Results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence, while exposing limits in long-horizon execution.
Abstract
Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.
Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.
Qing-Yang Shao, Xin Zhang, Zhou-Yang Yuan et al.· 0 citations
Scientific agents increasingly analyze data, execute code, and produce research artifacts, yet most benchmarks emphasize final answers, isolated programs, or a single domain. We introduce FrontierChallenge, a cross-domain benchmark comprising 300 end-to-end scientific workflows. In this paper, we release and evaluate 97 of these tasks, spanning quantum chemistry, molecular dynamics, materials characterization, analytical chemistry, life science, and electrochemistry/environment. Each task provides fixed inputs and specifies a bundle of required scientific deliverables. We evaluate twelve frontier models with three agent scaffolds. Pass Rate measures the fraction of tasks satisfying the full-completion criterion, while Avg. Score captures partial progress. Each of the best-performing configurations completed only 20 of the 97 released tasks, yielding a Pass Rate of 20.6%. Partial progress translated especially poorly into complete delivery in analytical chemistry and electrochemistry/environment: Avg. Scores reached 87.6 and 94.9, but the highest Pass Rates were only 4% and 0%. Among non-passing Claude Code trajectories, 75.5% still ended with language claiming completion. These findings show that neither high partial scores nor confident claims of completion reliably indicate that a scientific task has been fully delivered, highlighting the need to evaluate end-to-end workflow execution and the completeness of scientific deliverables together.
Liangcai Su, Zhaopeng Feng, Zhuo Chen et al.· 0 citations
It is argued that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone, and the Function--Evidence--Validation (FEV) framework is introduced, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation.
This work introduces an executable benchmark and a budget-aware meta-router that composes heterogeneous operations from raw task text that establishes a reproducible testbed and a bounded proof of concept, not evidence of live-LLM performance.
Natan Vidra, Alina Kapanova, Arun Kanhai et al.· 0 citations
SyntheticAgentTraceQA is proposed, an execution- first framework for generating scalable supervision data for tool- augmented agents and shows that execution-grounded supervision improves tool execution behavior, reference-trace agreement, and answer-generation performance on the evaluated tasks.
Hafsa Ouajdi, Francesco Giannuzzo, Alaa Boukhary et al.· arXiv.org· 1 citation· ⚡1
This work systematically study AI products with demonstrated adoption, together with their product workflows and users, to identify real-world tasks for which AI has established practical demand across diverse professional domains and establishes StartupBench as an empirical measure of progress toward E2E completions of real-world user tasks.
Li-Ya Zhu, Xin Ma, Tao Liu et al.· 0 citations
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