arXiv subjects

Yongrui Chen

Publications and source records attributed to Yongrui Chen.

At least 19 recordsLinked to original sources

arXiv2026

Code as Representation: A Compilable Parsing Paradigm for Academic Documents

Academic papers are a primary carrier of scientific knowledge, yet most of this knowledge remains locked in PDFs that are optimized for human reading rather than machine use. For Multimodal Large Language Models (MLLMs), the core challenge is not only perception, but representation: scientific pages interleave text with Structured Academic Elements (SAEs) such as tables, formulas, charts, and pseudocode, whose structure, data, and logic are poorly preserved by common surrogates like Markdown. We therefore propose Compilable Academic Document Parsing (CADP), a paradigm that reconstructs a full page as contextual \LaTeX{} plus executable Python, so that structure-preserving elements and executable chart representations can be reconstructed, recompiled, and directly verified against the source page. To support this setting, we introduce CADP-Bench, an expert-verified benchmark of full academic pages containing tightly coupled text and multiple SAE types, evaluated through a re-injection compilation protocol. We further study current capabilities using SOTA MLLMs and an exploratory multi-agent baseline that incorporates common agentic techniques. Results show that even frontier models still struggle to produce high-fidelity executable reconstructions, highlighting substantial room for improvement in structure-aware scientific document parsing. CADP-Bench is released for future research.

cs.CV↗

arXiv2026

Pandora: Leveraging Code-driven Knowledge Transfer for Unified Structured Knowledge Reasoning

Unified Structured Knowledge Reasoning (USKR) aims to answer natural language questions by using structured sources such as tables, databases, and knowledge graphs in a unified way. Existing USKR methods rely on task-specific strategies or bespoke representations, which hinder their ability to dismantle barriers between different SKR tasks, thereby constraining their overall performance in cross-task scenarios. In this paper, we introduce \textsc{Pandora}, a novel USKR framework that addresses the limitations of existing methods by leveraging two key innovations. First, we propose a code-based unified knowledge representation using \textsc{Python}'s \textsc{Pandas} API, which aligns seamlessly with the pre-training of LLMs. This representation facilitates a cohesive approach to handling different structured knowledge sources. Building on this foundation, we employ knowledge transfer to bolster the unified reasoning process of LLMs by automatically building cross-task memory. By adaptively correcting reasoning using feedback from code execution, \textsc{Pandora} showcases impressive unified reasoning capabilities. Extensive experiments on six widely used benchmarks across three SKR tasks demonstrate that \textsc{Pandora} outperforms existing unified reasoning frameworks and competes effectively with task-specific methods.

cs.CL↗

arXiv2026

KG2Code: Bridging Knowledge Graphs and Large Language Models via Executable Code for Question Answering

Recent research has explored the integration of knowledge graphs (KGs) with large language models (LLMs) to enhance their performance on downstream knowledge-intensive tasks, particularly knowledge graph question answering (KGQA). Existing approaches primarily combine LLMs with KGs through retrieval-augmented generation (RAG)-based, agent-based, and SPARQL-based methods. Although these methods have achieved notable success, they still suffer from several limitations, including structural information loss, unfaithful reasoning, and limited flexibility and generalization. To address these challenges, this paper proposes KG2Code, a novel approach that transforms knowledge graphs into a code-based representation, preserving structural semantics while naturally aligning with the code-aware pretraining of modern LLMs. Based on KG2Code, KG2Code-QA is further introduced as a KGQA framework that formulates KGQA as a code generation task. This formulation enables the generation of verifiable reasoning traces and executable code, thereby substantially mitigating the impact of hallucinations. In addition, an automated pipeline is developed to construct a large-scale, high-quality code corpus for effectively training open-source LLMs on KG2Code-QA. After training, LLMs are able to perform KGQA in zero-shot scenarios. Extensive experiments demonstrate that the proposed approach significantly outperforms existing KG-enhanced LLM methods for KGQA, while exhibiting strong generalization to unseen KGs. The code and data are available at Github.

cs.AI↗

arXiv2026

StressEval: Failure-Driven Dynamic Benchmarking for Knowledge-Intensive Reasoning in Large Language Models

