arXiv subjects

Yu Kang

Publications and source records attributed to Yu Kang.

At least 55 records · Page 3Linked to original sources

arXiv2025

Graph Neural Networks in Modern AI-aided Drug Discovery

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive framework for learning the complex topological and geometric features of drug-like molecules, cementing their role in modern molecular modeling. This review provides a comprehensive overview of the methodological foundations and representative applications of GNNs in drug discovery, spanning tasks such as molecular property prediction, virtual screening, molecular generation, biomedical knowledge graph construction, and synthesis planning. Particular attention is given to recent methodological advances, including geometric GNNs, interpretable models, uncertainty quantification, scalable graph architectures, and graph generative frameworks. We also discuss how these models integrate with modern deep learning approaches, such as self-supervised learning, multi-task learning, meta-learning and pre-training. Throughout this review, we highlight the practical challenges and methodological bottlenecks encountered when applying GNNs to real-world drug discovery pipelines, and conclude with a discussion on future directions.

q-bio.BM↗

arXiv2025

SWE-bench Goes Live!

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a critical benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench and its variants have become standard in this domain, they suffer from key limitations: they have not been updated since their initial releases, cover a narrow set of repositories, and depend heavily on manual effort for instance construction and environment setup. These factors hinder scalability and introduce risks of overfitting and data contamination. In this work, we present SWE-bench-Live, a live-updatable benchmark designed to overcome these challenges. Our initial release consists of 1,319 tasks derived from real GitHub issues created since 2024, spanning 93 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Central to our benchmark is \method, an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art agent frameworks and LLMs on SWE-bench-Live, revealing a substantial performance gap compared to static benchmarks like SWE-bench, even under controlled evaluation conditions. To better understand this discrepancy, we perform detailed analyses across repository origin, issue recency, and task difficulty. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live facilitates rigorous, contamination-resistant evaluation of LLMs and agents in dynamic, real-world software development settings.

cs.SE↗

arXiv2025

Large Language Model-Brained GUI Agents: A Survey

GUIs have long been central to human-computer interaction, providing an intuitive and visually-driven way to access and interact with digital systems. The advent of LLMs, particularly multimodal models, has ushered in a new era of GUI automation. They have demonstrated exceptional capabilities in natural language understanding, code generation, and visual processing. This has paved the way for a new generation of LLM-brained GUI agents capable of interpreting complex GUI elements and autonomously executing actions based on natural language instructions. These agents represent a paradigm shift, enabling users to perform intricate, multi-step tasks through simple conversational commands. Their applications span across web navigation, mobile app interactions, and desktop automation, offering a transformative user experience that revolutionizes how individuals interact with software. This emerging field is rapidly advancing, with significant progress in both research and industry. To provide a structured understanding of this trend, this paper presents a comprehensive survey of LLM-brained GUI agents, exploring their historical evolution, core components, and advanced techniques. We address research questions such as existing GUI agent frameworks, the collection and utilization of data for training specialized GUI agents, the development of large action models tailored for GUI tasks, and the evaluation metrics and benchmarks necessary to assess their effectiveness. Additionally, we examine emerging applications powered by these agents. Through a detailed analysis, this survey identifies key research gaps and outlines a roadmap for future advancements in the field. By consolidating foundational knowledge and state-of-the-art developments, this work aims to guide both researchers and practitioners in overcoming challenges and unlocking the full potential of LLM-brained GUI agents.

cs.AI↗

arXiv2025

AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy

Protein structure prediction is a critical and longstanding challenge in biology, garnering widespread interest due to its significance in understanding biological processes. A particular area of focus is the prediction of missing loops in proteins, which are vital in determining protein function and activity. To address this challenge, we propose AutoLoop, a novel computational model designed to automatically generate accurate loop backbone conformations that closely resemble their natural structures. AutoLoop employs a bidirectional training approach while merging atom- and residue-level embedding, thus improving robustness and precision. We compared AutoLoop with twelve established methods, including FREAD, NGK, AlphaFold2, and AlphaFold3. AutoLoop consistently outperforms other methods, achieving a median RMSD of 1.12 Angstrom and a 2-Angstrom success rate of 73.23% on the CASP15 dataset, while maintaining strong performance on the HOMSTARD dataset. It demonstrates the best performance across nearly all loop lengths and secondary structural types. Beyond accuracy, AutoLoop is computationally efficient, requiring only 0.10 s per generation. A post-processing module for side-chain packing and energy minimization further improves results slightly, confirming the reliability of the predicted backbone. A case study also highlights AutoLoop's potential for precise predictions based on dominant loop conformations. These advances hold promise for protein engineering and drug discovery.

