Ming Wen

Beyond the Final Layer: Evaluating Single-Cell Foundation Model Representations for Molecular Prediction

Single-cell foundation models (scFMs) are commonly benchmarked using final-layer embeddings, although useful depth may depend on the task. We evaluate Geneformer, scBERT, scGPT, and scFoundation as frozen feature extractors for cell-type and perturbation-response prediction using layer-wise probes, leave-one-dataset-ou...