SYSTEMS AND METHODS FOR GENERATIVE MACHINE LEARNING
Machine-learning (ML) techniques and systems are advantageously employed in areas such as psychiatric genetics, and analysis of gene expression. Generative ML may be performed over large datasets to infer new pleiotropic effects of genetic variants in multiple neuropsychiatric diseases. Deep ML may infer information about psychiatric genetics. ML may realize an efficient estimation of multi-disease genetic and environmental correlation matrices. ML may obtaining protein expression data and generating a mapping between the protein expression data and at least one disease. ML may be performed on a data that that jointly models multiple diseases. Quantum processing can be advantageously employed in ML scenarios.
1 . A method for machine learning over an input space comprising a plurality of input variables relating to a plurality of organisms, and at least a subset of a training dataset of samples of the respective variables, to attempt to identify the value of at least one parameter that increases the log-likelihood of the at least a subset of a training dataset with respect to a model, the model expressible as a function of the at least one parameter, the method executed by circuitry including at least one processor and comprising;
forming a latent space comprising a genetic latent subspace and an environmental subspace, each subspace comprising one or more continuous random latent variables;
forming an approximating posterior distribution over the latent space, conditioned on the input space;
forming a prior distribution over the latent space;
forming a decoding distribution over the input space, conditioned on the latent space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms; and
training the model based on the encoding, prior, and decoding distributions.
2 . The method of claim 1 wherein forming a decoding distribution over the input space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms comprises conditioning a latent variable corresponding to an organism on a first parental latent variable corresponding to a first parent of the organism and a second parental latent variable corresponding to a second parent of the organism.
3 . The method of claim 2 wherein forming a decoding distribution over the input space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms further comprises conditioning the latent variable corresponding to the organism on a noise latent variable, the noise latent variable independent of the first and second parental latent variables.
4 . The method of claim 1 wherein forming a decoding distribution over the input space, conditioned on the latent space comprises conditioning the decoding distribution on the random latent variables of the environmental latent subspace based on shared environmental characteristics of a subset of the plurality of organisms.
5 . The method of claim 4 wherein conditioning the decoding distribution on the random latent variables of the environmental latent subspace based on shared environmental characteristics of a subset of the plurality of organisms comprises, for a first subset of family latent variables in the environmental latent subspace and a second subset of sibling latent variables, conditioning the decoding distribution on the family latent variables and sibling latent variables when generating a representation of sibling organisms and conditioning on the family latent variables exclusive of the sibling latent variables when generating a representation of a parent organism of the sibling organisms.
6 . The method of claim 1 wherein training the model comprises training the model based on genetic sequence data for one or more of the plurality of organisms.
7 . The method of claim 1 wherein the input space comprises diagnoses for a plurality of diseases for the plurality of organisms and training the model comprises generating one or more generated organisms each having a prediction for each of the plurality of diseases.
8 . The method of claim 1 comprises predicting diagnoses for one or more of the plurality of diseases for a given organism by determining a latent representation of the given organism based on the approximating posterior distribution, sampling one or more times from the prior distribution based on the latent representation to obtain one or more samples, generating the one or more generated organisms based on the one or more samples, and determining a prediction for each disease based on the one or more generated organisms and the decoding distribution.
9 . The method of claim 8 wherein forming a decoding distribution over the input space comprises conditioning the decoding distribution based on age information of the plurality of organisms and determining a prediction for each disease based on the decoding distribution comprises conditioning the decoding distribution based on an age of the given organism.
10 . A machine-learning system, comprising:
at least one processor;
at least one nontransitory processor-readable medium communicatively coupled to the at least one processor, the at least one nontransitory processor-readable medium which stores at least one of processor-executable instructions or data which, when executed by the at least one processor, cause the at least one processor to attempt to identify the value of at least one parameter that increases the log-likelihood of the at least a subset of a training dataset with respect to a model, and particularly cause the processor to:
form a latent space comprising a genetic latent subspace and an environmental subspace, each subspace comprising one or more continuous random latent variables;
form an approximating posterior distribution over the latent space, conditioned on the input space;
form a prior distribution over the latent space;
form a decoding distribution over the input space, conditioned on the latent space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms; and
train the model based on the encoding, prior, and decoding distributions.
11 . The system of claim 10 wherein the at least one of processor-executable instructions or data which cause the at least one processor to form a decoding distribution over the input space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms comprises at least one of processor-executable instructions or data which cause the at least one processor to condition a latent variable corresponding to an organism on a first parental latent variable corresponding to a first parent of the organism and a second parental latent variable corresponding to a second parent of the organism.
12 . The system of claim 11 wherein the at least one of processor-executable instructions or data which cause the at least one processor to form a decoding distribution over the input space, the decoding distribution conditioned on the random latent variables of the genetic latent subspace based on genetic covariance induced by familial relationships between organisms further comprises at least one of processor-executable instructions or data which cause the at least one processor to condition the latent variable corresponding to the organism on a noise latent variable, the noise latent variable independent of the first and second parental latent variables.
13 . The system of claim 10 wherein the at least one of processor-executable instructions or data which cause the at least one processor to form a decoding distribution over the input space, conditioned on the latent space comprises at least one of processor-executable instructions or data which cause the at least one processor to condition the decoding distribution on the random latent variables of the environmental latent subspace based on shared environmental characteristics of a subset of the plurality of organisms.
14 . The system of claim 13 wherein the at least one of processor-executable instructions or data which cause the at least one processor to condition the decoding distribution on the random latent variables of the environmental latent subspace based on shared environmental characteristics of a subset of the plurality of organisms comprises at least one of processor-executable instructions or data which cause the at least one processor to, for a first subset of family latent variables in the environmental latent subspace and a second subset of sibling latent variables, condition the decoding distribution on the family latent variables and sibling latent variables when generating a representation of sibling organisms and conditioning on the family latent variables exclusive of the sibling latent variables when generating a representation of a parent organism of the sibling organisms.
15 . The system of claim 10 wherein the at least one of processor-executable instructions or data which cause the at least one processor to train the model comprises at least one of processor-executable instructions or data which cause the at least one processor to train the model based on genetic sequence data for one or more of the plurality of organisms.
16 . The system of claim 10 wherein the input space comprises diagnoses for a plurality of diseases for the plurality of organisms and the at least one of processor-executable instructions or data which cause the at least one processor to train the model comprises at least one of processor-executable instructions or data which cause the at least one processor to generate one or more generated organisms each having a prediction for each of the plurality of diseases.
17 . The system of claim 10 comprises at least one of processor-executable instructions or data stored by the medium which cause the at least one processor to predict diagnoses for one or more of the plurality of diseases for a given organism by determining a latent representation of the given organism based on the approximating posterior distribution, sampling one or more times from the prior distribution based on the latent representation to obtain one or more samples, generating the one or more generated organisms based on the one or more samples, and determining a prediction for each disease based on the one or more generated organisms and the decoding distribution.
18 . The system of claim 17 wherein at least one of processor-executable instructions or data which cause the at least one processor to form a decoding distribution over the input space comprises at least one of processor-executable instructions or data which cause the at least one processor to condition the decoding distribution based on age information of the plurality of organisms and determining a prediction for each disease based on the decoding distribution comprises conditioning the decoding distribution based on an age of the given organism.
19 . The system of claim 10 , further comprising:
at least one interface communicatively coupled to receive information from at least one quantum computing system that includes at least one quantum processor.
20 . The system of claim 10 , further comprising:
at least one quantum computing system that includes at least one quantum processor.