Static benchmarks for LLMs are increasingly compromised by contamination and overfitting especially on knowledge intensive reasoning tasks While recent dynamic benchmarks can alleviate staleness they often increase difficulty at the expense of answerability and controllability In this paper we propose StressEval a failure driven data synthesis framework that turns observed model failures into dynamic challenging and controllable test instances StressEval consists of three stages first it constructs a semi structured difficulty card that identifies the failed reasoning step and its root cause second it applies a dual perspective instance synthesis method that targets both knowledge gaps and reasoning breakdowns while preserving the underlying difficulty factors and third it applies a gating mechanism to retain only grounded unambiguous instances Seeding from multiple knowledge intensive reasoning datasets we employ StressEval to build Dynamic OneEval a focused suite of challenging dynamic benchmark Across several state of the art LLMs Dynamic OneEval yields substantially larger performance drops than the original benchmarks while retaining explicit difficulty factors enabling more actionable iteration

cs.CL↗

arXiv2026

After Retrieval, Before Generation: Enhancing the Trustworthiness of Large Language Models in Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) is a promising paradigm, yet its trustworthiness remains a critical concern. A major vulnerability arises prior to generation: models often fail to balance parametric (internal) and retrieved (external) knowledge, particularly when the two sources conflict or are unreliable. To analyze these scenarios comprehensively, we construct the Trustworthiness Response Dataset (TRD) with 36,266 questions spanning four RAG settings. We reveal that existing approaches address isolated scenarios-prioritizing one knowledge source, naively merging both, or refusing answers-but lack a unified framework to handle different real-world conditions simultaneously. Therefore, we propose the BRIDGE framework, which dynamically determines a comprehensive response strategy of large language models (LLMs). BRIDGE leverages an adaptive weighting mechanism named soft bias to guide knowledge collection, followed by a Maximum Soft-bias Decision Tree to evaluate knowledge and select optimal response strategies (trust internal/external knowledge, or refuse). Experiments show BRIDGE outperforms baselines by 5-15% in accuracy while maintaining balanced performance across all scenarios. Our work provides an effective solution for LLMs' trustworthy responses in real-world RAG applications.

cs.CL↗

arXiv2026

ELAIPBench: A Benchmark for Expert-Level Artificial Intelligence Paper Understanding

While large language models (LLMs) excel at many domain-specific tasks, their ability to deeply comprehend and reason about full-length academic papers remains underexplored. Existing benchmarks often fall short of capturing such depth, either due to surface-level question design or unreliable evaluation metrics. To address this gap, we introduce ELAIPBench, a benchmark curated by domain experts to evaluate LLMs' comprehension of artificial intelligence (AI) research papers. Developed through an incentive-driven, adversarial annotation process, ELAIPBench features 403 multiple-choice questions from 137 papers. It spans three difficulty levels and emphasizes non-trivial reasoning rather than shallow retrieval. Our experiments show that the best-performing LLM achieves an accuracy of only 39.95%, far below human performance. Moreover, we observe that frontier LLMs equipped with a thinking mode or a retrieval-augmented generation (RAG) system fail to improve final results-even harming accuracy due to overthinking or noisy retrieval. These findings underscore the significant gap between current LLM capabilities and genuine comprehension of academic papers.

cs.AI↗

arXiv2025

Question Answering Over Spatio-Temporal Knowledge Graph

Spatio-temporal knowledge graphs (STKGs) enhance traditional KGs by integrating temporal and spatial annotations, enabling precise reasoning over questions with spatio-temporal dependencies. Despite their potential, research on spatio-temporal knowledge graph question answering (STKGQA) remains limited. This is primarily due to the lack of datasets that simultaneously contain spatio-temporal information, as well as methods capable of handling implicit spatio-temporal reasoning. To bridge this gap, we introduce the spatio-temporal question answering dataset (STQAD), the first comprehensive benchmark comprising 10,000 natural language questions that require both temporal and spatial reasoning. STQAD is constructed with real-world facts containing spatio-temporal information, ensuring that the dataset reflects practical scenarios. Furthermore, our experiments reveal that existing KGQA methods underperform on STQAD, primarily due to their inability to model spatio-temporal interactions. To address this, we propose the spatio-temporal complex question answering (STCQA) method, which jointly embeds temporal and spatial features into KG representations and dynamically filters answers through constraint-aware reasoning. STCQA achieves state-of-the-art performance, significantly outperforming existing baselines. Our work not only provides a valuable resource for future research but also advances the field by offering a robust baseline for answering complex spatio-temporal questions.

cs.CL↗

arXiv2025

Harnessing Diverse Perspectives: A Multi-Agent Framework for Enhanced Error Detection in Knowledge Graphs

