PEARL: Auditable Repair for Scientific Reasoning Graph Extraction

Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.

Large reasoning models (LRMs) produce reasoning traces with non-linear structures, such as backtracking and self-correction, that complicate the evaluation and monitoring of the reasoning process. We introduce ReasoningFlow, a framework that captures the discourse structures of LRM reasoning traces into fine-grained directed acyclic graphs (DAGs). We develop and validate our annotation schema through careful manual annotation of 31 traces (2.1k steps), achieving high inter-annotator agreement, then scale to automatic annotation of 1,260 traces (247.7k steps) spanning three tasks (math, science, argumentation) and five models (Qwen2.5-32B-Inst, QwQ-32B, DeepSeek-V3, DeepSeek-R1, GPT-oss-120B). By analyzing ReasoningFlow graphs, we find: (1) LRMs exhibit structurally similar traces, despite being trained from different base models and potentially non-overlapping post-training data. (2) ReasoningFlow reveals diverse fine-grained reasoning behaviors (e.g., local verification, self-reflection, and assumptions) that can be used for better reasoning trace monitorability. (3) In LRMs, most of the erroneous steps are not used to derive final answers. (4) Mechanistic causal dependencies between steps do not reflect the language-level discourse structure. We release the dataset and code in: https://github.com/jinulee-v/reasoningflow.

Large-Language Models (LLMs) can be prone to flawed and unfaithful reasoning that decoding strategies like Self-Consistency (SC) fail to detect as they evaluate only final-answer agreement while ignoring the logical validity of intermediate steps. This raises three fundamental questions: How can we reliably quantify uncertainty in LLM reasoning? Can semantic, structural, and causal awareness select more faithful reasoning compared to naïve majority voting? and How robust is reasoning topology under adversarial conditions? To address these questions, we introduce GRAPHEVAL, a graph-based reasoning framework that re-frames uncertainty quantification (UQ) as a holistic reasoning fidelity problem. We propose a novel UQ metric, Graph Reasoning Coherence Score (GRCS), that quantifies semantic-structural consensus of the reasoning space and captures pathological mode collapse and confident hallucinations. We find that GRCS is the only metric that is consistently negatively correlated with reasoning faithfulness across both more capable and smaller models. Additionally, we introduce Graph Self-Consistency (GSC), a medoid-based decoding strategy that trades nominal accuracy for reasoning fidelity, exposing the degree to which SC is inflated by unfaithful lucky guesses in smaller models, while preserving or improving accuracy in more capable ones. Finally, through adversarial medoid ablation, we demonstrate that the GSC-selected path acts as a "load-bearing path" and forcing models away from it degrades reasoning faithfulness and, in targeted cases, causes drops in accuracy.