Patent Grant
9898687
The present disclosure relates generally to an apparatus, and related methods, for processing data, and more specifically, for identifying association variables, such as biological variables, which are associated with a trait.
Many mathematical problems involve analyzing data to determine relationships between variables. For example, in regression analysis an expression can be determined to describe data (which is sometimes referred to as ‘fitting’ the expression to the data). This is shown in
y=mx+b,
where x (the data) is the dependent variable, and m and b are unknown coefficients (the slope and y-intercept, respectively) that are to be determined during the fitting. In this example, each datum in the data corresponds to a point in the x-y plane (such as x0, y0).
Typically, the minimum number of data points needed to uniquely determine the fitting equation equals the number of unknowns in the fitting equation (as shown in
Unfortunately, many interesting problems are underdetermined. For example, in biology, important differences between different individual's genomes can be described by single nucleotide polymorphisms (SNPs). As shown in
However, even after eliminating correlated SNPs using a haplotype map (which includes information about closely related alleles that are inherited as a unit), there may still be several hundred thousand or more SNPs for each individual in a population. In order to identify the associations, these SNPs may be compared to the expression of a trait in the population, such as the occurrence of a disease. Typically, the population may include several thousand individuals. Consequently, identifying the associations involves ‘fitting’ several hundred thousand SNPs (the fitting space) to several thousand data points, which is an extremely underdetermined problem that increases the complexity, time and expense when trying to identify the associations.
Furthermore, it is unusual for a disease (or, more generally, an expressed trait) to be associated with a single gene. More typically, the disease is associated with multiple genes (i.e., it is polygenetic), as well as one or more environmental factors. In the case of SNPs, including these additional variables and/or combinations of variables causes a power-law increase in the size of the fitting space. If the population size (several thousand people) remains unchanged, the problem becomes vastly underdetermined. Unfortunately, increasing the size of the population is often difficult because of the associated expense and time needed to obtain biological samples.
Therefore, there is a need for an analysis technique to identify associations in underdetermined problems without the problems listed above.
One embodiment of the present disclosure describes an apparatus, such as a computer system or a circuit, to identify one or more association variables that are associated with a trait. This apparatus may determine patterns of occurrence of compound variables based on a set of mathematical interactions and patterns of occurrence of a set of biological variables of a group of life forms (such as humans, animals, bacteria, fungi and/or plants), where a pattern of occurrence of a given compound variable may be determined based on a given mathematical interaction in the set of mathematical interactions and patterns of occurrence of a given pair of biological variables in the set of biological variables. Moreover, the apparatus may calculate statistical relationships corresponding to a pattern of occurrence of the trait in the group of life forms and the patterns of occurrence of the compound variables. Note that a given statistical relationship corresponds to the pattern of occurrence of the trait in the group of life forms and a pattern of occurrence of a given compound variable, and the calculation may include contributions from presence and absence information in the patterns of occurrence of the trait and the pattern of occurrence of the given compound variable.
Using the statistical relationships, the apparatus may determine numbers of occurrences of biological variables that were used to determine the compound variables in at least a subset of the compound variables, where the subset of the compound variables have statistical relationships greater than a statistical confidence value. Furthermore, the apparatus may determine numbers of different mathematical interactions used to determine the compound variables in the subset of the compound variables for the biological variables that are associated with the corresponding numbers of occurrences. Then, the apparatus may identify one or more of the biological variables in the set of biological variables as the one or more association variables based on the numbers of occurrences and/or the numbers of different mathematical interactions.
In some embodiments, the given compound variable is determined by performing a mathematical operation specified by the given mathematical interaction on corresponding entries in a pattern of occurrence of a first biological variable in the given pair of biological variables and a pattern of occurrence of the second biological variable in the given pair of biological variables.
Moreover, the calculating may involve a non-parametric statistical analysis technique, such as: a chi-square analysis technique, a log-likelihood ratio analysis technique, a goodness-of-fit (G-test) technique, and/or a Fisher's exact probability analysis technique. More generally, the calculating may involve a supervised learning technique. This supervised learning technique may include a support vector machines (SVM) analysis technique and/or a classification and regression tree (CART) analysis technique.
Note that the statistical confidence value may correspond to a statistical significance value associated with the statistical relationships. For example, the statistical confidence value may correspond to a noise floor in the statistical relationships. This noise floor may be determined based on approximate stability of at least a portion of a ranking of the biological variables that were used to determine compound variables in at least a subset of the compound variables, where the ranking is based on the numbers of occurrences of the biological variables. Moreover, the approximate stability may be for statistical confidence values between the statistical confidence value and another statistical confidence value, where the other statistical confidence value corresponds to a larger statistical significance value associated with the statistical relationships than the statistical confidence value.
In some embodiments, the apparatus calculates additional statistical relationships corresponding to a pattern of occurrence of a sequence of values and the patterns of occurrence of the compound variables, where a given additional statistical relationship corresponds to the pattern of occurrence of the sequence of values and the pattern of occurrence of the given compound variable. This calculation may include contributions from presence and absence information in the patterns of occurrence of the sequence of values and the pattern of occurrence of the given compound variable. Then, the apparatus determines additional numbers of occurrences of biological variables that were used to determine additional compound variables in at least another subset of the compound variables, where the other subset of the compound variables have statistical relationships greater than the statistical confidence value or another statistical confidence value. Moreover, the apparatus corrects the numbers of occurrences of biological variables based on the additional numbers of occurrences of biological variables prior to identifying the one or more association variables. Note that the sequence of values include a random or a pseudo-random sequence of values, and a number of entries in the sequence of values may equal a number of life forms in the group of life forms.
The set of biological variables may include information associated with at least single nucleotide polymorphisms (SNPs) and/or copy number variations (CNVs). More generally, the set of biological variables may include epigenetic information, information associated with deoxyribonucleic acid, information associated with ribonucleic acid, information associated with one or more proteins, and/or information associated with another biological marker. In some embodiments, the set of biological variables includes one or more environmental factors. Note that the trait may include phenotype information, such as that for a disease and, more generally, for a characteristic.
Furthermore, a given pattern of occurrence of a given variable, which can include the trait in the group of life forms, the given compound variable, or either one of the given pair of biological variables, may include presence and absence information of the given variable. For example, the presence information of the given variable may include expression or suppression of the given variable, and the absence information of the given variable includes an absence of expression or an absence of suppression of the given variable.
In some embodiments, the apparatus excludes at least some of the compound variables prior to calculating the statistical relationships. Note that a given excluded compound variable may have a number of presences or absences in the pattern of occurrence of the given excluded compound variable that is greater than a first value or less than a second value.
The set of biological variables may include categorical data. Alternatively, the apparatus may convert the set of biological variables into categorical data prior to calculating the compound variables. Note that the converting for a given genetic locus (such as a base-pair location) may be based on a minor allele frequency and/or a major allele frequency of a SNP at the given genetic locus. Additionally, the apparatus may exclude at least some of the biological variables in the set of biological variables prior to calculating the compound variables. Note that a given excluded biological variable may have a number of presences or absences in the pattern of occurrence of the given excluded biological variable that is greater than a third value or less than a fourth value.
In some embodiments, the apparatus determines the set of biological variables of the group of life forms based on biological samples associated with the group of life forms.
Note that identifying the one or more association variables constitutes an underdetermined problem. For example, a number of life forms in the group of life forms may be significantly less than a number of biological variables in the set of biological variables.
Another embodiment provides a method that includes at least some of the operations performed by the apparatus.
Another embodiment provides a computer-program product for use with the apparatus. This computer-program product includes instructions for at least some of the operations performed by the apparatus.
Table 1 provides identified association variables in an exemplary embodiment.
Table 2 provides a contingency table in an exemplary embodiment.
Note that like reference numerals refer to corresponding parts throughout the drawings. Moreover, multiple instances of the same part are designated by a common prefix separated from an instance number by a dash.
