Agentic AI Scientists Are Not Built For Autonomous Scientific Discovery
Authors: Harshit Bisht, Vinay Kumar, Kevin Maik Jablonka, Mausam, N. M. Anoop Krishnan
Organizations: Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi · Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena · Center for Energy and Environmental Chemistry Jena, Friedrich Schiller University Jena · Helmholtz Institute for Polymers in Energy Applications Jena (HIPOLE Jena) · Department of Computer Science and Engineering, Indian Institute of Technology Delhi · Department of Civil and Environmental Engineering, Indian Institute of Technology Delhi
Abstract
A growing body of work pursues AI scientists capable of end-to-end autonomous scientific discovery. This position paper argues that although they already function as co-scientists, agentic AI scientists are not built for autonomous scientific discovery. We identify the following challenges in building and deploying autonomous AI scientists: (1) Problem selection is influenced by the McNamara fallacy; (2) Agents are built on large language models (LLMs) whose training corpora omit tacit procedural and failure knowledge of laboratory practice; (3) Preference optimisation during post-training compresses output diversity toward consensus; and (4) Most scientific benchmarks measure single-turn prediction accuracy and lack feedback from physical experiments back to the computational model. These challenges are not just questions of scale and scaffolding; they require revisiting fundamental design choices. To build truly autonomous AI scientists, we recommend the use of scientific simulations as verifiers for training, the design of persistent world models that represent the shifting objectives governing real investigations, the establishment of a centralized preregistration repository for all AI-generated hypotheses, and application driven by scientific need rather than tool affordance.
Agentic artificial intelligence (AI) systems are beginning to assist, accelerate, and partially automate scientific discovery, performing tasks that span literature synthesis, code generation, data analysis, hypothesis proposal, and model criticism. We argue that this transition is qualitative rather than incremental, and that suitably designed multi-agent systems may evolve from passive computational tools into ``AI scientists'' that can expand the hypothesis-generating and verification capacity of science. Such systems must be developed and deployed within a scientific ecosystem fit for purpose: institutions must be redesigned for verification, accountability, interpretability, and dual-use safety. We sketch how multi-agent architectures, illustrated by the prototype framework \textit{Denario}, accelerate the discovery cycle and traverse model spaces beyond human reach; examine what this implies for authorship, peer review, and the enduring role of human scientists; and close with recommendations for governing AI as an epistemic actor rather than a mere instrument.
Raul Jimenez, Boris Bolliet, Francisco Villaescusa-Navarro +7
AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.
Scientific discovery is defined by the ability to identify the boundaries of existing knowledge and venture into unexplored territory. The ultimate vision for AI in science is problem-driven autonomous research: given a fundamental challenge by a human expert, the AI independently navigates the scientific landscape, uncovers theoretical and empirical bottlenecks, and systematically expands the frontier of knowledge. In this paper, we introduce ScientistTwo, a fully autonomous multi-agent framework designed to realize this vision. Specifically, ScientistTwo takes an initial problem as input, establishes state-of-the-art baselines, formulates novel hypotheses, and coordinates specialized agents to orchestrate an end-to-end discovery cycle without human intervention. Moreover, the framework rigorously conducts experiments using diverse datasets and metrics, refines methodologies through automated ablation studies, and validates research findings via a closed-loop simulated peer-review rebuttal engine. To evaluate ScientistTwo's capabilities against the highest standards of human scientific achievement, we benchmark it across papers accepted at top-tier conferences such as ICLR, ICML, and NeurIPS. As a result, ScientistTwo autonomously generates expert-level, publishable papers and fully verified, executable codebases. Its solutions consistently outperform human state-of-the-art models, and achieve higher average review ratings than human-authored papers under automated AI review agents. These results show that ScientistTwo is not merely an assistive tool but an autonomous scientific pioneer capable of pushing the frontiers of human discovery. Project website: https://scientist-two.github.io/