Knowledge graphs are widely used in industrial applications, making error detection crucial for ensuring the reliability of downstream applications. Existing error detection methods often fail to effectively utilize fine-grained subgraph information and rely solely on fixed graph structures, while also lacking transparency in their decision-making processes, which results in suboptimal detection performance. In this paper, we propose a novel Multi-Agent framework for Knowledge Graph Error Detection (MAKGED) that utilizes multiple large language models (LLMs) in a collaborative setting. By concatenating fine-grained, bidirectional subgraph embeddings with LLM-based query embeddings during training, our framework integrates these representations to produce four specialized agents. These agents utilize subgraph information from different dimensions to engage in multi-round discussions, thereby improving error detection accuracy and ensuring a transparent decision-making process. Extensive experiments on FB15K and WN18RR demonstrate that MAKGED outperforms state-of-the-art methods, enhancing the accuracy and robustness of KG evaluation. For specific industrial scenarios, our framework can facilitate the training of specialized agents using domain-specific knowledge graphs for error detection, which highlights the potential industrial application value of our framework. Our code and datasets are available at https://github.com/kse-ElEvEn/MAKGED.

cs.AI↗

arXiv2025

K-DeCore: Facilitating Knowledge Transfer in Continual Structured Knowledge Reasoning via Knowledge Decoupling

Continual Structured Knowledge Reasoning (CSKR) focuses on training models to handle sequential tasks, where each task involves translating natural language questions into structured queries grounded in structured knowledge. Existing general continual learning approaches face significant challenges when applied to this task, including poor generalization to heterogeneous structured knowledge and inefficient reasoning due to parameter growth as tasks increase. To address these limitations, we propose a novel CSKR framework, \textsc{K-DeCore}, which operates with a fixed number of tunable parameters. Unlike prior methods, \textsc{K-DeCore} introduces a knowledge decoupling mechanism that disentangles the reasoning process into task-specific and task-agnostic stages, effectively bridging the gaps across diverse tasks. Building on this foundation, \textsc{K-DeCore} integrates a dual-perspective memory consolidation mechanism for distinct stages and introduces a structure-guided pseudo-data synthesis strategy to further enhance the model's generalization capabilities. Extensive experiments on four benchmark datasets demonstrate the superiority of \textsc{K-DeCore} over existing continual learning methods across multiple metrics, leveraging various backbone large language models.

cs.CL↗

arXiv2025

Pandora: A Code-Driven Large Language Model Agent for Unified Reasoning Across Diverse Structured Knowledge

Unified Structured Knowledge Reasoning (USKR) aims to answer natural language questions (NLQs) by using structured sources such as tables, databases, and knowledge graphs in a unified way. Existing USKR methods either rely on employing task-specific strategies or custom-defined representations, which struggle to leverage the knowledge transfer between different SKR tasks or align with the prior of LLMs, thereby limiting their performance. This paper proposes a novel USKR framework named \textsc{Pandora}, which takes advantage of \textsc{Python}'s \textsc{Pandas} API to construct a unified knowledge representation for alignment with LLM pre-training. It employs an LLM to generate textual reasoning steps and executable Python code for each question. Demonstrations are drawn from a memory of training examples that cover various SKR tasks, facilitating knowledge transfer. Extensive experiments on four benchmarks involving three SKR tasks demonstrate that \textsc{Pandora} outperforms existing unified frameworks and competes effectively with task-specific methods.

cs.CL↗

arXiv2025

Large Language Models Meet Knowledge Graphs for Question Answering: Synthesis and Opportunities

Large language models (LLMs) have demonstrated remarkable performance on question-answering (QA) tasks because of their superior capabilities in natural language understanding and generation. However, LLM-based QA struggles with complex QA tasks due to poor reasoning capacity, outdated knowledge, and hallucinations. Several recent works synthesize LLMs and knowledge graphs (KGs) for QA to address the above challenges. In this survey, we propose a new structured taxonomy that categorizes the methodology of synthesizing LLMs and KGs for QA according to the categories of QA and the KG's role when integrating with LLMs. We systematically survey state-of-the-art methods in synthesizing LLMs and KGs for QA and compare and analyze these approaches in terms of strength, limitations, and KG requirements. We then align the approaches with QA and discuss how these approaches address the main challenges of different complex QA. Finally, we summarize the advancements, evaluation metrics, and benchmark datasets and highlight open challenges and opportunities.

cs.CL↗

arXiv2025

Can LLMs Evaluate Complex Attribution in QA? Automatic Benchmarking using Knowledge Graphs

