From Task Executors to Research Partners: Evaluating AI Co-Pilots Through Workflow Integration in Biomedical Research

Lukas Weidener; Marko Brkić; Chiara Bacci; Mihailo Jovanović; Emre Ulgac; Alex Dobrin; Johannes Weniger; Martin Vlas; Ritvik Singh; Aakaash Meduri

arXiv · 2512.04854

From Task Executors to Research Partners: Evaluating AI Co-Pilots Through Workflow Integration in Biomedical Research

Lukas Weidener·Marko Brkić·Chiara Bacci·Mihailo Jovanović·Emre Ulgac·Alex Dobrin·Johannes Weniger·Martin Vlas·Ritvik Singh·Aakaash Meduri

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Abstract

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

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Lukas Weidener, Marko Brkić, Chiara Bacci, Mihailo Jovanović, Emre Ulgac, Alex Dobrin, Johannes Weniger, Martin Vlas, Ritvik Singh, Aakaash Meduri. 2025-12-04. From Task Executors to Research Partners: Evaluating AI Co-Pilots Through Workflow Integration in Biomedical Research. https://arxiv.org/abs/2512.04854

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