Embodiments of an apparatus (such as a computer system or a circuit), a method (which is sometimes referred to as an ‘identification technique’), and a computer-program product (e.g., software) for use with the apparatus are described. This apparatus may be used to identify one or more association variables that are associated with a trait. In particular, compound variables may be determined for biological variables in a set of biological variables of a group of life forms (such as genetic data for a group of people, animals, bacteria, fungi and/or plants) based on a set of mathematical interactions. (Alternatively, the compound variables may be pre-determined.) A given compound variable may be determined using a given mathematical interaction and one or more biological variables (such as a given pair of biological variables), where a given entry in the compound variable for a given one of the life forms is based on a presence or absence of the one or more biological variables for the given one of the life forms. For example, the given entry may be determined by performing a logical operation (AND, OR, NOT, XOR and/or another Boolean operation) or a mathematical operation specified by the given mathematical interaction on the values of one or more biological variables of the given life form. Alternatively or additionally, the given entry in the compound variable for the given one of the life forms may be based on an expression or suppression of one or more biological variables for the given one of the life forms.
Then, the apparatus may calculate statistical relationships between a pattern of occurrence of the trait associated with a group of life forms (e.g., presence or absence of the trait in the group of life forms) with patterns of occurrence of compound variables in the set of biological variables of the group of life forms (e.g., presence or absence entries in the compound variables). These calculations may involve a non-parametric statistical analysis technique and/or a supervised learning technique.
Next, the apparatus may determine numbers of occurrences of biological variables that were used to determine compound variables in at least a subset of the compound variables that have statistical relationships greater than a statistical significance value, which may correspond to a noise floor in the statistical relationships. This noise floor may be determined based on approximate stability of at least a portion of an occurrence ranking based on the numbers of occurrences for statistical confidence values between the statistical confidence value and another statistical confidence value, i.e., a range of statistical confidence values.
Moreover, the apparatus may determine numbers of different mathematical interactions that were used to determine the compound variables in the subset of the compound variables for the biological variables that are associated with the corresponding numbers of occurrences.
Furthermore, the apparatus may identify one or more of the biological variables as one or more association variables based on the numbers of occurrences and/or the numbers of different mathematical interactions. For example, N association variables may be the top-N values in rankings based on the numbers of occurrences and/or the numbers of different mathematical interactions.
In some embodiments, the apparatus performs a correction for a background prior to identifying the one or more association variables. For example, the apparatus may subtract from the occurrence ranking another occurrence ranking which is associated with numbers of occurrences of the biological variables that were used to determine compound variables in other statistically significant statistical relationships (i.e., those compound variables which have statistical relationship values greater than the same or another statistical significance value) between the patterns of occurrence of the compound variables and a pattern of occurrence of a sequence of values (such as a random or a pseudo-random sequence of values).
In the discussion that follows, the following definitions are used:
the meaning of ‘configured’ may include ‘to set up for operation especially in a particular way’, such as a circuit configured for a particular function or a program configured to be executed on a particular processor or computer;
the meaning of ‘configurable’ may include ‘capable of being configured in a particular way’, such as a programmable circuit that is configurable or a program (source code or compiled) that can be configured to executed on the particular processor at run time;
the meaning of ‘based on’ may include ‘is a function of’, ‘using’ and/or ‘according to’;
the meaning of ‘group of life forms’ may include ‘a group that includes one or more people, animals, bacteria, fungi, plants and/or an engineered life form (such as a genetically engineered life form);
the meaning of ‘pattern of occurrence of a variable or a trait for a group of life forms’ may include ‘values corresponding to presence and/or absence information for the variable or the trait for each of the life forms in the group’, ‘values corresponding to expression and/or non-expression information for the variable or the trait for each of the life forms in the group’, ‘values corresponding to suppression and/or non-suppression information for the variable or the trait for each of the life forms in the group’, and/or ‘values corresponding to expression and/or suppression information for the variable or the trait for each of the life forms in the group’ (note that non-expression or non-suppression may be equivalent and may correspond to a value between expression and suppression);
the meaning of ‘ranking’ may include ‘a listing of items in a group according to a system of rating’;
the meaning of ‘allele’ may include two or more alternative forms of a genetic locus, where a single allele for each genetic locus may be inherited separately from each parent (e.g., at a genetic locus for eye color an allele might result in blue or brown eyes);
the meaning of ‘phenotype’ may include ‘the observable traits or characteristics of an organism, such as hair color, weight, or the presence or absence of a disease, which may not be genetic or may not be solely genetic’;
the meaning of ‘epigenetic’ may include ‘something that affects a cell, organ, plant, animal or individual (i.e., a human) without directly affecting its DNA, which may indirectly influence the expression of the genome’; and
the meaning of ‘disease’ may include ‘an illness or sickness characterized by an impairment of health or a condition of abnormal functioning’.
In general, the trait includes phenotype information, such as: how life forms (for example, humans) develop diseases and respond to pathogens, chemicals, drugs (or pharmacological agents), vaccines, and/or other agents. In some embodiments, the trait includes a disease. This disease may include: a type of cancer, an auto-immune disease, an immune-related disease, a form of arthritis, a disease of at least a portion of the endocrine system, a metabolic disease, cardiovascular disease, a neurological disease, a respiratory disease, joint disease, gastrointestinal disease, a disease of a component in blood, a psychological disease or mental illness, asthma, an allergy, an inflammatory disease, a disease involving a histamine response, a type of skin disease, a circadian rhythm disorder a degenerative disease, a chronic disease, and/or an episodic disease. For example, the disease may include: rheumatoid arthritis, lupus, thyroid disease, gout, diabetes, chronic fatigue syndrome, insomnia, depression, anxiety, bipolar disorder, colitis, ulcerative colitis, inflammatory bowel disease, Crohn's disease, candida, celiac disease, hepatitis, irritable bowel syndrome, one or more food allergies, one or more food sensitivities, menstrual cramps, chronic pain, back pain, facial pain, fibromyalgia, asthma, migraines, abdominal migraines, cyclic vomiting syndrome, cluster headaches, chronic headaches, tension headaches, another type of headaches, seizures, epilepsy, neurodermatitis, acne, psoriasis, adiposity, hypertonia, heart disease, hypertension, arteriosclerosis, and/or acquired immune deficiency syndrome. In some embodiments, the trait may include multiple illnesses, which may or may not have an associated comorbidity. However, as noted above, in some embodiments the trait includes a characteristic, such as: intelligence, a physical attribute, a skill, longevity, etc. Thus, the trait may not be confided to a disease; instead it may include a positive or desirable attribute.
We now describe embodiments of a technique for identifying one or more association variables that are associated with a trait. In the discussion that follows, SNPs are used as an illustration of biological variables. However, in other embodiments the biological variables may include: epigenetic information (such as methylation or demethylation), information associated with DNA (such as one or more copy number variations or frame shifts), information associated with ribonucleic acid (RNA), information associated with one or more proteins (such as one or more enzymes), and/or information associated with another biological marker or type of biological marker.
Note that in some embodiments the biological variables include environmental factors, such as: environmental stimuli (for example, light or sound), weather conditions, behaviors, patterns of behaviors (when the behaviors occur or do not occur), diet (including foods or beverages consumed or not consumed), dietary patterns (when the foods or beverages are consumed or are not consumed), use of drugs (prescription or recreational), activities, exposure to chemicals, exposure to toxins, exposure to one or more fungi, and/or exposure to infectious agents (for example, bacteria, viruses, fungi, and/or prions).
Continuing the discussion of
Most common SNPs have only two alleles. It is important to note that there are variations between populations (such as between groups of humans), so a SNP allele that is common in one geographical or ethnic group (such as a given population or a given group of life forms) may be much rarer in another. Typically, in order for a variation to be considered a SNP, it occurs in at least 1% of a given population.
SNPs can be assigned a minor allele frequency, which is the lowest allele frequency at a genetic locus (such as a base-pair location) that is observed in a particular or given population. This is simply the lesser of the two allele frequencies for SNPs. Similarly, SNPs can be assigned a major allele frequency, which is the largest allele frequency at the genetic locus (such as the base-pair location) that is observed in the given population. This is simply the larger of the two allele frequencies for SNPs.