Attributed Question Answering (AQA) has attracted wide attention, but there are still several limitations in evaluating the attributions, including lacking fine-grained attribution categories, relying on manual annotations, and failing to compare attributions with only subtle differences. To bridge these gaps, we introduce Complex Attributed Question Answering (CAQA), a large-scale benchmark containing comprehensive attribution categories, automatically generated using Knowledge Graphs (KGs), and complex attribution scenarios. We have conducted extensive experiments to verify the effectiveness of CAQA, including the benchmarking of 25 automatic evaluators, their comparison with human evaluators, the testing of LLM evaluators fine-tuned by CAQA and so on. These experiments also lead to a series of important findings that can benefit the future research of AQA. All the codes and data are publicly accessible at https://github.com/HuuuNan/CAQA-Benchmark.

cs.CL↗

arXiv2025

OneEval: Benchmarking LLM Knowledge-intensive Reasoning over Diverse Knowledge Bases

Large Language Models (LLMs) have demonstrated substantial progress on reasoning tasks involving unstructured text, yet their capabilities significantly deteriorate when reasoning requires integrating structured external knowledge such as knowledge graphs, code snippets, or formal logic. This limitation is partly due to the absence of benchmarks capable of systematically evaluating LLM performance across diverse structured knowledge modalities. To address this gap, we introduce \textbf{\textsc{OneEval}}, a comprehensive benchmark explicitly designed to assess the knowledge-intensive reasoning capabilities of LLMs across four structured knowledge modalities, unstructured text, knowledge graphs, code, and formal logic, and five critical domains (general knowledge, government, science, law, and programming). \textsc{OneEval} comprises 4,019 carefully curated instances and includes a challenging subset, \textsc{OneEval}\textsubscript{Hard}, consisting of 1,285 particularly difficult cases. Through extensive evaluation of 18 state-of-the-art open-source and proprietary LLMs, we establish three core findings: a) \emph{persistent limitations in structured reasoning}, with even the strongest model achieving only 32.2\% accuracy on \textsc{OneEval}\textsubscript{Hard}; b) \emph{performance consistently declines as the structural complexity of the knowledge base increases}, with accuracy dropping sharply from 53\% (textual reasoning) to 25\% (formal logic); and c) \emph{diminishing returns from extended reasoning chains}, highlighting the critical need for models to adapt reasoning depth appropriately to task complexity. We release the \textsc{OneEval} datasets, evaluation scripts, and baseline results publicly, accompanied by a leaderboard to facilitate ongoing advancements in structured knowledge reasoning.

cs.CL↗

arXiv2025

Table-r1: Self-supervised and Reinforcement Learning for Program-based Table Reasoning in Small Language Models

Table reasoning (TR) requires structured reasoning over semi-structured tabular data and remains challenging, particularly for small language models (SLMs, e.g., LLaMA-8B) due to their limited capacity compared to large LMs (LLMs, e.g., GPT-4o). To narrow this gap, we explore program-based TR (P-TR), which circumvents key limitations of text-based TR (T-TR), notably in numerical reasoning, by generating executable programs. However, applying P-TR to SLMs introduces two challenges: (i) vulnerability to heterogeneity in table layouts, and (ii) inconsistency in reasoning due to limited code generation capability. We propose Table-r1, a two-stage P-TR method designed for SLMs. Stage 1 introduces an innovative self-supervised learning task, Layout Transformation Inference, to improve tabular layout generalization from a programmatic view. Stage 2 adopts a mix-paradigm variant of Group Relative Policy Optimization, enhancing P-TR consistency while allowing dynamic fallback to T-TR when needed. Experiments on four TR benchmarks demonstrate that Table-r1 outperforms all SLM-based methods, achieving at least a 15% accuracy improvement over the base model (LLaMA-8B) across all datasets and reaching performance competitive with LLMs.

cs.LG↗

arXiv2025

Magic Mushroom: A Customizable Benchmark for Fine-grained Analysis of Retrieval Noise Erosion in RAG Systems

