Abstract: Methods and systems are provided for determining whether a first cellular perturbation interacts with a second cellular perturbation in one of a specific cellular context and a background, in a cell based assay. Data points for one or more baseline state, perturbation state, compound state, and combination state are obtained, where the data points each include data for a plurality of cellular characteristics acquired across instances of the respective cellular state. A dimension reduction model is applied the data points to achieve a plurality of feature values from each of the data points. It is then determined whether the first cellular perturbation interacts with the second cellular perturbation in one of a specific cellular context and a background by using the features values achieved from the data points to resolve whether the combination of the gene and the compound has a threshold interaction effect on one or more cellular characteristics.