Hongfu Huang, Yuzhe Li, Ao Xu +14cond-mat.mtrl-sci cs.AI
Despite the powerful multi-scale modeling methods and high-throughput infrastructures established in the materials community, real material computation workflows remain fragmented and heavily manual, requiring researchers to constantly bridge software tools, data analysis, and intermediate decisions. This growing gap between methodological capability and practical execution highlights the need for a new kind of autonomous computational framework, one that can coordinate tools, knowledge, and workflows in a more unified and adaptive way. Here, we introduce ALKEMIE Agent, an agentic platform in which retrieval-augmented generation, a materials-computation knowledge base, registered skills, database-supported provenance, AI-assisted structure modeling, bounded task execution, tool-calling iteration, and error-diagnostic assistance are integrated within a traceable control loop. The capabilities of ALKEMIE Agent are demonstrated through applications including materials recommendation, structure modeling, phonon calculations, machine-learned interatomic potential training, LAMMPS simulations, Ab Initio Monte Carlo (AIMC) sampling, and active-learning-based materials screening. Finally, we outline the future directions and challenges for the development of agentic platforms for computational materials design.
Large Language Model (LLM) agents have significantly improved coding and programming workflows. Claude Code, in particular, is one of the most powerful LLM coding agents and is capable of conducting complex coding tasks. However, several drawbacks can undermine long-term agentic workflows. (1) Irrecoverable agent teams: The Agent Teams feature is powerful, but the working state accumulated by each teammate is lost and cannot be resumed once the process stops, for example, when a terminal is closed. (2) Compaction erodes working detail: Compaction condenses the conversation into a summary, causing an agent's working details to become vague. (3) Agentic "technical debt": Over time, a user's decisions and the agents' operations become trapped in compacted old chats, making the project increasingly difficult to maintain and review. (4) Heavy prompt writing: Assigning or handing off tasks requires users to repeatedly write long prompts to achieve the expected agentic performance. We propose ATWZ (Agent Team Work Zone), a filesystem-based operations layer built around Claude Code's native Agent Teams that addresses these problems. Its central design principle is to treat each agent and teammate as a human employee and preserve their important working state in files stored in a dedicated directory called a "workstation," together with the skills, hooks, and scripts that use and maintain these files. With ATWZ, an agent team can periodically back up its working state, allowing an agent's knowledge to be recovered after compaction. After a process ends, the team can be restored with a single command. These features also substantially mitigate the agentic "technical debt" described above. Moreover, within ATWZ, agent "employees" can send documents to one another, greatly reducing the effort required to write prompts.
Jiazhen Jiang, Boxi Cao, Lingyong Yan +6cs.AI cs.CL cs.LG
As autonomous agents rapidly evolve, their ability to reliably manipulate ubiquitous digital documents has become critical for enabling general-purpose AI assistants and automating complex workspace workflows. In this paper, we introduce DocOps, a deterministically verifiable evaluation framework underpinned by a hierarchical taxonomy that deconstructs document operations inspired by real-world practices into atomic dimensions and escalating workflow complexities. Based on DocOps, we systematically evaluate representative closed- and open-source models across various agentic harnesses, revealing that even the most advanced frontier configurations still exhibit profound limitations when handling highly coupled, long-range tasks. Furthermore, a fine-grained analysis of existing agents' manipulation behaviors uncovers 3 key failure modes: long-term state tracking collapse, shallow semantic verification, and destructive editing of structural metadata. Ultimately, our work exposes the capability boundaries of agents in maintaining global document consistency, shedding light on the future design of robust, non-destructive agents for complex digital ecosystems.
Mohammad Arvan, Amber E. Osterholt, Bailee Rue +5cs.CL cs.AI cs.DL cs.HC
Introduction. Clinical and Translational Science Award (CTSA) programs must document their scholars' research impact, but assembling each scholar's record by hand takes staff an estimated 15 hours and does not scale to a full cohort. An artificial intelligence (AI) agent could serve as a tool to gather scholar data across platforms and disciplines. Methods. We built a human-in-the-loop AI agent that assembles a dossier of sourced evidence for each scholar and drafts one-sentence Translational Science Benefits Model (TSBM) impact summaries for staff review. We evaluated it in the impact-reporting workflow of one CTSA hub across 10 career-development (KL2/K12) scholars. Two evaluation staff independently coded all 507 findings as accept, edit, or reject; the primary measure was the unanimous usable rate, defined as the share both accepted or edited. Results. Both reviewers accepted or edited 81.7% of the agent's findings. Reviewers each spent a median of 14 minutes per scholar, replacing an estimated 15 hours of manual assembly. Inter-rater agreement was moderate (Cohen's kappa 0.43 on the usable-versus-reject decision). A profile discovery study found the agent's recall close to human search. The agent's impact evidence spanned all four TSBM domains, and about a third of the reviewed findings fell in non-scholarly categories that routine processes tend to miss. Reviewers rated synthesis accuracy 4.5 and usefulness 4.8 on a 5-point scale. Conclusions. A human-in-the-loop AI agent can serve as the first-pass author of a scholar's impact record, shifting staff from collecting and writing to reviewing, and making cohort-scale impact reporting feasible.
