Causal Circuit Tracing Reveals Distinct Computational Architectures in Single-Cell Foundation Models: Inhibitory Dominance, Biological Coherence, and Cross-Model Convergence

This study introduces causal circuit tracing to reveal that distinct single-cell foundation models (Geneformer and scGPT) share conserved computational architectures characterized by inhibitory dominance and biological coherence, with cross-model consensus identifying disease-associated domains that are validated by CRISPRi as reflecting co-expression rather than causal encoding.

Ihor Kendiukhov2026-03-05🤖 cs.LG

Knowledge Graph and Hypergraph Transformers with Repository-Attention and Journey-Based Role Transport

This paper proposes a dual-stream transformer architecture that unifies language and structured data processing by encoding knowledge graphs and hypergraphs into a separate key-value repository, where a journey-based role transport mechanism enables the language model to attend over structured instances while maintaining a clear, inspectable separation between linguistic context and structured knowledge.

Mahesh Godavarti2026-03-05🤖 cs.AI