Mol-R1: Towards Explicit Long-CoT Reasoning in Molecule Discovery

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.

LoSemB: Logic-Guided Semantic Bridging for Inductive Tool Retrieval

Tool learning has emerged as a promising paradigm for large language models (LLMs) to solve many real-world tasks. Nonetheless, with the tool repository rapidly expanding, it is impractical to contain all tools within the limited input length of LLMs. To alleviate these issues, researchers have explored incorporating a tool retrieval module to select the most relevant tools or represent tools as unique tokens within LLM parameters. However, most state-of-the-art methods are under transductive settings, assuming all tools have been observed during training. Such a setting deviates from reality as the real-world tool repository is evolving and incorporates new tools frequently. When dealing with these unseen tools, which refer to tools not encountered during the training phase, these methods are limited by two key issues, including the large distribution shift and the vulnerability of similarity-based retrieval. To this end, inspired by human cognitive processes of mastering unseen tools through discovering and applying the logical information from prior experience, we introduce a novel Logic-Guided Semantic Bridging framework for inductive tool retrieval, namely, LoSemB, which aims to mine and transfer latent logical information for inductive tool retrieval without costly retraining. Specifically, LoSemB contains a logic-based embedding alignment module to mitigate distribution shifts and implements a relational augmented retrieval mechanism to reduce the vulnerability of similarity-based retrieval. Extensive experiments demonstrate that LoSemB achieves advanced performance in inductive settings while maintaining desirable effectiveness in the transductive setting.

You Don't Need Pre-built Graphs for RAG: Retrieval Augmented Generation with Adaptive Reasoning Structures

Large language models (LLMs) often suffer from hallucination, generating factually incorrect statements when handling questions beyond their knowledge and perception. Retrieval-augmented generation (RAG) addresses this by retrieving query-relevant contexts from knowledge bases to support LLM reasoning. Recent advances leverage pre-constructed graphs to capture the relational connections among distributed documents, showing remarkable performance in complex tasks. However, existing Graph-based RAG (GraphRAG) methods rely on a costly process to transform the corpus into a graph, introducing overwhelming token cost and update latency. Moreover, real-world queries vary in type and complexity, requiring different logic structures for accurate reasoning. The pre-built graph may not align with these required structures, resulting in ineffective knowledge retrieval. To this end, we propose a \textbf{\underline{Logic}}-aware \textbf{\underline{R}}etrieval-\textbf{\underline{A}}ugmented \textbf{\underline{G}}eneration framework (\textbf{LogicRAG}) that dynamically extracts reasoning structures at inference time to guide adaptive retrieval without any pre-built graph. LogicRAG begins by decomposing the input query into a set of subproblems and constructing a directed acyclic graph (DAG) to model the logical dependencies among them. To support coherent multi-step reasoning, LogicRAG then linearizes the graph using topological sort, so that subproblems can be addressed in a logically consistent order. Besides, LogicRAG applies graph pruning to reduce redundant retrieval and uses context pruning to filter irrelevant context, significantly reducing the overall token cost. Extensive experiments demonstrate that LogicRAG achieves both superior performance and efficiency compared to state-of-the-art baselines.

LAG: Logic-Augmented Generation from a Cartesian Perspective

Large language models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks, yet exhibit critical limitations in knowledge-intensive tasks, often generating hallucinations when faced with questions requiring specialized expertise. While retrieval-augmented generation (RAG) mitigates this by integrating external knowledge, it struggles with complex reasoning scenarios due to its reliance on direct semantic retrieval and lack of structured logical organization. Inspired by Cartesian principles from \textit{Discours de la m\'ethode}, this paper introduces Logic-Augmented Generation (LAG), a novel paradigm that reframes knowledge augmentation through systematic question decomposition and dependency-aware reasoning. Specifically, LAG first decomposes complex questions into atomic sub-questions ordered by logical dependencies. It then resolves these sequentially, using prior answers to guide context retrieval for subsequent sub-questions, ensuring stepwise grounding in logical chain. To prevent error propagation, LAG incorporates a logical termination mechanism that halts inference upon encountering unanswerable sub-questions and reduces wasted computation on excessive reasoning. Finally, it synthesizes all sub-resolutions to generate verified responses. Experiments on four benchmark datasets demonstrate that LAG significantly enhances reasoning robustness, reduces hallucination, and aligns LLM problem-solving with human cognition, offering a principled alternative to existing RAG systems.