Harris Borman, Herman Wandabwa, Fusun Yu +4cs.SE cs.AI
Large Language Models (LLMs) have accelerated the adoption of software development agents, now widely available as Integrated Development Environment (IDE) extensions and standalone applications. While these agents are typically general-purpose, it remains unclear whether specialist agents justify their additional development effort. We investigate this question in the context of business process automation, focusing on the transformation of Business Process Model and Notation (BPMN) diagrams into executable agentic workflows. Since BPMN specifies explicit control-flow semantics, we focus on deterministic workflows in which a fixed process model and inputs uniquely determine the executed path. We introduce a specialist workflow for this task and compare it against generalist agents such as Roo and Cline. Our results show that the specialist solution produces agents that outperform generalist baselines by approximately 9-20 percentage points in tool-use exactness, 2-4x in penalty-adjusted latency, and 3x fewer tool-call errors, while reducing generation token cost by over 95% and eliminating repair iterations. We also find that generalist agents generate code inconsistently in both functionality and quality, limiting their suitability for industrial settings where reliability and maintainability are essential.
Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical. However, existing methods require extensive manual intervention and proficiency in heterogeneous tools, posing a significant barrier to efficient TI analysis. To bridge this gap, we propose SpaCellAgent, an autonomous large language model (LLM) multi-agent framework that automates end-to-end spatiotemporal analysis and narrative generation. SpaCellAgent utilizes a multi-agent architecture for strategic workflow planning, a dynamic tool-orchestration engine for adaptive algorithm selection, and a self-evolution module that iteratively refines performance through feedback. We evaluate SpaCellAgent on six heterogeneous datasets encompassing complex temporal developmental trajectories, diverse sequencing platforms, and spatially-resolved tissue architectures. SpaCellAgent consistently demonstrates over 40\% improvement in analytical efficiency while maintaining expert-aligned performance. By converting natural language specifications into optimized analytical workflows and fully automating the pipeline, SpaCellAgent democratizes advanced spatiotemporal modeling and establishes a scalable, agent-driven paradigm for computational biology. The code and materials are available at https://github.com/LittleXH-shw/SpaCellAgent.
Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fragmented, requiring expert manual orchestration of heterogeneous tools and limiting research scalability and reproducibility. We present SP-Mind, the first autonomous AI agent designed to unify the spatial proteomics analysis pipeline, from raw multiplexed tissue imaging to downstream phenotype discovery. Equipped with expert-curated biological analysis skills and specialized computational tools, SP-Mind converts natural-language queries into end-to-end analytical workflows without task-specific fine-tuning. To rigorously evaluate its capabilities, we introduce SP-Bench, a comprehensive benchmark spanning diverse tissue types, comprising 102 tasks across 18 distinct categories. Through extensive evaluation on SP-Bench and established downstream tasks, SP-Mind achieves state-of-the-art performance compared to existing open-source biomedical agent baselines.
Computational pathology has advanced rapidly with the emergence of foundation models, yet widespread adoption remains limited by substantial technical complexity and programming requirements. Here we present PathLab, an autonomous agentic framework that translates natural-language research objectives into executable and validated computational pathology workflows through the structured composition of domain-specific skills and tools. By organizing workflow generation around reusable methodological modules, including data preprocessing, model development, evaluation and interpretation, PathLab enables studies to be specified at the level of scientific intent rather than implementation details. We evaluated PathLab across 12 public datasets spanning four representative task families: region-of-interest classification, whole-slide image classification, segmentation and survival prediction. Across all task categories, PathLab achieved non-inferior performance relative to expert implementations, while consistently enforcing semantic validity of user prompts and proactively rejecting incompatible workflow specifications prior to execution. In controlled user studies, PathLab substantially reduced the time required to generate executable analytical pipelines and enabled domain experts without programming experience to independently design, execute and evaluate computational pathology studies. Together, these results establish PathLab as a reliable interface between biomedical intent and computational execution, enabling computational pathology studies to be designed at the level of scientific questions rather than programming expertise. By lowering technical barriers to advanced AI methodologies, PathLab provides a foundation for the broader democratization of computational pathology.
