Daily Papers

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) in natural language to perform complex reasoning. However, chemical reasoning is inherently continuous and structural, and forcing it into discrete linguistic tokens introduces a fundamental representation mismatch that constrains both efficiency and performance. We introduce LatentChem, a latent reasoning interface that decouples chemical computation from textual generation, enabling models to perform multi-step reasoning directly in continuous latent space while emitting language only for final outputs. Remarkably, we observe a consistent emergent behavior: when optimized solely for task success, models spontaneously internalize reasoning, progressively abandoning verbose textual derivations in favor of implicit latent computation. This shift is not merely stylistic but computationally advantageous. Across diverse chemical reasoning benchmarks, LatentChem achieves a 59.88\% non-tie win rate over strong CoT-based baselines on ChemCoTBench, while delivering a 10.84times average inference speedup. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

Chemical reasoning inherently integrates visual, textual, and symbolic modalities, yet existing benchmarks rarely capture this complexity, often relying on simple image-text pairs with limited chemical semantics. As a result, the actual ability of Multimodal Large Language Models (MLLMs) to process and integrate chemically meaningful information across modalities remains unclear. We introduce ChemVTS-Bench, a domain-authentic benchmark designed to systematically evaluate the Visual-Textual-Symbolic (VTS) reasoning abilities of MLLMs. ChemVTS-Bench contains diverse and challenging chemical problems spanning organic molecules, inorganic materials, and 3D crystal structures, with each task presented in three complementary input modes: (1) visual-only, (2) visual-text hybrid, and (3) SMILES-based symbolic input. This design enables fine-grained analysis of modality-dependent reasoning behaviors and cross-modal integration. To ensure rigorous and reproducible evaluation, we further develop an automated agent-based workflow that standardizes inference, verifies answers, and diagnoses failure modes. Extensive experiments on state-of-the-art MLLMs reveal that visual-only inputs remain challenging, structural chemistry is the hardest domain, and multimodal fusion mitigates but does not eliminate visual, knowledge-based, or logical errors, highlighting ChemVTS-Bench as a rigorous, domain-faithful testbed for advancing multimodal chemical reasoning. All data and code will be released to support future research.

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

While large language models (LLMs) have achieved impressive progress, their application in scientific domains such as chemistry remains hindered by shallow domain understanding and limited reasoning capabilities. In this work, we focus on the specific field of chemistry and develop a Chemical Reasoner LLM, ChemDFM-R. We first construct a comprehensive dataset of atomized knowledge points to enhance the model's understanding of the fundamental principles and logical structure of chemistry. Then, we propose a mix-sourced distillation strategy that integrates expert-curated knowledge with general-domain reasoning skills, followed by domain-specific reinforcement learning to enhance chemical reasoning. Experiments on diverse chemical benchmarks demonstrate that ChemDFM-R achieves state-of-the-art performance while providing interpretable, rationale-driven outputs. Further case studies illustrate how explicit reasoning chains significantly improve the reliability, transparency, and practical utility of the model in real-world human-AI collaboration scenarios.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents. Code available at https://github.com/HowardLi1984/ChemCraft.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. However, the landscape remains fragmented and lacks a unified taxonomy or comprehensive survey. Therefore, we present a side-by-side comparison of benchmarks developed between 2019 and 2025 that evaluate these models and agents across multiple domains. In addition, we propose a taxonomy of approximately 60 benchmarks that cover general and academic knowledge reasoning, mathematical problem-solving, code generation and software engineering, factual grounding and retrieval, domain-specific evaluations, multimodal and embodied tasks, task orchestration, and interactive assessments. Furthermore, we review AI-agent frameworks introduced between 2023 and 2025 that integrate large language models with modular toolkits to enable autonomous decision-making and multi-step reasoning. Moreover, we present real-world applications of autonomous AI agents in materials science, biomedical research, academic ideation, software engineering, synthetic data generation, chemical reasoning, mathematical problem-solving, geographic information systems, multimedia, healthcare, and finance. We then survey key agent-to-agent collaboration protocols, namely the Agent Communication Protocol (ACP), the Model Context Protocol (MCP), and the Agent-to-Agent Protocol (A2A). Finally, we discuss recommendations for future research, focusing on advanced reasoning strategies, failure modes in multi-agent LLM systems, automated scientific discovery, dynamic tool integration via reinforcement learning, integrated search capabilities, and security vulnerabilities in agent protocols.

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose MPPReasoner, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

Large Language Models(LLMs) have demonstrated remarkable performance across various domains, yet their capabilities in molecular reasoning remain insufficiently explored. Current approaches tend to rely heavily on general-purpose prompting, which lacks domain-specific molecular semantics, while those that use fine-tuning strategies often face challenges with interpretability and reasoning depth. To address these issues, we introduce MolReasoner, a two-stage framework designed to transition LLMs from memorization towards chemical reasoning. First, we propose Mol-SFT, which initializes the model's reasoning abilities via synthetic Chain-of-Thought(CoT) samples generated by GPT-4o and verified for chemical accuracy. Subsequently, Mol-RL applies reinforcement learning with specialized reward functions designed explicitly to align chemical structures with linguistic descriptions, thereby enhancing molecular reasoning capabilities. Our approach notably enhances interpretability, improving the model 's molecular understanding and enabling better generalization. Extensive experiments demonstrate that MolReasoner outperforms existing methods, and marking a significant shift from memorization-based outputs to robust chemical reasoning.

Olympiad-level benchmarks in mathematics and physics are crucial testbeds for advanced AI reasoning, but chemistry, with its unique multimodal symbolic language, has remained an open challenge. We introduce ChemO, a new benchmark built from the International Chemistry Olympiad (IChO) 2025. ChemO features two key innovations for automated assessment: Assessment-Equivalent Reformulation (AER), which converts problems requiring visual outputs (e.g., drawing molecules) into computationally tractable formats, and Structured Visual Enhancement (SVE), a diagnostic mechanism to disentangle a model's visual perception capabilities from its core chemical reasoning. To tackle this benchmark, we propose ChemLabs, a hierarchical multi-agent framework that mimics human expert collaboration through specialized agents for problem decomposition, perception, reasoning, and auditing. Experiments on state-of-the-art multimodal models demonstrate that combining SVE with our multi-agent system yields dramatic performance gains. Our top configuration achieves a score of 93.6 out of 100, surpassing an estimated human gold medal threshold and establishing a new state-of-the-art in automated chemical problem-solving. ChemO Dataset: https://huggingface.co/datasets/IDEA-AI4SCI/ChemO

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 46% on molecular tasks and 66% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery.

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their robustness and reliability in scientific applications. To support more rigorous evaluation of LLMs in chemical reasoning, we present the MolErr2Fix benchmark, designed to assess LLMs on error detection and correction in molecular descriptions. Unlike existing benchmarks focused on molecule-to-text generation or property prediction, MolErr2Fix emphasizes fine-grained chemical understanding. It tasks LLMs with identifying, localizing, explaining, and revising potential structural and semantic errors in molecular descriptions. Specifically, MolErr2Fix consists of 1,193 fine-grained annotated error instances. Each instance contains quadruple annotations, i.e,. (error type, span location, the explanation, and the correction). These tasks are intended to reflect the types of reasoning and verification required in real-world chemical communication. Evaluations of current state-of-the-art LLMs reveal notable performance gaps, underscoring the need for more robust chemical reasoning capabilities. MolErr2Fix provides a focused benchmark for evaluating such capabilities and aims to support progress toward more reliable and chemically informed language models. All annotations and an accompanying evaluation API will be publicly released to facilitate future research.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful and widely used tools for molecular structure elucidation in organic chemistry. However, the interpretation of NMR spectra to determine unknown molecular structures remains a labor-intensive and expertise-dependent process, particularly for complex or novel compounds. Although recent methods have been proposed for molecular structure elucidation, they often underperform in real-world applications due to inherent algorithmic limitations and limited high-quality data. Here, we present NMR-Solver, a practical and interpretable framework for the automated determination of small organic molecule structures from ^1H and ^{13}C NMR spectra. Our method introduces an automated framework for molecular structure elucidation, integrating large-scale spectral matching with physics-guided fragment-based optimization that exploits atomic-level structure-spectrum relationships in NMR. We evaluate NMR-Solver on simulated benchmarks, curated experimental data from the literature, and real-world experiments, demonstrating its strong generalization, robustness, and practical utility in challenging, real-life scenarios. NMR-Solver unifies computational NMR analysis, deep learning, and interpretable chemical reasoning into a coherent system. By incorporating the physical principles of NMR into molecular optimization, it enables scalable, automated, and chemically meaningful molecular identification, establishing a generalizable paradigm for solving inverse problems in molecular science.

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science. With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation. Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20-35% gains over domain-specific baselines and outperforms general-purpose LLMs by 10-15% in Top-1 accuracy, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

Computer-aided synthesis planning (CASP) has long been envisioned as a complementary tool for synthetic chemists. However, existing frameworks often lack mechanisms to allow interaction with human experts, limiting their ability to integrate chemists' insights. In this work, we introduce Synthelite, a synthesis planning framework that uses large language models (LLMs) to directly propose retrosynthetic transformations. Synthelite can generate end-to-end synthesis routes by harnessing the intrinsic chemical knowledge and reasoning capabilities of LLMs, while allowing expert intervention through natural language prompts. Our experiments demonstrate that Synthelite can flexibly adapt its planning trajectory to diverse user-specified constraints, achieving up to 95\% success rates in both strategy-constrained and starting-material-constrained synthesis tasks. Additionally, Synthelite exhibits the ability to account for chemical feasibility during route design. We envision Synthelite to be both a useful tool and a step toward a paradigm where LLMs are the central orchestrators of synthesis planning.

While Vision-Language Models (VLMs) have demonstrated significant potential in chemical visual understanding, current models are predominantly optimized for direct visual question-answering tasks. This paradigm often results in "black-box" systems that fail to utilize the inherent capability of Large Language Models (LLMs) to infer underlying reaction mechanisms. In this work, we introduce ChemVLR, a chemical VLM designed to prioritize reasoning within the perception process. Unlike conventional chemical VLMs, ChemVLR analyzes visual inputs in a fine-grained manner by explicitly identifying granular chemical descriptors, such as functional groups, prior to generating answers. This approach ensures the production of explicit and interpretable reasoning paths for complex visual chemical problems. To facilitate this methodology, we implement a cross-modality reverse-engineering strategy, combined with a rigorous filtering pipeline, to curate a large-scale reasoning-and-captioning dataset comprising 760k high-quality samples across molecular and reaction tasks. Furthermore, we adopt a three-stage training framework that systemically builds model perception and reasoning capacity. Experiments demonstrate that ChemVLR achieves state-of-the-art (SOTA) performance, surpassing both leading proprietary models and domain-specific open-source baselines. We also provide comprehensive ablation studies to validate our training strategy and data generation designs. Code and model weights will be available at https://github.com/xxlllz/ChemVLR.

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.

Retrosynthesis planning, essential in organic synthesis and drug discovery, has greatly benefited from recent AI-driven advancements. Nevertheless, existing methods frequently face limitations in both applicability and explainability. Traditional graph-based and sequence-to-sequence models often lack generalized chemical knowledge, leading to predictions that are neither consistently accurate nor easily explainable. To address these challenges, we introduce RetroDFM-R, a reasoning-based large language model (LLM) designed specifically for chemical retrosynthesis. Leveraging large-scale reinforcement learning guided by chemically verifiable rewards, RetroDFM-R significantly enhances prediction accuracy and explainability. Comprehensive evaluations demonstrate that RetroDFM-R significantly outperforms state-of-the-art methods, achieving a top-1 accuracy of 65.0% on the USPTO-50K benchmark. Double-blind human assessments further validate the chemical plausibility and practical utility of RetroDFM-R's predictions. RetroDFM-R also accurately predicts multistep retrosynthetic routes reported in the literature for both real-world drug molecules and perovskite materials. Crucially, the model's explicit reasoning process provides human-interpretable insights, thereby enhancing trust and practical value in real-world retrosynthesis applications.

Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We introduce Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), an active learning framework where large language models autonomously design, execute, and interpret atomistic simulations. In MASTER, a multimodal system translates natural language into density functional theory workflows, while higher-level reasoning agents guide discovery through a hierarchy of strategies, including a single agent baseline and three multi-agent approaches: peer review, triage-ranking, and triage-forms. Across two chemical applications, CO adsorption on Cu-surface transition metal (M) adatoms and on M-N-C catalysts, reasoning-driven exploration reduces required atomistic simulations by up to 90% relative to trial-and-error selection. Reasoning trajectories reveal chemically grounded decisions that cannot be explained by stochastic sampling or semantic bias. Altogether, multi-agent collaboration accelerates materials discovery and marks a new paradigm for autonomous scientific exploration.

