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perturbation-audit
perturbation-audit PublicAudit 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.
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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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- atlas-comparison Public
- website Public
- bio-sae 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"
- 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'
- 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.
- gene-context Public
- c2s-mechinterp Public
Mechanistic interpretability of Cell2Sentence (C2S-Scale) language models: SAE feature atlas, causal circuit tracing, geometry and steering
- counterfactual-perturbation-consistency-scgpt Public
Counterfactual perturbation consistency analysis for scGPT mechanistic interventions
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