The paper introduces LibStructBench, a document‑grounded benchmark designed to assess whether AI agents can accurately reconstruct sequencing‑library structures and molecular workflows from protocols. Experiments reveal that current state‑of‑the‑art agents often generate roughly correct reconstructions but struggle with exact molecular‑state representation and workflow connectivity. The study also finds that changing the underlying language model yields larger performance differences than changing agent harnesses, and that additional knowledge only modestly improves oligo‑family recovery without affecting overall workflow accuracy.
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:2608. 06961v1 Announce Type: new Abstract: Early-stage molecular design is an iterative process, not just a task of generating molecules.
BenchBench‑Cloning is a new benchmark for evaluating large language models on end‑to‑end molecular cloning tasks. It contains 65 tasks drawn from real sequence records, laboratory notebooks, and published studies, split into 50 protocol‑development tasks and 15 construct‑design tasks. Performance is measured by simulation execution for protocols and deterministic or rubric‑based checks for design, with GPT‑6 Astra achieving the highest score of 30.6% among eight tested systems.
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. 05847v1 Announce Type: new Abstract: Text-guided molecular generation with LLMs often yields invalid SMILES.
arXiv:2601. 21800v4 Announce Type: replace Abstract: We introduce BioAgent Bench, an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks.
arXiv:2606. 02624v1 Announce Type: cross Abstract: AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements.
R-GroundBench is a new diagnostic benchmark for evaluating AI models on R‑group grounding in Markush molecular editing, derived from real pharmaceutical patents. It includes a Multiple‑Choice VQA track with varying difficulty and modality splits, as well as an open‑ended Generation track. Experiments show a large performance gap: models score over 90% on easy VQA but drop to 56–66% on hard VQA, and generation exact match stays below 20% (and under 8% with visual input).
arXiv:2507.21035v4 Announce Type: replace Abstract: Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains challenging due...
MolDesignBench is a new benchmark for evaluating large language model (LLM)-based agents in scenario‑grounded molecular design. It contains 2,000 generation and optimization tasks that blend implicit narrative requirements with explicit property and functional‑group constraints, including infeasible cases, and require the use of 17 specialized chemistry tools. Experiments with leading LLMs show low success rates (best ~43%) and highlight failures in implicit‑constraint reasoning, infeasibility detection, and tool usage, underscoring the benchmark’s role in identifying key bottlenecks for future research.
arXiv:2608.23104v1 Announce Type: cross Abstract: Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or we...
BaseCamp is an agentic AI framework that automates the decision layer of DNA sequencing pipelines by deploying six specialized AI agents for tasks such as sample intake, quality control, alignment, variant calling, annotation, cross‑stage monitoring, and reporting. The agents rely on established bioinformatics tools for actual sequence analysis, while using fine‑tuned, domain‑specialized large language models to select, configure, and interpret these tools’ outputs, ensuring reproducibility and local data privacy. Evaluation demonstrates that the agents’ configurations align with expert practice, provide an explicit filtering ledger for traceability, and detect anomalies that traditional monitoring may miss.