arXiv subjects

Fangzhi Xu

Publications and source records attributed to Fangzhi Xu.

At least 37 records · Page 2Linked to original sources

arXiv2025

BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning

The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting biological phenomena, formulating hypotheses, and designing experiments. This work explores the potential of LLMs in pathway reasoning. We introduce BioMaze, a dataset with 5.1K complex pathway problems derived from real research, covering various biological contexts including natural dynamic changes, disturbances, additional intervention conditions, and multi-scale research targets. Our evaluation of methods such as CoT and graph-augmented reasoning, shows that LLMs struggle with pathway reasoning, especially in perturbed systems. To address this, we propose PathSeeker, an LLM agent that enhances reasoning through interactive subgraph-based navigation, enabling a more effective approach to handling the complexities of biological systems in a scientifically aligned manner. The dataset and code are available at https://github.com/zhao-ht/BioMaze.

cs.LG↗

arXiv2025

Towards Unified Neurosymbolic Reasoning on Knowledge Graphs

Knowledge Graph (KG) reasoning has received significant attention in the fields of artificial intelligence and knowledge engineering, owing to its ability to autonomously deduce new knowledge and consequently enhance the availability and precision of downstream applications. However, current methods predominantly concentrate on a single form of neural or symbolic reasoning, failing to effectively integrate the inherent strengths of both approaches. Furthermore, the current prevalent methods primarily focus on addressing a single reasoning scenario, presenting limitations in meeting the diverse demands of real-world reasoning tasks. Unifying the neural and symbolic methods, as well as diverse reasoning scenarios in one model is challenging as there is a natural representation gap between symbolic rules and neural networks, and diverse scenarios exhibit distinct knowledge structures and specific reasoning objectives. To address these issues, we propose a unified neurosymbolic reasoning framework, namely Tunsr, for KG reasoning. Tunsr first introduces a consistent structure of reasoning graph that starts from the query entity and constantly expands subsequent nodes by iteratively searching posterior neighbors. Based on it, a forward logic message-passing mechanism is proposed to update both the propositional representations and attentions, as well as first-order logic (FOL) representations and attentions of each node. In this way, Tunsr conducts the transformation of merging multiple rules by merging possible relations at each step. Finally, the FARI algorithm is proposed to induce FOL rules by constantly performing attention calculations over the reasoning graph. Extensive experimental results on 19 datasets of four reasoning scenarios (transductive, inductive, interpolation, and extrapolation) demonstrate the effectiveness of Tunsr.

cs.AI↗

arXiv2025

OS-Genesis: Automating GUI Agent Trajectory Construction via Reverse Task Synthesis

Graphical User Interface (GUI) agents powered by Vision-Language Models (VLMs) have demonstrated human-like computer control capability. Despite their utility in advancing digital automation, a critical bottleneck persists: collecting high-quality trajectory data for training. Common practices for collecting such data rely on human supervision or synthetic data generation through executing pre-defined tasks, which are either resource-intensive or unable to guarantee data quality. Moreover, these methods suffer from limited data diversity and significant gaps between synthetic data and real-world environments. To address these challenges, we propose OS-Genesis, a novel GUI data synthesis pipeline that reverses the conventional trajectory collection process. Instead of relying on pre-defined tasks, OS-Genesis enables agents first to perceive environments and perform step-wise interactions, then retrospectively derive high-quality tasks to enable trajectory-level exploration. A trajectory reward model is then employed to ensure the quality of the generated trajectories. We demonstrate that training GUI agents with OS-Genesis significantly improves their performance on highly challenging online benchmarks. In-depth analysis further validates OS-Genesis's efficiency and its superior data quality and diversity compared to existing synthesis methods. Our codes, data, and checkpoints are available at https://qiushisun.github.io/OS-Genesis-Home/.

cs.AI↗

arXiv2025

ChartSketcher: Reasoning with Multimodal Feedback and Reflection for Chart Understanding