For the given population, the minor allele frequencies and/or the major allele frequencies may be used to convert a sequence of SNPs at multiple genetic loci to categorical or discrete data. In an exemplary embodiment, the categorical data includes two classes or categories, i.e., binary categorical data. This is shown in
More generally, categorical data may be represented by codes. For categorical variables having two class or categories, a single binary digit may be used, such as 0 or 1, or −1 or 1. Thus, in the case of SNPs, genetic loci corresponding to minor frequencies may be coded as −1s and genetic loci corresponding to major frequencies may be coded as 1s. Note that a wide variety of code choices may be used. Thus, considering both copies of a chromosome, the presence of two copies of a SNP at a genetic location on both copies of the chromosome having a minor allele frequency may be coded as a ‘0’; the presence of the SNP having the minor allele frequency at the genetic location on one of the copies and the presence of the SNP having a major allele frequency at the genetic location on the other of the copies may be coded as a ‘1’; and the presence of two copies of the SNP at the genetic location on both copies of the chromosome having the major allele frequency may be coded as a ‘2’.
Also note that, when there are more than two categories, such as A, T, C, and G for a DNA sequence, a dummy variable having K values or bits may be used. Moreover, data having qualitative or continuous values can be converted in to categorical data by partitioning using one or more thresholds. In some embodiments, different thresholds may be used for different biological variables or different types of biological variables (such as SNPs versus environmental factors). Furthermore, in some embodiments categorical data is converted into continuous values using interpolation (such as minimum bandwidth interpolation), subject to the limitations associated with the Nyquist sampling criterion.
In some embodiments, either before conversion to categorical data or after, SNP data for a given population may be windowed or reduced using a haplotype map for the given population. This windowing operation may remove SNPs at genetic loci in the data that are highly correlated with one or more other SNPs in the data. For example, many SNPs are highly spatially correlated with each other over or across one or more regions in the genomes or sequences of most or all of the given population. For each group of highly correlated SNPs in the data, all but one may be removed from the set of biological variables associated with the given population before attempting to identify the one or more association variables.
Then, the set of biological variables may be optionally converted into categorical data (operation 412), as described previously in the discussion of
Next, at least some of the biological variables in the set of biological variables may be optionally excluded (operation 414) prior to determining compound variables based on at least some of the biological variables in the set of biological variables (operation 416) (or a remainder of the set of biological variables after the optional excluding in operation 414) and one or more mathematical interactions. For example, a given excluded biological variable may have a number of presence or absences (or, alternatively, expression and/or suppression) in a pattern of occurrence in the set of biological variables (i.e., in the data determined from the biological samples of the group of life forms) which is greater than a first value or less than a second value. This may exclude biological variables that have too few or too many presences or absences for there to be a statistically significant relationship with a pattern of occurrence of the trait associated with the group of life forms. For these excluded biological variables, it may not be possible to determine whether or not there is a relationship with the trait. In an exemplary embodiment, the first value is 5, 10 or 15% presence or absence (respectively) and/or the second value is 85, 90 or 95% absence or presence (respectively).
Additionally, or alternatively, in some embodiments at least some of the determined compound variables may be optionally excluded (operation 418) after determining the compound variables (416). For example, a given excluded compound variable may have a number of presence or absences (or, alternatively, expression and/or suppression) in a pattern of occurrence of the compound variable (i.e., based on the data associated with the group of life forms) which is greater than a third value or less than a fourth value. This may exclude compound variables that have too few or too many presences or absences for there to be a statistically significant relationship with a pattern of occurrence of the trait associated with the group of life forms. For these excluded compound variables, it may not be possible to determine whether or not there is a relationship with the trait. In an exemplary embodiment, the third value is 5, 10, or 15% presence or absence (respectively) and/or the fourth value is 85, 90 or 95% absence or presence (respectively).
As noted above, the compound variables may be determined (416). (Alternatively, the compound variables may be pre-determined, stored in a computer-readable memory, and accessed during process 400.) Moreover, as described further below, this determining or accessing may be iterated in operation 428 (
Then, at second order, a given compound variable may correspond to a pattern of occurrence of one biological variable in the set of biological variables of the group of life forms and a pattern of occurrence of a another biological variable in the set of biological variables of the group of life forms. This process may be repeated at ever high order (i.e., with larger groups of biological variables) until the resulting model complexity is sufficient to ‘fit’ the data or until diminishing returns occur (as described further below).
Note that the given compound variable for an order n may be determined by performing a mathematical operation and/or a logical operation on corresponding entries in the patterns of occurrence of n biological variables. For example, at second order, a particular compound variable may be determined by performing the mathematical operation and/or the logical operation on corresponding entries in a pattern of occurrence of a first biological variable and a pattern of occurrence of the second biological variable (which is described further below with reference to
More generally, for ternary encoded biological variables (such as {0, 1 or 2} for a SNP at a genetic location on two copies of a chromosome across the group of life forms, e.g., a patient population) the mathematical operation used to determine the given compound variable may be one of a set of mathematical operations. For example, the set of mathematical operations may be represented by 3×3 matrices, such as at least some of those provided in Wentian Li et al., “A Complete Enumeration and Classification of Two-Locus Disease Models,” Human Heredity vol. 50, pp. 334-349 (2000). (Note that the set of mathematical operations may be selected based on those 3×3 matrices that are expected to provide the largest signal in the identification technique, such as the largest numbers of occurrences in the occurrence ranking.) Thus, the given compound variable may be determined by performing a mathematical operation specified by a given mathematical interaction on corresponding entries in a pattern of occurrence of the first biological variable in the given pair of biological variables and a pattern of occurrence of the second biological variable in the given pair of biological variables.
In some embodiments, one or more compound variables may be a weighted summation of one or more biological variables. For example, for order n, n biological variables may be multiplied by corresponding weights and summed to determine the given compound variable. Moreover, in some embodiments the resulting one or more compound variables may be converted into categorical data using one or more thresholds (thus, converting operation 412 may occur before and/or after the determining operation 416).
Continuing the discussion of process 400 in
As described further below, the statistical relationships may be determined using a supervised-learning analysis technique and/or a non-parametric analysis technique, which makes few assumptions about an existence of a probability distribution function (such as a normal distribution) corresponding to the given population from which biological samples and, thus, the data are obtained, or regarding independence of the biological variables and/or the compound variables. In some embodiments, a given statistical relationship may be used to perform hypothesis testing to determine if the associated given compound variable and the trait are statistically independent (or dependent) based on a statistical confidence value (for example, based on a statistical significance value or criterion). In the process, the effective signal-to-noise ratio in an underdetermined problem (e.g., sparse sampling in a multi-dimensional variable space, such as when a number of life forms in the group of life forms is significantly less than a number of biological variables in the set of biological variables) may be improved by restricting a number of local fitting neighborhoods (e.g., a number of relevant biological variables and/or compound variables), thereby reducing the requirements associated with the Bonferonni correction.
Note that in some embodiments ‘significantly less than’ includes a multiplicative factor of 2, 5, 10, 100, 1000, 104, 105, 106, 107, or more. Thus, the number of life forms in the group of life forms may be at least 1000 times less than the number of biological variables in the set of biological variables. In an exemplary embodiment, the number of life forms is 3700 and the number of biological variables in the set of biological variables is 500,000.
Next, numbers of occurrences of biological variables that were used to determine the compound variables in a subset of the compound variables that have statistical relationships greater than a statistical confidence value may be determined (422). For example, an occurrence ranking based on the numbers of occurrences may be determined. (This is described further below with reference to
Moreover, a background correction may be performed (operation 424). For example, the additional statistical relationships may be calculated (as in operation 420) using a sequence of values (such as a random or a pseudorandom sequence having the same number of entries as the number of life forms in the group of life forms) instead of the pattern of occurrence of the trait. Then, another occurrence ranking for another subset of these additional statistical relationships that are significant may be determined (as in operation 422) and may be subtracted from the occurrence ranking. Note that significance of the other subset of the additional statistical relationships may be determined using another statistical confidence value, which may be different that the statistical confidence value.
