Committee

arXiv:2510.13908v1 Announce Type: new Abstract: Large Language Models (LLMs) have demonstrated impressive reasoning capabilities but continue to struggle with arithmetic tasks. Prior works largely focus on outputs or prompting strategies, leaving the open question of the internal structure through which models do arithmetic computation. In this work, we investigate whether LLMs encode operator precedence in their internal representations via the open-source instruction-tuned LLaMA 3.2-3B model. We constructed a dataset of arithmetic expressions with three operands and two operators, varying the order and placement of parentheses. Using this dataset, we trace whether intermediate results appear in the residual stream of the instruction-tuned LLaMA 3.2-3B model. We apply interpretability techniques such as logit lens, linear classification probes, and UMAP geometric visualization. Our results show that intermediate computations are present in the residual stream, particularly after MLP blocks. We also find that the model linearly encodes precedence in each operator’s embeddings post attention layer. We introduce partial embedding swap, a technique that modifies operator precedence by exchanging high-impact embedding dimensions between operators.

arXiv:2510.13909v1 Announce Type: new Abstract: Inductive Knowledge Graph Reasoning (KGR) aims to discover facts in open-domain KGs containing unknown entities and relations, which poses a challenge for KGR models in comprehending uncertain KG components. Existing studies have proposed Knowledge Graph Foundation Models (KGFMs) that learn structural invariances across KGs to handle this uncertainty. Recently, Large Language Models (LLMs) have demonstrated strong capabilities for open-domain knowledge reasoning. As a result, the latest research has focused on LLM-based KGFMs that integrate LLM knowledge with KG context for inductive KGR. However, the intrinsic knowledge of LLMs may be overshadowed by sparse KG context, leading to LLM knowledge distortion, which can cause irreversible damage to model reasoning. Moreover, existing LLM-based KGR methods still struggle to fully constrain generative hallucinations in LLMs, severely limiting the credibility of reasoning results. To address these limitations, we propose a Knowledge Reasoning Language Model (KRLM) that achieves unified coordination between LLM knowledge and KG context throughout the KGR process. Specifically, we design a Knowledge Reasoning Language (KRL) instruction format and a KRL tokenizer to align LLM knowledge with KG representations. Then, we propose a KRL attention layer that coordinates intrinsic LLM knowledge with additional KG context through a dynamic knowledge memory mechanism. Finally, a structure-aware next-entity predictor is proposed, which strictly constrains the reasoning results within a trustworthy knowledge domain. Extensive experimental results on 25 real-world inductive KGR datasets demonstrate the significant superiority of the proposed KRLMfootnote{Our source codes are available at https://anonymous.4open.science/r/KRLM-EA36 in both zero-shot reasoning and fine-tuning scenarios.

arXiv:2509.06917v2 Announce Type: replace-cross Abstract: We introduce Paper2Agent, an automated framework that converts research papers into AI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate downstream use, adoption, and discovery. Conventional research papers require readers to invest substantial effort to understand and adapt a paper’s code, data, and methods to their own work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by automatically converting a paper into an AI agent that acts as a knowledgeable research assistant. It systematically analyzes the paper and the associated codebase using multiple agents to construct a Model Context Protocol (MCP) server, then iteratively generates and runs tests to refine and robustify the resulting MCP. These paper MCPs can then be flexibly connected to a chat agent (e.g. Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the original paper. We demonstrate Paper2Agent’s effectiveness in creating reliable and capable paper agents through in-depth case studies. Paper2Agent created an agent that leverages AlphaGenome to interpret genomic variants and agents based on ScanPy and TISSUE to carry out single-cell and spatial transcriptomics analyses. We validate that these paper agents can reproduce the original paper’s results and can correctly carry out novel user queries. Paper2Agent automatically created AI co-scientist that identified new splicing variant associated with ADHD risk. By turning static papers into dynamic, interactive AI agents, Paper2Agent introduces a new paradigm for knowledge dissemination and a foundation for the collaborative ecosystem of AI co-scientists.

arXiv:2506.02132v4 Announce Type: replace Abstract: Large transformer-based language models dominate modern NLP, yet our understanding of how they encode linguistic information relies primarily on studies of early models like BERT and GPT-2. Building on classic BERTology work, we analyze 25 models spanning from classical architectures (BERT, DeBERTa, GPT-2) to modern large language models (Pythia, OLMo-2, Gemma-2, Qwen2.5, Llama-3.1), probing layer-by-layer representations across eight linguistic tasks in English. Consistent with earlier findings, we find that hierarchical organization persists in modern models: early layers capture syntax, middle layers handle semantics and entity-level information, and later layers encode discourse phenomena. We dive deeper, conducting an in-depth multilingual analysis of two specific linguistic properties – lexical identity and inflectional morphology – that help disentangle form from meaning. We find that lexical information concentrates linearly in early layers but becomes increasingly nonlinear deeper in the network, while inflectional information remains linearly accessible throughout all layers. Additional analyses of attention mechanisms, steering vectors, and pretraining checkpoints reveal where this information resides within layers, how it can be functionally manipulated, and how representations evolve during pretraining. Taken together, our findings suggest that, even with substantial advances in LLM technologies, transformer models learn to organize linguistic information in similar ways, regardless of model architecture, size, or training regime, indicating that these properties are important for next token prediction. Our code is available at https://github.com/ml5885/model_internal_sleuthing

