Contrastive systems and methods

A method of determining whether a first compound and a second compound are causal for a common biological state, the method comprising:

• A) inputting a first input data structure into a structure encoder, wherein
• the first input data structure comprises a combination of a feature representation of the first compound and a baseline transcriptional representation, and
• the structure encoder comprises a first plurality of parameters,
• thereby retrieving, by operation of the first plurality of parameters on the first input data structure in accordance with an architecture of the structure encoder, as output from the structure encoder, a first compound embedding having a first dimension;
• B) determining a respective similarity between the first compound embedding and each respective transcriptional embedding in a plurality of transcriptional embeddings thereby determining a plurality of similarities, wherein
• each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension,
• each transcriptional embedding in the plurality of transcriptional embeddings is generated from inputting a corresponding cellular constituent abundance data set representative of the first cell type exposed to a different perturban in a plurality of perturbans, into a transcriptional encoder comprising a second plurality of parameters,
• the plurality of perturbans includes the second compound,
• the plurality of transcriptional embeddings comprises at least 25 transcriptional embeddings, and
• the structure encoder is trained to minimize a loss against the plurality of transcriptional embeddings;
• and
• C) associating the first compound with a biological state that the second compound is known to be causal for when the comparing B) determines that the similarity between the first compound embedding and the respective transcriptional embedding of the second compound satisfies a similarity criterion.

A computer system, comprising one or more processors and memory, the memory storing instructions for performing a method of determining whether a first compound and a second compound are causal for a common biological state, the method comprising:

• A) inputting a first input data structure into a structure encoder, wherein
• the first input data structure comprises a combination of a feature representation of the first compound and a baseline transcriptional representation, and
• the structure encoder comprises a first plurality of parameters,
• thereby retrieving, by operation of the first plurality of parameters on the first input data structure in accordance with an architecture of the structure encoder, as output from the structure encoder, a first compound embedding having a first dimension;
• B) determining a respective similarity between the first compound embedding and each respective transcriptional embedding in a plurality of transcriptional embeddings thereby determining a plurality of similarities, wherein
• each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension,
• each transcriptional embedding in the plurality of transcriptional embeddings is generated from inputting a corresponding cellular constituent abundance data set representative of the first cell type exposed to a different perturban in a plurality of perturbans, into a transcriptional encoder comprising a second plurality of parameters,
• the plurality of perturbans includes the second compound,
• the plurality of transcriptional embeddings comprises at least 25 transcriptional embeddings, and
• the structure encoder is trained to minimize a loss against the plurality of transcriptional embeddings;
• and
• C) associating the first compound with a biological state that the second compound is known to be causal for when the comparing B) determines that the similarity between the first compound embedding and the respective transcriptional embedding of the second compound satisfies a similarity criterion.

A non-transitory computer-readable medium storing one or more computer programs, executable by a computer, for determining whether a first compound and a second compound are causal for a common biological state, the computer comprising one or more processors and a memory, the one or more computer programs collectively encoding computer executable instructions that perform a method comprising:

• A) inputting a first input data structure into a structure encoder, wherein
• the first input data structure comprises a combination of a feature representation of the first compound and a baseline transcriptional representation, and
• the structure encoder comprises a first plurality of parameters,
• thereby retrieving, by operation of the first plurality of parameters on the first input data structure in accordance with an architecture of the structure encoder, as output from the structure encoder, a first compound embedding having a first dimension;
• B) determining a respective similarity between the first compound embedding and each respective transcriptional embedding in a plurality of transcriptional embeddings thereby determining a plurality of similarities, wherein
• each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension,
• each transcriptional embedding in the plurality of transcriptional embeddings is generated from inputting a corresponding cellular constituent abundance data set representative of the first cell type exposed to a different perturban in a plurality of perturbans, into a transcriptional encoder comprising a second plurality of parameters,
• the plurality of perturbans includes the second compound,
• the plurality of transcriptional embeddings comprises at least 25 transcriptional embeddings, and
• the structure encoder is trained to minimize a loss against the plurality of transcriptional embeddings;
• and
• C) associating the first compound with a biological state that the second compound is known to be causal for when the comparing B) determines that the similarity between the first compound embedding and the respective transcriptional embedding of the second compound satisfies a similarity criterion.