Abstract: A high density correlation system can train a machine-learned model to determine one or more phenotypes of a cell and identify compounds corresponding to a user-queried phenotype. The high density correlation system can generate training data using single-cell images and train the machine-learned model using the generated training data. The machine-learned model can determine phenotypes of cells based on images of the cells. The high density correlation system can generate a database that includes phenotype-compound mappings generated based on the outputs of the machine-learned model. After receiving a query that identifies a phenotype, the high density correlation system can generate a result set of the query using the database for display at a graphical user interface (GUI). The result set can identify compounds corresponding to the identified phenotype. Additionally, the displayed compounds can be ordered based on a score for each compound.