentration, mixture composition, time, location, and energetic state (rotational, vibrational, electronic, magnetic). A chemical ensemble in storage having a static and unique system state can be measured as a unique spectral state. Moreover, a chemical ensemble in a reaction-based state can also be measured as a unique spectral state. The ongoing assays to test data storage includes (1) sparse mapping for higher data capacity with the same experimental throughput; (2) coding and redundancy for accurate data recovery; (3) improvements towards zero-characterization libraries; (4) on-demand synthesis in data write flow instead of pre-synthesis. In addition to single-peak identification of spectra, the invention also provides multipeak regressions that improve accuracy and combinatorically increases capacity.
Some Themes of this EXAMPLE Include:
Defining the space of opportunities for representing information using the continuum from precisely-specified molecules to imprecisely-specified mixtures. (1) Explicit molecular identity: DNA; proteins; and purified Ugis. (2) Unspecified molecular identity: Nominally one substance, but not necessarily purified, so that one does not know the readout signature ahead of time. (3) Specified mixtures: Active control over the relative proportions of multiple species per library component. (4) Unspecified mixtures: Natural samples that are known to contain many species, but not controlled. Mixtures may correspond to other contextual states or environmental states.
Defining the space of opportunities for representing information using the spectrum from precisely-specified molecules to imprecisely-specified mixtures. The opportunities include explicit molecular identity and explicit molecular identity, such as DNA; proteins; and purified Ugis.
Defining the space of opportunities for representing information using the spectrum from precisely-specified molecules to imprecisely-specified mixtures. Unspecified molecular identity: Nominally one substance, but not necessarily purified, so that one does not know the readout signature ahead of time.
diphosphate sodium
hydrate
indicates data missing or illegible when filed
See also, TABLE 6.
Defining the space of opportunities for representing information using the spectrum from precisely-specified molecules to imprecisely-specified mixtures. Using specified mixtures, one can achieve active control over the relative proportions of multiple species per library component.
Defining the space of opportunities for representing information using the spectrum from precisely-specified molecules to imprecisely-specified mixtures. An under-represented category. Using specified mixtures, one can achieve active over the relative proportions of multiple species per library component. Traditional DNA data encodes one base per position. For composite DNA data encoding, one position might be 25% A, 0% C, 25% G, 50% T. See Anavy et al., Nature Biotechnology (2019).
Also, scaling up information density can use deeper reagent sequences, rather than a larger set of starting materials.
Determining differences in the speeds of molecular kinds (DNA, small molecule, etc.). Molecular computing approaches may have the same dimensionality, but these are not the same as silicon. The elements of the search processes that persons having ordinary skill in the molecular computing art can measure include kinetics (time to successful search reaction) and thermodynamics (free energy dissipated). See Lakin, Bioinformatics (2011).
Continued testing of the optimal space in which to encode data. Work is continuing on how small molecules are clustered in the chemical libraries that have been created. New interconnections arise, whose spectral networks could have different features and scalings. The different relationships in spectral space can lead to improved molecular fingerprinting assays. See Grzybowski et al., Nature Chemistry (2009). The techniques of the invention can be used to understand the structure (interconnectedness, scales) of those spaces. See FIGS.
So far, the inventors synthesized mixtures of Ugi molecules representing >1,000,000 bits of data, the most reported in small molecules.
The inventors developed new time-dependent storage techniques that can increase capacity, while using the same amount of resources.
The inventors demonstrated volumetric and chemical perceptrons and used them for image processing. See
In addition to the explicit mixtures from pre-synthesized molecular libraries that the inventors created in the EXAMPLES above, persons having ordinary skill in the molecular computing art can use the time-order of reactive components to store additional information in relative concentrations of products. In addition to the single-peak identification of spectra disclosed in the EXAMPLES above, persons having ordinary skill in the molecular computing art can measure and compute multipeak regressions that substantially improve accuracy and combinatorically increase capacity.
Computation risks and mitigation. See also EXAMPLE 11. For scaling molecular computation to storage capacity, computational scaling is limited by cross-reactivity, reaction speed in solution. In mitigation: The initial use of metabolic pathways evolved to cofunction, so development of techniques that require fewer molecular than in silico operations is possible.
For marrying storage and computing media, the stability required for storage is inconsistent with the malleability needed for computation. In mitigation, one can use metabolite computation or use of multistability.
For computation speed, the reaction-based, classical molecular computation is slower and limited by reaction times. In mitigation, one can encode more complex operations into each reaction, exploration of degrees of freedom that may be more quickly manipulated.
The contents of all references cited herein are incorporated by reference in their entireties. In case of conflict, the present application, including any definitions herein, will control.