Additionally, numbers of different mathematical interactions used to determine the compound variables in the subset of the compound variables for the biological variables that are associated with the corresponding numbers of occurrences may be optionally determined (operation 426). For example, an interaction ranking of the biological variables in the subset may be determined based on the numbers of different mathematical interactions associated with these biological variables. (This is described further below with reference to
As noted previously, operations 416-426 may be iterated (operation 428) using progressively higher-order compound variables to determine the statistical relationships and the rankings. In some embodiments, at least a portion of the occurrence ranking for the current order is used to determine the compound variables (416) (
Next, one or more of the biological variables in the set of biological variables may be identified (operation 430) as the one or more association variables based on the numbers of occurrences (e.g., the occurrence ranking) and/or the numbers of different mathematical interactions (e.g., the interaction ranking). As described further below with reference to
In some embodiments, process 400 includes additional or fewer operations. Moreover, the order of the operations may be changed and/or two or more operations may be combined into a single operation. For example, in some embodiments compound variables may be determined (416) (
In some embodiments, at least some of the operations in process 400 (
We now describe examples of operations in process 400 (
Similarly, information for the occurrence of trait 514 may vary across or over the group of life forms (the rows in trait 514). For example, trait 514 may be present in one life form (as indicated by a ‘1’) and absent in another (as indicated by a ‘0’). (Alternatively, ‘0’s and ‘1’s may indicate suppression and expression, respectively, of trait 514.) This variation defines the patterns of occurrence 516-3 of trait 514.
Moreover, one or more biological variables in the set of biological variables 510 may be used to determine 518 compound variable 512. For example, at second order, entries in two of the set of biological variables 510 may be combined according to a particular mathematical operation, such as the M21 penetrance table in Wentian Li et al., “A Complete Enumeration and Classification of Two-Locus Disease Models,” Human Heredity vol. 50, pp. 334-349 (2000). In this case, if an entry in a first biological variable is a ‘0’ and an entry in a second biological variable is a ‘1’, this specifies row 0, column 1 in the M21 penetrance table, which results in a row entry of a ‘0’ in compound variable 512. In general, the resulting entries in compound variable 512 may vary across or over the group of life forms (the rows in compound variable 512). This variation defines the patterns of occurrence 516-2 of compound variable 512.
Then, patterns of occurrence 516-2 and 516-3 may be used to calculate a statistical relationship for each life form in the group of life forms (i.e., using the entries in compound variable 512 and trait 514 on a row by row basis). For example, the statistical relationship may be determined by comparing 520 entries in compound variable 512 and trait 514 using a statistical analysis technique. This process may be repeated for multiple combinations of the biological variables in the set of biological variables 510 (i.e., multiple compound variables based on the same or different mathematical operations in the set of mathematical operations) to generate a set of statistical relationships with trait 514 for a given order in the analysis.
Next, the set of statistical relationships may be compared to statistical confidence values (such as a statistical significance value or criterion) to identify a noise floor in the set of statistical relationships. This is shown in
Note that portion 718 may include one or more biological variables, such as environmental factor 716-1 and/or one or more of biological variables 714. Moreover, at least portion 718 in occurrence rankings 712-2 and 712-2 may indicate or specify a pareto. Furthermore, the one or more association variables may be identified in portion 718 or in occurrence rankings 712-2 and 712-3 that are substantially or approximately stable.
Once a substantially or approximately stable occurrence ranking is determined, it can be used to determine an interaction ranking. This is shown in
Note that the assumption that underlies occurrence rankings 712 (
Similarly, the mathematical interactions provide very selective filtering as the biological variables are combined to determine compound variables. As the order n is increased, it is increasingly difficult to find a pattern of occurrence of a given biological variable for a given mathematical interaction that, in conjunction with a compound variable of order n−1, improves the statistical association with the pattern of occurrence of the trait. (In fact, using the given mathematical interaction the pattern of occurrence of the given biological variable typically results in a weaker statistical association.) In general, if a first mathematical interaction for a pair of biological variables results in a statistically significant association, a different mathematical interaction is needed to determine a statistically significant association between a third biological variable and either of the biological variables in the pair of biological variables. Thus, assuming that the graph includes sequences of multiple interacting nodes (i.e., biological variables), these can be identified by looking for biological variables that are associated with multiple different mathematical interactions in an interaction ranking.
In an exemplary embodiment, the identification technique was used to identify association variables for major depressive disorder using the GAIN SNP dataset (available via dbGaP) for 3741 individuals (about 50% of whom had major depressive disorder). After correcting for linkage disequilibrium and excluding data for the Y chromosome, there were approximately 240,000 SNP variables (which were the biological variables in this example). Using 28 mathematical interactions specified in Wentian Li et al., “A Complete Enumeration and Classification of Two-Locus Disease Models,” Human Heredity vol. 50, pp. 334-349 (2000), approximately a half a trillion compound variables were determined at second order (i.e., pairs of biological variables). (In particular, the penetrance tables used were: M1, M3, M7, M10, M11, M13, M14, M17, M21, M26, M27, M30, M41, M42, M45, M58, M69, M78, M85, M86, M97, M99, M101, M106, M113, M114, M170, and M186.) The noise floor in the occurrence rankings occurred for a log-likelihood ratio of 9. As a consequence, occurrence rankings were determined for log-likelihood ratios between 9 and 24. After subtracting the background associated with a pseudorandom sequence of values, the association variables were identified from the occurrence ranking using the interaction ranking.
These association variables are summarized in Table 1, including: the SNP identifier, the occurrence ranking position, the interaction ranking position and, if appropriate, the gene name and gene identifier. Note that 70-80% of the genetic locations specified by these association variables are within or proximate to (within 10,000 base pairs) of genes (far larger than would be expected for random results). The top association variables in Table 1 include known genes that have been determined to be associated with major depressive disorder (such as the glutamate receptor GRM7) and new genes that have not been previously reported. These new genes appear to be associated with low-level synaptic signaling, which seems plausible based on a biological model of the disease. Moreover, the genetic loci that do not include genes may not be false positives. Instead, these locations may play another role, for example, they may be regulators. Furthermore, p-values for the results in Table 1 are estimated to be smaller than 10−10.
The results in Table 1 are considered surprising because prior analyses of this dataset using existing techniques were unsuccessful. Indeed, the expectation value for false-positive but statistically significant compound variables (for example, for log-likelihood ratios larger than 25 or 30) is 2-4× larger than the number of statistically significant compound variables that were determined using the identification technique (i.e., the results in Table 1 were obtained even though the dataset is theoretically too small for existing analysis techniques to obtain meaningful results). Furthermore, the results in Table 1 were obtained via the identification technique using no adjustable parameters (i.e., the analysis has not be optimized for this dataset or at all).
Collectively, these results suggest that the interaction technique has information gain relative to existing analysis techniques, and that it can be applied to an arbitrary dataset. This indicates that the interaction technique may be able to identify association variables even for extremely underdetermined problems, such as those associated with full genome sequencing.
We now further describe embodiments of the statistical analysis. This statistical analysis may include classification and/or regression (such as determining a model of the one or more traits, which includes one or more biological variables and/or one or more compound variables, along with corresponding weights).
A wide variety of computational techniques may be used to determine the one or more statistical relationships, including: one or more parametric analysis techniques, one or more non-parametric analysis techniques, one or more supervised learning techniques and/or one or more unsupervised learning techniques. In some embodiments, one or more non-parametric analysis techniques may be used. As noted previously, non-parametric analysis techniques make few assumptions about an existence of a probability distribution function, such as a normal distribution, corresponding to the given population (or group of life forms) from which samples or associated data are obtained, or regarding independence of the biological variables and/or the compound variables. In general, non-parametric analysis techniques may use rank or naturally occurring frequency information in the data to draw conclusions about the differences between different populations or subsets of the given population.
