TEM-Scientist

Verified experimental protocols for agentic electron microscopy

TEM-Scientist is a compile–rehearse–execute–reflect architecture for autonomous transmission electron microscopy. Rather than placing a language model in the millisecond-scale instrument control loop — where its stochasticity, latency, and silent failures compromise experimental safety — TEM-Scientist moves the model above the loop: it compiles a natural-language experimental goal into a typed, verifiable protocol, rehearses that protocol against a physics-aware simulator under injected faults, and then executes it with a deterministic runtime that requires no further model involvement.

The architecture separates deliberation from protection, and detection from correction. The compiled protocol is a finite state machine over a closed set of instrument primitives, carrying declared dose and motion invariants and a table of edge-triggered reflexes; a two-layer verification gate (static lints plus behavioral rehearsal) admits only protocols that satisfy the frozen objective contract; and a runtime with frame-rate reflexes responds to safety-critical events five orders of magnitude faster than a per-step model round-trip. The compiled protocol is itself the reviewable artifact — reproducible, citable, and diffable.

Status: Active development · Preprint 2026

Role: First author and lead developer, in collaboration with Yuqing Huang (ANL/CNM), Rama Vasudevan (ORNL/CNMS), Yuzi Liu (ANL/CNM), and Subramanian Sankaranarayanan (UIC/ANL).

Key contributions

  • Compile–rehearse–execute architecture — separates model deliberation from deterministic execution
  • Objective contract — an immutable, verifiable specification of what the experiment must achieve
  • TWINTEM behavioral simulator — physics-aware digital twin with Poisson-limited imaging, drift, defocus, cumulative beam damage, and fault injection
  • Frame-rate reflexes — protective response with median 6.6 µs latency, against 2.1 s for per-step LLM control
  • 114-task benchmark catalog with 25-task executable subset and a held-out locked evaluation suite
  • Failure taxonomy and repair loop — legible, layer-localized failure classes with static and behavioral diagnostics

Citation

@article{manna2026temscientist,
  title   = {Verified Experimental Protocols for Agentic Electron Microscopy},
  author  = {Manna, Sukriti and Huang, Yuqing and Vasudevan, Rama and
             Liu, Yuzi and Sankaranarayanan, Subramanian K. R. S.},
  journal = {arXiv preprint},
  year    = {2026},
  note    = {Under review}
}