Having thus described in detail preferred embodiments of the present invention, other embodiments will be evident to those skilled in the molecular computing art. The foregoing detailed description is illustrative and not restrictive. The spirit and scope of the present invention are not limited to the above examples but are encompassed by the following claims.
Among other embodiments, the invention provides:
A method for computing with chemicals, the method comprising the steps of: encoding an abstract digital data into a plurality of liquid volumes of a plurality of chemicals to obtain a dataset; translating the dataset into a chemical form; creating the data set using spectrometry, spectroscopy, or a combination of both assay methods; querying the dataset by performing a volumetric operation to obtain a perceptron; and analyzing the perceptron for identifying chemical structure, concentration, or another characteristic of at least one of the chemicals, thereby developing a chemical computational language.
The method described above, wherein the abstract digital data comprises a binary computer language.
The method described above, wherein translating further comprises assembling a library of chemicals in the dataset.
The method described above, wherein volumetric operation is performed robotically.
The method described above, wherein volumetric operation further comprises a programmed standard volumetric transfer.
The method described above, wherein the plurality of liquid volumes of the plurality of chemicals are a mixture of different chemical molecules, and optionally, wherein the abstract digital data comprises presence or absence of chemical molecules in the mixture.
The method described above, wherein spectrometry comprises mass spectrometry.
The method of described above, wherein spectroscopy comprises at least one of: ultraviolet-visible spectroscopy, Rydberg spectroscopy, Infrared spectroscopy, fluorescence spectroscopy, and absorption spectroscopy.
A method for molecular computing using a chemical perceptron, the method comprising the steps of: preparing a plurality of distinct mixtures of molecules to obtain a chemical data set, wherein the mixtures of molecules are an input unit of the perceptron; writing the data set on an array and applying an operation to the data set for transduction of the input unit; combining the input unit by an operation to obtain an operation product; and detecting a threshold of the operation product, thereby obtaining product of the chemical perceptron.
The method described above, wherein the array is a micro-well plate or a MALDI plate.
The method described above, further comprising applying a chemical multiply accumulate operation to obtain the mathematical equivalent of the perceptron, and optionally wherein the chemical multiply accumulate operation is z=Liwi·xi+b, where z is the output of the multiply accumulate operation, Wi is the weight of a species, xi is the initial amount of the species, and b is the bias.
A chemical perceptron comprising: a plurality of analytes; an array spectrum; a fluid handling robot; a computer; and a molecule quantifier or a molecule identifier.
The perceptron described above, wherein the molecule quantifier or molecule identifier is at least one selected from: a high performance liquid chromatography (HPLC), and a mass spectrometer, and optionally wherein the array spectrum is at least one selected from a micro-well plate, and a MALDI plate.
A method for obtaining an output of a linear classification operation, the method comprising the steps of: encoding binary data into a chemical composition of a plurality of liquid samples; receiving an input of binary data; performing multiplication operation by a plurality of fractional volume transfers of the liquid samples into a plurality of micro-wells corresponding to the input; pooling the liquid samples to obtain an output; and analyzing the concentration of the chemicals in the output by a HPLC, thereby obtaining the output for the linear classification operation.
The method described above, further comprising the step of scaling a classifier weight corresponding to maximum available volume in the micro-wells, and optionally wherein the classifier weight corresponds to amount of the plurality of fractional volume transfers of the liquid samples.
The method described above, further comprising performing the plurality of fractional volume transfers by a robot.
The method described above, wherein the liquid samples are nonreactive.
The method described above, further comprising performing parallel computing to obtain the output for the linear classification operation.
A method for coding information with a mixture of product molecules, the method comprising the steps of: mapping of a plurality of each pixels on an array corresponding to a plurality of known organic chemical entity molecules each in a known location within the array to obtain a pixel map; reacting a selected subset of the molecules corresponding to the pixel map thereby synthesizing the mixture of product molecules; and analyzing the mixture of product molecules to identify the product molecules.
The method described above, wherein the reacting step further comprises performing an Ugi reaction to obtain an Ugi product molecule, and optionally further comprising the step of creating a new Ugi product molecule, or optionally wherein the plurality of known organic chemical entity molecules comprise a chemical scaffold.
The method described above, wherein the plurality of known organic chemical entity molecules comprise reaction groups, optionally wherein the reacting step further comprises substituting the reaction groups.
The method described above, wherein the reacting step further comprises changing pH of at least one of the plurality of known organic chemical entity molecules.
A method for computing with chemicals, the method comprising the steps of: encoding digital data into a plurality of chemicals to obtain a dataset and translating the dataset into a chemical form; reading the data set using spectrometry and/or spectroscopy and querying the dataset by performing an operation to obtain a perceptron; and analyzing the perceptron for identifying chemical structure, concentration, or another characteristic of at least one of the chemicals, thereby developing a chemical computational language.