q-bio.BM↗

arXiv2025

Learning Multi-view Multi-class Anomaly Detection

The latest trend in anomaly detection is to train a unified model instead of training a separate model for each category. However, existing multi-class anomaly detection (MCAD) models perform poorly in multi-view scenarios because they often fail to effectively model the relationships and complementary information among different views. In this paper, we introduce a Multi-View Multi-Class Anomaly Detection model (MVMCAD), which integrates information from multiple views to accurately identify anomalies. Specifically, we propose a semi-frozen encoder, where a pre-encoder prior enhancement mechanism is added before the frozen encoder, enabling stable cross-view feature modeling and efficient adaptation for improved anomaly detection. Furthermore, we propose an Anomaly Amplification Module (AAM) that models global token interactions and suppresses normal regions to enhance anomaly signals, leading to improved detection performance in multi-view settings. Finally, we propose a Cross-Feature Loss that aligns shallow encoder features with deep decoder features and vice versa, enhancing the model's sensitivity to anomalies at different semantic levels under multi-view scenarios. Extensive experiments on the Real-IAD dataset for multi-view multi-class anomaly detection validate the effectiveness of our approach, achieving state-of-the-art performance of 91.0/88.6/82.1 and 99.1/43.9/48.2/95.2 for image-level and the pixel-level, respectively.

cs.CV↗

arXiv2025

Reservoir-enhanced Segment Anything Model for Subsurface Diagnosis

Urban roads and infrastructure, vital to city operations, face growing threats from subsurface anomalies like cracks and cavities. Ground Penetrating Radar (GPR) effectively visualizes underground conditions employing electromagnetic (EM) waves; however, accurate anomaly detection via GPR remains challenging due to limited labeled data, varying subsurface conditions, and indistinct target boundaries. Although visually image-like, GPR data fundamentally represent EM waves, with variations within and between waves critical for identifying anomalies. Addressing these, we propose the Reservoir-enhanced Segment Anything Model (Res-SAM), an innovative framework exploiting both visual discernibility and wave-changing properties of GPR data. Res-SAM initially identifies apparent candidate anomaly regions given minimal prompts, and further refines them by analyzing anomaly-induced changing information within and between EM waves in local GPR data, enabling precise and complete anomaly region extraction and category determination. Real-world experiments demonstrate that Res-SAM achieves high detection accuracy (>85%) and outperforms state-of-the-art. Notably, Res-SAM requires only minimal accessible non-target data, avoids intensive training, and incorporates simple human interaction to enhance reliability. Our research provides a scalable, resource-efficient solution for rapid subsurface anomaly detection across diverse environments, improving urban safety monitoring while reducing manual effort and computational cost.

eess.IV↗

arXiv2025

UFO2: The Desktop AgentOS

Recent Computer-Using Agents (CUAs), powered by multimodal large language models (LLMs), offer a promising direction for automating complex desktop workflows through natural language. However, most existing CUAs remain conceptual prototypes, hindered by shallow OS integration, fragile screenshot-based interaction, and disruptive execution. We present UFO2, a multiagent AgentOS for Windows desktops that elevates CUAs into practical, system-level automation. UFO2 features a centralized HostAgent for task decomposition and coordination, alongside a collection of application-specialized AppAgent equipped with native APIs, domain-specific knowledge, and a unified GUI--API action layer. This architecture enables robust task execution while preserving modularity and extensibility. A hybrid control detection pipeline fuses Windows UI Automation (UIA) with vision-based parsing to support diverse interface styles. Runtime efficiency is further enhanced through speculative multi-action planning, reducing per-step LLM overhead. Finally, a Picture-in-Picture (PiP) interface enables automation within an isolated virtual desktop, allowing agents and users to operate concurrently without interference. We evaluate UFO2 across over 20 real-world Windows applications, demonstrating substantial improvements in robustness and execution accuracy over prior CUAs. Our results show that deep OS integration unlocks a scalable path toward reliable, user-aligned desktop automation.

