The Hypothesis Evolution Protocol (HEP) is proposed, an agent harness that provides hypothesis generation, evaluation, and evolution as explicit, auditable operations and marks a step toward auditable AI scientists, whose scientific reasoning can be inspected, verified, and built upon.
Abstract
Large language model (LLM) agents are increasingly expected to play a central role in AI-driven scientific discovery. Equipped with broad knowledge, flexible reasoning, and tool use, they have the potential to autonomously explore and solve scientific problems by repeatedly proposing hypotheses, testing them, and revising their beliefs in the light of the evidence. In current agents, however, these hypotheses, tests, and belief updates are buried in unstructured logs, and no mechanism lets the agent or the human researcher audit that process. Here we propose the Hypothesis Evolution Protocol (HEP), an agent harness that provides hypothesis generation, evaluation, and evolution as explicit, auditable operations. On materials-science research tasks, a HEP-equipped agent operates the hypothesis--test--evidence--belief cycle that planning-style agents lack, generalizes across research questions, and exploits the protocol more fully as the base LLM becomes more capable. These results mark a step toward auditable AI scientists, whose scientific reasoning can be inspected, verified, and built upon.
Autonomous coding agents are increasingly proposed as AI-scientist systems that conduct analyses and write research reports, but executing a prescribed analysis is not the same as making a discovery. Existing benchmarks are configured for reproduction: tasks, data, and rubrics are built around a hidden target study, and recovery of its result is rewarded. We present TruthInsightBench, a benchmark configured for discovery. Its 40 blind tasks, drawn from 40 peer-reviewed studies across 10 scientific domains, expose only a neutral scientific objective and frozen data; source conclusions, expected values, and analysis paths are withheld, leaving the agent to determine what claim the data support. A fixed LLM-based judge scores the evidentiary maturity of an agent's own claims along six dimensions, operationalized as 29 artifact-grounded items, with automated, deterministic aggregation and no per-instance human grading, so evaluation can be repeated automatically as agents evolve. On one frozen base model, four coding agents form a narrow plateau (58.4-60.3 of 100) with no statistically reliable pairwise separation: they execute and document analyses competently, with comparatively strong evidence auditability and novelty, but largely lack the discriminating acts that establish a trustworthy claim (controls, robustness, falsifiability, and cross-dataset generalization). The bottleneck is scientific judgment rather than coding, and genuine discovery remains out of reach. TruthInsightBench makes this gap a measurable target; data and scoring code are at https://github.com/TruthInsight-stack/TruthInsightBench.
Zhi-Bo Yang, Chen Zhang, Yue-Wei Zhang et al.· 0 citations
It is argued that verification, not generation, is the binding constraint for trustworthy automated analysis in agentic data science: systems in which an LLM coordinates exploratory analysis, query generation, hypothesis formation, and reporting with limited human supervision.
M. Keerthika· Eduschool International Jour...· 0 citations
AgentHPOBench, a sequential benchmark comprising 30 executable machine learning tasks across seven research categories, shows that current agents exhibit measurable experimental optimization ability across domains, but still face clear limitations in sustained iterative refinement, complex log diagnosis, and consistent progress toward reported reference performance.
LLM agents deployed for software engineering fail expensively: they act confidently wrong, and bad actions are recognized only after costly execution and retry. We present Speculative Uncertainty (SU), a method that recovers a predictive failure signal for a black-box agent from its output tokens alone, with no access to logits, weights, activations, or repeated sampling. Inverting speculative decoding, a small open-weight draft model scores the agent's already-generated trajectory in a single forward pass. From these speculative cross-likelihoods we extract phase-aware features by separating the reasoning and action spans, and calibrate them against a verifiable objective. SU produces a failure-likelihood score that any downstream policy, such as routing, human intervention, or extra test-time compute, can consume directly. To show the signal is actionable, we instantiate one such policy, a pre-execution veto gate, on software engineering agents Qwen3-Coder-480B and closed-source Claude 3.5 Sonnet, cutting execution error rate by 6-8 percentage points and token cost by 14-19% in deployment, transferring to out-of-distribution benchmarks without retraining, and generalizing across agent models.
The Little Scientist is presented, a framework in which a LLM agent stepping through the scientific method can discover both new algorithms and new ensemble strategies that outperform prior solutions, and is demonstrated on two problems that require fundamentally different modes of discovery.
AI Agents are increasingly deployed in real-world settings, where they interact with external tools and make sequential decisions with limited human oversight. This creates a pressing need for reliable and auditable explanations of what an agent did and why. However, traditional Explainable AI (XAI) methods fall short of providing the process-level transparency required for such interactive, multi-step systems, motivating a paradigm shift toward approaches specifically designed for AI Agents. To address this gap, we present a post-hoc XAI framework that transforms a lengthy agent's execution trace into a structured report and a faithful natural-language explanation explicitly grounded in its observable behavior. Because it relies solely on execution traces, the framework applies across different agent architectures, environments, and tasks. Human and automated evaluations across multiple benchmarks and architectures show that our framework produces high-quality, trace-faithful explanations while reliably identifying unsupported claims, unjustified actions, and evidence gaps, outperforming naive LLM-generated explanations.
Vittoria Vineis, Fabiano Veglianti, Lorenzo Antonelli et al.· 0 citations
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