Note that the one or more non-parametric analysis techniques may perform hypothesis testing, e.g., to test a statistical significance of a hypothesis. In particular, the one or more non-parametric analysis techniques may determine if the one or more traits and/or the one or more compound variables are statistically independent (or dependent) based on a statistical significance value or criterion. As noted previously, one or more compound variables having a statistically significant relationship with the trait (and, in particular, the pattern of occurrence of the trait for the group of life forms) may be used to identify the one or more association variables.
In exemplary embodiments, the non-parametric analysis technique may include: a chi-square analysis technique, a log-likelihood ratio analysis technique (also referred to as G-test), and/or a Fisher's exact probability analysis technique. In addition to their other advantages, these techniques may be well suited to analyzing an underdetermined problem, i.e., sparse sampling in a multi-dimensional variable space, in which there may be multiple biological variables and/or compound variables and a smaller number of members of the group of life forms (and, thus, a smaller number of entries in these variables and in the trait information).
In some embodiments, the chi-square analysis technique, the log-likelihood ratio analysis technique, and/or the Fisher's exact probability analysis technique may be determined using a cross-tabulation or contingency tables (which are sometimes referred to as bivariate tables). Note that the Fisher's exact probability analysis technique computes the sum of conditional probabilities of obtaining the observed frequencies in a given contingency table and the conditional probabilities of obtaining exactly the same observed frequencies for any configuration that is more extreme, i.e., having a smaller conditional probability. Moreover, the chi-square (χ2) may be determined using
and the log-likelihood ratio (LLR) using
where the summation is over the entries in the given contingency table, Oi is the i-th observed frequency value, and Ei is the i-th expected frequency value. The following example illustrates an exemplary embodiment of determining a statistical relationship using the log-likelihood ratio for binary categorical data.
Consider the example contingency table in Table 2. The first column contains the number of entries in the pattern of occurrence where a compound variable is present and the trait is present (which is henceforth denoted by X11) in the data (such as genetic data) associated with the group of life forms plus the number of entries in the pattern or occurrence where the compound variable is absent and the trait is absent in the data associated with the group of life forms (which is henceforth denoted by X00). X11 is sometimes referred to as a true-true and X00 is sometimes referred to as a false-false. X11 and X00 are henceforth referred to as co-occurrences.
The second column in Table 2 contains the number of entries in the pattern of occurrence where the compound variable is present and the trait is absent (henceforth denoted by X10) in the data associated with the group of life forms plus the number of entries in the pattern of occurrence where the compound variable is absent and the trait is present (henceforth denoted by X01) in the data associated with the group of life forms. X10 is sometimes referred to as a true-false and X01 is sometimes referred to as a false-true. X10 and X01 are henceforth referred to as cross occurrences.
If the compound variable and the trait are completely independent, the expected frequency values for each column, E1 and E2, would equal 28.5, one half of the sum of the number of co-occurrences and cross occurrences, i.e., the total number of observations (data points or samples) in Table 2. Therefore, for Table 2,
A one-sided minimal statistical significance confidence value or criterion of 5% (α=0.05) or a statistical confidence threshold based on the number of degrees of freedom (the size of the contingency table, which in this example is one) corresponds to an LLR of 3.841. (Note that if the biological variables have more than two categories, the contingency table may have a larger number of degrees of freedom.) Because the LLR for Table 2 is greater than 3.841, it is statistically significant. Therefore, from a statistical perspective, the null hypothesis is rejected and the patterns of occurrence of the compound variable and the trait in the data associated with the group of life forms in this example are dependent.
Note that it is possible for statistically significant LLR values to occur even when X11 is zero. In some embodiments, compound variables that have X11 equal to zero when compared with the pattern of occurrence of the trait are excluded prior to determining the rankings and identifying the one or more association variables. Additionally, note that the LRR value is the same when there is a relationship (when the number of co-occurrences is greater than the number of cross occurrences) or an anti-relationship (when the number of co-occurrences is less than the number of cross occurrences) between the pattern of occurrence of the compound variable and the pattern of occurrence of the trait. Consequently, in embodiments where association variables corresponding to relationships are desired, statistical relationships where the number of co-occurrences is less than the number of cross occurrences may be excluded. Similarly, in embodiments where association variables corresponding to anti-relationships are desired, statistical relationships where the number of co-occurrences is greater than the number of cross occurrences may be excluded. Furthermore, in some embodiments, instead of using an occurrence ranking corresponding to the sequence of values to perform the background correction, an occurrence ranking of the number of occurrences of biological variables in statistical relationships corresponding to no relationship (i.e., an LLR of infinity, or when the number of co-occurrences equals the number of cross occurrences) may be used.
In the preceding example, the calculation of the statistical relationship for the trait and the compound variable uses presence and absence information in the patterns of occurrence of the compound variable and the trait. In some embodiments, one or more of the statistical relationships may be determined using presence information, i.e., the presence only (or absence only) of one or more compound variables in the data associated with the group of life forms, without using absence information (or without using presence information). In alternate embodiments, a wide variety of analysis techniques may be used to calculate the one or more statistical relationships.
In parametric analysis, a Pearson's product-moment correlation coefficient r may be useful in summarizing a statistical relationship. For some contingency tables, Cramer's phi φ, the square root of χ2 or the LLR divided by the number of observations N, may have a similar interpretation to r (although, it is known that Cramer's phi φ may underestimate r). In the example illustrated in Table 2,
The chi-square analysis technique and the log-likelihood ratio analysis technique may have a maximal sensitivity for contingency tables based on patterns of occurrence of compound variables having 50% presence entries and 50% absence entries in the data associated with the group of life forms. In addition, maximal sensitivity may occur if 50% of the life forms in the group of life forms have the trait, e.g., presence entries. In some embodiments, one or more contingency tables may be generated to achieve approximately 50% presence entries for patterns of occurrence of one or more compound variables and/or 50% having the trait by using a subset of the data associated with the group of life forms. In an exemplary embodiment, one or more contingency tables may be generated by randomly or pseudo-randomly selecting (for example, using a pseudo-random number generator or technique) a subset of the data associated with the group of life forms, such that the one or more contingency tables may have approximately 50% presence entries and 50% absence entries distributed over X00, X11, X10, and X01. For infrequently occurring events, biological variables and/or compound variables, there may be more absence entries than presence entries in the data associated with the group of life forms. As a consequence, different sampling ratios may be used for presence and absence entries in the data associated with the group of life forms.
In some embodiments, boosting may be used when generating one or more contingency tables. A subset of the data associated with group of life forms may be selected randomly or pseudo-randomly in order to determine one or more contingency tables. A given contingency table may be generated L times using approximate random sampling. Statistical relationships for at least M of these L contingency tables may be used (including combining and/or averaging) to determine whether or not the trait and the corresponding compound variable are independent in the data associated with the group of life forms. In an exemplary embodiment, L may be 5, 10, 25, 50, 100, 500 or more, and M may be 50% (rounded to the nearest integer), 60%, 66%, 70%, 75%, 80% or more of L.
In some embodiments, there may be too few presence entries or too many presence entries in one or more patterns of occurrence of one or more biological variables or compound variables in the data associated with the group of life forms to reliably determine statistically significant independence (or dependence) based on the trait information for the group of life forms, i.e., the pattern of occurrence of the trait in data associated with the group of life forms. As a consequence, one or more of these biological variables or one or more of these compound variables may be excluded when determining one or more statistical relationships. In an exemplary embodiment, one or more biological variables or one or more compound variables having patterns of occurrence with less than 15% presence entries or more than 85% presence entries in the data associated with the group of life forms may be excluded.
Overfitting or developing a model that is too complex is a risk in a statistical learning problem. In some embodiments, the model complexity may correspond to a number of compound variables that have statistically significant dependence on the trait information. Moreover, in some embodiments the model complexity may, at least in part, correspond to a number of biological variables included when determining a given compound variable, i.e., the order n.
