The Tell-Tale Trace: Detecting Reasoning Failures in LLMs Using Chain-of-Thought Dynamics

Chain-of-thought (CoT) reasoning improves large language model (LLM) performance while also providing an observable interface to the model's reasoning process. Existing approaches that leverage verbalized CoTs to monitor reasoning correctness, however, largely evaluate the semantic correctness or consistency of individual intermediate steps, rather than how the reasoning process evolves across the trace. As a result, failures distributed across the reasoning trajectory, rather than those localized to a single incorrect step, remain comparatively underexplored. Furthermore, verbalized CoTs need not faithfully reflect the model's internal reasoning, motivating analyses that do not treat individual statements as literal accounts of internal computation. In this work, we therefore ask whether the dynamics of visible CoT can be leveraged to systematically distinguish successful from failed reasoning without assuming such semantic faithfulness. We study a range of LLMs on verifiable Boolean satisfiability tasks with variable complexity, enabling controlled comparisons near each model's capability frontier. Tagging CoT sentences by reasoning function reveals premature verification collapse on SAT problems: incorrect traces enter clause checking earlier, repeat similar operations, and finalize sooner. On UNSAT problems, models presumptuously move towards incorrect SAT conclusions, checking candidate assignments rather than deriving contradictions across constructed cases. Subsequently, a targeted proof-search prompt intervention raises Llama3-70B accuracy from 13.3% to 85%, correcting 84.6% of these errors. These results show that capability failures can manifest as distributed, task-dependent changes in the structure of visible reasoning, and that CoT dynamics agnostic to whether the verbalized trace reflects the model's internal computations can help diagnose and correct failures.

Visualizing Graph-to-Answer Mechanism Recovery in Materials-Science Hypothesis Generation

AI co-scientists can generate fluent materials-science hypotheses, but fluency does not show that an answer preserves a scientifically meaningful mechanism. We present a graph-to-answer mechanism-tracing case study for Graph-PRefLexOR-8B, a Qwen3-8B model adapted to expose distinct stages for brainstorming, graph construction, pattern extraction, and synthesis. We organize semantic backtracking, graph corruption, activation-based recovery measurements, and layer-by-token-region grids into a visual diagnostic workflow for inspecting this pathway. Across 100 open-ended materials-science questions, final answers remain closest to the model's own structured stages, especially synthesis. Under graph corruption, a full sweep over 37 residual-stream checkpoints, the embedding output and 36 transformer blocks, shows little mechanism recovery in the earlier transition region at layers 7--10, recovery instead concentrates in late synthesis and answer-start regions around layers 30 and 36. The workflow is intended to help scientists and model developers identify where a generated hypothesis loses or regains mechanism support before it is passed to downstream experimental planning.

Graph-Native Reinforcement Learning Enables Traceable Scientific Hypothesis Generation through Conceptual Recombination

Accelerating materials discovery requires AI systems that can generate scientifically valid hypotheses through multi-step, domain-grounded reasoning. Standard large language models often produce fluent but weakly traceable responses to open-ended materials design problems, making it difficult to determine whether final answers are supported by coherent intermediate reasoning. We develop Graph-PRefLexOR, a family of graph-native reasoning models fine-tuned with Group Relative Policy Optimization (GRPO) to organize reasoning into explicit phases for mechanism exploration, graph construction, pattern extraction, and hypothesis synthesis. This design links neural language generation with symbolic relational structure, enabling causal connections to be constructed, inspected, and reused. On 100 open-ended questions from materials science and mechanics literature, Graph-PRefLexOR achieves 40-65% improvements over corresponding base models, with the largest gains in reasoning traceability. Embedding analyses show broader semantic exploration and approximately 2-3 times greater semantic diversity than baselines. Semantic backtracking and layer-wise hidden-state analyses further show stronger alignment between structured reasoning and final answers. Finally, test-time graph expansion reveals that additional compute primarily increases long-range conceptual recombination within a bounded semantic space, rather than simply expanding semantic coverage. These results establish graph-native reinforcement learning as a pathway toward interpretable AI systems for scientific hypothesis generation in materials design and other scientific applications.