Charts are high-density visualization carriers for complex data, serving as a crucial medium for information extraction and analysis. Automated chart understanding poses significant challenges to existing multimodal large language models (MLLMs) due to the need for precise and complex visual reasoning. Current step-by-step reasoning models primarily focus on text-based logical reasoning for chart understanding. However, they struggle to refine or correct their reasoning when errors stem from flawed visual understanding, as they lack the ability to leverage multimodal interaction for deeper comprehension. Inspired by human cognitive behavior, we propose ChartSketcher, a multimodal feedback-driven step-by-step reasoning method designed to address these limitations. ChartSketcher is a chart understanding model that employs Sketch-CoT, enabling MLLMs to annotate intermediate reasoning steps directly onto charts using a programmatic sketching library, iteratively feeding these visual annotations back into the reasoning process. This mechanism enables the model to visually ground its reasoning and refine its understanding over multiple steps. We employ a two-stage training strategy: a cold start phase to learn sketch-based reasoning patterns, followed by off-policy reinforcement learning to enhance reflection and generalization. Experiments demonstrate that ChartSketcher achieves promising performance on chart understanding benchmarks and general vision tasks, providing an interactive and interpretable approach to chart comprehension.

cs.CV↗

arXiv2025

Genius: A Generalizable and Purely Unsupervised Self-Training Framework For Advanced Reasoning

Advancing LLM reasoning skills has captivated wide interest. However, current post-training techniques rely heavily on supervisory signals, such as outcome supervision or auxiliary reward models, which face the problem of scalability and high annotation costs. This motivates us to enhance LLM reasoning without the need for external supervision. We introduce a generalizable and purely unsupervised self-training framework, named Genius. Without external auxiliary, Genius requires to seek the optimal response sequence in a stepwise manner and optimize the LLM. To explore the potential steps and exploit the optimal ones, Genius introduces a stepwise foresight re-sampling strategy to sample and estimate the step value by simulating future outcomes. Further, we recognize that the unsupervised setting inevitably induces the intrinsic noise and uncertainty. To provide a robust optimization, we propose an advantage-calibrated optimization (ACO) loss function to mitigate estimation inconsistencies. Combining these techniques together, Genius provides an advanced initial step towards self-improve LLM reasoning with general queries and without supervision, revolutionizing reasoning scaling laws given the vast availability of general queries. The code will be released at https://github.com/xufangzhi/Genius.

cs.CL↗

arXiv2025

$ϕ$-Decoding: Adaptive Foresight Sampling for Balanced Inference-Time Exploration and Exploitation

Inference-time optimization scales computation to derive deliberate reasoning steps for effective performance. While previous search-based strategies address the short-sightedness of auto-regressive generation, the vast search space leads to excessive exploration and insufficient exploitation. To strike an efficient balance to derive the optimal step, we frame the decoding strategy as foresight sampling, leveraging simulated future steps to obtain globally optimal step estimation. Built on it, we propose a novel decoding strategy, named $ϕ$-Decoding. To provide a precise and expressive estimation of step value, $ϕ$-Decoding approximates two distributions via foresight and clustering. Sampling from the joint distribution, the optimal steps can be selected for exploitation. To support adaptive computation allocation, we propose in-width and in-depth pruning strategies, featuring a light-weight solution to achieve inference efficiency. Extensive experiments across seven benchmarks show $ϕ$-Decoding outperforms strong baselines in both performance and efficiency. Additional analysis demonstrates its generalization across various LLMs and scalability across a wide range of computing budgets. The code will be released at https://github.com/xufangzhi/phi-Decoding, and the open-source PyPI package is coming soon.

cs.LG↗

arXiv2025

CapArena: Benchmarking and Analyzing Detailed Image Captioning in the LLM Era

Image captioning has been a longstanding challenge in vision-language research. With the rise of LLMs, modern Vision-Language Models (VLMs) generate detailed and comprehensive image descriptions. However, benchmarking the quality of such captions remains unresolved. This paper addresses two key questions: (1) How well do current VLMs actually perform on image captioning, particularly compared to humans? We built CapArena, a platform with over 6000 pairwise caption battles and high-quality human preference votes. Our arena-style evaluation marks a milestone, showing that leading models like GPT-4o achieve or even surpass human performance, while most open-source models lag behind. (2) Can automated metrics reliably assess detailed caption quality? Using human annotations from CapArena, we evaluate traditional and recent captioning metrics, as well as VLM-as-a-Judge. Our analysis reveals that while some metrics (e.g., METEOR) show decent caption-level agreement with humans, their systematic biases lead to inconsistencies in model ranking. In contrast, VLM-as-a-Judge demonstrates robust discernment at both the caption and model levels. Building on these insights, we release CapArena-Auto, an accurate and efficient automated benchmark for detailed captioning, achieving 94.3% correlation with human rankings at just $4 per test. Data and resources will be open-sourced at https://caparena.github.io.

cs.CV↗

arXiv2025

Self-supervised Quantized Representation for Seamlessly Integrating Knowledge Graphs with Large Language Models