Retrosynthesis prediction aims to infer the reactant molecule based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing models rely on static pattern-matching paradigm, which limits their ability to perform effective logic decision-making, leading to black-box decision-making. Building on this, we propose Retro-Expert, an interpretable retrosynthesis framework that performs collaborative reasoning by combining the complementary reasoning strengths of Large Language Models and specialized models via reinforcement learning. It outputs natural language explanations grounded in chemical logic through three components: (1) specialized models perform shallow reasoning to construct high-quality chemical decision space, (2) LLM-driven critical reasoning to generate predictions and corresponding interpretable reasoning path, and (3) reinforcement learning optimizing interpretable decision policy. Experiments show that Retro-Expert not only surpasses both LLM-based and specialized models across different metrics but also provides expert-aligned explanations that bridge the gap between AI predictions and actionable chemical insights.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

Question Answering (QA) effectively evaluates language models' reasoning and knowledge depth. While QA datasets are plentiful in areas like general domain and biomedicine, academic chemistry is less explored. Chemical QA plays a crucial role in both education and research by effectively translating complex chemical information into readily understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a QAMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. We first address the issue of imbalanced label distribution by re-weighting the instance-wise loss based on the inverse frequency of each class, ensuring minority classes are not dominated by majority ones during optimization. Next, we utilize the unlabeled data to enrich the learning process, generating a variety of augmentations based on a SoftMix operation and ensuring their predictions align with the same target, i.e., pseudo-labels. To ensure the quality of the pseudo-labels, we propose a calibration procedure aimed at closely aligning the pseudo-label estimates of individual samples with a desired ground truth distribution. Experiments show that our QAMatch significantly outperforms the recent similar-scale baselines and Large Language Models (LLMs) not only on our ScholarChemQA dataset but also on four benchmark datasets. We hope our benchmark and model can facilitate and promote more research on chemical QA.

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains underexplored. Here, we introduce RxnBench, a multi-tiered benchmark designed to rigorously evaluate MLLMs on chemical reaction understanding from scientific PDFs. RxnBench comprises two tasks: Single-Figure QA (SF-QA), which tests fine-grained visual perception and mechanistic reasoning using 1,525 questions derived from 305 curated reaction schemes, and Full-Document QA (FD-QA), which challenges models to synthesize information from 108 articles, requiring cross-modal integration of text, schemes, and tables. Our evaluation of MLLMs reveals a critical capability gap: while models excel at extracting explicit text, they struggle with deep chemical logic and precise structural recognition. Notably, models with inference-time reasoning significantly outperform standard architectures, yet none achieve 50\% accuracy on FD-QA. These findings underscore the urgent need for domain-specific visual encoders and stronger reasoning engines to advance autonomous AI chemists.

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce Mol-R1, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation. Our approach begins with a high-quality reasoning dataset curated through Prior Regulation via In-context Distillation (PRID), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce MoIA, Molecular Iterative Adaptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery. Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

The next frontier for video generation lies in developing models capable of zero-shot reasoning, where understanding real-world scientific laws is crucial for accurate physical outcome modeling under diverse conditions. However, existing video benchmarks are physical commonsense-based, offering limited insight into video models' scientific reasoning capability. We introduce VideoScience-Bench, a benchmark designed to evaluate undergraduate-level scientific understanding in video models. Each prompt encodes a composite scientific scenario that requires understanding and reasoning across multiple scientific concepts to generate the correct phenomenon. The benchmark comprises 200 carefully curated prompts spanning 14 topics and 103 concepts in physics and chemistry. We conduct expert-annotated evaluations across seven state-of-the-art video models in T2V and I2V settings along five dimensions: Prompt Consistency, Phenomenon Congruency, Correct Dynamism, Immutability, and Spatio-Temporal Continuity. Using a VLM-as-a-Judge to assess video generations, we observe strong correlation with human assessments. To the best of our knowledge, VideoScience-Bench is the first benchmark to evaluate video models not only as generators but also as reasoners, requiring their generations to demonstrate scientific understanding consistent with expected physical and chemical phenomena. Our data and evaluation code are available at: https://github.com/hao-ai-lab/VideoScience{github.com/hao-ai-lab/VideoScience}.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

We introduce MMMU: a new benchmark designed to evaluate multimodal models on massive multi-discipline tasks demanding college-level subject knowledge and deliberate reasoning. MMMU includes 11.5K meticulously collected multimodal questions from college exams, quizzes, and textbooks, covering six core disciplines: Art & Design, Business, Science, Health & Medicine, Humanities & Social Science, and Tech & Engineering. These questions span 30 subjects and 183 subfields, comprising 30 highly heterogeneous image types, such as charts, diagrams, maps, tables, music sheets, and chemical structures. Unlike existing benchmarks, MMMU focuses on advanced perception and reasoning with domain-specific knowledge, challenging models to perform tasks akin to those faced by experts. Our evaluation of 14 open-source LMMs and the proprietary GPT-4V(ision) highlights the substantial challenges posed by MMMU. Even the advanced GPT-4V only achieves a 56% accuracy, indicating significant room for improvement. We believe MMMU will stimulate the community to build next-generation multimodal foundation models towards expert artificial general intelligence.

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Autonomous agents driven by Large Language Models (LLMs) have revolutionized reasoning and problem-solving but remain static after training, unable to grow with experience as intelligent beings do during deployment. We introduce Forward Learning with EXperience (FLEX), a gradient-free learning paradigm that enables LLM agents to continuously evolve through accumulated experience. Specifically, FLEX cultivates scalable and inheritable evolution by constructing a structured experience library through continual reflection on successes and failures during interaction with the environment. FLEX delivers substantial improvements on mathematical reasoning, chemical retrosynthesis, and protein fitness prediction (up to 23% on AIME25, 10% on USPTO50k, and 14% on ProteinGym). We further identify a clear scaling law of experiential growth and the phenomenon of experience inheritance across agents, marking a step toward scalable and inheritable continuous agent evolution. Project Page: https://flex-gensi-thuair.github.io.

Despite deep learning's success in chemistry, its impact is hindered by a lack of interpretability and an inability to resolve activity cliffs, where minor structural nuances trigger drastic property shifts. Current representation learning, bound by the similarity principle, often fails to capture these structural-activity discontinuities. To address this, we introduce MolEvolve, an evolutionary framework that reformulates molecular discovery as an autonomous, look-ahead planning problem. Unlike traditional methods that depend on human-engineered features or rigid prior knowledge, MolEvolve leverages a Large Language Model (LLM) to actively explore and evolve a library of executable chemical symbolic operations. By utilizing the LLM to cold start and an Monte Carlo Tree Search (MCTS) engine for test-time planning with external tools (e.g. RDKit), the system self-discovers optimal trajectories autonomously. This process evolves transparent reasoning chains that translate complex structural transformations into actionable, human-readable chemical insights. Experimental results demonstrate that MolEvolve's autonomous search not only evolves transparent, human-readable chemical insights, but also outperforms baselines in both property prediction and molecule optimization tasks.

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. There have been considerable attempts to address this problem, but given the exponentially large combinatorial space of synthesizable molecules, existing methods have shown limited coverage of the space and poor molecular optimization performance. To tackle these problems, we introduce ReaSyn, a generative framework for synthesizable projection where the model explores the neighborhood of given molecules in the synthesizable space by generating pathways that result in synthesizable analogs. To fully utilize the chemical knowledge contained in the synthetic pathways, we propose a novel perspective that views synthetic pathways akin to reasoning paths in large language models (LLMs). Specifically, inspired by chain-of-thought (CoT) reasoning in LLMs, we introduce the chain-of-reaction (CoR) notation that explicitly states reactants, reaction types, and intermediate products for each step in a pathway. With the CoR notation, ReaSyn can get dense supervision in every reaction step to explicitly learn chemical reaction rules during supervised training and perform step-by-step reasoning. In addition, to further enhance the reasoning capability of ReaSyn, we propose reinforcement learning (RL)-based finetuning and goal-directed test-time compute scaling tailored for synthesizable projection. ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.

Quantitative chemistry is central to modern chemical research, yet the ability of large language models (LLMs) to perform its rigorous, step-by-step calculations remains underexplored. To fill this blank, we propose QCBench, a Quantitative Chemistry oriented benchmark comprising 350 computational chemistry problems across 7 chemistry subfields, which contains analytical chemistry, bio/organic chemistry, general chemistry, inorganic chemistry, physical chemistry, polymer chemistry and quantum chemistry. To systematically evaluate the mathematical reasoning abilities of large language models (LLMs), they are categorized into three tiers: easy, medium, and difficult. Each problem, rooted in realistic chemical scenarios, is structured to prevent heuristic shortcuts and demand explicit numerical reasoning. QCBench enables fine-grained diagnosis of computational weaknesses, reveals model-specific limitations across difficulty levels, and lays the groundwork for future improvements such as domain-adaptive fine-tuning or multi-modal integration. Evaluations on 24 LLMs demonstrate a consistent performance degradation with increasing task complexity, highlighting the current gap between language fluency and scientific computation accuracy. Code for QCBench is available at https://github.com/jiaqingxie/QCBench.

Reasoning is a fundamental cognitive process that enables logical inference, problem-solving, and decision-making. With the rapid advancement of large language models (LLMs), reasoning has emerged as a key capability that distinguishes advanced AI systems from conventional models that empower chatbots. In this survey, we categorize existing methods along two orthogonal dimensions: (1) Regimes, which define the stage at which reasoning is achieved (either at inference time or through dedicated training); and (2) Architectures, which determine the components involved in the reasoning process, distinguishing between standalone LLMs and agentic compound systems that incorporate external tools, and multi-agent collaborations. Within each dimension, we analyze two key perspectives: (1) Input level, which focuses on techniques that construct high-quality prompts that the LLM condition on; and (2) Output level, which methods that refine multiple sampled candidates to enhance reasoning quality. This categorization provides a systematic understanding of the evolving landscape of LLM reasoning, highlighting emerging trends such as the shift from inference-scaling to learning-to-reason (e.g., DeepSeek-R1), and the transition to agentic workflows (e.g., OpenAI Deep Research, Manus Agent). Additionally, we cover a broad spectrum of learning algorithms, from supervised fine-tuning to reinforcement learning such as PPO and GRPO, and the training of reasoners and verifiers. We also examine key designs of agentic workflows, from established patterns like generator-evaluator and LLM debate to recent innovations. ...

Scientific reasoning, the process through which humans apply logic, evidence, and critical thinking to explore and interpret scientific phenomena, is essential in advancing knowledge reasoning across diverse fields. However, despite significant progress, current scientific reasoning models still struggle with generalization across domains and often fall short of multimodal perception. Multimodal Large Language Models (MLLMs), which integrate text, images, and other modalities, present an exciting opportunity to overcome these limitations and enhance scientific reasoning. Therefore, this position paper argues that MLLMs can significantly advance scientific reasoning across disciplines such as mathematics, physics, chemistry, and biology. First, we propose a four-stage research roadmap of scientific reasoning capabilities, and highlight the current state of MLLM applications in scientific reasoning, noting their ability to integrate and reason over diverse data types. Second, we summarize the key challenges that remain obstacles to achieving MLLM's full potential. To address these challenges, we propose actionable insights and suggestions for the future. Overall, our work offers a novel perspective on MLLM integration with scientific reasoning, providing the LLM community with a valuable vision for achieving Artificial General Intelligence (AGI).

Reasoning is a fundamental aspect of human intelligence that plays a crucial role in activities such as problem solving, decision making, and critical thinking. In recent years, large language models (LLMs) have made significant progress in natural language processing, and there is observation that these models may exhibit reasoning abilities when they are sufficiently large. However, it is not yet clear to what extent LLMs are capable of reasoning. This paper provides a comprehensive overview of the current state of knowledge on reasoning in LLMs, including techniques for improving and eliciting reasoning in these models, methods and benchmarks for evaluating reasoning abilities, findings and implications of previous research in this field, and suggestions on future directions. Our aim is to provide a detailed and up-to-date review of this topic and stimulate meaningful discussion and future work.

