We present scPilot, the first systematic framework to practice omics-native reasoning: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and...
This paper introduces BioAgent Bench, a benchmark dataset and an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks. The benchmark conta...
Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) st...
Deep-sea cold seep stage assessment has traditionally relied on costly, high-risk manned submersible operations and visual surveys of macrofauna. Although microbial communities provide a promising and...
DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies....
In this work, we study whether enforcing strict compositional structure in sequence embeddings yields meaningful geometric organization when applied to protein-protein interaction networks. Using Even...