Retrieval-Augmented Generation (RAG) systems enhance Large Language Models (LLMs) by incorporating external retrieved information, mitigating issues such as hallucination and outdated knowledge. However, RAG systems are highly sensitive to retrieval noise prevalent in real-world scenarios. Existing benchmarks fail to emulate the complex and heterogeneous noise distributions encountered in real-world retrieval environments, undermining reliable robustness assessment. In this paper, we define four categories of retrieval noise based on linguistic properties and noise characteristics, aiming to reflect the heterogeneity of noise in real-world scenarios. Building on this, we introduce Magic Mushroom, a benchmark for replicating "magic mushroom" noise: contexts that appear relevant on the surface but covertly mislead RAG systems. Magic Mushroom comprises 7,468 single-hop and 3,925 multi-hop question-answer pairs. More importantly, Magic Mushroom enables researchers to flexibly configure combinations of retrieval noise according to specific research objectives or application scenarios, allowing for highly controlled evaluation setups. We evaluate LLM generators of varying parameter scales and classic RAG denoising strategies under diverse noise distributions to investigate their performance dynamics during progressive noise encroachment. Our analysis reveals that both generators and denoising strategies have significant room for improvement and exhibit extreme sensitivity to noise distributions. Magic Mushroom emerges as a promising tool for evaluating and advancing noise-robust RAG systems, accelerating their widespread deployment in real-world applications. The Magic Mushroom benchmark is available at https://drive.google.com/file/d/1aP5kyPuk4L-L_uoI6T9UhxuTyt8oMqjT/view?usp=sharing.

cs.CL↗

arXiv2025

Single Image Unlearning: Efficient Machine Unlearning in Multimodal Large Language Models

Machine unlearning empowers individuals with the `right to be forgotten' by removing their private or sensitive information encoded in machine learning models. However, it remains uncertain whether MU can be effectively applied to Multimodal Large Language Models (MLLMs), particularly in scenarios of forgetting the leaked visual data of concepts. To overcome the challenge, we propose an efficient method, Single Image Unlearning (SIU), to unlearn the visual recognition of a concept by fine-tuning a single associated image for few steps. SIU consists of two key aspects: (i) Constructing Multifaceted fine-tuning data. We introduce four targets, based on which we construct fine-tuning data for the concepts to be forgotten; (ii) Jointly training loss. To synchronously forget the visual recognition of concepts and preserve the utility of MLLMs, we fine-tune MLLMs through a novel Dual Masked KL-divergence Loss combined with Cross Entropy loss. Alongside our method, we establish MMUBench, a new benchmark for MU in MLLMs and introduce a collection of metrics for its evaluation. Experimental results on MMUBench show that SIU completely surpasses the performance of existing methods. Furthermore, we surprisingly find that SIU can avoid invasive membership inference attacks and jailbreak attacks. To the best of our knowledge, we are the first to explore MU in MLLMs. We will release the code and benchmark in the near future.

cs.CV↗

arXiv2024

HeGTa: Leveraging Heterogeneous Graph-enhanced Large Language Models for Few-shot Complex Table Understanding

Table understanding (TU) has achieved promising advancements, but it faces the challenges of the scarcity of manually labeled tables and the presence of complex table structures.To address these challenges, we propose HGT, a framework with a heterogeneous graph (HG)-enhanced large language model (LLM) to tackle few-shot TU tasks.It leverages the LLM by aligning the table semantics with the LLM's parametric knowledge through soft prompts and instruction turning and deals with complex tables by a multi-task pre-training scheme involving three novel multi-granularity self-supervised HG pre-training objectives.We empirically demonstrate the effectiveness of HGT, showing that it outperforms the SOTA for few-shot complex TU on several benchmarks.

cs.CL↗

arXiv2024

DoG-Instruct: Towards Premium Instruction-Tuning Data via Text-Grounded Instruction Wrapping

The improvement of LLMs' instruction-following capabilities relies heavily on the availability of high-quality instruction-response pairs. Unfortunately, the current methods used to collect the pairs suffer from either unaffordable labor costs or severe hallucinations in the self-generation of LLM. To tackle these challenges, this paper proposes a scalable solution. It involves training LLMs to generate instruction-response pairs based on human-written documents, rather than relying solely on self-generation without context. Our proposed method not only exploits the advantages of human-written documents in reducing hallucinations but also utilizes an LLM to wrap the expression of documents, which enables us to bridge the gap between various document styles and the standard AI response. Experiments demonstrate that our method outperforms existing typical methods on multiple benchmarks. In particular, compared to the best-performing baseline, the LLM trained using our generated dataset exhibits a 10\% relative improvement in performance on AlpacaEval, despite utilizing only 1/5 of its training data. Furthermore, a comprehensive manual evaluation validates the quality of the data we generated. Our trained wrapper is publicly available at https://github.com/Bahuia/Dog-Instruct.

cs.CL↗