In some embodiments, this risk may be addressed using a fraction or percentage of the data associated with the group of life forms (such as the patterns of occurrence) for training, i.e., to develop the model, and a remainder for testing the resulting model. Typically training error decreases as the model complexity increases (the model better fits or predicts a training set of data), and a testing error exhibits a minimum. Additional model complexity beyond this minimum usually does not generalize well (the model offers a poorer fit or prediction for a test set of data). Therefore, beyond the minimum point the training set of data may be overfit. In an exemplary embodiment, the percentage of the data associated with the group of life forms used for training may be 70%, 75%, 80%, 85% or 90%.
An additional metric of the model complexity may be determined. This metric may be used in conjunction with or independently of the training set of data and the test set of data. The additional metric is described below. In some problems and/or embodiments, calculating one or more statistical relationships for one or more biological variables (or, said differently, for one or more compound variables of order 1) may not be sufficient to determine statistically significant independence (or dependence) with respect to trait information. For example, in multi-dimensional problems, where two or more biological variables are necessary and sufficient to give rise to a trait (such as migraine), a value of the Fisher's exact probability, χ2, and/or LLR for a compound variable of order 1 may be reduced since there is a penalty for the presence of the cross occurrences, X10 and X01.
More generally, the value of the Fisher's exact probability, χ2, and/or LLR may be reduced if the order n of one or more compound variables is less than an intrinsic order of the multi-dimensional problem. In the case of X10, a trait may or may not occur unless a certain number of biological variables or a set of biological variables (which may be inter-operative) are present for particular life forms in the group of life forms. And in the case of X01, more than one set of biological variables may be present, i.e., one or more biological variables in another set of biological variables may lead to the trait in the particular life forms. (Moreover, for environmental factors, there may be one or more thresholds, which may be a function of time.)
To assess whether or not the model has sufficient complexity, i.e., whether or not one or more compound variables have been determined to sufficient order n, a ratio R may be determined. For contingency Table 2, R is defined as X11 divided by the total number of occurrences of the compound variable of order n in the data associated with the group of life forms, i.e.,
An increasing value of R, and/or Cramer's phi φ, as statistical analysis is performed to higher order (i.e., n+1) may be metrics of goodness, i.e., it may indicate that the higher order does a better job determining statistically significant independence or dependence between one or more compound variables and the trait information. In some embodiments, contingency tables for one or more compound variables may be generated for progressively higher orders (e.g., by iterating at least some of the operations in process 400 in
One or more variables and/or compound variables having statistically significant statistical relationships with the trait information for the group of life forms may be identified as one or more association variables. For a given compound variable of order n having a significant statistical relationship with the trait information, the n constituent biological variables may be identified as n association variables and/or as a set of association variables. In some embodiments, one or more statistically significant compound variables of order n having the ratio R approximately equal to 1 may be identified as one or more association variables.
In some embodiments, one or more compound variables of order n and/or one or more constituent biological variables in the one or more compound variables of order n may be ranked based on the corresponding calculated statistical relationships that are statistically significant. In some embodiments, an occurrence ranking of a given constituent biological variable is based on a number of occurrences of the given constituent biological variable in one or more compound variables of order n having statistical relationships that are statistically significant. As noted previously, occurrence rankings may be performed as the statistical significance confidence value or criterion (a) is progressively increased, which can be used to determine the noise floor in the statistical relationships (as described previously in the discussion of
In exemplary embodiments, a may be 0.05 or lower. For a given occurrence ranking, a pareto corresponding to at least a portion of the given occurrence ranking may be defined. This pareto may correspond to biological variables or compound variables having a statistical relationship or a number of occurrences in the statistically significant compound variables exceeding a threshold. In some embodiments, a top-10, 20, 50 or 100 biological variables or compound variables may be used, or a majority of the top-10, 20, 50 or 100 biological variables or compound variables may be used. For compound variables of order n, approximate stability of the pareto as the statistical significance value or criterion is increased may be used to identify the noise floor. Approximately stability may include an approximately unchanged order of the ranking or a presence of approximately the same biological variables and/or compound variables (for example, more than 70 or 80%) in the portion of the occurrence ranking. In exemplary embodiments, the noise floor may correspond to an α of 0.01 or lower, an α of 0.001 or lower, or an α of 0.0001 or lower.
Additionally, once a suitable statistical significance confidence value or criterion is found (based on substantial or approximate stability of the occurrence rankings), an interaction ranking may be determined based on the numbers of different mathematical interactions used to determine the compound variables in the subset of the compound variables for the biological variables that are associated with the corresponding numbers of occurrences. One or more biological variables and/or one or more compound variables in paretos corresponding to one or more statistical significance values or criteria that exceed the noise floor and which may be associated with the largest numbers of different mathematical interactions may be identified as association variables.
In some embodiments, the analysis is repeated using a random or pseudo-random sequence of values instead of the trait information. This sequence of values may have the same length (or number of entries) as the number of life forms in the group of life forms. Moreover, the resulting occurrence ranking, which may be determined using the same or a different statistical significance value or criterion as the occurrence ranking described above, may be subtracted from the occurrence ranking described above before the one or more association variables are identified.
In some embodiments, one or more biological variables and/or one or more compound variables in paretos corresponding to one or more statistical significance values or criteria that exceed the noise floor may be used as a seed set in additional statistical analysis. The additional statistical analysis may determine statistical relationships for compound variables of a higher order. In some embodiments, the additional analysis may utilize an analysis technique such as SVM or CART.
Alternatively, the additional analysis technique may be used as the initial or first stage, to refine the model (including adding or removing one or more biological variables and/or one or more compound variables), and/or to identify one or more association variables.
Note that the additional analysis technique may include classification and/or regression (such as determining a model of the trait information including one or more biological variables and/or one or more compound variables, along with corresponding weights). As with the statistical analysis technique described previously, a wide variety of techniques may be used in the additional analysis technique. Two such techniques, SVM and CART, are described further below.
Embodiments of SVM are instances of supervised learning techniques that may be applied to classification and regression problems. For binary classification, a set of binary labeled data points (training data or examples) is provided. SVMs may be used to determine an optimal separation boundary, defined by the biological variables and/or compound variables, between two classes of data points. A separation boundary is optimal if using it as a decision rule to classify future data points minimizes an expected classification error. For linearly separable data sets (e.g., a class of absences, which may be indicated by −1, and a class of presences, which may be indicated by +1, that may be separated from each other by a line in 2 dimensions, or a so-called hyperplane in higher dimensions), SVMs may be used to determine a maximal margin hyperplane. For the maximal margin hyperplane, a linear decision boundary may be positioned such that it separates both classes and such that the distance to the closest point from each class is maximized. For non-linearly separable data sets, some training data points may be allowed on the opposite or ‘wrong’ side of the hyperplane, e.g., a classification error on the training data set may be allowed and may be minimized, while the margin, measured between points on the ‘correct’ side of the hyperplane, may be maximized.
If a linear decision boundary is not sufficiently complicated to model the separation between classes accurately, the corresponding linear model may be transformed into a non-linear model by non-linearly transforming the biological variables and/or compound variables into a possibly higher dimensional Euclidean space. A linear decision boundary constructed in such a higher dimensional Euclidean space may correspond to a non-linear decision boundary in the original space of biological variables and/or compound variables. This approach is referred to as kernel SVM.
Depending on how the margin and training error are measured, and how a trade-off between maximizing the margin and minimizing the training error is established, different types of SVMs may be obtained. In some embodiments, SVM may include standard 1-norm SVM (measuring the margin using Euclidean distance, i.e., a L2-norm, and the training error using a L1-norm), standard 2-norm SVM (measuring the margin using Euclidean distance, i.e., the L2-norm, and the training error using the L1-norm), and/or LP-SVM (measuring the margin using the L1-norm and the training error using the L1-norm). Each of these 3 types of SVM may be a C-type or η-type SVM. These two varieties correspond to different ways of trading-off maximizing the margin against minimizing the training error. The 1-norm SVM, standard 2-norm SVM, and/or LP-SVM may be a C+/C− or η+/η− type, where errors on positive (+1) labeled training data are weighted differently than errors on negative (−1) labeled training data.
