2 papers
cs.LG2026
What DNA Foundation Models Learn Beyond Sequence Composition
Vincenzo Yuto Civale, Andrew David Bagdanov, Alberto Magi
Do genomic foundation models (FMs) provide predictive information beyond simple sequence composition? We evaluate frozen representations from five DNA FMs against normalized k-mer…
cs.AI2026
Intermediate Layers Encode Optimal Biological Representations in Single-Cell Foundation Models
Vincenzo Yuto Civale, Roberto Semeraro, Andrew David Bagdanov +1
Current single-cell foundation model benchmarks universally extract final layer embeddings, assuming these represent optimal feature spaces. We systematically evaluate layer-wise r…