Exploiting large language models (LLMs) to tackle deductive reasoning has garnered growing attention. It still remains highly challenging to achieve satisfactory results in complex deductive problems, characterized by plenty of premises (i.e., facts or rules) entailing intricate relationships among entities and requiring multi-hop reasoning. One intuitive solution is to decompose the original task into smaller sub-tasks, and then chain the multiple casual reasoning steps together in a forward (e.g., Selection-Inference) or backward (e.g., LAMBADA) direction. However, these techniques inevitably necessitate a large number of overall stages, leading to computationally expensive operations and a higher possibility of making misleading steps. In addition to stage-by-stage decomposition, we draw inspiration from another aspect of human problem-solving. Humans tend to distill the most relevant information and organize their thoughts systematically (e.g., creating mind maps), which assists them in answering questions or drawing conclusions precisely and quickly. In light of this, we propose a novel reasoning approach named Concise and Organized Perception (COP). COP carefully analyzes the given statements to efficiently identify the most pertinent information while eliminating redundancy. It then prompts the LLMs in a more organized form that adapts to the model's inference process. By perceiving concise and organized proofs, the deductive reasoning abilities of LLMs can be better elicited, and the risk of acquiring errors caused by excessive reasoning stages is mitigated. Furthermore, our approach can be combined with the aforementioned ones to further boost their performance. Extensive experimental results on three popular deductive benchmarks (i.e., ProofWriter, PrOntoQA and PrOntoQA-OOD) show that COP significantly outperforms previous state-of-the-art methods.

Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffe and the hard and soft acids and bases concept of Pearson. The sound theoretical basis allows for a systematic definition of such concepts. However, while they are often used to describe and compare chemical processes in terms of reactivity, their predictive power remains unclear. In this work, we elaborate on the predictive potential of chemical reactivity concepts, which can be crucial for autonomous reaction exploration protocols to guide them by first-principles heuristics that expoit these concepts.

Rule-based reasoning, a fundamental type of legal reasoning, enables us to draw conclusions by accurately applying a rule to a set of facts. We explore causal language models as rule-based reasoners, specifically with respect to compositional rules - rules consisting of multiple elements which form a complex logical expression. Reasoning about compositional rules is challenging because it requires multiple reasoning steps, and attending to the logical relationships between elements. We introduce a new prompting method, Chain of Logic, which elicits rule-based reasoning through decomposition (solving elements as independent threads of logic), and recomposition (recombining these sub-answers to resolve the underlying logical expression). This method was inspired by the IRAC (Issue, Rule, Application, Conclusion) framework, a sequential reasoning approach used by lawyers. We evaluate chain of logic across eight rule-based reasoning tasks involving three distinct compositional rules from the LegalBench benchmark and demonstrate it consistently outperforms other prompting methods, including chain of thought and self-ask, using open-source and commercial language models.

Most scientific materials compress reasoning, presenting conclusions while omitting the derivational chains that justify them. This compression hinders verification by lacking explicit, step-wise justifications and inhibits cross-domain links by collapsing the very pathways that establish the logical and causal connections between concepts. We introduce a scalable framework that decompresses scientific reasoning, constructing a verifiable Long Chain-of-Thought (LCoT) knowledge base and projecting it into an emergent encyclopedia, SciencePedia. Our pipeline operationalizes an endpoint-driven, reductionist strategy: a Socratic agent, guided by a curriculum of around 200 courses, generates approximately 3 million first-principles questions. To ensure high fidelity, multiple independent solver models generate LCoTs, which are then rigorously filtered by prompt sanitization and cross-model answer consensus, retaining only those with verifiable endpoints. This verified corpus powers the Brainstorm Search Engine, which performs inverse knowledge search -- retrieving diverse, first-principles derivations that culminate in a target concept. This engine, in turn, feeds the Plato synthesizer, which narrates these verified chains into coherent articles. The initial SciencePedia comprises approximately 200,000 fine-grained entries spanning mathematics, physics, chemistry, biology, engineering, and computation. In evaluations across six disciplines, Plato-synthesized articles (conditioned on retrieved LCoTs) exhibit substantially higher knowledge-point density and significantly lower factual error rates than an equally-prompted baseline without retrieval (as judged by an external LLM). Built on this verifiable LCoT knowledge base, this reasoning-centric approach enables trustworthy, cross-domain scientific synthesis at scale and establishes the foundation for an ever-expanding encyclopedia.

Scientific problem solving poses unique challenges for LLMs, requiring both deep domain knowledge and the ability to apply such knowledge through complex reasoning. While automated scientific reasoners hold great promise for assisting human scientists, there is currently no widely adopted holistic benchmark for evaluating scientific reasoning, and few approaches systematically disentangle the distinct roles of knowledge and reasoning in these tasks. To address these gaps, we introduce SciReas, a diverse suite of existing benchmarks for scientific reasoning tasks, and SciReas-Pro, a selective subset that requires more complex reasoning. Our holistic evaluation surfaces insights about scientific reasoning performance that remain hidden when relying on individual benchmarks alone. We then propose KRUX, a probing framework for studying the distinct roles of reasoning and knowledge in scientific tasks. Combining the two, we conduct an in-depth analysis that yields several key findings: (1) Retrieving task-relevant knowledge from model parameters is a critical bottleneck for LLMs in scientific reasoning; (2) Reasoning models consistently benefit from external knowledge added in-context on top of the reasoning enhancement; (3) Enhancing verbalized reasoning improves LLMs' ability to surface task-relevant knowledge. Finally, we conduct a lightweight analysis, comparing our science-focused data composition with concurrent efforts on long CoT SFT, and release SciLit01, a strong 8B baseline for scientific reasoning.

Reasoning is a fundamental cognitive process underlying inference, problem-solving, and decision-making. While large language models (LLMs) demonstrate strong reasoning capabilities in closed-world settings, they struggle in open-ended and dynamic environments. Agentic reasoning marks a paradigm shift by reframing LLMs as autonomous agents that plan, act, and learn through continual interaction. In this survey, we organize agentic reasoning along three complementary dimensions. First, we characterize environmental dynamics through three layers: foundational agentic reasoning, which establishes core single-agent capabilities including planning, tool use, and search in stable environments; self-evolving agentic reasoning, which studies how agents refine these capabilities through feedback, memory, and adaptation; and collective multi-agent reasoning, which extends intelligence to collaborative settings involving coordination, knowledge sharing, and shared goals. Across these layers, we distinguish in-context reasoning, which scales test-time interaction through structured orchestration, from post-training reasoning, which optimizes behaviors via reinforcement learning and supervised fine-tuning. We further review representative agentic reasoning frameworks across real-world applications and benchmarks, including science, robotics, healthcare, autonomous research, and mathematics. This survey synthesizes agentic reasoning methods into a unified roadmap bridging thought and action, and outlines open challenges and future directions, including personalization, long-horizon interaction, world modeling, scalable multi-agent training, and governance for real-world deployment.

While reasoning in LLMs plays a natural role in math, code generation, and multi-hop factual questions, its effect on simple, single-hop factual questions remains unclear. Such questions do not require step-by-step logical decomposition, making the utility of reasoning highly counterintuitive. Nevertheless, we find that enabling reasoning substantially expands the capability boundary of the model's parametric knowledge recall, unlocking correct answers that are otherwise effectively unreachable. Why does reasoning aid parametric knowledge recall when there are no complex reasoning steps to be done? To answer this, we design a series of hypothesis-driven controlled experiments, and identify two key driving mechanisms: (1) a computational buffer effect, where the model uses the generated reasoning tokens to perform latent computation independent of their semantic content; and (2) factual priming, where generating topically related facts acts as a semantic bridge that facilitates correct answer retrieval. Importantly, this latter generative self-retrieval mechanism carries inherent risks: we demonstrate that hallucinating intermediate facts during reasoning increases the likelihood of hallucinations in the final answer. Finally, we show that our insights can be harnessed to directly improve model accuracy by prioritizing reasoning trajectories that contain hallucination-free factual statements.

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.

Reasoning is central to human intelligence, enabling structured problem-solving across diverse tasks. Recent advances in large language models (LLMs) have greatly enhanced their reasoning abilities in arithmetic, commonsense, and symbolic domains. However, effectively extending these capabilities into multimodal contexts-where models must integrate both visual and textual inputs-continues to be a significant challenge. Multimodal reasoning introduces complexities, such as handling conflicting information across modalities, which require models to adopt advanced interpretative strategies. Addressing these challenges involves not only sophisticated algorithms but also robust methodologies for evaluating reasoning accuracy and coherence. This paper offers a concise yet insightful overview of reasoning techniques in both textual and multimodal LLMs. Through a thorough and up-to-date comparison, we clearly formulate core reasoning challenges and opportunities, highlighting practical methods for post-training optimization and test-time inference. Our work provides valuable insights and guidance, bridging theoretical frameworks and practical implementations, and sets clear directions for future research.

Recently, slow-thinking reasoning systems, such as o1, have demonstrated remarkable capabilities in solving complex reasoning tasks. These systems typically engage in an extended thinking process before responding to a query, allowing them to generate more thorough, accurate, and well-reasoned solutions. These systems are primarily developed and maintained by industry, with their core techniques not publicly disclosed. In response, an increasing number of studies from the research community aim to explore the technical foundations underlying these powerful reasoning systems. Building on these prior efforts, this paper presents a reproduction report on implementing o1-like reasoning systems. We introduce an "imitate, explore, and self-improve" framework as our primary technical approach to train the reasoning model. In the initial phase, we use distilled long-form thought data to fine-tune the reasoning model, enabling it to invoke a slow-thinking mode. The model is then encouraged to explore challenging problems by generating multiple rollouts, which can result in increasingly more high-quality trajectories that lead to correct answers. Furthermore, the model undergoes self-improvement by iteratively refining its training dataset. To verify the effectiveness of this approach, we conduct extensive experiments on three challenging benchmarks. The experimental results demonstrate that our approach achieves competitive performance compared to industry-level reasoning systems on these benchmarks.

Large language models (LLMs) have established great success in the general domain of natural language processing. Their emerging task generalization and free-form dialogue capabilities can greatly help to design Chemical General Intelligence (CGI) to assist real-world research in chemistry. However, the existence of specialized language and knowledge in the field of chemistry, such as the highly informative SMILES notation, hinders the performance of general-domain LLMs in chemistry. To this end, we develop ChemDFM, the first LLM towards CGI. ChemDFM-13B is trained on 34B tokens from chemical literature, textbooks, and instructions as well as various data from the general domain. Therefore, it can store, understand, and reason over chemical knowledge and languages while still possessing advanced free-form language comprehension capabilities. Extensive quantitative evaluation shows that ChemDFM can significantly outperform the representative open-sourced LLMs. Moreover, ChemDFM can also surpass GPT-4 on a great portion of chemical tasks, despite the significant size difference. Further qualitative evaluations demonstrate the efficiency and effectiveness of ChemDFM in real-world research scenarios. We will open-source the ChemDFM model soon.

Large Language Models (LLMs) have demonstrated remarkable abilities in scientific reasoning, yet their reasoning capabilities in materials science remain underexplored. To fill this gap, we introduce MatSciBench, a comprehensive college-level benchmark comprising 1,340 problems that span the essential subdisciplines of materials science. MatSciBench features a structured and fine-grained taxonomy that categorizes materials science questions into 6 primary fields and 31 sub-fields, and includes a three-tier difficulty classification based on the reasoning length required to solve each question. MatSciBench provides detailed reference solutions enabling precise error analysis and incorporates multimodal reasoning through visual contexts in numerous questions. Evaluations of leading models reveal that even the highest-performing model, Gemini-2.5-Pro, achieves under 80% accuracy on college-level materials science questions, highlighting the complexity of MatSciBench. Our systematic analysis of different reasoning strategie--basic chain-of-thought, tool augmentation, and self-correction--demonstrates that no single method consistently excels across all scenarios. We further analyze performance by difficulty level, examine trade-offs between efficiency and accuracy, highlight the challenges inherent in multimodal reasoning tasks, analyze failure modes across LLMs and reasoning methods, and evaluate the influence of retrieval-augmented generation. MatSciBench thus establishes a comprehensive and solid benchmark for assessing and driving improvements in the scientific reasoning capabilities of LLMs within the materials science domain.

Reasoning, as an essential ability for complex problem-solving, can provide back-end support for various real-world applications, such as medical diagnosis, negotiation, etc. This paper provides a comprehensive survey of cutting-edge research on reasoning with language model prompting. We introduce research works with comparisons and summaries and provide systematic resources to help beginners. We also discuss the potential reasons for emerging such reasoning abilities and highlight future research directions. Resources are available at https://github.com/zjunlp/Prompt4ReasoningPapers (updated periodically).