Atomistic simulations are central to materials design, but their execution involves complex, multi-step workflows that require significant human expertise. Here, we present an agent-based system embedded within the URSA (Universal Research and Scientific Agent) framework that automates the design, execution, and validation of atomistic simulations, demonstrated using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) tool. Our system autonomously selects interatomic potentials, constructs and runs simulations, and performs iterative error recovery within a closed-loop workflow. We evaluate the scientific reliability of the agent by benchmarking its outputs against LAVA, a high-throughput toolkit for LAMMPS and the Vienna Ab initio Simulation Package (VASP) calculations. Our framework reduces manual intervention and trial-and-error, thereby improving the rigor, reproducibility, and scalability of atomistic modeling.
Undergraduate research programs such as the Summer Undergraduate Research Fellowship (SURF) at Purdue University receive thousands of applications every year, requiring significant time and effort for program staff to evaluate each submission consistently and within tight timelines. This work-in-progress paper describes the development and initial deployment of a large language model (LLM)-based tool to assist in the evaluation of approximately 1,200 student Statements of Purpose (SoPs) for the SURF 2026 cycle at Purdue University. The workflow utilizes OpenAI GPT models (GPT-4o, GPT-5-mini, and GPT-5.2) and uses a structured rubric across six subcategories, each scored on a 0-3 scale. A few SoPs, graded by program staff, were used to tune the model responses. The model prompt was designed to generate both numerical scores, rationales (including positive and negative aspects) and short excerpts from each submission. Using GPT-5.2, the full batch of 1,200 SoPs was processed in approximately 4.6 hours of compute time, averaging roughly 14 seconds per SoP (with per-SoP timing varying with SoP length, which ranged from 500 to 2,000 words). Notable differences in rubric adherence were observed across model versions, with GPT-5.2 adhering most closely. Disagreement in model scores was more pronounced for lower-scoring submissions. The LLM outputs replicated the role previously played by distributed human graders, providing the program coordinator with scored and rationale-annotated outputs for the entire applicant pool. The program coordinator then reviewed these outputs alongside each applicant's SoP, applying the same downstream office criteria used in prior SURF cycles, to produce a shortlist of strong candidates. This coordinator review was completed in approximately 4 hours, compared to the multi-week coordination effort required in prior program cycles.
Biological image analysis increasingly demands integration across heterogeneous tools, programming environments, and domain knowledge that few researchers can command simultaneously. We present Agentic-J, a containerised, multi-agent AI assistant, primarily for ImageJ/Fiji that enables biologists to specify analysis tasks in natural language, from nuclei segmentation and cell tracking to multi-condition quantification. The agent generates executable scripts organised into a documented project structure, so every analysis decision is traceable and the workflow can be reproduced or shared. The specialised sub-agents handle plugin management, code generation, debugging, quality assurance, and statistical reporting. In this paper we introduce the system's design, demonstrate real biological microscopy image analysis workflows, and detailed the technical implementation.
Chenxin Li, Zhengyang Tang, Huangxin Lin +8cs.SE cs.AI
LLM agents are expected to complete end-to-end units of work across software tools, business services, and local workspaces. Yet many agent benchmarks freeze a curated task set at release time and grade mainly the final response, making it difficult to evaluate agents against evolving workflow demand or verify whether a task was executed. We introduce Claw-Eval-Live, a live benchmark for workflow agents that separates a refreshable signal layer, updated across releases from public workflow-demand signals, from a reproducible, time-stamped release snapshot. Each release is constructed from public workflow-demand signals, with ClawHub Top-500 skills used in the current release, and materialized as controlled tasks with fixed fixtures, services, workspaces, and graders. For grading, Claw-Eval-Live records execution traces, audit logs, service state, and post-run workspace artifacts, using deterministic checks when evidence is sufficient and structured LLM judging only for semantic dimensions. The release contains 105 tasks spanning controlled business services and local workspace repair, and evaluates 13 frontier models under a shared public pass rule. Experiments reveal that reliable workflow automation remains far from solved: the leading model passes only 66.7% of tasks and no model reaches 70%. Failures are structured by task family and execution surface, with HR, management, and multi-system business workflows as persistent bottlenecks and local workspace repair comparatively easier but unsaturated. Leaderboard rank alone is insufficient because models with similar pass rates can diverge in overall completion, and task-level discrimination concentrates in a middle band of tasks. Claw-Eval-Live suggests that workflow-agent evaluation should be grounded twice, in fresh external demand and in verifiable agent action.