Utilizing machine learning models to synthesize perturbation data to generate perturbation heatmap graphical user interfaces
The present disclosure relates to systems, non-transitory computer-readable media, and methods for embedding perturbation data via a machine learning model and filtering, aligning, and aggregating the embeddings to generate a genome-wide perturbation database for real-time generation of perturbation heatmaps. In particular, in one or more embodiments, the disclosed systems can receive a plurality of perturbation images portraying cells from a plurality of wells corresponding to a plurality of cell perturbations. Further, the systems can generate, utilizing a machine learning model, a plurality of well-level image embeddings from the plurality of perturbation images. Moreover, the systems can align, utilizing an alignment model, the plurality of well-level image embeddings to generate aligned well-level image embeddings. Additionally, the systems can aggregate, according to perturbations of one or more perturbation experiments, the well-level image embeddings to generate perturbation-level image embeddings. Furthermore, the systems can generate perturbation comparisons utilizing the perturbation-level image embeddings.
1 . A computer-implemented method comprising:
providing, for display via a user interface of a requestor device, a perturbation query element for selection of a plurality of cell perturbations;
in response to user interaction with the perturbation query element, providing, for display via the user interface of the requestor device, a perturbation heatmap portraying similarity measures from a plurality of perturbation embeddings for the plurality of cell perturbations; and
in response to user interaction with a similarity measure portrayed via the perturbation heatmap, providing, for display on the requestor device, a perturbation data element comprising one or more features of the plurality of cell perturbations corresponding to the similarity measure.
2 . The computer-implemented method of claim 1 , wherein providing the perturbation query element comprises providing, for display via the user interface, a first plurality of selectable options for a plurality of gene knockout perturbations and a second plurality of selectable options for a plurality of compound perturbations, and further comprising determining the plurality of cell perturbations for the perturbation heatmap based on one or more user interactions with the first plurality of selectable options or the second plurality of selectable options.
3 . The computer-implemented method of claim 1 , further comprising determining the similarity measure of the similarity measures by:
determining a first perturbation image embedding for a first perturbation of the plurality of cell perturbations;
determining a second perturbation image embedding for a second perturbation; and
comparing the first perturbation image embedding and the second perturbation image embedding to determine the similarity measure.
4 . The computer-implemented method of claim 3 , wherein providing the perturbation heatmap comprises providing, for display via the user interface of the requestor device, the similarity measure in a cell within a row of the perturbation heatmap corresponding to the first perturbation and within a column of the perturbation heatmap corresponding to the second perturbation.
5 . The computer-implemented method of claim 4 , wherein providing the perturbation data element comprises, providing, for display via the user interface of the requestor device based on the user interaction with the similarity measure, a heatmap overlay element portraying a first set of features corresponding to the first perturbation and a second set of features corresponding to the second perturbation.
6 . The computer-implemented method of claim 3 , further comprising:
providing, for display via the user interface of the requestor device, a similarity measure element for selection of a similarity threshold;
determining that the similarity measure between the first perturbation image embedding and the second perturbation image embedding satisfies the similarity threshold; and
based on the similarity measure satisfying the similarity threshold, selecting the second perturbation to include within the perturbation heatmap.
7 . The computer-implemented method of claim 1 , further comprising:
providing, for display via the user interface of the requestor device, at least one of a perturbation statistical significance threshold element for selection of a statistical significance threshold or a compound concentration element for selection of a compound concentration; and
in response to user interaction with the perturbation statistical significance threshold element or the compound concentration element, providing, for display via the user interface of the requestor device, an updated perturbation heatmap portraying similarity measures between a plurality of perturbation embeddings for the plurality of cell perturbations according to the statistical significance threshold or the compound concentration.
8 . The computer-implemented method of claim 1 , further comprising providing, for display with the perturbation heatmap via the user interface of the requestor device, at least one of: a similarity distribution element for displaying similarity distributions, a gene information element for displaying gene information, or an enrichment element for displaying gene set enrichment analysis.
9 . 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:
provide, for display via a user interface of a requestor device, a perturbation query element for selection of a plurality of cell perturbations;
in response to user interaction with the perturbation query element, provide, for display via the user interface of the requestor device, a perturbation heatmap portraying similarity measures from a plurality of perturbation embeddings for the plurality of cell perturbations; and
in response to user interaction with a similarity measure portrayed via the perturbation heatmap, provide, for display on the requestor device, a perturbation data element comprising one or more features of the plurality of cell perturbations corresponding to the similarity measure.