Large-scale pre-trained language models (PLMs) bring new opportunities to challenging problems, especially those that need high-level intelligence, such as the math word problem (MWPs). However, directly applying existing PLMs to MWPs can fail as the generation process lacks sufficient supervision and thus lacks fast adaptivity as humans. We notice that human reasoning has a dual reasoning framework that consists of an immediate reaction system (system 1) and a delicate reasoning system (system 2), where the entire reasoning is determined by their interaction. This inspires us to develop a cooperative reasoning-induced PLM for solving MWPs, called Cooperative Reasoning (CoRe), resulting in a human-like reasoning architecture with system 1 as the generator and system 2 as the verifier. In our approach, the generator is responsible for generating reasoning paths, and the verifiers are used to supervise the evaluation in order to obtain reliable feedback for the generator. We evaluate our CoRe framework on several mathematical reasoning datasets and achieve decent improvement over state-of-the-art methods, up to 9.6% increase over best baselines. Our codes are available at https://github.com/TianHongZXY/CoRe

Mathematical reasoning, a core aspect of human cognition, is vital across many domains, from educational problem-solving to scientific advancements. As artificial general intelligence (AGI) progresses, integrating large language models (LLMs) with mathematical reasoning tasks is becoming increasingly significant. This survey provides the first comprehensive analysis of mathematical reasoning in the era of multimodal large language models (MLLMs). We review over 200 studies published since 2021, and examine the state-of-the-art developments in Math-LLMs, with a focus on multimodal settings. We categorize the field into three dimensions: benchmarks, methodologies, and challenges. In particular, we explore multimodal mathematical reasoning pipeline, as well as the role of (M)LLMs and the associated methodologies. Finally, we identify five major challenges hindering the realization of AGI in this domain, offering insights into the future direction for enhancing multimodal reasoning capabilities. This survey serves as a critical resource for the research community in advancing the capabilities of LLMs to tackle complex multimodal reasoning tasks.

This paper presents ReasonFormer, a unified reasoning framework for mirroring the modular and compositional reasoning process of humans in complex decision-making. Inspired by dual-process theory in cognitive science, the representation module (automatic thinking) and reasoning modules (controlled thinking) are decoupled to capture different levels of cognition. Upon the top of the representation module, the pre-trained reasoning modules are modular and professional in specific and fundamental reasoning skills (e.g., logic, simple QA, etc). To mimic the controlled compositional thinking process, different reasoning modules are dynamically activated and composed in both parallel and cascaded manners to control what reasoning skills are activated and how deep the reasoning process will be reached to solve the current problems. The unified reasoning framework solves multiple tasks with a single model, and is trained and inferred in an end-to-end manner. Evaluated on 11 datasets requiring different reasoning skills and complexity, ReasonFormer demonstrates substantial performance boosts, revealing the compositional reasoning ability. Few-shot experiments exhibit better generalization ability by learning to compose pre-trained skills for new tasks with limited data, and decoupling the representation module and the reasoning modules. Further analysis shows the modularity of reasoning modules as different tasks activate distinct reasoning skills at different reasoning depths.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

Reasoning is an essential component of human intelligence as it plays a fundamental role in our ability to think critically, support responsible decisions, and solve challenging problems. Traditionally, AI has addressed reasoning in the context of logic-based representations of knowledge. However, the recent leap forward in natural language processing, with the emergence of language models based on transformers, is hinting at the possibility that these models exhibit reasoning abilities, particularly as they grow in size and are trained on more data. Despite ongoing discussions about what reasoning is in language models, it is still not easy to pin down to what extent these models are actually capable of reasoning. The goal of this workshop is to create a platform for researchers from different disciplines and/or AI perspectives, to explore approaches and techniques with the aim to reconcile reasoning between language models using transformers and using logic-based representations. The specific objectives include analyzing the reasoning abilities of language models measured alongside KR methods, injecting KR-style reasoning abilities into language models (including by neuro-symbolic means), and formalizing the kind of reasoning language models carry out. This exploration aims to uncover how language models can effectively integrate and leverage knowledge and reasoning with it, thus improving their application and utility in areas where precision and reliability are a key requirement.

Deductive reasoning plays a pivotal role in the formulation of sound and cohesive arguments. It allows individuals to draw conclusions that logically follow, given the truth value of the information provided. Recent progress in the domain of large language models (LLMs) has showcased their capability in executing deductive reasoning tasks. Nonetheless, a significant portion of research primarily assesses the accuracy of LLMs in solving such tasks, often overlooking a deeper analysis of their reasoning behavior. In this study, we draw upon principles from cognitive psychology to examine inferential strategies employed by LLMs, through a detailed evaluation of their responses to propositional logic problems. Our findings indicate that LLMs display reasoning patterns akin to those observed in humans, including strategies like supposition following or chain construction. Moreover, our research demonstrates that the architecture and scale of the model significantly affect its preferred method of reasoning, with more advanced models tending to adopt strategies more frequently than less sophisticated ones. Importantly, we assert that a model's accuracy, that is the correctness of its final conclusion, does not necessarily reflect the validity of its reasoning process. This distinction underscores the necessity for more nuanced evaluation procedures in the field.

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

Large Language Models (LLMs) significantly benefit from Chain-of-Thought (CoT) prompting in performing various reasoning tasks. While CoT allows models to produce more comprehensive reasoning processes, its emphasis on intermediate reasoning steps can inadvertently introduce hallucinations and accumulated errors, thereby limiting models' ability to solve complex reasoning tasks. Inspired by how humans engage in careful and meticulous deductive logical reasoning processes to solve tasks, we seek to enable language models to perform explicit and rigorous deductive reasoning, and also ensure the trustworthiness of their reasoning process through self-verification. However, directly verifying the validity of an entire deductive reasoning process is challenging, even with advanced models like ChatGPT. In light of this, we propose to decompose a reasoning verification process into a series of step-by-step subprocesses, each only receiving their necessary context and premises. To facilitate this procedure, we propose Natural Program, a natural language-based deductive reasoning format. Our approach enables models to generate precise reasoning steps where subsequent steps are more rigorously grounded on prior steps. It also empowers language models to carry out reasoning self-verification in a step-by-step manner. By integrating this verification process into each deductive reasoning stage, we significantly enhance the rigor and trustfulness of generated reasoning steps. Along this process, we also improve the answer correctness on complex reasoning tasks. Code will be released at https://github.com/lz1oceani/verify_cot.

Large language models (LLMs) have shown remarkable reasoning capabilities given chain-of-thought prompts (examples with intermediate reasoning steps). Existing benchmarks measure reasoning ability indirectly, by evaluating accuracy on downstream tasks such as mathematical reasoning. However, it is unclear how these models obtain the answers and whether they rely on simple heuristics rather than the generated chain-of-thought. To enable systematic exploration of the reasoning ability of LLMs, we present a new synthetic question-answering dataset called PrOntoQA, where each example is generated from a synthetic world model represented in first-order logic. This allows us to parse the generated chain-of-thought into symbolic proofs for formal analysis. Our analysis on InstructGPT and GPT-3 shows that LLMs are quite capable of making correct individual deduction steps, and so are generally capable of reasoning, even in fictional contexts. However, they have difficulty with proof planning: When multiple valid deduction steps are available, they are not able to systematically explore the different options.

Large Language Models (LLMs) have demonstrated significant potential in handling complex reasoning tasks through step-by-step rationale generation. However, recent studies have raised concerns regarding the hallucination and flaws in their reasoning process. Substantial efforts are being made to improve the reliability and faithfulness of the generated rationales. Some approaches model reasoning as planning, while others focus on annotating for process supervision. Nevertheless, the planning-based search process often results in high latency due to the frequent assessment of intermediate reasoning states and the extensive exploration space. Additionally, supervising the reasoning process with human annotation is costly and challenging to scale for LLM training. To address these issues, in this paper, we propose a framework to learn planning-based reasoning through direct preference optimization (DPO) on collected trajectories, which are ranked according to synthesized process rewards. Our results on challenging logical reasoning benchmarks demonstrate the effectiveness of our learning framework, showing that our 7B model can surpass the strong counterparts like GPT-3.5-Turbo.

A physically motivated equation that determines the number of electrons of a molecule is proposed based on chemical common sense. It shows that all molecules are entangled in the number of electrons and results in the fundamental assumption of molecular energy convexity that underpins molecular quantum mechanics. The proposed physical principle includes the molecular size consistency principle as a special case. Application of wavefunction theory to the principle shows that an individual molecule with a noninteger number of electrons is locally physical albeit locally unreal. The energy of a molecule is piecewise linear with respect to its continuous number of electrons. The continuity of the number of electrons allows the definition of an electronic chemical potential of a single molecule. A state function equivalent to the energy of a molecule can be defined using the chemical potential as a variable. The aforementioned physical principle can alternatively be expressed as a simple additivity with the new state function. The latter also shows that the quantum entanglement in the number of electrons can be viewed as all molecules sharing the same chemical potential.

Scientific reasoning relies not only on logical inference but also on activating prior knowledge and experiential structures. Memory can efficiently reuse knowledge and enhance reasoning consistency and stability. However, existing benchmarks mainly evaluate final answers or step-by-step coherence, overlooking the memory-driven mechanisms that underlie human reasoning, which involves activating anchors and attractors, then integrating them into multi-step inference. To address this gap, we propose A^3-Bench~ https://a3-bench.github.io, a benchmark designed to evaluate scientific reasoning through dual-scale memory-driven activation, grounded in Anchor and Attractor Activation. First, we annotate 2,198 science reasoning problems across domains using the SAPM process(subject, anchor & attractor, problem, and memory developing). Second, we introduce a dual-scale memory evaluation framework utilizing anchors and attractors, along with the AAUI(Anchor--Attractor Utilization Index) metric to measure memory activation rates. Finally, through experiments with various base models and paradigms, we validate A^3-Bench and analyze how memory activation impacts reasoning performance, providing insights into memory-driven scientific reasoning.

Reasoning is a distinctive human capacity, enabling us to address complex problems by breaking them down into a series of manageable cognitive steps. Yet, complex logical reasoning is still cumbersome for language models. Based on the dual process theory in cognitive science, we are the first to unravel the cognitive reasoning abilities of language models. Our framework employs an iterative methodology to construct a Cognitive Tree (CogTree). The root node of this tree represents the initial query, while the leaf nodes consist of straightforward questions that can be answered directly. This construction involves two main components: the implicit extraction module (referred to as the intuitive system) and the explicit reasoning module (referred to as the reflective system). The intuitive system rapidly generates multiple responses by utilizing in-context examples, while the reflective system scores these responses using comparative learning. The scores guide the intuitive system in its subsequent generation step. Our experimental results on two popular and challenging reasoning tasks indicate that it is possible to achieve a performance level comparable to that of GPT-3.5 (with 175B parameters), using a significantly smaller language model that contains fewer parameters (<=7B) than 5% of GPT-3.5.

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, e.g., Large Language Models (LLMs), there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

Mathematical reasoning is a fundamental aspect of human intelligence and is applicable in various fields, including science, engineering, finance, and everyday life. The development of artificial intelligence (AI) systems capable of solving math problems and proving theorems has garnered significant interest in the fields of machine learning and natural language processing. For example, mathematics serves as a testbed for aspects of reasoning that are challenging for powerful deep learning models, driving new algorithmic and modeling advances. On the other hand, recent advances in large-scale neural language models have opened up new benchmarks and opportunities to use deep learning for mathematical reasoning. In this survey paper, we review the key tasks, datasets, and methods at the intersection of mathematical reasoning and deep learning over the past decade. We also evaluate existing benchmarks and methods, and discuss future research directions in this domain.

Hierarchical reasoning model (HRM) achieves extraordinary performance on various reasoning tasks, significantly outperforming large language model-based reasoners. To understand the strengths and potential failure modes of HRM, we conduct a mechanistic study on its reasoning patterns and find three surprising facts: (a) Failure of extremely simple puzzles, e.g., HRM can fail on a puzzle with only one unknown cell. We attribute this failure to the violation of the fixed point property, a fundamental assumption of HRM. (b) "Grokking" dynamics in reasoning steps, i.e., the answer is not improved uniformly, but instead there is a critical reasoning step that suddenly makes the answer correct; (c) Existence of multiple fixed points. HRM "guesses" the first fixed point, which could be incorrect, and gets trapped there for a while or forever. All facts imply that HRM appears to be "guessing" instead of "reasoning". Leveraging this "guessing" picture, we propose three strategies to scale HRM's guesses: data augmentation (scaling the quality of guesses), input perturbation (scaling the number of guesses by leveraging inference randomness), and model bootstrapping (scaling the number of guesses by leveraging training randomness). On the practical side, by combining all methods, we develop Augmented HRM, boosting accuracy on Sudoku-Extreme from 54.5% to 96.9%. On the scientific side, our analysis provides new insights into how reasoning models "reason".