Due to the presence of the natural gap between Knowledge Graph (KG) structures and the natural language, the effective integration of holistic structural information of KGs with Large Language Models (LLMs) has emerged as a significant question. To this end, we propose a two-stage framework to learn and apply quantized codes for each entity, aiming for the seamless integration of KGs with LLMs. Firstly, a self-supervised quantized representation (SSQR) method is proposed to compress both KG structural and semantic knowledge into discrete codes (\ie, tokens) that align the format of language sentences. We further design KG instruction-following data by viewing these learned codes as features to directly input to LLMs, thereby achieving seamless integration. The experiment results demonstrate that SSQR outperforms existing unsupervised quantized methods, producing more distinguishable codes. Further, the fine-tuned LLaMA2 and LLaMA3.1 also have superior performance on KG link prediction and triple classification tasks, utilizing only 16 tokens per entity instead of thousands in conventional prompting methods.

cs.CL↗

arXiv2025

A Survey of Neural Code Intelligence: Paradigms, Advances and Beyond

Neural Code Intelligence -- leveraging deep learning to understand, generate, and optimize code -- holds immense potential for transformative impacts on the whole society. Bridging the gap between Natural Language and Programming Language, this domain has drawn significant attention from researchers in both research communities over the past few years. This survey presents a systematic and chronological review of the advancements in code intelligence, encompassing over 50 representative models and their variants, more than 20 categories of tasks, and an extensive coverage of over 680 related works. We follow the historical progression to trace the paradigm shifts across different research phases (e.g., from modeling code with recurrent neural networks to the era of Large Language Models). Concurrently, we highlight the major technical transitions in models, tasks, and evaluations spanning through different stages. For applications, we also observe a co-evolving shift. It spans from initial endeavors to tackling specific scenarios, through exploring a diverse array of tasks during its rapid expansion, to currently focusing on tackling increasingly complex and varied real-world challenges. Building on our examination of the developmental trajectories, we further investigate the emerging synergies between code intelligence and broader machine intelligence, uncovering new cross-domain opportunities and illustrating the substantial influence of code intelligence across various domains. Finally, we delve into both the opportunities and challenges associated with this field, alongside elucidating our insights on the most promising research directions. An ongoing, dynamically updated project and resources associated with this survey have been released at https://github.com/QiushiSun/Awesome-Code-Intelligence.

cs.SE↗

arXiv2024

OS-ATLAS: A Foundation Action Model for Generalist GUI Agents

Existing efforts in building GUI agents heavily rely on the availability of robust commercial Vision-Language Models (VLMs) such as GPT-4o and GeminiProVision. Practitioners are often reluctant to use open-source VLMs due to their significant performance lag compared to their closed-source counterparts, particularly in GUI grounding and Out-Of-Distribution (OOD) scenarios. To facilitate future research in this area, we developed OS-Atlas - a foundational GUI action model that excels at GUI grounding and OOD agentic tasks through innovations in both data and modeling. We have invested significant engineering effort in developing an open-source toolkit for synthesizing GUI grounding data across multiple platforms, including Windows, Linux, MacOS, Android, and the web. Leveraging this toolkit, we are releasing the largest open-source cross-platform GUI grounding corpus to date, which contains over 13 million GUI elements. This dataset, combined with innovations in model training, provides a solid foundation for OS-Atlas to understand GUI screenshots and generalize to unseen interfaces. Through extensive evaluation across six benchmarks spanning three different platforms (mobile, desktop, and web), OS-Atlas demonstrates significant performance improvements over previous state-of-the-art models. Our evaluation also uncovers valuable insights into continuously improving and scaling the agentic capabilities of open-source VLMs.

cs.CL↗

arXiv2024

Vision-Language Models Can Self-Improve Reasoning via Reflection

Chain-of-thought (CoT) has proven to improve the reasoning capability of large language models (LLMs). However, due to the complexity of multimodal scenarios and the difficulty in collecting high-quality CoT data, CoT reasoning in multimodal LLMs has been largely overlooked. To this end, we propose a simple yet effective self-training framework, R3V, which iteratively enhances the model's Vision-language Reasoning by Reflecting on CoT Rationales. Our framework consists of two interleaved parts: (1) iteratively bootstrapping positive and negative solutions for reasoning datasets, and (2) reflection on rationale for learning from mistakes. Specifically, we introduce the self-refine and self-select losses, enabling the model to refine flawed rationale and derive the correct answer by comparing rationale candidates. Experiments on a wide range of vision-language tasks show that R3V consistently improves multimodal LLM reasoning, achieving a relative improvement of 23 to 60 percent over GPT-distilled baselines. Additionally, our approach supports self-reflection on generated solutions, further boosting performance through test-time computation.

