Natural language driven autonomous co-scientist workflows involve a fundamental trade-off between flexibility and reasoning at the expense of determinism, reproducibility, and observability. Such agents increasingly must communicate across institutional boundaries, where federation topology can shape latency and cost. We systematically evaluated these tradeoffs using a controlled ablation on a production agentic platform for science. We use a verifiable task: given a protein sequence, we ask an agent to confidently characterize its function by routing across common tools. We compare federation topology, classic RL vs LLM-driven harnesses, language model, and prompt expertise. We also stratify results by protein novelty. We find that the choice of LLM dominated prediction quality far more than topology or prompting (Opus ~92%-94% vs o4-mini ~40%-50%). The PPO policy was nearly as accurate as the best LLM (88%) at zero token cost, fastest latency, and perfect consistency, but yields no reasoning trace. Expert prompted LLMs reached the highest accuracy but were high-cost and less consistent; prompt dependence was largest when the task was hardest. Federation imposed a negligible penalty on performance. These results offer actionable guidance for deploying agents for scientific workflows: for routine, verifiable tasks, a cheap deterministic policy delivers near-frontier accuracy with complete reproducibility, while flexible LLM reasoning is best reserved for open-ended discovery.
Scientific workflow systems automate execution -- scheduling, fault tolerance, resource management -- but not the semantic translation that precedes it. Scientists still manually convert research questions into workflow specifications, a task requiring both domain knowledge and infrastructure expertise. We propose an agentic architecture that closes this gap through three layers: an LLM interprets natural language into structured intents (semantic layer); validated generators produce reproducible workflow DAGs (deterministic layer); and domain experts author ``Skills'': markdown documents encoding vocabulary mappings, parameter constraints, and optimization strategies (knowledge layer). This decomposition confines LLM non-determinism to intent extraction: identical intents always yield identical workflows. We implement and evaluate the architecture on the 1000 Genomes population genetics workflow and Hyperflow WMS running on Kubernetes. In an ablation study on 150 queries, Skills raise full-match intent accuracy from 44% to 83%; skill-driven deferred workflow generation reduces data transfer by 92%; and the end-to-end pipeline completes queries on Kubernetes with LLM overhead below 15 seconds and cost under $0.001 per query.
Bartosz Balis, Michal Orzechowski, Piotr Kica +2
AGH University of Krakow, Krakow, Poland · Sano Centre for Computational Medicine, Krakow, Poland
Multi-agent systems built from teams of large language models (LLMs) are increasingly deployed for collaborative scientific reasoning and problem-solving. These systems require agents to coordinate under shared constraints, such as GPUs or credit balances, where cooperative behavior matters. Behavioral economics provides a rich toolkit of games that isolate distinct cooperation mechanisms, yet it remains unknown whether a model's behavior in these stylized settings predicts its performance in realistic collaborative tasks. Here, we benchmark 41 open-weight LLMs across six behavioral economics games and show that game-derived cooperative profiles robustly predict downstream performance in AI-for-Science tasks, where teams of LLM agents collaboratively analyze data, build models, and produce scientific reports under shared budget constraints. Models that effectively coordinate in games and invest in multiplicative team production (rather than greedy strategies) produce better scientific reports across three outcomes, accuracy, quality, and completeness. These associations hold after controlling for multiple factors, indicating that cooperative disposition is a distinct, measurable property of LLMs not reducible to general ability. Our behavioral games framework thus offers a fast diagnostic for screening cooperative fitness before costly multi-agent deployment.
Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broad design pipelines. We introduce Agent Rosetta, an LLM agent paired with a structured environment for operating Rosetta, the leading physics-based heteropolymer design software, capable of modeling non-canonical building blocks and geometries. Agent Rosetta iteratively refines designs to achieve user-defined objectives, combining LLM reasoning with Rosetta's generality. We evaluate Agent Rosetta on design with canonical amino acids, matching specialized models and expert baselines, and with non-canonical residues -- where ML approaches fail -- achieving comparable performance. Critically, prompt engineering alone often fails to generate Rosetta actions, demonstrating that environment design is essential for integrating LLM agents with specialized software. Our results show that properly designed environments enable LLM agents to make scientific software accessible while matching specialized tools and human experts.
Jacopo Teneggi, S. M. Bargeen A. Turzo, Tanya Marwah +4
Polymathic AI · Johns Hopkins University · Center for Computational Biology, Flatiron Institute +3