Language has long been conceived as an essential tool for human reasoning. The breakthrough of Large Language Models (LLMs) has sparked significant research interest in leveraging these models to tackle complex reasoning tasks. Researchers have moved beyond simple autoregressive token generation by introducing the concept of "thought" -- a sequence of tokens representing intermediate steps in the reasoning process. This innovative paradigm enables LLMs' to mimic complex human reasoning processes, such as tree search and reflective thinking. Recently, an emerging trend of learning to reason has applied reinforcement learning (RL) to train LLMs to master reasoning processes. This approach enables the automatic generation of high-quality reasoning trajectories through trial-and-error search algorithms, significantly expanding LLMs' reasoning capacity by providing substantially more training data. Furthermore, recent studies demonstrate that encouraging LLMs to "think" with more tokens during test-time inference can further significantly boost reasoning accuracy. Therefore, the train-time and test-time scaling combined to show a new research frontier -- a path toward Large Reasoning Model. The introduction of OpenAI's o1 series marks a significant milestone in this research direction. In this survey, we present a comprehensive review of recent progress in LLM reasoning. We begin by introducing the foundational background of LLMs and then explore the key technical components driving the development of large reasoning models, with a focus on automated data construction, learning-to-reason techniques, and test-time scaling. We also analyze popular open-source projects at building large reasoning models, and conclude with open challenges and future research directions.

The ability to organically reason over and with both text and images is a pillar of human intelligence, yet the ability of Multimodal Large Language Models (MLLMs) to perform such multimodal reasoning remains under-explored. Existing benchmarks often emphasize text-dominant reasoning or rely on shallow visual cues, failing to adequately assess integrated visual and textual reasoning. We introduce EMMA (Enhanced MultiModal reAsoning), a benchmark targeting organic multimodal reasoning across mathematics, physics, chemistry, and coding. EMMA tasks demand advanced cross-modal reasoning that cannot be addressed by reasoning independently in each modality, offering an enhanced test suite for MLLMs' reasoning capabilities. Our evaluation of state-of-the-art MLLMs on EMMA reveals significant limitations in handling complex multimodal and multi-step reasoning tasks, even with advanced techniques like Chain-of-Thought prompting and test-time compute scaling underperforming. These findings underscore the need for improved multimodal architectures and training paradigms to close the gap between human and model reasoning in multimodality.

Reasoning lies at the heart of intelligence, shaping the ability to make decisions, draw conclusions, and generalize across domains. In artificial intelligence, as systems increasingly operate in open, uncertain, and multimodal environments, reasoning becomes essential for enabling robust and adaptive behavior. Large Multimodal Reasoning Models (LMRMs) have emerged as a promising paradigm, integrating modalities such as text, images, audio, and video to support complex reasoning capabilities and aiming to achieve comprehensive perception, precise understanding, and deep reasoning. As research advances, multimodal reasoning has rapidly evolved from modular, perception-driven pipelines to unified, language-centric frameworks that offer more coherent cross-modal understanding. While instruction tuning and reinforcement learning have improved model reasoning, significant challenges remain in omni-modal generalization, reasoning depth, and agentic behavior. To address these issues, we present a comprehensive and structured survey of multimodal reasoning research, organized around a four-stage developmental roadmap that reflects the field's shifting design philosophies and emerging capabilities. First, we review early efforts based on task-specific modules, where reasoning was implicitly embedded across stages of representation, alignment, and fusion. Next, we examine recent approaches that unify reasoning into multimodal LLMs, with advances such as Multimodal Chain-of-Thought (MCoT) and multimodal reinforcement learning enabling richer and more structured reasoning chains. Finally, drawing on empirical insights from challenging benchmarks and experimental cases of OpenAI O3 and O4-mini, we discuss the conceptual direction of native large multimodal reasoning models (N-LMRMs), which aim to support scalable, agentic, and adaptive reasoning and planning in complex, real-world environments.

Large language models (LLMs) achieve promising performance, yet their ability to reason remains poorly understood. Existing evaluations largely emphasize task-level accuracy, often conflating pattern matching with reasoning capability. We present X-RAY, an explainable reasoning analysis system that maps the LLM reasoning capability using calibrated, formally verified probes. We model reasoning capability as a function of extractable structure, operationalized through formal properties such as constraint interaction, reasoning depth, and solution-space geometry. X-Ray generates probes via formal tools with controlled structural variations, enabling precise isolation of incremental structural information through formal calibration and verification. We evaluate state-of-the-art LLMs on problems ranging from junior-level to advanced in mathematics, physics, and chemistry. Our analysis reveals a systematic asymmetry in LLM reasoning: models are relatively robust to constraint refinement, where additional conditions shrink an existing solution space, but degrade sharply under solution-space restructuring, where modifications alter the underlying structural form of the solution manifold. Moreover, calibrated formal probes differentiate models that appear indistinguishable on standard benchmarks and reveal failure modes that are structurally interpretable rather than opaque. Beyond evaluation, our framework is contamination-free and supports the training and testing of reasoning models.

Mathematical reasoning---a core ability within human intelligence---presents some unique challenges as a domain: we do not come to understand and solve mathematical problems primarily on the back of experience and evidence, but on the basis of inferring, learning, and exploiting laws, axioms, and symbol manipulation rules. In this paper, we present a new challenge for the evaluation (and eventually the design) of neural architectures and similar system, developing a task suite of mathematics problems involving sequential questions and answers in a free-form textual input/output format. The structured nature of the mathematics domain, covering arithmetic, algebra, probability and calculus, enables the construction of training and test splits designed to clearly illuminate the capabilities and failure-modes of different architectures, as well as evaluate their ability to compose and relate knowledge and learned processes. Having described the data generation process and its potential future expansions, we conduct a comprehensive analysis of models from two broad classes of the most powerful sequence-to-sequence architectures and find notable differences in their ability to resolve mathematical problems and generalize their knowledge.

Human reasoning relies on constructing and manipulating mental models-simplified internal representations of situations that we use to understand and solve problems. Conceptual diagrams (for example, sketches drawn by humans to aid reasoning) externalize these mental models, abstracting irrelevant details to efficiently capture relational and spatial information. In contrast, Large Language Models (LLMs) and Large Multimodal Models (LMMs) predominantly reason through textual representations, limiting their effectiveness in complex multi-step combinatorial and planning tasks. In this paper, we propose a zero-shot fully automatic framework that enables LMMs to reason through multiple chains of self-generated intermediate conceptual diagrams, significantly enhancing their combinatorial planning capabilities. Our approach does not require any human initialization beyond a natural language description of the task. It integrates both textual and diagrammatic reasoning within an optimized graph-of-thought inference framework, enhanced by beam search and depth-wise backtracking. Evaluated on multiple challenging PDDL planning domains, our method substantially improves GPT-4o's performance (for example, from 35.5% to 90.2% in Blocksworld). On more difficult planning domains with solution depths up to 40, our approach outperforms even the o1-preview reasoning model (for example, over 13% improvement in Parking). These results highlight the value of conceptual diagrams as a complementary reasoning medium in LMMs.

Recent advances in large language models (LLMs) have demonstrated notable progress on many mathematical benchmarks. However, most of these benchmarks only feature problems grounded in junior and senior high school subjects, contain only multiple-choice questions, and are confined to a limited scope of elementary arithmetic operations. To address these issues, this paper introduces an expansive benchmark suite SciBench that aims to systematically examine the reasoning capabilities required for complex scientific problem solving. SciBench contains two carefully curated datasets: an open set featuring a range of collegiate-level scientific problems drawn from mathematics, chemistry, and physics textbooks, and a closed set comprising problems from undergraduate-level exams in computer science and mathematics. Based on the two datasets, we conduct an in-depth benchmark study of two representative LLMs with various prompting strategies. The results reveal that current LLMs fall short of delivering satisfactory performance, with an overall score of merely 35.80%. Furthermore, through a detailed user study, we categorize the errors made by LLMs into ten problem-solving abilities. Our analysis indicates that no single prompting strategy significantly outperforms others and some strategies that demonstrate improvements in certain problem-solving skills result in declines in other skills. We envision that SciBench will catalyze further developments in the reasoning abilities of LLMs, thereby ultimately contributing to scientific research and discovery.

Reasoning is a core capability in artificial intelligence systems, for which large language models (LLMs) have recently shown remarkable progress. However, most work focuses exclusively on deductive reasoning, which is problematic since other types of reasoning are also essential in solving real-world problems, and they are less explored. This work focuses on evaluating LLMs' inductive and abductive reasoning capabilities. We introduce a programmable and synthetic dataset, InAbHyD (pronounced in-a-bid), where each reasoning example consists of an incomplete world model and a set of observations. The task for the intelligent agent is to produce hypotheses to explain observations under the incomplete world model to solve each reasoning example. We propose a new metric to evaluate the quality of hypotheses based on Occam's Razor. We evaluate and analyze some state-of-the-art LLMs. Our analysis shows that LLMs can perform inductive and abductive reasoning in simple scenarios, but struggle with complex world models and producing high-quality hypotheses, even with popular reasoning-enhancing techniques such as in-context learning and RLVR.

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it is natural to explore how a general-purpose language model can be efficiently adapted for molecular science applications. In this work, we introduce BioMedGPT-Mol, a molecular language model designed to support molecular understanding and generation tasks. By curating and unifying existing public instruction datasets, we have assembled a large-scale, comprehensive, and high-quality training dataset. The model is then fine-tuned through a meticulously designed multi-task learning framework. On a consolidated benchmark derived from LlaSMol, TOMG-Bench, and MuMOInstruct, BioMedGPT-Mol achieves remarkable performance. Our experimental results demonstrate that a general-purpose reasoning model can be effectively and efficiently post-trained into a professional molecular language model through a well-structured multi-task curriculum. Leveraging these capabilities, we further apply the model to multi-step retrosynthetic planning, achieving state-of-the-art performance on RetroBench and demonstrating its superior efficacy as an end-to-end retrosynthetic planner. We anticipate that our approach can be extended to other biomedical scientific domains.

The reasoning ability of large language models (LLMs) can be unleashed with reinforcement learning (RL) (OpenAI, 2024; DeepSeek-AI et al., 2025a; Zeng et al., 2025). The success of existing RL attempts in LLMs usually relies on high-quality samples of thousands or beyond. In this paper, we challenge fundamental assumptions about data requirements in RL for LLMs by demonstrating the remarkable effectiveness of one-shot learning. Specifically, we introduce polymath learning, a framework for designing one training sample that elicits multidisciplinary impact. We present three key findings: (1) A single, strategically selected math reasoning sample can produce significant performance improvements across multiple domains, including physics, chemistry, and biology with RL; (2) The math skills salient to reasoning suggest the characteristics of the optimal polymath sample; and (3) An engineered synthetic sample that integrates multidiscipline elements outperforms training with individual samples that naturally occur. Our approach achieves superior performance to training with larger datasets across various reasoning benchmarks, demonstrating that sample quality and design, rather than quantity, may be the key to unlock enhanced reasoning capabilities in language models. Our results suggest a shift, dubbed as sample engineering, toward precision engineering of training samples rather than simply increasing data volume.

Recent work has shown that language models (LMs) have strong multi-step (i.e., procedural) reasoning capabilities. However, it is unclear whether LMs perform these tasks by cheating with answers memorized from pretraining corpus, or, via a multi-step reasoning mechanism. In this paper, we try to answer this question by exploring a mechanistic interpretation of LMs for multi-step reasoning tasks. Concretely, we hypothesize that the LM implicitly embeds a reasoning tree resembling the correct reasoning process within it. We test this hypothesis by introducing a new probing approach (called MechanisticProbe) that recovers the reasoning tree from the model's attention patterns. We use our probe to analyze two LMs: GPT-2 on a synthetic task (k-th smallest element), and LLaMA on two simple language-based reasoning tasks (ProofWriter & AI2 Reasoning Challenge). We show that MechanisticProbe is able to detect the information of the reasoning tree from the model's attentions for most examples, suggesting that the LM indeed is going through a process of multi-step reasoning within its architecture in many cases.

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

Large Language Models (LLMs) have succeeded remarkably in various natural language processing (NLP) tasks, yet their reasoning capabilities remain a fundamental challenge. While LLMs exhibit impressive fluency and factual recall, their ability to perform complex reasoning-spanning logical deduction, mathematical problem-solving, commonsense inference, and multi-step reasoning-often falls short of human expectations. This survey provides a comprehensive review of emerging techniques enhancing reasoning in LLMs. We categorize existing methods into key approaches, including prompting strategies (e.g., Chain-of-Thought reasoning, Self-Consistency, and Tree-of-Thought reasoning), architectural innovations (e.g., retrieval-augmented models, modular reasoning networks, and neuro-symbolic integration), and learning paradigms (e.g., fine-tuning with reasoning-specific datasets, reinforcement learning, and self-supervised reasoning objectives). Additionally, we explore evaluation frameworks used to assess reasoning in LLMs and highlight open challenges, such as hallucinations, robustness, and reasoning generalization across diverse tasks. By synthesizing recent advancements, this survey aims to provide insights into promising directions for future research and practical applications of reasoning-augmented LLMs.