cs.LG↗

arXiv2024

AgentStore: Scalable Integration of Heterogeneous Agents As Specialized Generalist Computer Assistant

Digital agents capable of automating complex computer tasks have attracted considerable attention due to their immense potential to enhance human-computer interaction. However, existing agent methods exhibit deficiencies in their generalization and specialization capabilities, especially in handling open-ended computer tasks in real-world environments. Inspired by the rich functionality of the App store, we present AgentStore, a scalable platform designed to dynamically integrate heterogeneous agents for automating computer tasks. AgentStore empowers users to integrate third-party agents, allowing the system to continuously enrich its capabilities and adapt to rapidly evolving operating systems. Additionally, we propose a novel core \textbf{MetaAgent} with the \textbf{AgentToken} strategy to efficiently manage diverse agents and utilize their specialized and generalist abilities for both domain-specific and system-wide tasks. Extensive experiments on three challenging benchmarks demonstrate that AgentStore surpasses the limitations of previous systems with narrow capabilities, particularly achieving a significant improvement from 11.21\% to 23.85\% on the OSWorld benchmark, more than doubling the previous results. Comprehensive quantitative and qualitative results further demonstrate AgentStore's ability to enhance agent systems in both generalization and specialization, underscoring its potential for developing the specialized generalist computer assistant. All our codes will be made publicly available in https://chengyou-jia.github.io/AgentStore-Home.

cs.AI↗

arXiv2024

Are Large Language Models Really Good Logical Reasoners? A Comprehensive Evaluation and Beyond

Logical reasoning consistently plays a fundamental and significant role in the domains of knowledge engineering and artificial intelligence. Recently, Large Language Models (LLMs) have emerged as a noteworthy innovation in natural language processing (NLP). However, the question of whether LLMs can effectively address the task of logical reasoning, which requires gradual cognitive inference similar to human intelligence, remains unanswered. To this end, we aim to bridge this gap and provide comprehensive evaluations in this paper. Firstly, to offer systematic evaluations, we select fifteen typical logical reasoning datasets and organize them into deductive, inductive, abductive and mixed-form reasoning settings. Considering the comprehensiveness of evaluations, we include 3 early-era representative LLMs and 4 trending LLMs. Secondly, different from previous evaluations relying only on simple metrics (e.g., \emph{accuracy}), we propose fine-level evaluations in objective and subjective manners, covering both answers and explanations, including \emph{answer correctness}, \emph{explain correctness}, \emph{explain completeness} and \emph{explain redundancy}. Additionally, to uncover the logical flaws of LLMs, problematic cases will be attributed to five error types from two dimensions, i.e., \emph{evidence selection process} and \emph{reasoning process}. Thirdly, to avoid the influences of knowledge bias and concentrate purely on benchmarking the logical reasoning capability of LLMs, we propose a new dataset with neutral content. Based on the in-depth evaluations, this paper finally forms a general evaluation scheme of logical reasoning capability from six dimensions (i.e., \emph{Correct}, \emph{Rigorous}, \emph{Self-aware}, \emph{Active}, \emph{Oriented} and \emph{No hallucination}). It reflects the pros and cons of LLMs and gives guiding directions for future works.

cs.CL↗

arXiv2024

Interactive Evolution: A Neural-Symbolic Self-Training Framework For Large Language Models

One of the primary driving forces contributing to the superior performance of Large Language Models (LLMs) is the extensive availability of human-annotated natural language data, which is used for alignment fine-tuning. This inspired researchers to investigate self-training methods to mitigate the extensive reliance on human annotations. However, the current success of self-training has been primarily observed in natural language scenarios, rather than in the increasingly important neural-symbolic scenarios. To this end, we propose an environment-guided neural-symbolic self-training framework named ENVISIONS. It aims to overcome two main challenges: (1) the scarcity of symbolic data, and (2) the limited proficiency of LLMs in processing symbolic language. Extensive evaluations conducted on three distinct domains demonstrate the effectiveness of our approach. Additionally, we have conducted a comprehensive analysis to uncover the factors contributing to ENVISIONS's success, thereby offering valuable insights for future research in this area. Code will be available at \url{https://github.com/xufangzhi/ENVISIONS}.

