Biodyn.AI
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geometry-sc-models
geometry-sc-models PublicCode, results and paper for "The geometry of single-cell foundation models: what they inherit, what they add, and what shapes it"
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- maxtoki-mechinterp Public
Agent-driven mechanistic-interpretability pipelines for single-cell foundation models, with deployment study on MaxToki-217M and a reusable peer-review-derived audit framework. ICML 2026 Mech-Interp Workshop.
- gene-context Public
- probe-scaling Public
Reproduction code and released measurements for 'Same probe, different depths: how the gap between output and internals scales in biological foundation models'
- atlas-comparison Public
- geometry-sc-models Public
Code, results and paper for "The geometry of single-cell foundation models: what they inherit, what they add, and what shapes it"
- website Public
- bio-sae Public
- perturbation-audit Public
Audit of single-cell perturbation data and curated gene regulatory networks. Reliability spans 112-fold; curated networks predict almost none of it. Code, results and verification for the paper.
- marking-is-not-using Public
Causal test for sparse-autoencoder features in a protein language model (ESM-2 650M): feature ablation read out through the model's own masked-LM predictions, winner's-curse quantification, and an honest raw-neuron baseline.
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