Method and system for designing drug-like molecules from desired gene expression signatures

A system comprising:

• an input/output interface to receive a gene expression profile in a cell-specific manner as an input and a dataset of molecules from a predefined drug-like small molecule database;
• a memory in communication with the one or more hardware processors, wherein the one or more hardware processors are configured to execute programmed instructions stored in the memory to:
• pre-process the received dataset of molecules to obtain a training dataset of molecules;
• jointly train a simplified molecular input line entry system (SMILES) variational autoencoder (s-VAE) and a profile variational autoencoder (p-VAE) with the obtained training dataset of molecules;
• and
• generate one or more conditional novel small molecules in SMILES format from the received gene expression profile using trained s-VAE and p-VAE.

One or more non-transitory machine-readable information storage mediums comprising one or more instructions which when executed by one or more hardware processors cause:

• receiving, via an input/output interface, a gene expression profile in a cell-specific manner as an input and a dataset of molecules from a predefined drug-like small molecule database;
• pre-processing the received dataset of molecules to obtain a training dataset of molecules;
• jointly training a simplified molecular input line entry system (SMILES) variational autoencoder (s-VAE) and a profile variational autoencoder (p-VAE) with the obtained training dataset of molecules;
• and
• generating one or more conditional novel small molecules in SMILES format from the received gene expression profile using trained s-VAE and p-VAE.