The method described above, wherein the operation further comprises at least one of a volumetric transfer or a chemical reaction, optionally further comprising the step of measuring a rate constant and/or an equilibrium constant of the chemical reaction, or optionally wherein the chemical reaction further comprises an Ugi reaction to obtain at least one Ugi product molecule.
The method described above, further comprising the step of synthesizing a new chemical.
The method described above, wherein digital data comprises a computer language.
The method described above, wherein the plurality of chemicals further comprises a plurality of liquid volumes.
The method described above, wherein the plurality of chemicals are a mixture of different chemical molecules, and optionally wherein the digital data comprises presence or absence of chemical molecules in the mixture.
The method described above, wherein spectrometry comprises mass spectrometry.
The method described above, wherein spectroscopy comprises at least one of: ultraviolet-visible spectroscopy, Rydberg spectroscopy, Infrared spectroscopy, fluorescence spectroscopy, and absorption spectroscopy.
The method described above, wherein the plurality of chemicals comprise reaction groups, and optionally wherein reacting further comprises substituting the reaction groups.
The method described above, wherein reacting further comprises changing pH of at least one of the plurality of chemicals.
An information storage system, comprising a solid surface with plurality of addressable locations, wherein each addressable location comprises a mixture of small molecules, and each mixture contains one set of small molecules per addressable location.
The information storage system described above, wherein the small molecules are metabolomic elements.
The information storage system of described above, wherein the solid surface is a MALDI plate.
The information storage system described above, wherein the addressable locations comprise at least 1024 independent mixture spots.
The information storage system described above, wherein the addressable locations comprise thousands of spatially arrayed nanoliter spots.
The information storage system described above, wherein the storage system comprises more than 100 kbits of data.
The information storage system described above, wherein the storage system comprises a gigabyte of data.
A method of storing information in a plurality of metabolomic elements, comprising the steps of converting a format of information into a plurality of digital sequences; converting the plurality of digital sequences into a plurality of corresponding metabolomic elements using one bit per metabolomic element, and storing the plurality of corresponding metabolomic elements on a solid surface, where the location of a metabolomic element is an addressable location.
The method described above, wherein the converting the plurality of digital sequences into a plurality of corresponding metabolomic elements Is performed using robotic liquid handling.
A method of retrieving a format of information from a plurality of metabolomic elements encoding digital sequences of the format of information, comprising the steps of assaying a solid surface comprising a set of metabolomic elements; where the location of a metabolomic element is an addressable location; converting the metabolomic elements to digital sequences; and converting the digital sequences to a format of information.
The method of described above, wherein the assay method is mass-spectroscopy, and optionally wherein the mass-spectroscopy is MALDI mass spectroscopy.
The method described above, wherein the retrieving a format of information from a plurality of metabolomic elements results in an information recovery at >99% accuracy.
The method described above, further comprising the step of visualizing the format of information.
The method described above, further comprising the step of mitigating errors in the converting of the metabolomic elements to digital sequences.
The method of described above, wherein the mitigating errors comprises logistic regression analysis.
The method described above, wherein the converting the digital sequences to a format of information is performed using one m/z peak selected per metabolomic element.
The method described above, wherein the converting the digital sequences to a format of information is performed using multiple m/z peaks selected per metabolomic element.
A chemical perceptron, comprising the mathematical framework described herein for quantifying chemical memory.
The chemical perceptron described above, further comprising autocatalytic thresholding.
Persons having ordinary skill in the molecular computing art can rely on the following patents, patent applications, scientific books, and scientific publications for enabling methods:
This document is a continuation-in-part of U.S. Ser. No. 17/378,988, filed Jul. 19, 2021, which is a divisional patent application of U.S. Ser. No. 17/253,013, filed Jun. 20, 2019, now U.S. Pat. No. 11,093,865, granted on Aug. 17, 2021, which is a national phase filing under 35 U.S.C. § 371 of International Application No. PCT/US2019/038301, filed Jun. 20, 2019, which claims the benefit of priority to patent applications U.S. Ser. No. 62/687,366, filed Jun. 20, 2018, and U.S. Ser. No. 62/791,504 filed Jan. 11, 2019, the entire contents of which are hereby incorporated by reference herein.
This invention was made with government support under grant number W911NF-18-2-0031 awarded by the Defense Advanced Research Projects Agency (DARPA). This invention was made with government support under grant number 1941344 awarded by the National Science Foundation. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 62687366 | Jun 2018 | US | |
| 62791504 | Jan 2019 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 17253013 | Dec 2020 | US |
| Child | 17378988 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 17378988 | Jul 2021 | US |
| Child | 17929279 | US |
