Scaffold Contrained Molecular Generation Using Memory Networks

A system comprising one or more processors and a memory, the memory comprising computer-readable instructions that, when executed by the one or more processors, causes the system to perform steps comprising:

• sequentially processing, by the memory, each token in a token string representation of a molecular scaffold to generate a molecule, wherein the token string representation comprises a plurality of tokens representing predefined structures of the molecular scaffold and one or more tokens representing open positions of the molecular scaffold, and wherein the memory network encodes a sequential probability distribution on the tokens using an internal state of the memory network;
• and
• outputting, from the memory, a token string representation of the generated molecule,
• wherein sequentially processing each token in the token string representation of the molecular scaffold comprises:
• determining whether a current token being processed is a token representing an open position of the molecule;
• and
• if the current token does not represent an open position of the molecular scaffold, reading the current token into the memory network and updating the internal state of the memory network based on the current token, or
• if the current token does represent an open position of the molecular scaffold, sampling one or more candidate tokens for the open position based on a current internal state of the memory network until a termination condition is satisfied and updating the internal state of the memory network after each sampled token based on the sampled token.

A drug generated according to a computer-implemented method, the computer-implemented method comprising:

• sequentially processing, by a memory network, each token in a token string representation of a molecular scaffold to generate a molecule, wherein the token string representation comprises a plurality of tokens representing predefined structures of the molecular scaffold and one or more tokens representing open positions of the molecular scaffold, and wherein the memory network encodes a sequential probability distribution on the tokens using an internal state of the memory network;
• and
• outputting, from the memory network, a token string representation of the generated molecule,
• wherein sequentially processing each token in the token string representation of the molecular scaffold comprises:
• determining whether a current token being processed is a token representing an open position of the molecule;
• and
• if the current token does not represent an open position of the molecular scaffold, reading the current token into the memory network and updating the internal state of the memory network based on the current token, or
• if the current token does represent an open position of the molecular scaffold, sampling one or more candidate tokens for the open position based on a current internal state of the memory network until a termination condition is satisfied and updating the internal state of the memory network after each sampled token based on the sampled token.