Enhancing Large Language Models with Reliable Knowledge Graphs

Large Language Models (LLMs) have demonstrated remarkable capabilities in text generation and understanding, yet their reliance on implicit, unstructured knowledge often leads to factual inaccuracies and limited interpretability. Knowledge Graphs (KGs), with their structured, relational representations, offer a promising solution to ground LLMs in verified knowledge. However, their potential remains constrained by inherent noise, incompleteness, and the complexity of integrating their rigid structure with the flexible reasoning of LLMs. This thesis presents a systematic framework to address these limitations, advancing the reliability of KGs and their synergistic integration with LLMs through five interconnected contributions. This thesis addresses these challenges through a cohesive framework that enhances LLMs by refining and leveraging reliable KGs. First, we introduce contrastive error detection, a structure-based method to identify incorrect facts in KGs. This approach is extended by an attribute-aware framework that unifies structural and semantic signals for error correction. Next, we propose an inductive completion model that further refines KGs by completing the missing relationships in evolving KGs. Building on these refined KGs, KnowGPT integrates structured graph reasoning into LLMs through dynamic prompting, improving factual grounding. These contributions form a systematic pipeline (from error detection to LLM integration), demonstrating that reliable KGs significantly enhance the robustness, interpretability, and adaptability of LLMs.

Reliable Reasoning Path: Distilling Effective Guidance for LLM Reasoning with Knowledge Graphs

Large language models (LLMs) often struggle with knowledge-intensive tasks due to a lack of background knowledge and a tendency to hallucinate. To address these limitations, integrating knowledge graphs (KGs) with LLMs has been intensively studied. Existing KG-enhanced LLMs focus on supplementary factual knowledge, but still struggle with solving complex questions. We argue that refining the relationships among facts and organizing them into a logically consistent reasoning path is equally important as factual knowledge itself. Despite their potential, extracting reliable reasoning paths from KGs poses the following challenges: the complexity of graph structures and the existence of multiple generated paths, making it difficult to distinguish between useful and redundant ones. To tackle these challenges, we propose the RRP framework to mine the knowledge graph, which combines the semantic strengths of LLMs with structural information obtained through relation embedding and bidirectional distribution learning. Additionally, we introduce a rethinking module that evaluates and refines reasoning paths according to their significance. Experimental results on two public datasets show that RRP achieves state-of-the-art performance compared to existing baseline methods. Moreover, RRP can be easily integrated into various LLMs to enhance their reasoning abilities in a plug-and-play manner. By generating high-quality reasoning paths tailored to specific questions, RRP distills effective guidance for LLM reasoning.

FaithfulRAG: Fact-Level Conflict Modeling for Context-Faithful Retrieval-Augmented Generation

Large language models (LLMs) augmented with retrieval systems have demonstrated significant potential in handling knowledge-intensive tasks. However, these models often struggle with unfaithfulness issues, generating outputs that either ignore the retrieved context or inconsistently blend it with the LLM`s parametric knowledge. This issue is particularly severe in cases of knowledge conflict, where the retrieved context conflicts with the model`s parametric knowledge. While existing faithful RAG approaches enforce strict context adherence through well-designed prompts or modified decoding strategies, our analysis reveals a critical limitation: they achieve faithfulness by forcibly suppressing the model`s parametric knowledge, which undermines the model`s internal knowledge structure and increases the risk of misinterpreting the context. To this end, this paper proposes FaithfulRAG, a novel framework that resolves knowledge conflicts by explicitly modeling discrepancies between the model`s parametric knowledge and retrieved context. Specifically, FaithfulRAG identifies conflicting knowledge at the fact level and designs a self-thinking process, allowing LLMs to reason about and integrate conflicting facts before generating responses. Extensive experiments demonstrate that our method outperforms state-of-the-art methods. The code is available at https:// github.com/DeepLearnXMU/Faithful-RAG

When to use Graphs in RAG: A Comprehensive Analysis for Graph Retrieval-Augmented Generation

