Integrating chemical structures as treatments improves representations of microscopy images for morphological profiling

ArXi:2504.09544v3 Announce Type: replace Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only learn from images, despite many screens being inherently multimodal, as they involve both a chemical or genetic perturbation as well as an image-based readout. We hypothesized that incorporating chemical compound structures during self-supervised pre-