arXiv:2510.13163v1 Announce Type: new Abstract: Most large language models (LLMs) today excel at generating raw, sequential code with minimal abstractions and custom structures. However, there has been little work on graph-based abstract code generation, where significant logic is encapsulated in predefined nodes and execution flow is determined by edges. This is relevant for visual programming languages, and in cases where raw source code is inaccessible to users and LLM training sets. In this work, we propose and evaluate JSON representations for graphs to enable high accuracy graph-based abstract code generation. We evaluate these representations on ScratchTest, a mini-benchmark based on our custom Python re-implementation of Scratch, which tests the LLM in code graph space. Our findings demonstrate that LLMs can indeed perform the aforementioned generation task in a single pass without relying on specialized or complex pipelines, given the correct graph representations. We also show that different representations induce significantly different accuracies, highlighting the instrumental role of representations in this generation task. All in all, this work establishes the first steps towards representation learning for graph-based abstract code generation.

arXiv:2510.12915v1 Announce Type: cross Abstract: Critical thinking represents a fundamental competency in today’s education landscape. Developing critical thinking skills through timely assessment and feedback is crucial; however, there has not been extensive work in the learning analytics community on defining, measuring, and supporting critical thinking. In this paper, we investigate the feasibility of measuring core “subskills” that underlie critical thinking. We ground our work in an authentic task where students operationalize critical thinking: student-written argumentative essays. We developed a coding rubric based on an established skills progression and completed human coding for a corpus of student essays. We then evaluated three distinct approaches to automated scoring: zero-shot prompting, few-shot prompting, and supervised fine-tuning, implemented across three large language models (GPT-5, GPT-5-mini, and ModernBERT). GPT-5 with few-shot prompting achieved the strongest results and demonstrated particular strength on subskills with separable, frequent categories, while lower performance was observed for subskills that required detection of subtle distinctions or rare categories. Our results underscore critical trade-offs in automated critical thinking assessment: proprietary models offer superior reliability at higher cost, while open-source alternatives provide practical accuracy with reduced sensitivity to minority categories. Our work represents an initial step toward scalable assessment of higher-order reasoning skills across authentic educational contexts.

arXiv:2505.10113v3 Announce Type: replace Abstract: In this paper, we introduce S-MedQA, an English medical question-answering (QA) dataset for benchmarking large language models (LLMs) in fine-grained clinical specialties. S-MedQA has over 20k examples, covers 15 medical specialties, and QA pairs can have multiple specialty annotations (e.g., when a question is cross-disciplinary), constructed with both machine and expert verification to maximize data availability. We use S-MedQA to investigate the role of clinical specialty data in the knowledge-intensive scenario of medical QA. Our results show that 1) training on data from a clinical specialty does not necessarily lead to best performance on that specialty, and 2) regardless of the specialty the LLM was fine-tuned on, token probabilities of clinically relevant terms increase consistently across all specialties. Thus, we hypothesize improvement gains are derived mostly from domain shifting (e.g., general to medical) rather than specialty-specific knowledge injection, and suggest rethinking the role of fine-tuning data in the medical domain.

arXiv:2510.13302v1 Announce Type: new Abstract: Computational stylometry analyzes writing style through quantitative patterns in text, supporting applications from forensic tasks such as identity linking and plagiarism detection to literary attribution in the humanities. Supervised and contrastive approaches rely on data with spurious correlations and often confuse style with topic. Despite their natural use in AI-generated text detection, the CLM pre-training of modern LLMs has been scarcely leveraged for general authorship problems. We propose a novel unsupervised approach based on this extensive pre-training and the in-context learning capabilities of LLMs, employing the log-probabilities of an LLM to measure style transferability from one text to another. Our method significantly outperforms LLM prompting approaches of comparable scale and achieves higher accuracy than contrastively trained baselines when controlling for topical correlations. Moreover, performance scales fairly consistently with the size of the base model and, in the case of authorship verification, with an additional mechanism that increases test-time computation; enabling flexible trade-offs between computational cost and accuracy.

arXiv:2510.12121v1 Announce Type: cross Abstract: Precise attribute intensity control–generating Large Language Model (LLM) outputs with specific, user-defined attribute intensities–is crucial for AI systems adaptable to diverse user expectations. Current LLM alignment methods, however, typically provide only directional or open-ended guidance, failing to reliably achieve exact attribute intensities. We address this limitation with three key designs: (1) reformulating precise attribute intensity control as a target-reaching problem, rather than simple maximization; (2) training a lightweight value function via temporal-difference learning to predict final attribute intensity scores from partial generations, thereby steering LLM outputs; and (3) employing gradient-based interventions on hidden representations to navigate the model precisely towards specific attribute intensity targets. Our method enables fine-grained, continuous control over attribute intensities, moving beyond simple directional alignment. Experiments on LLaMA-3.2-3b and Phi-4-mini confirm our method’s ability to steer text generation to user-specified attribute intensities with high accuracy. Finally, we demonstrate efficiency enhancements across three downstream tasks: preference data synthesis, Pareto frontier approximation and optimization, and distillation of aligned behaviors for intervention-free inference. Our code is available on https://github.com/Pre-Control/pre-control