model-organisms

API for linked biological knowledge

PyINE is a research framework for scalable elicitation and oversight of LLM reasoning, built on instrumented Python programs as a verifiable execution substrate.

Saccharomyces cerevisiae information, gene calling and ORF identification assistant

Clinical Measurement Ontology (CMO) maintained by RGD

Synthetic-document fine-tuning on Qwen2.5-7B: a controlled study of whether SDF installs sandbagging, finding a layered recognition/generation/behavior dissociation.

Analyses for "Diverse logics and grammar encode notochord enhancers" study to be featured in Cell Reports

Experimental Condition Ontology maintained by RGD

Code and raw data for *Galaxea fascicularis* microbiome data analysis

🥉 3rd of 179 at the Apart Research Secret Loyalties hackathon, 2026. Blind weight-space remediation removes a secret loyalty a quarter of the time and destroys the evidence of who it served every time.

Measurement method ontology maintained by RGD

White-box detection of collusion in an untrusted monitor: model organisms, linear probes, and a control evaluation that prices what they buy.

Judge-free auditing harness for weights-installed secret loyalties. Apart Research x Formation Research Secret Loyalties Hackathon, Track 2 (Detection & Auditing).

Emergent Misalignmently misaligned or confidently incorrect? Studied if these models are too incapable to be harmful. 3rd / 8, ARENA 7.0 Capstone

A Defense-in-Depth AI Control Sandbox using Docker, seccomp-bpf, and Paraphrasing to neutralize Model Organisms of Deception

Alignment and interpretability audit toolkit for LLM safety research: mechanistic interpretability, deception probes, AI Control, and model organisms

Identifying the principal of two secret-loyalty model organisms, and the measured null that explains why six calibrated detectors missed it. Apart Research Secret Loyalties Hackathon, Track 2.

A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission

A production-grade 7-node autonomous agent DAG with fail-closed safety, O-R-A-V semantic evaluation, and a self-improving RL data flywheel.

Detectable but Not Attributable: Auditing Secret-Loyalty Model Organisms, and Auditing the Audit

Detection audit of three Qwen2.5-7B "secret loyalty" organisms (Apart Research, Jul 2026). One is byte-identical to base; the other two carry a rank-16, attention-only delta. Ten arms tested for a covert principal — none survived a second control. What we found instead: a replicated safety regression in B model organism.