Graph retrieval-augmented generation (GraphRAG) has emerged as a powerful paradigm for enhancing large language models (LLMs) with external knowledge. It leverages graphs to model the hierarchical structure between specific concepts, enabling more coherent and effective knowledge retrieval for accurate reasoning.Despite its conceptual promise, recent studies report that GraphRAG frequently underperforms vanilla RAG on many real-world tasks. This raises a critical question: Is GraphRAG really effective, and in which scenarios do graph structures provide measurable benefits for RAG systems? To address this, we propose GraphRAG-Bench, a comprehensive benchmark designed to evaluate GraphRAG models onboth hierarchical knowledge retrieval and deep contextual reasoning. GraphRAG-Bench features a comprehensive dataset with tasks of increasing difficulty, coveringfact retrieval, complex reasoning, contextual summarization, and creative generation, and a systematic evaluation across the entire pipeline, from graph constructionand knowledge retrieval to final generation. Leveraging this novel benchmark, we systematically investigate the conditions when GraphRAG surpasses traditional RAG and the underlying reasons for its success, offering guidelines for its practical application. All related resources and analyses are collected for the community at https://github.com/GraphRAG-Bench/GraphRAG-Benchmark.

Nondeterministic Polynomial-time Problem Challenge: An Ever-Scaling Reasoning Benchmark for LLMs

Reasoning is the fundamental capability of large language models (LLMs). Due to the rapid progress of LLMs, there are two main issues of current benchmarks: i) these benchmarks can be crushed in a short time (less than 1 year), and ii) these benchmarks may be easily hacked. To handle these issues, we propose the ever-scalingness for building the benchmarks which are uncrushable, unhackable, auto-verifiable and general. This paper presents Nondeterministic Polynomial-time Problem Challenge (NPPC), an ever-scaling reasoning benchmark for LLMs. Specifically, the NPPC has three main modules: i) npgym, which provides a unified interface of 25 well-known NP-complete problems and can generate any number of instances with any levels of complexities, ii) npsolver: which provides a unified interface to evaluate the problem instances with both online and offline models via APIs and local deployments, respectively, and iii) npeval: which provides the comprehensive and ready-to-use tools to analyze the performances of LLMs over different problems, the number of tokens, the aha moments, the reasoning errors and the solution errors. Extensive experiments over widely-used LLMs demonstrate: i) NPPC can successfully decrease the performances of advanced LLMs' performances to below 10%, demonstrating that NPPC is uncrushable, ii) DeepSeek-R1, Claude-3.7-Sonnet, and o1/o3-mini are the most powerful LLMs, where DeepSeek-R1 outperforms Claude-3.7-Sonnet and o1/o3-mini in most NP-complete problems considered, and iii) the numbers of tokens, aha moments in the advanced LLMs, e.g., Claude-3.7-Sonnet and DeepSeek-R1, are observed first to increase and then decrease when the problem instances become more and more difficult. We believe that NPPC is the first ever-scaling reasoning benchmark, serving as the uncrushable and unhackable testbed for LLMs toward artificial general intelligence (AGI).

Knapsack Optimization-based Schema Linking for LLM-based Text-to-SQL Generation

Generating SQLs from user queries is a long-standing challenge, where the accuracy of initial schema linking significantly impacts subsequent SQL generation performance. However, current schema linking models still struggle with missing relevant schema elements or an excess of redundant ones. A crucial reason for this is that commonly used metrics, recall and precision, fail to capture relevant element missing and thus cannot reflect actual schema linking performance. Motivated by this, we propose an enhanced schema linking metric by introducing a restricted missing indicator. Accordingly, we introduce Knapsack optimization-based Schema Linking Agent (KaSLA), a plug-in schema linking agent designed to prevent the missing of relevant schema elements while minimizing the inclusion of redundant ones. KaSLA employs a hierarchical linking strategy that first identifies the optimal table linking and subsequently links columns within the selected table to reduce linking candidate space. In each linking process, it utilize a knapsack optimization approach to link potentially relevant elements while accounting for a limited tolerance of potential redundant ones.With this optimization, KaSLA-1.6B achieves superior schema linking results compared to large-scale LLMs, including deepseek-v3 with state-of-the-art (SOTA) schema linking method. Extensive experiments on Spider and BIRD benchmarks verify that KaSLA can significantly improve the SQL generation performance of SOTA text-to-SQL models by substituting their schema linking processes.