cs.AI↗

arXiv2025

CA+: Cognition Augmented Counselor Agent Framework for Long-term Dynamic Client Engagement

Current AI counseling systems struggle with maintaining effective long-term client engagement. Through formative research with counselors and a systematic literature review, we identified five key design considerations for AI counseling interactions. Based on these insights, we propose CA+, a Cognition Augmented counselor framework enhancing contextual understanding through three components: (1) Therapy Strategies Module: Implements hierarchical Goals-Session-Action planning with bidirectional adaptation based on client feedback; (2) Communication Form Module: Orchestrates parallel guidance and empathy pathways for balanced therapeutic progress and emotional resonance; (3) Information Management: Utilizes client profile and therapeutic knowledge databases for dynamic, context-aware interventions. A three-day longitudinal study with 24 clients demonstrates CA+'s significant improvements in client engagement, perceived empathy, and overall satisfaction compared to a baseline system. Besides, two licensed counselors confirm its high professionalism. Our research demonstrates the potential for enhancing LLM engagement in psychological counseling dialogues through cognitive theory, which may inspire further innovations in computational interaction in the future.

cs.HC↗

arXiv2025

Large Language Model Compression via the Nested Activation-Aware Decomposition

In this paper, we tackle the critical challenge of compressing large language models (LLMs) to facilitate their practical deployment and broader adoption. We introduce a novel post-training compression paradigm that focuses on low-rank decomposition of LLM weights. Our analysis identifies two main challenges in this task: the variability in LLM activation distributions and handling unseen activations from different datasets and models. To address these challenges, we propose a nested activation-aware framework (NSVD) for LLMs, a training-free approach designed to enhance the accuracy of low-rank decompositions by managing activation outliers through transforming the weight matrix based on activation distribution and the original weight matrix. This method allows for the absorption of outliers into the transformed weight matrix, improving decomposition accuracy. Our comprehensive evaluation across eight datasets and six models from three distinct LLM families demonstrates the superiority of NSVD over current state-of-the-art methods, especially at medium to large compression ratios or in multilingual and multitask settings.

cs.LG↗

arXiv2025

Boosting the Generalization and Reasoning of Vision Language Models with Curriculum Reinforcement Learning

While state-of-the-art vision-language models (VLMs) have demonstrated remarkable capabilities in complex visual-text tasks, their success heavily relies on massive model scaling, limiting their practical deployment. Small-scale VLMs offer a more practical alternative but face significant challenges when trained with traditional supervised fine-tuning (SFT), particularly in two aspects: out-of-domain (OOD) generalization and reasoning abilities, which significantly lags behind the contemporary Large language models (LLMs). To address these challenges, we propose Curriculum Reinforcement Finetuning (Curr-ReFT), a novel post-training paradigm specifically designed for small-scale VLMs. Inspired by the success of reinforcement learning in LLMs, Curr-ReFT comprises two sequential stages: (1) Curriculum Reinforcement Learning, which ensures steady progression of model capabilities through difficulty-aware reward design, transitioning from basic visual perception to complex reasoning tasks; and (2) Rejected Sampling-based Self-improvement, which maintains the fundamental capabilities of VLMs through selective learning from high-quality multimodal and language examples. Extensive experiments demonstrate that models trained with Curr-ReFT paradigm achieve state-of-the-art performance across various visual tasks in both in-domain and out-of-domain settings. Moreover, our Curr-ReFT enhanced 3B model matches the performance of 32B-parameter models, demonstrating that efficient training paradigms can effectively bridge the gap between small and large models.

cs.CV↗

arXiv2025

Discovery of novel antimicrobial peptides with notable antibacterial potency by a LLM-based foundation model

