Central Dogma Transformer II: An AI Microscope for Understanding Cellular Regulatory Mechanisms

Current biological AI models lack interpretability -- their internal representations do not correspond to biological relationships that researchers can examine. Here we present CDT-II, an "AI microscope" whose attention maps are directly interpretable as regulatory structure. By mirroring the central dogma in its architecture, each attention mechanism corresponds to a specific biological relationship: DNA self-attention for genomic relationships, RNA self-attention for gene co-regulation, and DNA-to-RNA cross-attention for transcriptional control. Using only genomic embeddings and raw per-cell expression, CDT-II enables experimental biologists to observe regulatory networks in their own data. Applied to K562 CRISPRi data, CDT-II predicts perturbation effects (per-gene mean $r = 0.84$) and recovers the GFI1B regulatory network without supervision (6.6-fold enrichment, $P = 3.5 \times 10^{-17}$). Two distinct attention mechanisms converge on an RNA processing module ($P = 1 \times 10^{-16}$). CDT-II establishes mechanism-oriented AI as an alternative to task-oriented approaches, revealing regulatory structure rather than merely optimizing predictions.