cs.CL↗

arXiv2024

PathReasoner: Modeling Reasoning Path with Equivalent Extension for Logical Question Answering

Logical reasoning task has attracted great interest since it was proposed. Faced with such a task, current competitive models, even large language models (e.g., ChatGPT and PaLM 2), still perform badly. Previous promising LMs struggle in logical consistency modeling and logical structure perception. To this end, we model the logical reasoning task by transforming each logical sample into reasoning paths and propose an architecture \textbf{PathReasoner}. It addresses the task from the views of both data and model. To expand the diversity of the logical samples, we propose an atom extension strategy supported by equivalent logical formulas, to form new reasoning paths. From the model perspective, we design a stack of transformer-style blocks. In particular, we propose a path-attention module to joint model in-atom and cross-atom relations with the high-order diffusion strategy. Experiments show that PathReasoner achieves competitive performances on two logical reasoning benchmarks and great generalization abilities.

cs.CL↗

arXiv2024

A Semantic Mention Graph Augmented Model for Document-Level Event Argument Extraction

Document-level Event Argument Extraction (DEAE) aims to identify arguments and their specific roles from an unstructured document. The advanced approaches on DEAE utilize prompt-based methods to guide pre-trained language models (PLMs) in extracting arguments from input documents. They mainly concentrate on establishing relations between triggers and entity mentions within documents, leaving two unresolved problems: a) independent modeling of entity mentions; b) document-prompt isolation. To this end, we propose a semantic mention Graph Augmented Model (GAM) to address these two problems in this paper. Firstly, GAM constructs a semantic mention graph that captures relations within and between documents and prompts, encompassing co-existence, co-reference and co-type relations. Furthermore, we introduce an ensembled graph transformer module to address mentions and their three semantic relations effectively. Later, the graph-augmented encoder-decoder module incorporates the relation-specific graph into the input embedding of PLMs and optimizes the encoder section with topology information, enhancing the relations comprehensively. Extensive experiments on the RAMS and WikiEvents datasets demonstrate the effectiveness of our approach, surpassing baseline methods and achieving a new state-of-the-art performance.

cs.CL↗

arXiv2024

SeeClick: Harnessing GUI Grounding for Advanced Visual GUI Agents

Graphical User Interface (GUI) agents are designed to automate complex tasks on digital devices, such as smartphones and desktops. Most existing GUI agents interact with the environment through extracted structured data, which can be notably lengthy (e.g., HTML) and occasionally inaccessible (e.g., on desktops). To alleviate this issue, we propose a novel visual GUI agent -- SeeClick, which only relies on screenshots for task automation. In our preliminary study, we have discovered a key challenge in developing visual GUI agents: GUI grounding -- the capacity to accurately locate screen elements based on instructions. To tackle this challenge, we propose to enhance SeeClick with GUI grounding pre-training and devise a method to automate the curation of GUI grounding data. Along with the efforts above, we have also created ScreenSpot, the first realistic GUI grounding benchmark that encompasses mobile, desktop, and web environments. After pre-training, SeeClick demonstrates significant improvement in ScreenSpot over various baselines. Moreover, comprehensive evaluations on three widely used benchmarks consistently support our finding that advancements in GUI grounding directly correlate with enhanced performance in downstream GUI agent tasks. The model, data and code are available at https://github.com/njucckevin/SeeClick.

cs.HC↗

arXiv2024

Symbol-LLM: Towards Foundational Symbol-centric Interface For Large Language Models

Although Large Language Models (LLMs) demonstrate remarkable ability in processing and generating human-like text, they do have limitations when it comes to comprehending and expressing world knowledge that extends beyond the boundaries of natural language(e.g., chemical molecular formula). Injecting a collection of symbolic data directly into the training of LLMs can be problematic, as it disregards the synergies among different symbolic families and overlooks the need for a balanced mixture of natural and symbolic data. In this work, we tackle these challenges from both a data and framework perspective and introduce Symbol-LLM series models. First, we curated a data collection consisting of 34 tasks and incorporating approximately 20 distinct symbolic families, intending to capture the interrelations and foster synergies between symbols. Then, a two-stage tuning framework succeeds in injecting symbolic knowledge without loss of the generality ability. Extensive experiments on both symbol- and NL-centric tasks demonstrate the balanced and superior performances of Symbol-LLM series models. The project page is https://xufangzhi.github.io/symbol-llm-page/.

cs.CL↗