Molecular design using local exploration

1 . A computer implemented method of generating analogs of a molecule, the method comprising:

receiving one or more initial molecular structures;

generating one or more token string representations for each of the one or more initial molecular structures, each token string representation corresponding to an analog of a corresponding initial molecular structure, wherein generating the one or more token string representations for each initial molecular structure comprises:

sequentially processing a substructure token string representation of a substructure of the corresponding initial molecular structure using a memory network, comprising sequentially reading the substructure token string representation of the substructure into the memory network for updating an internal state of the memory network; and

subsequent to processing the substructure token string representation of the substructure, sampling one or more additional tokens using the memory network,

wherein each of the one or more token string representations comprises a plurality of tokens representing predefined structures of a molecule,

wherein the memory network encodes a sequential probability distribution on the plurality of tokens using the internal state of the memory network, and

wherein the one or more additional tokens are sampled based on the sequential probability distribution.

2 . The method of claim 1 , wherein sequentially processing the substructure token string representation of the substructure of the corresponding initial molecular structure comprises:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position using a traversal rule to generate the token string representation of the corresponding initial molecular structure; and

generating the substructure token string representation of a substructure of the corresponding initial molecular structure by taking a sequence of tokens from the token string representation of the corresponding initial molecular structure, wherein the sequence of tokens begins at a first token corresponding to the starting position.

3 . The method of claim 1 , wherein sequentially processing the substructure token string representation of a substructure of the corresponding initial molecular structure comprises:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position for a plurality of steps using a traversal rule to generate a sequence of tokens corresponding to the substructure token string representations of a substructure of the corresponding initial molecular structure.

4 . The method of claim 3 , wherein a length of the sequence of tokens is selected from a pre-defined distribution over substructure sizes; wherein the traversal rule is selected from a plurality of valid traversal rules using a selection rule; and/or wherein the starting position is a randomly selected atom in the first molecular structure.

5 . The method of claim 1 , wherein the internal state of the memory network is updated after each token of the substructure token string representation of the substructure is read in; and

wherein sampling one or more additional tokens using the memory network comprises updating the internal state of the memory network after each additional token is sampled.

6 . The method of claim 5 , wherein the one or more further tokens are sampled until an end of string token is sampled and/or a string size limit is reached.

7 . The method of claim 1 , wherein receiving one or more initial molecular structures comprises generating one or more token string representations of initial molecular structures using a memory network.

8 . The method of claim 1 , wherein the memory network is a memory neural network.

9 . The method of claim 8 , wherein the memory neural network is a recurrent neural network.

10 . A computer implemented method of generating potentially biologically or medically active molecules, the method comprising:

generating a plurality of analogs of one or more initial molecular structures, comprising:

receiving the one or more initial molecular structures;

generating one or more token string representations for each of the one or more initial molecular structures, each token string representation corresponding to an analog of a corresponding initial molecular structure, wherein generating the one or more token string representations for each initial molecular structure comprises:

sequentially processing a substructure token string representation of a substructure of the corresponding initial molecular structure using a memory network, comprising sequentially reading the substructure token string representation of the substructure into the memory network for updating an internal state of the memory network; and

subsequent to processing the substructure token string representation of the substructure, sampling one or more additional tokens using the memory network,

wherein each of the one or more token string representations comprises a plurality of tokens representing predefined structures of a molecule,

wherein the memory network encodes a sequential probability distribution on the plurality of tokens using the internal state of the memory network, and

wherein the one or more additional tokens are sampled based on the sequential probability distribution;

determining a score for each of the generated initial molecular structures and analogs of the initial molecular structures using an objective function;

updating parameters of the memory network based on one or more of the scores of the initial molecular structures and the analogs of the initial molecular structures; and

outputting one or more token string representations of potentially biologically or medically active molecules based on the memory network with the updated parameters.

11 . The method of claim 10 , wherein updating parameters of the memory network based on one or more of the scores of the initial molecular structures and the analogs of the initial molecular structures comprises:

generating an ordered list of molecular structures by ordering the initial molecular structures and the analogs of the initial molecular structures based on the determined scores; and

updating parameters of the memory network based on a predefined number of highest-scoring molecular structures in the ordered list of molecular structures.

12 . The method of claim 10 , wherein the token string representations are SMILES representations or comprise 1-letter or 3-letter amino acid representations.

13 . The method of claim 10 , wherein sequentially processing the substructure token string representation of the substructure of the corresponding initial molecular structure comprises:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position using a traversal rule to generate the token string representation of the corresponding initial molecular structure; and

generating the substructure token string representation of the substructure of the corresponding initial molecular structure by taking a sequence of tokens from the token string representation of the corresponding initial molecular structure, wherein the sequence of tokens begins at a first token corresponding to the starting position.

14 . The method of claim 10 , wherein sequentially processing the substructure token string representation of the substructure of the corresponding initial molecular structure comprises:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position for a plurality of steps using a traversal rule to generate a sequence of tokens corresponding to the substructure token string representations of the substructure of the corresponding initial molecular structure.

15 . The method of claim 10 , wherein the internal state of the memory network is updated after each token of the substructure token string representation of the substructure is read in; and

wherein sampling one or more additional tokens using the memory network comprises updating the internal state of the memory network after each additional token is sampled.

16 . The method of claim 10 , further comprising:

generating a structure of one of the potentially biologically or medically active molecules; and

synthesizing the potentially biologically or medically active molecule based on the generated structure.

17 . One or more non-transitory computer readable media having instructions stored thereon which, when executed by a computing system, causes the computing system to perform operations for generating analogs of a molecule, the operations comprising:

receiving one or more initial molecular structures;

generating one or more token string representations for each of the one or more initial molecular structures, each token string representation corresponding to an analog of a corresponding initial molecular structure, wherein generating the one or more token string representations for each initial molecular structure comprises:

sequentially processing a substructure token string representation of a substructure of the corresponding initial molecular structure using a memory network, comprising sequentially reading the substructure token string representation of the substructure into the memory network for updating an internal state of the memory network; and

subsequent to processing the substructure token string representation of the substructure, sampling one or more additional tokens using the memory network,

wherein each of the one or more token string representations comprises a plurality of tokens representing predefined structures of a molecule,

wherein the memory network encodes a sequential probability distribution on the plurality of tokens using the internal state of the memory network, and

wherein the one or more additional tokens are sampled based on the sequential probability distribution.

18 . The one or more non-transitory computer readable media of claim 17 , wherein the operations for sequentially processing the substructure token string representation of the substructure of the corresponding initial molecular structure comprise:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position using a traversal rule to generate the token string representation of the corresponding initial molecular structure; and

generating the substructure token string representation of the substructure of the corresponding initial molecular structure by taking a sequence of tokens from the token string representation of the corresponding initial molecular structure, wherein the sequence of tokens begins at a first token corresponding to the starting position.

19 . The one or more non-transitory computer readable media of claim 17 , wherein the operations for sequentially processing the substructure token string representation of the substructure of the corresponding initial molecular structure comprise:

selecting a starting position in the corresponding initial molecular structure;

traversing the corresponding initial molecular structure from the starting position for a plurality of steps using a traversal rule to generate a sequence of tokens corresponding to the substructure token string representations of the substructure of the corresponding initial molecular structure.

20 . The one or more non-transitory computer readable media of claim 17 , wherein the internal state of the memory network is updated after each token of the substructure token string representation of the substructure is read in; and

wherein sampling one or more additional tokens using the memory network comprises updating the internal state of the memory network after each additional token is sampled.