Large language models (LLMs) have shown remarkable advancements in chemistry and biomedical research, acting as versatile foundation models for various tasks. We introduce AMP-Designer, an LLM-based approach for swiftly designing novel antimicrobial peptides (AMPs) with desired properties. Within 11 days, AMP-Designer achieved the de novo design of 18 AMPs with broad-spectrum activity against Gram-negative bacteria. In vitro validation revealed a 94.4% success rate, with two candidates demonstrating exceptional antibacterial efficacy, minimal hemotoxicity, stability in human plasma, and low potential to induce resistance, as evidenced by significant bacterial load reduction in murine lung infection experiments. The entire process, from design to validation, concluded in 48 days. AMP-Designer excels in creating AMPs targeting specific strains despite limited data availability, with a top candidate displaying a minimum inhibitory concentration of 2.0 μg/ml against Propionibacterium acnes. Integrating advanced machine learning techniques, AMP-Designer demonstrates remarkable efficiency, paving the way for innovative solutions to antibiotic resistance.

q-bio.BM↗

arXiv2025

Skeleton-Guided-Translation: A Benchmarking Framework for Code Repository Translation with Fine-Grained Quality Evaluation

The advancement of large language models has intensified the need to modernize enterprise applications and migrate legacy systems to secure, versatile languages. However, existing code translation benchmarks primarily focus on individual functions, overlooking the complexities involved in translating entire repositories, such as maintaining inter-module coherence and managing dependencies. While some recent repository-level translation benchmarks attempt to address these challenges, they still face limitations, including poor maintainability and overly coarse evaluation granularity, which make them less developer-friendly. We introduce Skeleton-Guided-Translation, a framework for repository-level Java to C# code translation with fine-grained quality evaluation. It uses a two-step process: first translating the repository's structural "skeletons", then translating the full repository guided by these skeletons. Building on this, we present TRANSREPO-BENCH, a benchmark of high quality open-source Java repositories and their corresponding C# skeletons, including matching unit tests and build configurations. Our unit tests are fixed and can be applied across multiple or incremental translations without manual adjustments, enhancing automation and scalability in evaluations. Additionally, we develop fine-grained evaluation metrics that assess translation quality at the individual test case level, addressing traditional binary metrics' inability to distinguish when build failures cause all tests to fail. Evaluations using TRANSREPO-BENCH highlight key challenges and advance more accurate repository level code translation.

cs.SE↗

arXiv2025

DI-BENCH: Benchmarking Large Language Models on Dependency Inference with Testable Repositories at Scale

Large Language Models have advanced automated software development, however, it remains a challenge to correctly infer dependencies, namely, identifying the internal components and external packages required for a repository to successfully run. Existing studies highlight that dependency-related issues cause over 40\% of observed runtime errors on the generated repository. To address this, we introduce DI-BENCH, a large-scale benchmark and evaluation framework specifically designed to assess LLMs' capability on dependency inference. The benchmark features 581 repositories with testing environments across Python, C#, Rust, and JavaScript. Extensive experiments with textual and execution-based metrics reveal that the current best-performing model achieves only a 42.9% execution pass rate, indicating significant room for improvement. DI-BENCH establishes a new viewpoint for evaluating LLM performance on repositories, paving the way for more robust end-to-end software synthesis.

cs.CL↗

arXiv2024

C3oT: Generating Shorter Chain-of-Thought without Compromising Effectiveness

Generating Chain-of-Thought (CoT) before deriving the answer can effectively improve the reasoning capabilities of large language models (LLMs) and significantly improve the accuracy of the generated answer. However, in most cases, the length of the generated CoT is much longer than the desired final answer, which results in additional decoding costs. Furthermore, existing research has discovered that shortening the reasoning steps in CoT, even while preserving the key information, diminishes LLMs' abilities. These phenomena make it difficult to use LLMs and CoT in many real-world applications that only require the final answer and are sensitive to latency, such as search and recommendation. To reduce the costs of model decoding and shorten the length of the generated CoT, this paper presents $\textbf{C}$onditioned $\textbf{C}$ompressed $\textbf{C}$hain-of-$\textbf{T}$hought (C3oT), a CoT compression framework that involves a compressor to compress an original longer CoT into a shorter CoT while maintaining key information and interpretability, a conditioned training method to train LLMs with both longer CoT and shorter CoT simultaneously to learn the corresponding relationships between them, and a conditioned inference method to gain the reasoning ability learned from longer CoT by generating shorter CoT. We conduct experiments over four datasets from arithmetic and commonsense scenarios, showing that the proposed method is capable of compressing the length of generated CoT by up to more than 50% without compromising its effectiveness.

