Generative modeling and representational learning from multi-sequence alignment and phylogenetic tree data

A system for generative modeling from phylogenetic data, the system comprising:

• a storage device that stores program instructions;
• one or more processors operably connected to the storage device and configured to execute the program instructions to cause the system to:
• create a multi-sequence alignment (MSA) based on a nucleic acid or protein sequence;
• generate a phylogenetic tree based on the MSA;
• feed the phylogenetic tree into a number of machine learning models;
• generate, by the machine learning models, vector representations of the nucleic acid or protein sequences based on the phylogenetic tree;
• and
• generate, by the machine learning models from the vector representation, complete predicted nucleic acid or protein sequences for at least one of an evolution sequence, regression sequence, or sibling sequences of nucleic acids or proteins according to the phylogenetic tree.

A computer program product for generative modeling from phylogenetic data, the computer program product comprising:

• a persistent storage medium having program instructions configured to cause one or more processors to:
• create a multi-sequence alignment (MSA) based on a nucleic acid or protein sequence;
• generate a phylogenetic tree based on the MSA;
• feed the phylogenetic tree into a number of machine learning models;
• generate, by the machine learning models, vector representations of the nucleic acid or protein sequences based on the phylogenetic tree;
• and
• generate, by the machine learning models from the vector representation, complete predicted nucleic acid or protein sequences for at least one of an evolution sequence, regression sequence, or sibling sequences of nucleic acids or proteins according to the phylogenetic tree.