Recent Large Language Models (LLMs) have reported high accuracy on reasoning benchmarks. However, it is still unclear whether the observed results arise from true reasoning or from statistical recall of the training set. Inspired by the ladder of causation (Pearl, 2009) and its three levels (associations, interventions and counterfactuals), this paper introduces RE-IMAGINE, a framework to characterize a hierarchy of reasoning ability in LLMs, alongside an automated pipeline to generate problem variations at different levels of the hierarchy. By altering problems in an intermediate symbolic representation, RE-IMAGINE generates arbitrarily many problems that are not solvable using memorization alone. Moreover, the framework is general and can work across reasoning domains, including math, code, and logic. We demonstrate our framework on four widely-used benchmarks to evaluate several families of LLMs, and observe reductions in performance when the models are queried with problem variations. These assessments indicate a degree of reliance on statistical recall for past performance, and open the door to further research targeting skills across the reasoning hierarchy.

Deductive reasoning is a crucial logical capability that assists us in solving complex problems based on existing knowledge. Although augmented by Chain-of-Thought prompts, Large Language Models (LLMs) might not follow the correct reasoning paths. Enhancing the deductive reasoning abilities of LLMs, and leveraging their extensive built-in knowledge for various reasoning tasks, remains an open question. Attempting to mimic the human deductive reasoning paradigm, we propose a multi-stage Syllogistic-Reasoning Framework of Thought (SR-FoT) that enables LLMs to perform syllogistic deductive reasoning to handle complex knowledge-based reasoning tasks. Our SR-FoT begins by interpreting the question and then uses the interpretation and the original question to propose a suitable major premise. It proceeds by generating and answering minor premise questions in two stages to match the minor premises. Finally, it guides LLMs to use the previously generated major and minor premises to perform syllogistic deductive reasoning to derive the answer to the original question. Extensive and thorough experiments on knowledge-based reasoning tasks have demonstrated the effectiveness and advantages of our SR-FoT.

Recent advances in visual reasoning (VR), particularly with the aid of Large Vision-Language Models (VLMs), show promise but require access to large-scale datasets and face challenges such as high computational costs and limited generalization capabilities. Compositional visual reasoning approaches have emerged as effective strategies; however, they heavily rely on the commonsense knowledge encoded in Large Language Models (LLMs) to perform planning, reasoning, or both, without considering the effect of their decisions on the visual reasoning process, which can lead to errors or failed procedures. To address these challenges, we introduce HYDRA, a multi-stage dynamic compositional visual reasoning framework designed for reliable and incrementally progressive general reasoning. HYDRA integrates three essential modules: a planner, a Reinforcement Learning (RL) agent serving as a cognitive controller, and a reasoner. The planner and reasoner modules utilize an LLM to generate instruction samples and executable code from the selected instruction, respectively, while the RL agent dynamically interacts with these modules, making high-level decisions on selection of the best instruction sample given information from the historical state stored through a feedback loop. This adaptable design enables HYDRA to adjust its actions based on previous feedback received during the reasoning process, leading to more reliable reasoning outputs and ultimately enhancing its overall effectiveness. Our framework demonstrates state-of-the-art performance in various VR tasks on four different widely-used datasets.

Self-distillation has emerged as an effective post-training paradigm for LLMs, often improving performance while shortening reasoning traces. However, in mathematical reasoning, we find that it can reduce response length while degrading performance. We trace this degradation to the suppression of epistemic verbalization - the model's expression of uncertainty during reasoning. Through controlled experiments varying conditioning context richness and task coverage, we show that conditioning the teacher on rich information suppresses uncertainty expression, enabling rapid in-domain optimization with limited task coverage but harming OOD performance, where unseen problems benefit from expressing uncertainty and adjusting accordingly. Across Qwen3-8B, DeepSeek-Distill-Qwen-7B, and Olmo3-7B-Instruct, we observe performance drops of up to 40%. Our findings highlight that exposing appropriate levels of uncertainty is crucial for robust reasoning and underscore the importance of optimizing reasoning behavior beyond merely reinforcing correct answer traces.

With the widespread adoption of large language models (LLMs), hallucinations, which are non-factual fabrications in model outputs, have become serious concerns. Reasoning capabilities have received attention as a self-verification process to improve output reliability. However, the effect of reasoning within a closed system where LLMs cannot rely on external tools or knowledge has yet to be clarified. We therefore conduct experiments under strict constraints (recommending peer-reviewed journal articles in computer science) to examine the effect of reasoning across multiple models (GPT-5.2 and Gemini 3 Flash). Our results reveal a problematic trade-off between constraint compliance and factual accuracy. Non-reasoning models exhibit high constraint violation rates (66-75%) but maintain factual accuracy, while reasoning models reduce violations (13-26%) but systematically distort known facts to satisfy constraints and increase complete fabrication. This trade-off pattern is consistent across both models despite different architectures, indicating a fundamental limitation of reasoning. Furthermore, reasoning does not uniformly improve output authenticity: effects diverge by model, reflecting different allocations of the compliance-truthfulness trade-off. These findings challenge the assumption that reasoning universally improves reliability: reasoning models trade honest constraint violations for detection-resistant distortions.

Reasoning is central to a wide range of intellectual activities, and while the capabilities of large language models (LLMs) continue to advance, their performance in reasoning tasks remains limited. The processes and mechanisms underlying reasoning are not yet fully understood, but key elements include path exploration, selection of relevant knowledge, and multi-step inference. Problems are solved through the synthesis of these components. In this paper, we propose a benchmark that focuses on a specific aspect of reasoning ability: the direct evaluation of multi-step inference. To this end, we design a special reasoning task where multi-step inference is specifically focused by largely eliminating path exploration and implicit knowledge utilization. Our dataset comprises pairs of explicit instructions and corresponding questions, where the procedures necessary for solving the questions are entirely detailed within the instructions. This setup allows models to solve problems solely by following the provided directives. By constructing problems that require varying numbers of steps to solve and evaluating responses at each step, we enable a thorough assessment of state-of-the-art LLMs' ability to follow instructions. To ensure the robustness of our evaluation, we include multiple distinct tasks. Furthermore, by comparing accuracy across tasks, utilizing step-aware metrics, and applying separately defined measures of complexity, we conduct experiments that offer insights into the capabilities and limitations of LLMs in reasoning tasks. Our findings have significant implications for the development of LLMs and highlight areas for future research in advancing their reasoning abilities. Our dataset is available at https://huggingface.co/datasets/ifujisawa/procbench and code at https://github.com/ifujisawa/proc-bench.

Reasoning is a cognitive process of using evidence to reach a sound conclusion. The reasoning capability is essential for large language models (LLMs) to serve as the brain of the artificial general intelligence agent. Recent studies reveal that fine-tuning LLMs on data with the chain of thought (COT) reasoning process can significantly enhance their reasoning capabilities. However, we find that the fine-tuned LLMs suffer from an Assessment Misalignment problem, i.e., they frequently assign higher scores to subpar COTs, leading to potential limitations in their reasoning abilities. To address this problem, we introduce an Alignment Fine-Tuning (AFT) paradigm, which involves three steps: 1) fine-tuning LLMs with COT training data; 2) generating multiple COT responses for each question, and categorizing them into positive and negative ones based on whether they achieve the correct answer; 3) calibrating the scores of positive and negative responses given by LLMs with a novel constraint alignment loss. Specifically, the constraint alignment loss has two objectives: a) Alignment, which guarantees that positive scores surpass negative scores to encourage answers with high-quality COTs; b) Constraint, which keeps the negative scores confined to a reasonable range to prevent the model degradation. Beyond just the binary positive and negative feedback, the constraint alignment loss can be seamlessly adapted to the ranking situations when ranking feedback is accessible. Furthermore, we also delve deeply into recent ranking-based alignment methods, such as DPO, RRHF, and PRO, and discover that the constraint, which has been overlooked by these approaches, is also crucial for their performance. Extensive experiments on four reasoning benchmarks with both binary and ranking feedback demonstrate the effectiveness of AFT.

Large reasoning models (LRMs) achieve strong performance on mathematical reasoning tasks, often attributed to their capability to generate explicit chain-of-thought (CoT) explanations. However, recent work shows that LRMs often arrive at the correct answer before completing these textual reasoning steps, indicating the presence of latent reasoning -- internal, non-verbal computation encoded in hidden states. While this phenomenon has been explored in English, its multilingual behavior remains largely unknown. In this paper, we conduct a systematic investigation of multilingual latent reasoning in LRMs across 11 languages. Using a truncation-based strategy, we examine how the correct answer emerges as the model is given only partial reasoning traces, allowing us to measure stepwise latent prediction formation. Our results reveal clear evidence of multilingual latent reasoning, though unevenly: strong in resource-rich languages, weaker in low-resource ones, and broadly less observable on harder benchmarks. To understand whether these differences reflect distinct internal mechanisms, we further perform representational analyses. Despite surface-level disparities, we find that the internal evolution of predictions is highly consistent across languages and broadly aligns with English -- a pattern suggesting an English-centered latent reasoning pathway.

Large language models (LLMs) have exhibited complex reasoning abilities by generating question rationales and demonstrated exceptional performance in natural language processing (NLP) tasks. However, these reasoning capabilities generally emerge in models with tens of billions of parameters, creating significant computational challenges for real-world deployment. Recent research has concentrated on improving open-source smaller models through knowledge distillation (KD) from commercial LLMs. Nevertheless, most of these studies rely solely on the responses from one single LLM as the gold rationale for training. In this paper, we introduce a novel Mistake-Aware Peer-Review Distillation (MAPD) approach: 1) Instead of merely obtaining gold rationales from teachers, our method asks teachers to identify and explain the student's mistakes, providing customized instruction learning data. 2) We design a simulated peer-review process between teacher LLMs, which selects only the generated rationales above the acceptance threshold. This reduces the chance of teachers guessing correctly with flawed rationale, improving instructional data quality. Comprehensive experiments and analysis on mathematical, commonsense, and logical reasoning tasks demonstrate the effectiveness of our method.

To augment language models with the ability to reason, researchers usually prompt or finetune them to produce chain of thought reasoning steps before producing the final answer. However, although people use natural language to reason effectively, it may be that LMs could reason more effectively with some intermediate computation that is not in natural language. In this work, we explore an alternative reasoning approach: instead of explicitly producing the chain of thought reasoning steps, we use the language model's internal hidden states to perform implicit reasoning. The implicit reasoning steps are distilled from a teacher model trained on explicit chain-of-thought reasoning, and instead of doing reasoning "horizontally" by producing intermediate words one-by-one, we distill it such that the reasoning happens "vertically" among the hidden states in different layers. We conduct experiments on a multi-digit multiplication task and a grade school math problem dataset and find that this approach enables solving tasks previously not solvable without explicit chain-of-thought, at a speed comparable to no chain-of-thought.

Understanding how Large Language Models (LLMs) perform logical reasoning internally remains a fundamental challenge. While prior mechanistic studies focus on identifying taskspecific circuits, they leave open the question of what computational strategies LLMs employ for propositional reasoning. We address this gap through comprehensive analysis of Qwen3 (8B and 14B) on PropLogic-MI, a controlled dataset spanning 11 propositional logic rule categories across one-hop and two-hop reasoning. Rather than asking ''which components are necessary,'' we ask ''how does the model organize computation?'' Our analysis reveals a coherent computational architecture comprising four interlocking mechanisms: Staged Computation (layer-wise processing phases), Information Transmission (information flow aggregation at boundary tokens), Fact Retrospection (persistent re-access of source facts), and Specialized Attention Heads (functionally distinct head types). These mechanisms generalize across model scales, rule types, and reasoning depths, providing mechanistic evidence that LLMs employ structured computational strategies for logical reasoning.

We study reasoning for accessing world knowledge stored in a language model's parameters. For example, recalling that Canberra is Australia's capital may benefit from thinking through major cities and the concept of purpose-built capitals. While reasoning language models are trained via reinforcement learning to produce reasoning traces on tasks such as mathematics, they may not reason well for accessing their own world knowledge. We first find that models do not generate their best world knowledge reasoning by default: adding a simple "think step-by-step" cue demonstrates statistically significant improvement in knowledge recall but not math. Motivated by this, we propose training models to reason over their parametric knowledge using world-knowledge question answering as a verifiable reward. After reinforcement learning on TriviaQA (+9.9%), performance also improves on Natural Questions, HotpotQA, SimpleQA, and StrategyQA by 4.2%, 2.1%, 0.6%, and 3.0%, respectively. Reasoning models are under-optimized for parametric knowledge access, but can be easily trained to reason better.

