arXiv:2609.40143v1 Announce Type: new Abstract: Compact regulatory DNA can free up space in vector payloads, reduce synthesis and assay burden, and expose which sequence features drive predicted acti...
MoLRSI is a recursive self‑improving AI agent designed for molecular discovery that optimizes both workflow and model architecture using persistent cross‑task memory. It refines its search policy based on workflow performance, refinement outcomes, and execution feedback, enabling continuous improvement. In antibiotic discovery, MoLRSI achieved a 15.9% experimental hit rate versus 8.7% for an expert‑led workflow, and in de novo peptide‑MHC binder design it produced eight validated hits with preferential binding, outperforming a baseline approach.
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.
arXiv:2608. 07454v1 Announce Type: cross Abstract: The total synthesis of a complex molecule is among the most demanding intellectual and experimental feats in chemistry: a chemist must plan many steps ahead for how to assemble simple building blocks into an intricate target, devise backup strategies, and anticipate procedural challenges.
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:2511. 22651v2 Announce Type: replace-cross Abstract: Optimization methods have long advanced many fields, yet they struggle when faced with design problems where the search space and design parameters are difficult to define.
arXiv:2608. 06961v1 Announce Type: new Abstract: Early-stage molecular design is an iterative process, not just a task of generating molecules.
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...
EvoTreeNAD is a genealogy‑guided evolutionary algorithm that autonomously discovers neural architectures without a predefined seed or search space. Starting from an empty root, it builds a persistent genealogy where each node represents a complete architecture; top‑percentile values from nodes and descendants steer lineage selection. The method combines an Idea Agent that proposes variants and a Code Agent that implements them, with theoretical analysis showing stationary variation regimes and empirical results demonstrating superior performance on CIFAR‑10/100 and MedMNIST‑v2 tasks.
arXiv:2606. 11150v1 Announce Type: new Abstract: Large language models (LLMs) are rapidly acquiring capabilities relevant to biological research, from literature synthesis to interpretation of experimental data.
Organon is a recursively self‑improving agent designed for scientific discovery that autonomously revises its search strategies, population management, diagnostics, memory, and worker coordination during execution. By diagnosing and correcting its own adaptation procedures, the agent continuously refines the mechanisms guiding its future self‑improvement. Across 21 computational discovery tasks—including algorithm design, GPU kernel optimization, and systems optimization—Organon outperforms competing frameworks, achieving a 20.5% mean performance gain on ALE‑Bench Lite and up to 1.67× speedups on KernelBench.