The principle for binary classification described above may be extended to regression, for example, by copying the regression data twice, shifting both copies in opposite directions (over a distance epsilon) with respect to the continuous output dimension or variable and establishing a regression surface as a decision boundary between the two shifted copies that may be regarded as two classes for binary classification. As a consequence, in some embodiments, regression versions of SVMs corresponding to previously described SVMs may be used.
The decision boundary determined using one or more SVMs may be used to discriminate between presence and absence of the trait in the trait information associated with the group of life forms. For binary classification, measures of goodness for the resulting model include a prediction accuracy that is better than predicting 50% of the positive data (e.g., occurrences, which may be indicated by a +1) as positive (i.e., true positive predictions) and better than predicting 50% of the negative data (i.e., absences, which may be indicated by a −1) as negative (i.e., true negative predictions). Doing better than 50/50 corresponds to doing better than random.
CART is a non-parametric multivariate analysis technique. It involves the determination of a binary decision tree using the training set of data. Predictions based on the resulting tree may be compared to the test set of data (cross validation). A decision tree provides a hierarchical representation of the feature space in which explanatory variables are allocated to classes (such as presence or absence of the trait in the trait information) according to the result obtained by following decisions made at a sequence of nodes at which branches of the tree diverge. Branches or divisions of the tree may be chosen to provide the greatest reduction in the statistical entropy of the variables (for a classification tree based on categorical data), such as a small or zero standard deviation, or the greatest reduction in the deviation between the biological variables (and/or compound variables) and the trait being fit (for a regression tree based on quantitative data). A tree stops growing when no significant additional reduction can be obtained by division. A node that is not further sub-divided is a terminal node. It is associated with a class. A desirable decision tree is one having a relatively small number of branches, a relatively small number of intermediate nodes from which these branches diverge, terminal nodes with a non-zero number of entries, and high prediction power (correct classifications at the terminal nodes). In some embodiments, CART may be used in conjunction with a gradient boosting algorithm, where each boosted tree is combined with its mates using a weighted voting scheme. Gradient boosting may be used to force the binary decision tree to classify data that was previously misclassified.
As noted above, a wide variety of statistical analysis techniques may be used to determine the one or more statistical relationships. These may include: one or more supervised learning techniques, one or more unsupervised learning techniques, one or more parametric analysis techniques (such as a Pearson's product-moment correlation coefficient r or an inner product), and/or one or more non-parametric analysis techniques. Non-parametric analysis techniques may include: a Wilcoxon matched pairs signed-rank test (for ordinal or ranked data), a Kolmogorov-Smirnov one-sample test (for ordinal or ranked data), a dependent t-test (for interval or ratio data), a Pearson chi-square, a chi-square test with a continuity correction (such as Yate's chi-square), a Mantel Heanszel chi-square test, a linear-by-linear association test, a maximum likelihood test, a risk ratio, an odds ratio, a log odds ratio, a Yule Q, a Yule Y, a phi-square, a Kappa measure of agreement, a McNemar change test, a Mann Whitney U-test, a Spearman's rank order correlation coefficient, a Kendall's rank correlation, a Krushcal-Wallis One-Way Analysis of Variance, and/or a Turkey's quick test.
Supervised learning techniques may include: least-squares regression (including correlation), ridge regression, partial least-squares (also referred to as partial correlation), a perceptron algorithm, a Winnow algorithm, linear discriminant analysis (LDA), Fisher discriminant analysis (FDA), logistic regression (LR), a Parzen windows classifier, a (k-) nearest-neighbor classification, multivariate adaptive regression splines (MARS), multiple additive regression trees (MART), SVM, LASSO (a regularized linear regression technique like ridge regression, but with L1-norm regularization of the coefficients), least angle regression (LARS), decision trees (such as CART, with and without gradient boosting, such as ID3 and C4.5), bagging, boosting (such as, adaboost) of simple classifiers, kernel density classification, a minimax probability machine (MPM), multi-class classification, multi-label classification, a Gaussian Process classification and regression, Bayesian statistical analysis, a Naive Bayes classifier, and/or neural networks for regression and classification. While some of these supervised learning algorithms are linear, it should be understood that one or more additional non-linear versions may be derived using the same ‘kernel-methodology’, as previously described for the SVM, leading to a spectrum of kernel-based learning methods, for example, kernel FDA, kernelized logistic regression, the kernelized perceptron algorithm, etc. One or more of these non-linear versions may be used to perform the statistical analysis.
Unsupervised learning techniques may include: a kernel density estimation (using, for example, Parzen windows or k-nearest neighbors), more general density estimation techniques, quantile estimation, clustering, spectral clustering, k-means clustering, Gaussian mixture models, an algorithm using hierarchical clustering, dimensionality reduction, principal component analysis (PCA), multi-dimensional scaling (MDS'), isomap, local linear embedding (LLE), self-organizing maps (SOM), novelty detection (which is also referred to as single-class classification, such as single-class SVM or single-class MPM), canonical correlation analysis (CCA), independent component analysis (ICA), factor analysis, and/or non-parametric Bayesian techniques like Dirichlet processes. As noted above for the supervised learning techniques, one or more additional non-linear versions of one or more linear unsupervised learning techniques may be used to perform the statistical analysis, such as kernel PCA, kernel CCA and/or kernel ICA.
In some embodiments, at least a portion of the statistical analysis, such as determination of one or more statistical relationships and/or identification of one or more association variables includes spectral analysis. For example, a Fourier transform or a discrete Fourier transform may be performed on the trait information, one or more patterns of occurrence of one or more biological variables, and/or one or more patterns of occurrence of one or more compound variables. Analysis in the frequency domain may allow patterns in at least some of the data associated with the group of life forms to be determined.
In some embodiments, calculating one or more statistical relationships and/or identifying one or more association variables includes the use of design of experiments. For example, the data associated with the group of life forms may correspond to an orthogonal array.
In some embodiments, a signal-to-noise metric is used to adjust how the one or more association variables are identified. This signal-to-noise metric may be computed using the set of biological variables of the group of life forms. Based on the computed signal-to-noise metric, how the one or more association variables are identified may vary from only using the occurrence and/or interaction rankings (for low values of the signal-to-noise metric) to only using the largest values of statistical association (e.g., without the occurrence and/or interaction rankings), which may be appropriate for high values of the signal-to-noise metric. In general, for an arbitrary value of the signal-to-noise metric, the one or more association variables may be identified using a weighted combination of the occurrence and/or interaction rankings and the largest values of statistical association, where the weights λi of these terms may be a function of the signal-to-noise metric (for example, the weights of the two terms may be λ and 1−λ). Alternatively or additionally, such as weighted combination may be used in a modified version of a supervised learning technique, such as LASSO.
In some embodiments, the initial set of biological variables is pruned or reduced prior to identifying the one or more association variables based on known or pre-determined association variables for the trait, such as one or more genes associated with a disease that have been identified using: linkage analysis, the biochemistry of the disease, or another technique known to one of skill in the art.
We now describe embodiments of a circuit and a computer system that may perform at least a portion of the statistical analysis and/or the identifying of the one or more association variables. This circuit may contain one or more filters, including: analog filters, digital filters, adaptive filters (using, for example, a least-square error or gradient approach, such as steepest decent), and/or neural networks. The one or more filters may be implemented using one or more digital signal processors (DSPs). In some embodiments, the statistical analysis and/or the identifying of the one or more association variables are implemented in hardware, for example, using one or more application-specific integrated circuits (ASICs), and/or using software.
Note that filters Hi 818 may be adaptive. This adaptation may be based on trait information 812 and/or an error 826. In some embodiments, the adaptation includes one or more time intervals and/or one or more offsets between these time intervals, which are used when determining compound variables. Note that the adaptation may minimize or reduce error 826 or a portion of error 826.