In this work, we use large language models (LLMs) to augment and accelerate research on the P versus NP problem, one of the most important open problems in theoretical computer science and mathematics. Specifically, we propose Socratic reasoning, a general framework that promotes in-depth thinking with LLMs for complex problem-solving. Socratic reasoning encourages LLMs to recursively discover, solve, and integrate problems while facilitating self-evaluation and refinement. Our pilot study on the P vs. NP problem shows that GPT-4 successfully produces a proof schema and engages in rigorous reasoning throughout 97 dialogue turns, concluding "P neq NP", which is in alignment with (Xu and Zhou, 2023). The investigation uncovers novel insights within the extensive solution space of LLMs, shedding light on LLM for Science.

This work introduces Symbolic-Aided Chain-of-Thought (CoT), an improved approach to standard CoT, for logical reasoning in large language models (LLMs). The key idea is to integrate lightweight symbolic representations into few-shot prompts, structuring the inference steps with a consistent strategy to make reasoning patterns more explicit within a non-iterative reasoning process. By incorporating these symbolic structures, our method preserves the generalizability of standard prompting techniques while enhancing the transparency, interpretability, and analyzability of LLM logical reasoning. Extensive experiments on four well-known logical reasoning benchmarks -- ProofWriter, FOLIO, ProntoQA, and LogicalDeduction, which cover diverse reasoning scenarios -- demonstrate the effectiveness of the proposed approach, particularly in complex reasoning tasks that require navigating multiple constraints or rules. Notably, Symbolic-Aided CoT consistently improves LLMs' reasoning capabilities across various model sizes and significantly outperforms conventional CoT on three out of four datasets, ProofWriter, ProntoQA, and LogicalDeduction.

Logical reasoning, i.e., deductively inferring the truth value of a conclusion from a set of premises, is an important task for artificial intelligence with wide potential impacts on science, mathematics, and society. While many prompting-based strategies have been proposed to enable Large Language Models (LLMs) to do such reasoning more effectively, they still appear unsatisfactory, often failing in subtle and unpredictable ways. In this work, we investigate the validity of instead reformulating such tasks as modular neurosymbolic programming, which we call LINC: Logical Inference via Neurosymbolic Computation. In LINC, the LLM acts as a semantic parser, translating premises and conclusions from natural language to expressions in first-order logic. These expressions are then offloaded to an external theorem prover, which symbolically performs deductive inference. Leveraging this approach, we observe significant performance gains on FOLIO and a balanced subset of ProofWriter for three different models in nearly all experimental conditions we evaluate. On ProofWriter, augmenting the comparatively small open-source StarCoder+ (15.5B parameters) with LINC even outperforms GPT-3.5 and GPT-4 with Chain-of-Thought (CoT) prompting by an absolute 38% and 10%, respectively. When used with GPT-4, LINC scores 26% higher than CoT on ProofWriter while performing comparatively on FOLIO. Further analysis reveals that although both methods on average succeed roughly equally often on this dataset, they exhibit distinct and complementary failure modes. We thus provide promising evidence for how logical reasoning over natural language can be tackled through jointly leveraging LLMs alongside symbolic provers. All corresponding code is publicly available at https://github.com/benlipkin/linc

Scientific texts often convey authority due to their technical language and complex data. However, this complexity can sometimes lead to the spread of misinformation. Non-experts are particularly susceptible to misleading claims based on scientific tables due to their high information density and perceived credibility. Existing table claim verification models, including state-of-the-art large language models (LLMs), often struggle with precise fine-grained reasoning, resulting in errors and a lack of precision in verifying scientific claims. Inspired by Cognitive Load Theory, we propose that enhancing a model's ability to interpret table-based claims involves reducing cognitive load by developing modular, reusable reasoning components (i.e., atomic skills). We introduce a skill-chaining schema that dynamically composes these skills to facilitate more accurate and generalizable reasoning with a reduced cognitive load. To evaluate this, we create SciAtomicBench, a cross-domain benchmark with fine-grained reasoning annotations. With only 350 fine-tuning examples, our model trained by atomic reasoning outperforms GPT-4o's chain-of-thought method, achieving state-of-the-art results with far less training data.

Human reasoning often involves working over limited information to arrive at probabilistic conclusions. In its simplest form, this involves making an inference that is not strictly entailed by a premise, but rather only likely given the premise. While reasoning LLMs have demonstrated strong performance on logical and mathematical tasks, their behavior on such open-ended, non-deterministic inferences remains largely unexplored. We introduce ProbCOPA, a dataset of 210 handcrafted probabilistic inferences in English, each annotated for inference likelihood by 25--30 human participants. We find that human responses are graded and varied, revealing probabilistic judgments of the inferences in our dataset. Comparing these judgments with responses from eight state-of-the-art reasoning LLMs, we show that models consistently fail to produce human-like distributions. Finally, analyzing LLM reasoning chains, we find evidence of a common reasoning pattern used to evaluate such inferences. Our findings reveal persistent differences between humans and LLMs, and underscore the need to evaluate reasoning beyond deterministic settings.

Large Language Models (LLMs) are highly proficient in language-based tasks. Their language capabilities have positioned them at the forefront of the future AGI (Artificial General Intelligence) race. However, on closer inspection, Valmeekam et al. (2024); Zecevic et al. (2023); Wu et al. (2024) highlight a significant gap between their language proficiency and reasoning abilities. Reasoning in LLMs and Vision Language Models (VLMs) aims to bridge this gap by enabling these models to think and re-evaluate their actions and responses. Reasoning is an essential capability for complex problem-solving and a necessary step toward establishing trust in Artificial Intelligence (AI). This will make AI suitable for deployment in sensitive domains, such as healthcare, banking, law, defense, security etc. In recent times, with the advent of powerful reasoning models like OpenAI O1 and DeepSeek R1, reasoning endowment has become a critical research topic in LLMs. In this paper, we provide a detailed overview and comparison of existing reasoning techniques and present a systematic survey of reasoning-imbued language models. We also study current challenges and present our findings.

Reasoning is a fundamental capability for solving complex multi-step problems, particularly in visual contexts where sequential step-wise understanding is essential. Existing approaches lack a comprehensive framework for evaluating visual reasoning and do not emphasize step-wise problem-solving. To this end, we propose a comprehensive framework for advancing step-by-step visual reasoning in large language models (LMMs) through three key contributions. First, we introduce a visual reasoning benchmark specifically designed to evaluate multi-step reasoning tasks. The benchmark presents a diverse set of challenges with eight different categories ranging from complex visual perception to scientific reasoning with over 4k reasoning steps in total, enabling robust evaluation of LLMs' abilities to perform accurate and interpretable visual reasoning across multiple steps. Second, we propose a novel metric that assesses visual reasoning quality at the granularity of individual steps, emphasizing both correctness and logical coherence. The proposed metric offers deeper insights into reasoning performance compared to traditional end-task accuracy metrics. Third, we present a new multimodal visual reasoning model, named LlamaV-o1, trained using a multi-step curriculum learning approach, where tasks are progressively organized to facilitate incremental skill acquisition and problem-solving. The proposed LlamaV-o1 is designed for multi-step reasoning and learns step-by-step through a structured training paradigm. Extensive experiments show that our LlamaV-o1 outperforms existing open-source models and performs favorably against close-source proprietary models. Compared to the recent Llava-CoT, our LlamaV-o1 achieves an average score of 67.3 with an absolute gain of 3.8\% across six benchmarks while being 5 times faster during inference scaling. Our benchmark, model, and code are publicly available.

Achieving human-level intelligence requires refining the transition from the fast, intuitive System 1 to the slower, more deliberate System 2 reasoning. While System 1 excels in quick, heuristic decisions, System 2 relies on logical reasoning for more accurate judgments and reduced biases. Foundational Large Language Models (LLMs) excel at fast decision-making but lack the depth for complex reasoning, as they have not yet fully embraced the step-by-step analysis characteristic of true System 2 thinking. Recently, reasoning LLMs like OpenAI's o1/o3 and DeepSeek's R1 have demonstrated expert-level performance in fields such as mathematics and coding, closely mimicking the deliberate reasoning of System 2 and showcasing human-like cognitive abilities. This survey begins with a brief overview of the progress in foundational LLMs and the early development of System 2 technologies, exploring how their combination has paved the way for reasoning LLMs. Next, we discuss how to construct reasoning LLMs, analyzing their features, the core methods enabling advanced reasoning, and the evolution of various reasoning LLMs. Additionally, we provide an overview of reasoning benchmarks, offering an in-depth comparison of the performance of representative reasoning LLMs. Finally, we explore promising directions for advancing reasoning LLMs and maintain a real-time https://github.com/zzli2022/Awesome-Slow-Reason-System{GitHub Repository} to track the latest developments. We hope this survey will serve as a valuable resource to inspire innovation and drive progress in this rapidly evolving field.

Recent scholarship on reasoning in LLMs has supplied evidence of impressive performance and flexible adaptation to machine generated or human feedback. Nonmonotonic reasoning, crucial to human cognition for navigating the real world, remains a challenging, yet understudied task. In this work, we study nonmonotonic reasoning capabilities of seven state-of-the-art LLMs in one abstract and one commonsense reasoning task featuring generics, such as 'Birds fly', and exceptions, 'Penguins don't fly' (see Fig. 1). While LLMs exhibit reasoning patterns in accordance with human nonmonotonic reasoning abilities, they fail to maintain stable beliefs on truth conditions of generics at the addition of supporting examples ('Owls fly') or unrelated information ('Lions have manes'). Our findings highlight pitfalls in attributing human reasoning behaviours to LLMs, as well as assessing general capabilities, while consistent reasoning remains elusive.

In the rapidly evolving field of Large Language Models (LLMs), there is a critical need to thoroughly analyze their capabilities and risks. Central to our investigation are two novel elements. Firstly, it is the innovative parallels between the statistical patterns of word relationships within LLMs and Martin Heidegger's concepts of "ready-to-hand" and "present-at-hand," which encapsulate the utilitarian and scientific altitudes humans employ in interacting with the world. This comparison lays the groundwork for positioning LLMs as the digital counterpart to the Faculty of Verbal Knowledge, shedding light on their capacity to emulate certain facets of human reasoning. Secondly, a structural analysis of human reasoning, viewed through Heidegger's notion of truth as "unconcealment" is conducted This foundational principle enables us to map out the inputs and outputs of the reasoning system and divide reasoning into four distinct categories. Respective cognitive faculties are delineated, allowing us to place LLMs within the broader schema of human reasoning, thus clarifying their strengths and inherent limitations. Our findings reveal that while LLMs possess the capability for Direct Explicative Reasoning and Pseudo Rational Reasoning, they fall short in authentic rational reasoning and have no creative reasoning capabilities, due to the current lack of many analogous AI models such as the Faculty of Judgement. The potential and risks of LLMs when they are augmented with other AI technologies are also evaluated. The results indicate that although LLMs have achieved proficiency in some reasoning abilities, the aspiration to match or exceed human intellectual capabilities is yet unattained. This research not only enriches our comprehension of LLMs but also propels forward the discourse on AI's potential and its bounds, paving the way for future explorations into AI's evolving landscape.

When presented with questions involving visual thinking, humans naturally switch reasoning modalities, often forming mental images or drawing visual aids. Large language models have shown promising results in arithmetic and symbolic reasoning by expressing intermediate reasoning in text as a chain of thought, yet struggle to extend this capability to answer text queries that are easily solved by visual reasoning, even with extensive multimodal pretraining. We introduce a simple method, whiteboard-of-thought prompting, to unlock the visual reasoning capabilities of multimodal large language models across modalities. Whiteboard-of-thought prompting provides multimodal large language models with a metaphorical `whiteboard' to draw out reasoning steps as images, then returns these images back to the model for further processing. We find this can be accomplished with no demonstrations or specialized modules, instead leveraging models' existing ability to write code with libraries such as Matplotlib and Turtle. This simple approach shows state-of-the-art results on four difficult natural language tasks that involve visual and spatial reasoning. We identify multiple settings where GPT-4o using chain-of-thought fails dramatically, including more than one where it achieves 0% accuracy, while whiteboard-of-thought enables up to 92% accuracy in these same settings. We present a detailed exploration of where the technique succeeds as well as its sources of error.

Large Reasoning Models (LRMs) have shown impressive capabilities in multi-step reasoning tasks. However, alongside these successes, a more deceptive form of model error has emerged--Reasoning Hallucination--where logically coherent but factually incorrect reasoning traces lead to persuasive yet faulty conclusions. Unlike traditional hallucinations, these errors are embedded within structured reasoning, making them more difficult to detect and potentially more harmful. In this work, we investigate reasoning hallucinations from a mechanistic perspective. We propose the Reasoning Score, which quantifies the depth of reasoning by measuring the divergence between logits obtained from projecting late layers of LRMs to the vocabulary space, effectively distinguishing shallow pattern-matching from genuine deep reasoning. Using this score, we conduct an in-depth analysis on the ReTruthQA dataset and identify two key reasoning hallucination patterns: early-stage fluctuation in reasoning depth and incorrect backtracking to flawed prior steps. These insights motivate our Reasoning Hallucination Detection (RHD) framework, which achieves state-of-the-art performance across multiple domains. To mitigate reasoning hallucinations, we further introduce GRPO-R, an enhanced reinforcement learning algorithm that incorporates step-level deep reasoning rewards via potential-based shaping. Our theoretical analysis establishes stronger generalization guarantees, and experiments demonstrate improved reasoning quality and reduced hallucination rates.