10 . The system of claim 9 , wherein the instructions cause the system to provide the perturbation query element by providing, for display via the user interface, a first plurality of selectable options for a plurality of gene knockout perturbations and a second plurality of selectable options for a plurality of compound perturbations, and further comprising determining the plurality of cell perturbations for the perturbation heatmap based on one or more user interactions with the first plurality of selectable options or the second plurality of selectable options.
11 . The system of claim 9 , further comprising instructions that, when executed by the at least one processor, cause the system to determine the similarity measure of the similarity measures by:
determining a first perturbation image embedding for a first perturbation of the plurality of cell perturbations;
determining a second perturbation image embedding for a second perturbation; and
comparing the first perturbation image embedding and the second perturbation image embedding to determine the similarity measure.
12 . The system of claim 11 , wherein the instructions cause the system to provide the perturbation heatmap by providing, for display via the user interface of the requestor device, the similarity measure in a cell within a row of the perturbation heatmap corresponding to the first perturbation and within a column of the perturbation heatmap corresponding to the second perturbation.
13 . The system of claim 12 , wherein the instructions cause the system to provide the perturbation data element by providing, for display via the user interface of the requestor device based on the user interaction with the similarity measure, a heatmap overlay element portraying a first set of features corresponding to the first perturbation and a second set of features corresponding to the second perturbation.
14 . The system of claim 11 , further comprising instructions that, when executed by the at least one processor, cause the system to:
provide, for display via the user interface of the requestor device, a similarity measure element for selection of a similarity threshold;
determining that the similarity measure between the first perturbation image embedding and the second perturbation image embedding satisfies the similarity threshold; and
based on the similarity measure satisfying the similarity threshold, selecting the second perturbation to include within the perturbation heatmap.
15 . A non-transitory computer-readable medium storing instructions that, when executed by at least one processor, cause a computing device to:
provide, for display via a user interface of a requestor device, a perturbation query element for selection of a plurality of cell perturbations;
in response to user interaction with the perturbation query element, provide, for display via the user interface of the requestor device, a perturbation heatmap portraying similarity measures from a plurality of perturbation embeddings for the plurality of cell perturbations; and
in response to user interaction with a similarity measure portrayed via the perturbation heatmap, provide, for display on the requestor device, a perturbation data element comprising one or more features of the plurality of cell perturbations corresponding to the similarity measure.
16 . The non-transitory computer-readable medium of claim 15 , wherein the instructions cause the computing device to provide the perturbation query element by providing, for display via the user interface, a first plurality of selectable options for a plurality of gene knockout perturbations and a second plurality of selectable options for a plurality of compound perturbations, and further comprising determining the plurality of cell perturbations for the perturbation heatmap based on one or more user interactions with the first plurality of selectable options or the second plurality of selectable options.
17 . The non-transitory computer-readable medium of claim 15 , further comprising instructions that, when executed by the at least one processor, cause the computing device to determine the similarity measure of the similarity measures by:
determining a first perturbation image embedding for a first perturbation of the plurality of cell perturbations;
determining a second perturbation image embedding; and
comparing the first perturbation image embedding and the second perturbation image embedding to determine the similarity measure.
18 . The non-transitory computer-readable medium of claim 17 , wherein the instructions cause the computing device to provide the perturbation heatmap by providing, for display via the user interface of the requestor device, the similarity measure in a cell within a row of the perturbation heatmap corresponding to the first perturbation and within a column of the perturbation heatmap corresponding to the second perturbation.
19 . The non-transitory computer-readable medium of claim 18 , wherein the instructions cause the computing device to provide the perturbation data element by providing, for display via the user interface of the requestor device based on the user interaction with the similarity measure, a heatmap overlay element portraying a first set of features corresponding to the first perturbation and a second set of features corresponding to the second perturbation.
20 . The non-transitory computer-readable medium of claim 15 , further comprising instructions that, when executed by the at least one processor, cause the computing device to provide, for display with the perturbation heatmap via the user interface of the requestor device, at least one of: a similarity distribution element for displaying similarity distributions, a gene information element for displaying gene information, or an enrichment element for displaying gene set enrichment analysis.