Abstract
Synchrotron data reduction, detector calibration followed by azimuthal integration of terabyte-scale diffraction series, is a multi-step, expert-bound bottleneck that increasingly limits the science rate of user facilities. LLM agents promise to collapse it, but driving a real pipeline with a stochastic model creates a failure mode chat benchmarks cannot see: an agent can report a calibration that was never computed. Correctness here is a property of what executed, not of the transcript. We present APEXA, a deployed multi-agent framework (61 tools over heterogeneous compute, run as a single reasoning loop) automating calibration and integration from natural language at a major light source. We make three contributions. First, execution-integrity enforcement: a deterministic tool-layer guard that refuses to surface any result not backed by an executed tool call, with a parser tolerant of cross-model tool-call format drift: in deployment, a frontier model fabricated a complete calibration-comparison report for commands that never ran, which the guard converts to an explicit non-result; the same code gates an optional motor-control surface at 0/200 adversarial violations against a simulated IOC, versus 15/200 for an equivalent safety prompt. Second, we release APEXA-Bench, an evaluation harness of 58 facility tasks (50 base plus an 8-task cross-detector slice) organized by a four-class physical-consequence taxonomy, the first benchmark axis we know of separating a wasted compute cycle from a damaged instrument; its cross-detector grading against NIST-traceable lattice constants surfaced two latent pipeline bugs. Large-scale agent scoring is left to a full-length study. Third, we validate APEXA on real beamline data: from one natural-language prompt it recovers detector geometry and integrates a full attenuation/exposure sweep. We release the framework, harness and traces.
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URL
https://arxiv.org/abs/2609.24165
