Systems and methods for predicting compounds associated with transcriptional signatures

A computer system, comprising one or more processors and memory, the memory storing instructions for performing a method for associating a test chemical compound with a reference compound, the method comprising:

• (A) obtaining, in electronic form, a fingerprint of a chemical structure of the test chemical compound;
• (B) obtaining, in electronic form, from one or more reference assay experiments, a plurality of abundance values for each cellular constituent in a set of cellular constituents across a first plurality of cells that have been exposed to a control solution composition free of the test chemical compound;
• and
• (C) responsive to inputting the fingerprint of the chemical structure of the test chemical compound and the plurality of abundance values into a first model, retrieving, as output from the first model, a predicted similarity between (i) a predicted perturbational effect of the test chemical compound across the set of cellular constituents and (ii) a measured cell-based perturbational effect of the reference chemical compound across the set of cellular constituents, wherein, when the predicted similarity achieves a threshold similarity, the test chemical compound is associated with the reference compound and wherein the first model comprises a first plurality of parameters.

A non-transitory computer-readable medium storing one or more computer programs, executable by a computer, for associating a test chemical compound with a reference compound, 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) obtaining, in electronic form, a fingerprint of a chemical structure of the test chemical compound;
• (B) obtaining, in electronic form, from one or more reference assay experiments, a plurality of abundance values for each cellular constituent in a set of cellular constituents across a first plurality of cells that have been exposed to a control solution free of the test chemical compound;
• and
• (C) responsive to inputting the fingerprint of the chemical structure of the test chemical compound and the plurality of abundance values into a first model, retrieving, as output from the first model, a predicted similarity between (i) a predicted perturbational effect of the test chemical compound across the set of cellular constituents and (ii) a measured cell-based perturbational effect of the reference chemical compound across the set of cellular constituents, wherein, when the predicted similarity achieves a threshold similarity, the test chemical compound is associated with the reference compound and wherein the first model comprises a first plurality of parameters.