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Ambig-DS: A Benchmark for Task-Framing Ambiguity in Data-Science Agents
Josefa Lia Stoisser, Marc Boubnovski Martell, Sidsel Boldsen +2
As data-science agents shift from co-pilots to auto-pilots, silent misframing becomes a critical failure mode. Agents quietly commit to plausible but unintended task framings, prod…
Measuring Black-Box Confidence via Reasoning Trajectories: Geometry, Coverage, and Verbalization
Marc Boubnovski Martell, Josefa Lia Stoisser, Kaspar Märtens +4
Reliable confidence estimation enables safe deployment of chain-of-thought (CoT) reasoning through text-only APIs. Yet the dominant black-box baseline, self-consistency over K samp…
Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering
Josefa Lia Stoisser, Lawrence Phillips, Aditya Misra +5
Synthetic chain-of-thought (CoT) traces are widely used to train large reasoning models (LRMs), improving generalization by providing step-level supervision. Yet most approaches re…
Towards Agents That Know When They Don't Know: Uncertainty as a Control Signal for Structured Reasoning
Josefa Lia Stoisser, Marc Boubnovski Martell, Lawrence Phillips +6
Large language model (LLM) agents are increasingly deployed in structured biomedical data environments, yet they often produce fluent but overconfident outputs when reasoning over…
SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
Lawrence Phillips, Marc Boubnovski Martell, Aditya Misra +4
Predicting cellular responses to genetic perturbations represents a fundamental challenge in systems biology, critical for advancing therapeutic discovery and virtual cell modeling…