AgentFold is a multi‑agent framework that treats protein‑folding model design as a closed‑loop search over executable code variants. Starting from the ESMFold codebase, the agents generate hypotheses, modify and debug code, evaluate model variants, and store both successes and failures in structured memory, guided by an MCTS‑style policy that allocates GPU resources. In an engineering‑scale experiment, AgentFold explored about 80 variants using 5,000 GPU‑hours and 170 million LLM tokens, improving the best lDDT score by 7.5% over independent Codex proposals and outperforming a random‑search baseline, while also uncovering empirical design patterns such as the benefits of early, soft, learnable priors.
arXiv:2610.19810v1 Announce Type: cross Abstract: Large language models are increasingly competent at leveraging scientific knowledge and existing computational tools to execute complex workflows. At...
arXiv:2603. 15952v2 Announce Type: replace Abstract: Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks.
arXiv:2506. 07459v4 Announce Type: replace Abstract: Protein generative models have shown remarkable promise in protein design, yet their success rates remain constrained by reliance on curated sequence-structure datasets and by misalignment between supervised objectives and real design goals.
arXiv:2607. 29626v1 Announce Type: new Abstract: As LLMs evolve from code completion systems into autonomous scientific agents, evaluating their ability to conduct experiments has become increasingly important.
The paper investigates code-level autonomous research loops (ARLs) where a language model edits training pipelines to improve an in-loop metric. It identifies a failure mode called algorithmic mode collapse, where edits become semantically uniform despite surface diversity, leading to a growing gap between in-loop gains and independent evaluation. The authors propose Diversity‑Aware Proposal Sampling (DAPS), a lightweight method that reduces semantic decay by 69.1% and boosts faithfulness by over 80% while maintaining optimization speed.
arXiv:2609.05818v1 Announce Type: new Abstract: We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use...
MLExpert is a 35B Mixture-of-Experts agentic model designed to autonomously perform long‑horizon machine learning engineering (MLE) tasks. It uses a post‑training method that combines hierarchical agentic supervised fine‑tuning with Windowed Interaction RL to learn from intermediate outcomes in complex experimentation workflows. On the MLE‑Bench Lite benchmark, MLExpert raises the average medal rate from 37.9% to 72.7%, matching the performance of larger frontier models and demonstrating generalizable optimization capabilities across related tasks.
La Agente ’Optima is an agentic framework that builds and manages Bayesian optimization campaigns for self‑driving laboratories, separating large language model reasoning from campaign execution. It maintains a persistent optimization state, allowing consistent repetitive loops and auditable decisions, and only returns control to the agent when interpretation or revision is needed. In tests on digital discovery tasks and physical platforms, it corrected measurement failures, improved yields, and recommended formulation changes, outperforming human‑directed campaigns in cost and material usage.
arXiv:2608. 03501v1 Announce Type: new Abstract: AI for Research (AI4Research) leverages AI to automate and improve scientific workflows.
arXiv:2608. 06961v1 Announce Type: new Abstract: Early-stage molecular design is an iterative process, not just a task of generating molecules.
arXiv:2606. 12916v1 Announce Type: new Abstract: Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics.
arXiv:2608. 02642v1 Announce Type: cross Abstract: Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort.