Recent efforts toward fully automated AI scientists have demonstrated that language-model agents can generate hypotheses, execute experiments, and draft scientific manuscripts. However, during the early stages of research, when research problems are formulated, these AI scientists often rely heavily on proprietary frontier models. Their proposals are shaped by opaque parametric knowledge and by literature searches conditioned on the proposals themselves. Such knowledge is effectively a black box, and this dependence makes the evidential basis and validity of generated research problems difficult to audit and leaves the process vulnerable to model-specific hallucinations and biases. Furthermore, if proprietary research materials are transmitted to external APIs, the use of these models creates confidentiality, privacy, and data-governance concerns. We introduce the Structural Gap Hypothesis Agent (SGHA), a fully automated, corpus-first research-problem discovery system that runs entirely on a local LLM. SGHA structures a scientific literature corpus into evidence-linked paper objects and a typed evidence graph, detects unresolved structural patterns across papers, screens candidate gaps before formulation, and produces traceable research-problem families. In particular, it is able to output assumptions, objectives, success criteria, and remaining ambiguities. All LLM-based components of SGHA are executed using a locally served open-weight 9B language model, without requiring proprietary frontier-model APIs. We compare SGHA with the AI Scientist-v2 idea formulation module in five machine-learning domains. Our results suggest that explicit corpus structure and evidence-constrained reasoning can support promising, inspectable research-problem formulation without relying on frontier models during generation or verification.
Autonomous research agents can generate hypotheses, execute experiments, and draft manuscripts, yet their outputs often contain unsupported claims and inconsistencies between research questions, experiments, results, and conclusions. We argue that this problem is partly architectural: existing systems organize research as sequential pipelines but do not explicitly maintain or validate the evolving claim-evidence structure across stages.In this paper, we introduce EviGraph, an autonomous research framework that represents the research process as a typed evidence graph containing Problem, Gap, Hypothesis, Experiment, Finding, and Claim nodes. The graph serves as the operational state of the agent rather than a post-hoc record. EviGraph inspects evidence chains for missing dependencies, semantic misalignment, and result-claim inconsistencies, localizes the earliest weak node, and regenerates its affected downstream subgraph. Graph checkpointing prevents unsuccessful repairs from corrupting previously validated evidence. Manuscripts are generated only after every retained claim is grounded in a validated evidence chain.Experiments on ARC-Bench-ML and NanoResearch-20 show that EviGraph outperforms the compared end-to-end research-agent baselines in overall research performance, improves Claim Support Rate by 40.19% over the strongest baseline, and achieves 87.73% Experimental Data Consistency. These results demonstrate the value of explicit evidence-state maintenance for reliable autonomous research.
LLM-based agents have demonstrated strong capabilities in data-intensive analytical tasks, yet their outputs are rarely verifiable: a reliance on linear text trajectories makes their reasoning difficult to audit. In particular, deterministic computations over raw data and semantic deductions over natural-language claims are often entangled in an unstructured stream, leaving numerical conclusions hard to reproduce and qualitative judgments hard to inspect. To address this, we propose VeriGraph, a traceable neuro-symbolic reasoning framework that enables agents to construct an explicit heterogeneous evidence directed acyclic graph (DAG) during execution. VeriGraph introduces three evidence-expansion primitives, namely computational, grounding, and derivational expansion, to connect raw data, interpreter variables, computed results, and natural-language claims in a unified graph. Under this formulation, structural traceability is reduced to graph reachability from raw data sources to terminal claims, while semantic support is measured by claim-level evidence evaluation. To improve graph construction, we further design a graph-based policy optimization strategy with a composite reward that jointly supervises answer correctness, computational integrity, and derivational coherence. Experiments on four benchmarks show that VeriGraph-8B achieves the highest overall score among all baselines. More importantly, VeriGraph produces auditable evidence graphs with substantially stronger claim grounding, achieving a 87.61\% Grounding Rate under our claim-level evidence support evaluation. These results suggest that explicit evidence-graph construction is a promising path toward verifiable data-analytic agents. Our code is available at https://github.com/ignorejjj/VeriGraph.