Outputs from one or more of the filters Hi 818 may be coupled to filter HB 820. This filter may perform additional spectral modification. As a consequence, an arbitrary filtering operation may be implemented using one or more of the filters Hi 818 and/or the filter HB 820. Moreover, filter HB 820 may determine a pattern of occurrence for one or more biological variables 810 and/or one or more compound variables.
Trait information 812 may be filtered using filter H3 818-3. Comparisons between an output of filter H3 818-3 and an output of the filter HB 820 may be performed using statistical analysis element 824. In some embodiments, the statistical analysis element 824 may be a comparator. Statistical analysis element may implement one or more statistical analysis techniques, such as the log-likelihood ratio. Moreover, the statistical analysis element 824 may generate error 826. Note that error 826 may be: a scalar, a vector, and/or a matrix. In some embodiments, statistical analysis element 824 may perform a relative time shifting of the output of filter H3 818-3 and the output of the filter HB 820.
In an exemplary embodiment, statistical analysis element 824 calculates one or more statistical relationships between the trait information 812 and one or more patterns of occurrence of one or more compound variables. The one or more statistical relationships may be determined sequentially and/or substantially concurrently. Note that error 826 may correspond to the one or more statistical relationships.
In some embodiments, one or more optional additional inputs, such as optional additional input 814, is filtered using one or more filters, such as filter H4 818-4, and/or combined with trait information 812 using a filter, such as filter/combiner H5 822. An output from filter/combiner H5 822 may be included in the analysis performed by statistical analysis element 824. The one or more optional additional inputs may allow inclusion of cross-terms. In some embodiments, the one or more optional additional inputs may include other disease symptoms, other diseases (such as diseases that have a comorbidity with a trait), and/or environmental factors.
While a single output is shown for the filter HB 820, there may be additional outputs that are used by statistical analysis element 824. Similarly, there may be additional outputs from filter/combiner H5 822 that are used by statistical analysis element 824. While embodiment 800 uses presence and absence information in the one or more biological variables 810, trait information 812, and optional additional input 814, in some embodiments one or more of these items may only use presence information or may use only absence information. Alternatively or additionally, expression and/or suppression information may be used.
A more general description of a circuit to identify the one or more association variables is shown in
Circuits 800 (
Devices and circuits described herein may be implemented using computer-aided design tools available in the art, and embodied by computer-readable files containing software descriptions of such circuits. These software descriptions may be: behavioral, register transfer, logic component, transistor and/or layout geometry-level descriptions. Moreover, the software descriptions may be stored on non-transitory computer-readable storage media.
Data formats in which such descriptions may be implemented include, but are not limited to: formats supporting behavioral languages like C, formats supporting register transfer level (RTL) languages like Verilog and VHDL, formats supporting geometry description languages (such as GDSII, GDSIII, GDSIV, CIF, and MEBES), and other suitable formats and languages. Note that physical files may be implemented on machine-readable media such as: 4 mm magnetic tape, 8 mm magnetic tape, 3½ inch floppy media, CDs, DVDs, and so on.
Memory 924 in computer system 900 may include volatile memory and/or non-volatile memory. More specifically, memory 924 may include: ROM, RAM, EPROM, EEPROM, flash, one or more smart cards, one or more magnetic disc storage devices, and/or one or more optical storage devices. Memory 924 may store an operating system 926 that includes procedures (or a set of instructions) for handling various basic system services for performing hardware-dependent tasks. Moreover, memory 924 may also store communication procedures (or a set of instructions) in a communication module 928. These communication procedures may be used for communicating with one or more computers, devices and/or servers, including computers, devices and/or servers that are remotely located with respect to computer system 900.
Memory 924 may also include one or more program modules 930, including: statistical analysis module 930 (or a set of instructions), conversion module 932 (or a set of instructions), ranking module 934 (or a set of instructions), background-correction module 936 (or a set of instructions), compound-variable generator 942 (or a set of instructions), optional signal-processing module 946 (or a set of instructions), and/or sequence generator 950 (or a set of instructions). Conversion module 932 may convert biological variables 938 for a group of life forms, such as biological variable A 940-1 or biological variable B 940-2, into categorical data. In some embodiments, biological variables 938 and/or information for one or more traits 952 associated with the group of life forms are preconditioned using optional signal-processing module 946. For example, optional signal-processing module 946 may filter data and/or may perform a transform, such as: a fast Fourier transform, a Laplace transform, a discrete Fourier transform, a Z-transform, and/or any other transform technique now known or later developed.
Then, compound-variable generator 942 may determine one or more compound variables 954 using one or more mathematical interactions 958 and at least some of the biological variables 938 (for example, statistical analysis module 930 may exclude one or more of the biological variables 938 using optional haplotype map 948). Alternatively, compound variables 954 may be pre-determined. Note that in some embodiments compound variables 954 are determined using optional weights 944.
Next, statistical analysis module 930 may determine statistical relationships between a pattern of occurrence of one or more traits 952 and patterns of occurrence of at least some of the compound variables 954. (Note that statistical analysis module 930 may exclude one or more of the compound variables 954 prior to determining the statistical relationships.) Moreover, ranking module 934 may determine one or more rankings 960 of the number of occurrences of biological variables in statistically significant statistical compound variables above a noise floor. For example, the one or more rankings 960 may include one or more occurrence rankings at different statistical significance criteria and/or one or more interaction rankings.
Additionally, background-correction module 936 may determine another occurrence ranking based on statistical relationships between at least some of the compound variables 954 and a sequence of values generated using sequence generator 950. This other occurrence ranking may be subtracted from at least one of the occurrence rankings in one or more rankings 960.
Then, statistical analysis module 930 may identify one or more association variables 956 based on ranking 960 (which may include an occurrence ranking after correcting for the background). In some embodiments, the operations of the various modules are repeated to higher order, i.e., in compound variables that include additional biological variables in the biological variables 938.
Instructions in the various modules in the memory 924 may be implemented in: a high-level procedural language, an object-oriented programming language, and/or in an assembly or machine language. The programming language may be compiled or interpreted, i.e., configurable or configured, to be executed by the one or more processors (or processor cores) 910.
Although computer system 900 is illustrated as having a number of discrete components,
Computer system 900 may include fewer components or additional components. Moreover, two or more components may be combined into a single component and/or a position of one or more components may be changed. In some embodiments the functionality of computer system 900 may be implemented more in hardware and less in software, or less in hardware and more in software, as is known in the art.
We now describe embodiments of a data structure that may be used in computer system 900.
Note that in some embodiments of the data structures 1000 (
While embodiments of apparatuses and related methods for identifying one or more association variables have been described, the apparatuses and related methods may be applied generally to determine statistical relationships in a wide variety of underdetermined problems in medicine, psychology, statistics, engineering, finance, applied mathematics and operations research (and, thus, in general to an arbitrary supervised learning problem). Consequently, the one or more association variables may be identified based on traits or features other than those corresponding to biological variables.
The foregoing description is intended to enable any person skilled in the art to make and use the disclosure, and is provided in the context of a particular application and its requirements. Moreover, the foregoing descriptions of embodiments of the present disclosure have been presented for purposes of illustration and description only. They are not intended to be exhaustive or to limit the present disclosure to the forms disclosed. Accordingly, many modifications and variations will be apparent to practitioners skilled in the art, and the general principles defined herein may be applied to other embodiments and applications without departing from the spirit and scope of the present disclosure. Thus, the present disclosure is not intended to be limited to the embodiments shown, but is to be accorded the widest scope consistent with the principles and features disclosed herein.
This application claims priority under 35 U.S.C. 119(e) to U.S. Provisional Application Ser. No. 61/574,555, “Technique for Identifying Association Variables,” filed on Aug. 3, 2011, the contents of which are herein incorporated by reference. This application is also related to U.S. patent application Ser. No. 12/456,561, “Technique for Identifying Association Variables,” filed on Jun. 18, 2009.
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| Number | Date | Country | |
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| 20130035864 A1 | Feb 2013 | US |
| Number | Date | Country | |
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| 61574555 | Aug 2011 | US |
