cs.AIAug 5, 2026

Agentic self-driving microscopy benchmarks support qualification but do not necessarily generalize to unseen tasks

Authors: Nathan S Johnson, Ian Abshire

Organizations: Carl Zeiss Research Microscopy Solutions, 5300 Central Boulevard, Dublin, CA 94568

Abstract

Large language model agents are increasingly being developed to control a wide range of scientific characterization tools including microscopes and synchrotron beamlines. Research into agentic control of physical infrastructure is nascent and there are few well-established paradigms for how to engineer an agentic system. There are many choices to make when designing a microscopy agent, including the choice of LLM, the number of agents to use, agent responsibilities and delegation rules, retrieval-augmented generation parameters, and more. When designing and optimizing an agentic microscope controller, researchers not only want to ensure that the agent can correctly perform known tasks but also that the agent can generalize to new tasks that it has not encountered before. In this study, we develop a benchmark and trace-logging framework that reveals a) how different choices of agent architecture impact performance at microscopy tasks and b) the limitations of benchmarks for predicting if a particular agent will perform well on unseen microscopy tasks. The framework was used to evaluate one-, two-, and three-agent graph topologies, five LLMs, RAG and context parameters, and operational constraints across 53 microscopy benchmark tests. In total, 105 agent configurations, 1,949 individual test runs, and 49,109 RAG retrievals were recorded. Direct comparisons showed clear differences in latency, token use, cost, and failure mode between configurations. However, surrogate models trained on agent architecture and test results did not reliably predict an agent's performance on new, unseen tasks. These results show that these benchmarks are useful for qualification, regression testing, diagnosis, and direct comparison, but the current heterogeneous test suite does not support a task-independent global configuration model.

Explore similar work

CardsList
Jul 10, 2026cs.AI

DynamicMCPBench: A Trace-Grounded, Effect-Scored Benchmark for LLM Agents over Live MCP Servers

Large language model (LLM) agents are increasingly deployed over Model Context Protocol (MCP) servers, yet the benchmarks used to evaluate them score the final answer or a fixed "ground-truth" list of tools, both of which are fragile once the underlying data is live and stateful. We present DynamicMCPBench, a reusable framework rather than a fixed dataset. A practitioner can run it on their own MCP servers to test models on their own tasks, or let it collect servers automatically to measure a model's general ability to solve agentic tasks. Given the servers and any set of models, it generates realistic goals, pursues each one live to record a successful trajectory, distills that trajectory into path-agnostic effect checkpoints, and scores an agent on whether it reproduces those effects, never on the final answer. To show what the framework reveals, we run it at scale: 24 models over 121 servers and 750 tasks spread evenly over 15 task categories (50 each), where each category targets a distinct tool-use challenge of the generated questions. Each task is scored by pass^3: it counts as solved only if all three independent attempts succeed. Even the strongest agents solve only about half of the tasks, 31% of tasks are solved by no model at all, and accuracy collapses as the required tool chain grows longer (from 39% on the shortest chains to 13% on the longest). A human validation study confirms the automatic scoring is reliable (chance-corrected agreement of 0.76). DynamicMCPBench thus turns benchmark construction into something practitioners can rerun on their own servers and models, while exposing a consistent inability of current agents to handle long, multi-step agentic tasks.
Jerzy Kamiński, Ilya Galyukshev, Artem Kuznetsov +4
Agentic BenchmarksLarge Language Model AgentsModel Context ProtocolAgentic Tool Use
AskPDF
Jun 4, 2026cs.AI

Benchmark Everything Everywhere All at Once

Benchmarks are fundamental for evaluating and advancing LLMs and MLLMs by providing standardized and explicit measures of performance. However, their construction is labor-intensive and hard to reuse, raising concerns about sustainability and scalability. Moreover, existing benchmarks often quickly reach performance saturation after their release, resulting in insufficient discrimination among state-of-the-art models. To address these challenges, we introduce Benchmark Agent, a fully autonomous agentic system designed for benchmark building. Our framework orchestrates the complete benchmark construction pipeline, from user query analysis and subtask design to data annotation and quality control. To assess Benchmark Agent, we implement it to produce 15 representative benchmarks, spanning diverse evaluation scenarios, including text understanding, multimodal understanding, and domain-specific reasoning. Extensive experiments, including human evaluation, LLM-as-a-judge assessment, and consistency checks, demonstrate Benchmark Agent can generate high-quality benchmark samples with minimal human involvement. More importantly, through continual evaluation, we observe several insightful findings, including that current models struggle with certain domain-specific reasoning tasks. We believe that rapidly evolving benchmarks can contribute significantly to the research community. The preview and code will be publicly available at the demo page and code repository.
Shiyun Xiong, Dongming Wu, Peiwen Sun +5
Agentic BenchmarksAgentic Systems
AskPDF
Jun 15, 2026cs.AI

LabOSBench: Benchmarking Computer Use Agents for Scientific Instrument Control

Current computer-use benchmarks primarily focus on software operation tasks in virtualized systems, whereas scientific instrumentation scenarios require coordinated control over complex interfaces, and feedback-driven parameter adjustment. However, directly evaluating agents on physical high-precision instruments is impractical due to high cost, safety risks, limited accessibility, and difficulty in ensuring reproducible evaluation. This motivates the need for a simulated yet realistic testbed that preserves the operational challenges of scientific instruments while enabling scalable and safe benchmarking. To this end, we introduce LabOSBench, a challenging benchmark for multimodal GUI agents built on a suite of web-based scientific-instrument simulators. Operating directly via a browser, LabOSBench avoids resource-heavy OS virtualization while supporting flexible task configuration and execution-based evaluation. Specifically, LabOSBench constructs 96 subtasks across eight instrument simulators, covering workflows from sample loading, alignment, parameter tuning, and data acquisition to result inspection. We evaluate general-purpose vision-language models, specialized GUI agent models, and advanced agentic frameworks at both subtask and end-to-end levels. Our experiments reveal that while existing agents can complete many structured GUI subtasks, they still struggle with feedback-driven operations and long-horizon workflow execution. Overall, LabOSBench provides a reproducible, low-cost testbed for advancing computer-using agents toward scientific-instrument control.
Anqi Zou, Han Deng, Chengyu Zhang +9
Computer-Use AgentsGraphical User Interface AgentsReproducibility
AskPDF