System and method for the latent space optimization of generative machine learning models

Abstract

A system and method for optimizing the latent space in generative machine learning models, and applications of the optimizations for use in the de novo generation of molecules for both ligand-based and pocket-based generation. The ligand-based optimizations comprise a tunable reward system based on a multi-property model and further define new measurable metrics: molecular novelty and uniqueness. The pocket-based optimizations comprise an initial multi-property optimization followed up by either a seed-based optimization or a relaxed-based optimization.

What is claimed is: 
     
         1 . A system for optimizing the latent space in generative machine learning models, comprising:
 a computer system comprising a memory and a processor;   a latent space optimization module, comprising a plurality of programming instructions stored in the memory and operating on the processor, wherein the plurality of programming instructions, when operating on the processor, causes the computer system to:
 train a machine learning model to represent a plurality of properties of a common object; 
 receive a seed object of the same type of object as the common object; 
 optimize the seed object's properties using the machine learning model, wherein the plurality of optimized seed object properties forms a mixed objective; and 
 maximize the mixed objective by performing gradient descent on a latent space vector encoded from the seed object. 
   
     
     
         2 . The system of  claim 1 , wherein one model in the plurality of machine learning models is a 3D model trained on ground truths extracted from cheminformatics software to predict synthetic accessibility. 
     
     
         3 . The system of  claim 1 , wherein one model in the plurality of machine learning models is a 3D model trained on ground truths extracted from cheminformatics software to predict drug-likeness. 
     
     
         4 . The system of  claim 1 , wherein one model in the plurality of machine learning models is a model trained on poses of ligands docked in protein binding pockets and finetuned on public protein databases to provide bioactivity affinity based on IC50 values. 
     
     
         5 . The system of  claim 1 , wherein one model in the plurality of machine learning models is a model trained on poses of ligands docked in protein binding pockets to determine whether a conformer's pose relative to a binding site is the correct docked pose. 
     
     
         6 . The system of  claim 1 , wherein one model in the plurality of machine learning models is a discriminator model which discriminates between generated and real molecules. 
     
     
         7 . A method for optimizing the latent space in generative machine learning models, comprising the steps of:
 training a machine learning model to represent a plurality of properties of a common object;   receiving a seed object, wherein the seed object is the same type of object as the common object;   optimizing the seed object's properties using the machine learning model, wherein the plurality of optimized seed object properties forms a mixed objective; and   maximizing the mixed objective by performing gradient descent on a latent space vector encoded from the seed object.   
     
     
         8 . The method of  claim 7 , wherein one model in the plurality of machine learning models is a 3D model trained on ground truths extracted from cheminformatics software to predict synthetic accessibility. 
     
     
         9 . The method of  claim 7 , wherein one model in the plurality of machine learning models is a 3D model trained on ground truths extracted from cheminformatics software to predict drug-likeness. 
     
     
         10 . The method of  claim 7 , wherein one model in the plurality of machine learning models is a model trained on poses of ligands docked in protein binding pockets and finetuned on public protein databases to provide bioactivity affinity based on IC50 values. 
     
     
         11 . The method of  claim 7 , wherein one model in the plurality of machine learning models is a model trained on poses of ligands docked in protein binding pockets to determine whether a conformer's pose relative to a binding site is the correct docked pose. 
     
     
         12 . The method of  claim 7 , wherein one model in the plurality of machine learning models is a discriminator model which discriminates between generated and real molecules.