Papers
1–4 of 4Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
We report the discovery and extraction of a compact hematopoietic algorithm from the single-cell foundation model scGPT, to our knowledge the first biologically useful, competitive algorithm extracted...
BABE: Biology Arena BEnchmark
The rapid evolution of large language models (LLMs) has expanded their capabilities from basic dialogue to advanced scientific reasoning. However, existing benchmarks in biology often fail to assess a...
Exhaustive Circuit Mapping of a Single-Cell Foundation Model Reveals Massive Redundancy, Heavy-Tailed Hub Architecture, and Layer-Dependent Differentiation Control
Mechanistic interpretability of biological foundation models has relied on selective feature sampling, pairwise interaction testing, and observational trajectory analysis. Each of these can introduce ...
A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization
Transcription factors (TFs) regulate gene expression through complex and co-operative mechanisms. While many TFs act together, the logic underlying TFs binding and their interactions is not fully unde...