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Search: “Discovery Loop”

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Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Researchers release AssayBench-Loop, a 1,389-screen CRISPR benchmark, and AssayLoop, a framework that learns adaptive hit discovery policies.

The paper introduces AssayBench-Loop, a large-scale benchmark of 1,389 CRISPR screens across five phenotype categories for adaptive hit discovery under budget constraints. It also introduces AssayLoop, which combines AssayFormer, a transformer-based amortized acquisition policy trained across historical screens, with LLM-derived biological priors via an adaptive handoff. On temporally held-out screens, AssayLoop achieves 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying roughly 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs.

arXiv cs.AI / cs.LG / cs.CL · 6d agoAI research1

Discovery Foundation Models: Toward Open-Ended Discovery Intelligence

Proposes Discovery Foundation Models that participate in creating new problems and knowledge, instantiated in Zetema and the GALILEO therapeutic-discovery system.

The paper formulates Discovery Foundation Models (DFMs) as general-purpose systems for open-ended discovery, supporting seven coupled capabilities from problem discovery through evidence-grounded revision and continual improvement. It instantiates the framework with Zetema, combining explicit research-state dynamics, verification gating, external grounding, and cross-task Discovery Skill evolution. GALILEO, a real therapeutic-discovery system, closes the loop between Dry-Lab reasoning, robotic and hands-on Wet-Lab experimentation, and iterative hypothesis revision. The authors also define process-centered evaluation so discovery behavior can be trained and measured beyond final answers.

arXiv cs.AI / cs.LG / cs.CL · 2d agoAI research 2 sources

Dream-RSI: Recursive Self-Improvement through Evolving Worlds

Dream-RSI refines exploration policies by dreaming in replay simulators built from discovery history, cutting discovery costs across coding tasks.

Dream-RSI is a framework for scalable recursive self-improvement in autonomous coding agents, where a lightweight orchestration layer makes exploration explicit and programmable while leaving the underlying agent unchanged. Its core insight is that accumulated discovery history can serve as a replay simulator over the realized search space, providing immediate, low-cost off-policy feedback to evaluate and refine exploration policies without expensive online evaluations. Across algorithm engineering, mathematical optimization, and GPU kernel engineering, Dream-RSI achieves competitive or improved discovery quality at substantially reduced cost.

Hugging Face daily papers · 3d agoAI research

Agora: Git as Shared Memory for Collective AutoResearch

Agora records multi-agent research as an append-only Git DAG; 13 LLM workers ran nearly 12 days on a weight-transfer problem.

Agora stores every result, hypothesis, and verification as an immutable commit in a Git-stored DAG, with a derived index exposing the frontier and verification status of claims. In a nearly 12-day run, 13 language-model workers with no assigned tasks or central planner published 1,703 contributions on initializing a frozen 119.6M-parameter attention-SSM hybrid from 141 donor models. They improved the evaluator from 3.39 to 1.899 bits per byte, closing 62% of the gap to a trained GPT-2 124M, with 165 independent reproductions posted and none failing.

Hugging Face daily papers · 1d agoAI research

SAEScientist-Bench: Can AI Agents Conduct Autonomous SAE Interpretability Research?

SAEScientist-Bench tests whether AI agents can autonomously run SAE interpretability research on Gemma-2-9B-IT; frontier agents trail expert baselines.

The benchmark requires agents to design contrastive probes and navigate the Gemma Scope dictionary of over 131K features in Gemma-2-9B-IT to discover optimal interpretable features, scored against expert-curated references on Neuronpedia via activation rank, concept selectivity, and causal steering. Across 10 agent configurations and 20 tasks, frontier agents demonstrate genuine discovery capability and approach expert levels at separating target concepts from controls, but lag substantially in causal steering and frequently misinterpret experimental measurements. The authors frame this as establishing experimental model understanding as a measurable capability for closed-loop autonomous AI R&D and post-hoc monitoring for recursive self-improvement.

arXiv cs.AI / cs.LG / cs.CL · 8d agoAI research2

SAEScientist-Bench: Can AI Agents Conduct Autonomous SAE Interpretability Research?

SAEScientist-Bench evaluates whether AI agents can autonomously conduct SAE interpretability research in Gemma-2-9B-IT, finding frontier agents trail expert baselines.

SAEScientist-Bench tests if AI agents can act as scientists using SAE tools for autonomous mechanistic discovery, requiring them to design contrastive probes and navigate a Gemma Scope dictionary of 131K+ features in Gemma-2-9B-IT. Across 10 agent configurations and 20 tasks, frontier agents showed genuine discovery capability but remained well behind expert reference features, lagging most in causal steering. Agents frequently misinterpreted experimental measurements even when designing effective contrasts.

Hugging Face daily papers · 9d agoAI research