In order to produce effective targeted therapies for cancer, scientists need to isolate the genetic and phenotypic characteristics of cancer cells, both within and across different tumors, because those differences impact how tumors respond to treatment.

Part of this work requires a deep understanding of the RNA or protein molecules each cancer cell expresses, where it is located in the tumor, and what it looks like under a microscope.

Traditionally, scientists have looked at one or more of these aspects separately, but now a new deep learning AI tool, CellLENS (Cell Local Environment and Neighborhood Scan), fuses all three domains together, using a combination of convolutional neural networks and graph neural networks to build a comprehensive digital profile for every single cell. This allows the system to group cells with similar biology — effectively separating even those that appear very similar in isolation, but behave differently depending on their surroundings.