The Compressive Knowledge Graph Hypothesis: Which Graph Facts Matter for Scientific Hypothesis Generation?

Knowledge graphs (KGs) can provide structured scientific context to language models, but it remains unclear which graph facts actually shape the generated hypotheses. We study KG-guided hypothesis generation for battery materials across Mistral-7B, Llama-3.1-70B, and Gemini 2.5 Flash. We perturb local KGs by varying density, ontology richness, topology, and control structure, and evaluate outputs with both provided-graph and fixed-reference metrics. Across models, KG utility is selective and model-dependent: graph context changes outputs, but no-KG outputs also recover substantial graph content from model priors. Compact top-k subgraphs often approximate full-KG behavior, including when claimed-outcome triples are held out. At the same time, compression is not unique to one semantic ranking rule, random and topology-based subsets can also recover much of the signal. These results support a redundancy-aware Compressive KG hypothesis: useful KG signal is often recoverable from compact, scientifically structured subgraphs rather than requiring the full local graph.

A Survey on Hypothesis Generation for Scientific Discovery in the Era of Large Language Models

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in their potential to enhance and automate this process. This paper presents a comprehensive survey of hypothesis generation with LLMs by (i) reviewing existing methods, from simple prompting techniques to more complex frameworks, and proposing a taxonomy that categorizes these approaches; (ii) analyzing techniques for improving hypothesis quality, such as novelty boosting and structured reasoning; (iii) providing an overview of evaluation strategies; and (iv) discussing key challenges and future directions, including multimodal integration and human-AI collaboration. Our survey aims to serve as a reference for researchers exploring LLMs for hypothesis generation.

Partially Blinded Unlearning: Class Unlearning for Deep Networks a Bayesian Perspective

In order to adhere to regulatory standards governing individual data privacy and safety, machine learning models must systematically eliminate information derived from specific subsets of a user's training data that can no longer be utilized. The emerging discipline of Machine Unlearning has arisen as a pivotal area of research, facilitating the process of selectively discarding information designated to specific sets or classes of data from a pre-trained model, thereby eliminating the necessity for extensive retraining from scratch. The principal aim of this study is to formulate a methodology tailored for the purposeful elimination of information linked to a specific class of data from a pre-trained classification network. This intentional removal is crafted to degrade the model's performance specifically concerning the unlearned data class while concurrently minimizing any detrimental impacts on the model's performance in other classes. To achieve this goal, we frame the class unlearning problem from a Bayesian perspective, which yields a loss function that minimizes the log-likelihood associated with the unlearned data with a stability regularization in parameter space. This stability regularization incorporates Mohalanobis distance with respect to the Fisher Information matrix and $l_2$ distance from the pre-trained model parameters. Our novel approach, termed \textbf{Partially-Blinded Unlearning (PBU)}, surpasses existing state-of-the-art class unlearning methods, demonstrating superior effectiveness. Notably, PBU achieves this efficacy without requiring awareness of the entire training dataset but only to the unlearned data points, marking a distinctive feature of its performance.

A Bayesian Learning, Greedy agglomerative clustering approach and evaluation techniques for Author Name Disambiguation Problem

Author names often suffer from ambiguity owing to the same author appearing under different names and multiple authors possessing similar names. It creates difficulty in associating a scholarly work with the person who wrote it, thereby introducing inaccuracy in credit attribution, bibliometric analysis, search-by-author in a digital library, and expert discovery. A plethora of techniques for disambiguation of author names has been proposed in the literature. I try to focus on the research efforts targeted to disambiguate author names. I first go through the conventional methods, then I discuss evaluation techniques and the clustering model which finally leads to the Bayesian learning and Greedy agglomerative approach. I believe this concentrated review will be useful for the research community because it discusses techniques applied to a very large real database that is actively used worldwide. The Bayesian and the greedy agglomerative approach used will help to tackle AND problems in a better way. Finally, I try to outline a few directions for future work