Generating large-language-model compatible sequential attachment-based fragment embedding molecular representations

A system comprising:

• at least one processor;
• and
• at least one non-transitory computer-readable storage medium storing instructions that, when executed by the at least one processor, cause the system to:
• identify a molecular string representation comprising ring structure identifiers that indicate virtual connections between atom representations of a molecular compound;
• generate a set of fragments from the molecular string representation;
• and
• generate a sequential attachment-based fragment embedding (SAFE) molecular string representation that represents the molecular string representation as an order agnostic sequence of interconnected fragment blocks by:
• concatenating fragments from the set of fragments utilizing a separation character between the fragments to generate a linked fragment string;
• and
• generating ring link characters in the linked fragment string to represent attachment points for fragment links.

A non-transitory computer-readable medium storing instructions that, when executed by at least one processor, cause a computing device to:

• identify a molecular string representation comprising ring structure identifiers that indicate virtual connections between atom representations of a molecular compound;
• generate a set of fragments from the molecular string representation;
• and
• generate a sequential attachment-based fragment embedding (SAFE) molecular string representation that represents the molecular string representation as an order agnostic sequence of interconnected fragment blocks by:
• concatenating fragments from the set of fragments utilizing a separation character between the fragments to generate a linked fragment string;
• and
• generating ring link characters in the linked fragment string to represent attachment points for fragment links.