Large language models (LLMs) have dramatically enhanced the field of language intelligence, as demonstrably evidenced by their formidable empirical performance across a spectrum of complex reasoning tasks. Additionally, theoretical proofs have illuminated their emergent reasoning capabilities, providing a compelling showcase of their advanced cognitive abilities in linguistic contexts. Critical to their remarkable efficacy in handling complex reasoning tasks, LLMs leverage the intriguing chain-of-thought (CoT) reasoning techniques, obliging them to formulate intermediate steps en route to deriving an answer. The CoT reasoning approach has not only exhibited proficiency in amplifying reasoning performance but also in enhancing interpretability, controllability, and flexibility. In light of these merits, recent research endeavors have extended CoT reasoning methodologies to nurture the development of autonomous language agents, which adeptly adhere to language instructions and execute actions within varied environments. This survey paper orchestrates a thorough discourse, penetrating vital research dimensions, encompassing: (i) the foundational mechanics of CoT techniques, with a focus on elucidating the circumstances and justification behind its efficacy; (ii) the paradigm shift in CoT; and (iii) the burgeoning of language agents fortified by CoT approaches. Prospective research avenues envelop explorations into generalization, efficiency, customization, scaling, and safety. This paper caters to a wide audience, including beginners seeking comprehensive knowledge of CoT reasoning and language agents, as well as experienced researchers interested in foundational mechanics and engaging in cutting-edge discussions on these topics. A repository for the related papers is available at https://github.com/Zoeyyao27/CoT-Igniting-Agent.

Large Language Models (LLMs) have demonstrated exceptional proficiency in mathematical reasoning tasks due to their extensive parameter counts and training on vast datasets. Despite these capabilities, deploying LLMs is hindered by their computational demands. Distilling LLM mathematical reasoning into Smaller Language Models (SLMs) has emerged as a solution to this challenge, although these smaller models often suffer from errors in calculation and semantic understanding. Prior work has proposed Program-of-Thought Distillation (PoTD) to avoid calculation error. To further address semantic understanding errors, we propose Key-Point-Driven Mathematical Reasoning Distillation (KPDD). KPDD enhances the reasoning performance of SLMs by breaking down the problem-solving process into three stages: Core Question Extraction, Problem-Solving Information Extraction, and Step-by-Step Solution. This method is further divided into KPDD-CoT, which generates Chain-of-Thought rationales, and KPDD-PoT, which creates Program-of-Thought rationales. The experiment results show that KPDD-CoT significantly improves reasoning abilities, while KPDD-PoT achieves state-of-the-art performance in mathematical reasoning tasks. Our approach effectively mitigates misunderstanding errors, advancing the deployment of efficient and capable SLMs.

Mathematical reasoning, a core ability of human intelligence, presents unique challenges for machines in abstract thinking and logical reasoning. Recent large pre-trained language models such as GPT-3 have achieved remarkable progress on mathematical reasoning tasks written in text form, such as math word problems (MWP). However, it is unknown if the models can handle more complex problems that involve math reasoning over heterogeneous information, such as tabular data. To fill the gap, we present Tabular Math Word Problems (TabMWP), a new dataset containing 38,431 open-domain grade-level problems that require mathematical reasoning on both textual and tabular data. Each question in TabMWP is aligned with a tabular context, which is presented as an image, semi-structured text, and a structured table. There are two types of questions: free-text and multi-choice, and each problem is annotated with gold solutions to reveal the multi-step reasoning process. We evaluate different pre-trained models on TabMWP, including the GPT-3 model in a few-shot setting. As earlier studies suggest, since few-shot GPT-3 relies on the selection of in-context examples, its performance is unstable and can degrade to near chance. The unstable issue is more severe when handling complex problems like TabMWP. To mitigate this, we further propose a novel approach, PromptPG, which utilizes policy gradient to learn to select in-context examples from a small amount of training data and then constructs the corresponding prompt for the test example. Experimental results show that our method outperforms the best baseline by 5.31% on the accuracy metric and reduces the prediction variance significantly compared to random selection, which verifies its effectiveness in selecting in-context examples.

We present ScienceWorld, a benchmark to test agents' scientific reasoning abilities in a new interactive text environment at the level of a standard elementary school science curriculum. Despite the transformer-based progress seen in question-answering and scientific text processing, we find that current models cannot reason about or explain learned science concepts in novel contexts. For instance, models can easily answer what the conductivity of a known material is but struggle when asked how they would conduct an experiment in a grounded environment to find the conductivity of an unknown material. This begs the question of whether current models are simply retrieving answers by way of seeing a large number of similar examples or if they have learned to reason about concepts in a reusable manner. We hypothesize that agents need to be grounded in interactive environments to achieve such reasoning capabilities. Our experiments provide empirical evidence supporting this hypothesis -- showing that a 1.5 million parameter agent trained interactively for 100k steps outperforms a 11 billion parameter model statically trained for scientific question-answering and reasoning from millions of expert demonstrations.

Reasoning-enhanced large language models (RLLMs), whether explicitly trained for reasoning or prompted via chain-of-thought (CoT), have achieved state-of-the-art performance on many complex reasoning tasks. However, we uncover a surprising and previously overlooked phenomenon: explicit CoT reasoning can significantly degrade instruction-following accuracy. Evaluating 15 models on two benchmarks: IFEval (with simple, rule-verifiable constraints) and ComplexBench (with complex, compositional constraints), we consistently observe performance drops when CoT prompting is applied. Through large-scale case studies and an attention-based analysis, we identify common patterns where reasoning either helps (e.g., with formatting or lexical precision) or hurts (e.g., by neglecting simple constraints or introducing unnecessary content). We propose a metric, constraint attention, to quantify model focus during generation and show that CoT reasoning often diverts attention away from instruction-relevant tokens. To mitigate these effects, we introduce and evaluate four strategies: in-context learning, self-reflection, self-selective reasoning, and classifier-selective reasoning. Our results demonstrate that selective reasoning strategies, particularly classifier-selective reasoning, can substantially recover lost performance. To our knowledge, this is the first work to systematically expose reasoning-induced failures in instruction-following and offer practical mitigation strategies.

Logical reasoning is a fundamental aspect of human intelligence and an essential capability for multimodal large language models (MLLMs). Despite the significant advancement in multimodal reasoning, existing benchmarks fail to comprehensively evaluate their reasoning abilities due to the lack of explicit categorization for logical reasoning types and an unclear understanding of reasoning. To address these issues, we introduce MME-Reasoning, a comprehensive benchmark designed to evaluate the reasoning ability of MLLMs, which covers all three types of reasoning (i.e., inductive, deductive, and abductive) in its questions. We carefully curate the data to ensure that each question effectively evaluates reasoning ability rather than perceptual skills or knowledge breadth, and extend the evaluation protocols to cover the evaluation of diverse questions. Our evaluation reveals substantial limitations of state-of-the-art MLLMs when subjected to holistic assessments of logical reasoning capabilities. Even the most advanced MLLMs show limited performance in comprehensive logical reasoning, with notable performance imbalances across reasoning types. In addition, we conducted an in-depth analysis of approaches such as ``thinking mode'' and Rule-based RL, which are commonly believed to enhance reasoning abilities. These findings highlight the critical limitations and performance imbalances of current MLLMs in diverse logical reasoning scenarios, providing comprehensive and systematic insights into the understanding and evaluation of reasoning capabilities.

Large language models (LLMs) have achieved strong performance on medical exam-style tasks, motivating growing interest in their deployment in real-world clinical settings. However, clinical decision-making is inherently safety-critical, context-dependent, and conducted under evolving evidence. In such situations, reliable LLM performance depends not on factual recall alone, but on robust medical reasoning. In this work, we present a comprehensive review of medical reasoning with LLMs. Grounded in cognitive theories of clinical reasoning, we conceptualize medical reasoning as an iterative process of abduction, deduction, and induction, and organize existing methods into seven major technical routes spanning training-based and training-free approaches. We further conduct a unified cross-benchmark evaluation of representative medical reasoning models under a consistent experimental setting, enabling a more systematic and comparable assessment of the empirical impact of existing methods. To better assess clinically grounded reasoning, we introduce MR-Bench, a benchmark derived from real-world hospital data. Evaluations on MR-Bench expose a pronounced gap between exam-level performance and accuracy on authentic clinical decision tasks. Overall, this survey provides a unified view of existing medical reasoning methods, benchmarks, and evaluation practices, and highlights key gaps between current model performance and the requirements of real-world clinical reasoning.

The rapid advancement of large language models (LLMs) has significantly enhanced their reasoning abilities, enabling increasingly complex tasks. However, these capabilities often diminish in smaller, more computationally efficient models like GPT-2. Recent research shows that reasoning distillation can help small models acquire reasoning capabilities, but most existing methods focus primarily on improving teacher-generated reasoning paths. Our observations reveal that small models can generate high-quality reasoning paths during sampling, even without chain-of-thought prompting, though these paths are often latent due to their low probability under standard decoding strategies. To address this, we propose Self-Enhanced Reasoning Training (SERT), which activates and leverages latent reasoning capabilities in small models through self-training on filtered, self-generated reasoning paths under zero-shot conditions. Experiments using OpenAI's GPT-3.5 as the teacher model and GPT-2 models as the student models demonstrate that SERT enhances the reasoning abilities of small models, improving their performance in reasoning distillation.

Studies have underscored how, regardless of the recent breakthrough and swift advances in AI research, even state-of-the-art Large Language models (LLMs) continue to struggle when performing logical and mathematical reasoning. The results seem to suggest that LLMs still work as (highly advanced) data pattern identifiers, scoring poorly when attempting to generalise and solve reasoning problems the models have never previously seen or that are not close to samples presented in their training data. To address this compelling concern, this paper makes use of the notion of critical questions from the literature on argumentation theory, focusing in particular on Toulmin's model of argumentation. We show that employing these critical questions can improve the reasoning capabilities of LLMs. By probing the rationale behind the models' reasoning process, the LLM can assess whether some logical mistake is occurring and correct it before providing the final reply to the user prompt. The underlying idea is drawn from the gold standard of any valid argumentative procedure: the conclusion is valid if it is entailed by accepted premises. Or, to paraphrase such Aristotelian principle in a real-world approximation, characterised by incomplete information and presumptive logic, the conclusion is valid if not proved otherwise. This approach successfully steers the models' output through a reasoning pipeline, resulting in better performance against the baseline and its Chain-of-Thought (CoT) implementation. To this end, an extensive evaluation of the proposed approach on the MT-Bench Reasoning and Math tasks across a range of LLMs is provided.

With the emergence of advanced reasoning models like OpenAI o3 and DeepSeek-R1, large language models (LLMs) have demonstrated remarkable reasoning capabilities. However, their ability to perform rigorous logical reasoning remains an open question. This survey synthesizes recent advancements in logical reasoning within LLMs, a critical area of AI research. It outlines the scope of logical reasoning in LLMs, its theoretical foundations, and the benchmarks used to evaluate reasoning proficiency. We analyze existing capabilities across different reasoning paradigms - deductive, inductive, abductive, and analogical - and assess strategies to enhance reasoning performance, including data-centric tuning, reinforcement learning, decoding strategies, and neuro-symbolic approaches. The review concludes with future directions, emphasizing the need for further exploration to strengthen logical reasoning in AI systems.

Recently, Chain-of-Thought (CoT) prompting has delivered success on complex reasoning tasks, which aims at designing a simple prompt like ``Let's think step by step'' or multiple in-context exemplars with well-designed rationales to elicit Large Language Models (LLMs) to generate intermediate reasoning steps. However, the generated rationales often come with mistakes, making unfactual and unfaithful reasoning chains. To mitigate this brittleness, we propose a novel Chain-of-Knowledge (CoK) prompting, where we aim at eliciting LLMs to generate explicit pieces of knowledge evidence in the form of structure triple. This is inspired by our human behaviors, i.e., we can draw a mind map or knowledge map as the reasoning evidence in the brain before answering a complex question. Benefiting from CoK, we additionally introduce a F^2-Verification method to estimate the reliability of the reasoning chains in terms of factuality and faithfulness. For the unreliable response, the wrong evidence can be indicated to prompt the LLM to rethink. Extensive experiments demonstrate that our method can further improve the performance of commonsense, factual, symbolic, and arithmetic reasoning tasks.