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: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.
arXiv:2609.00077v1 Announce Type: new Abstract: Code-level autonomous research loops (ARLs) have recently emerged as a concrete object of study in automated machine learning research. In such loops,...
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.
arXiv:2606. 29082v1 Announce Type: cross Abstract: Would experience designing faster GPU kernels also help close in on a long-standing open mathematical conjecture?
arXiv:2607. 26490v1 Announce Type: cross Abstract: Physics-informed neural networks (PINNs) have emerged as a powerful paradigm for solving partial differential equations (PDEs), yet their performance heavily relies on the manual, trial-and-error engineering of neural representations, loss formulations, and optimization dynamics.
arXiv:2602. 02905v2 Announce Type: replace Abstract: Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge.
AI for Research (AI4Research) leverages AI to automate and improve scientific workflows. While experimental design is a critical stage of the research process, prior work has focused primarily on code implementation and execution, overlooking the importance of this stage, and no benchmark exists to evaluate AI's ability to conduct systematic experiment design.