cs.CL↗

arXiv2024

Descriptors-free Collective Variables From Geometric Graph Neural Networks

Enhanced sampling simulations make the computational study of rare events feasible. A large family of such methods crucially depends on the definition of some collective variables (CVs) that could provide a low-dimensional representation of the relevant physics of the process. Recently, many methods have been proposed to semi-automatize the CV design by using machine learning tools to learn the variables directly from the simulation data. However, most methods are based on feed-forward neural networks and require as input some user-defined physical descriptors. Here, we propose to bypass this step using a graph neural network to directly use the atomic coordinates as input for the CV model. This way, we achieve a fully automatic approach to CV determination that provides variables invariant under the relevant symmetries, especially the permutational one. Furthermore, we provide different analysis tools to favor the physical interpretation of the final CV. We prove the robustness of our approach using different methods from the literature for the optimization of the CV, and we prove its efficacy on several systems, including a small peptide, an ion dissociation in explicit solvent, and a simple chemical reaction.

physics.comp-ph↗

arXiv2024

Can Large Language Models Effectively Process and Execute Financial Trading Instructions?

The development of Large Language Models (LLMs) has created transformative opportunities for the financial industry, especially in the area of financial trading. However, how to integrate LLMs with trading systems has become a challenge. To address this problem, we propose an intelligent trade order recognition pipeline that enables the conversion of trade orders into a standard format in trade execution. The system improves the ability of human traders to interact with trading platforms while addressing the problem of misinformation acquisition in trade execution. In addition, we have created a trade order dataset of 500 pieces of data to simulate real-world trading scenarios. Moreover, we designed several metrics to provide a comprehensive assessment of dataset reliability and the generative power of big models in finance by experimenting with five state-of-the-art LLMs on our dataset. The results indicate that while LLMs demonstrate high generation rates (87.50% to 98.33%) and perfect follow-up rates, they face significant challenges in accuracy (5% to 10%) and completeness, with high missing rates (14.29% to 67.29%). In addition, LLMs tend to over-interrogate, suggesting that large models tend to collect more information, carrying certain challenges for information security.

cs.CE↗

arXiv2024

Towards Unifying Feature Interaction Models for Click-Through Rate Prediction

Modeling feature interactions plays a crucial role in accurately predicting click-through rates (CTR) in advertising systems. To capture the intricate patterns of interaction, many existing models employ matrix-factorization techniques to represent features as lower-dimensional embedding vectors, enabling the modeling of interactions as products between these embeddings. In this paper, we propose a general framework called IPA to systematically unify these models. Our framework comprises three key components: the Interaction Function, which facilitates feature interaction; the Layer Pooling, which constructs higher-level interaction layers; and the Layer Aggregator, which combines the outputs of all layers to serve as input for the subsequent classifier. We demonstrate that most existing models can be categorized within our framework by making specific choices for these three components. Through extensive experiments and a dimensional collapse analysis, we evaluate the performance of these choices. Furthermore, by leveraging the most powerful components within our framework, we introduce a novel model that achieves competitive results compared to state-of-the-art CTR models. PFL gets significant GMV lift during online A/B test in Tencent's advertising platform and has been deployed as the production model in several primary scenarios.

cs.IR↗

arXiv2024

Benchmarking General-Purpose In-Context Learning

In-context learning (ICL) empowers generative models to address new tasks effectively and efficiently on the fly, without relying on any artificially crafted optimization techniques. In this paper, we study extending ICL to address a broader range of tasks with an extended learning horizon and higher improvement potential, namely General Purpose In-Context Learning (GPICL). To this end, we introduce two lightweight benchmarks specifically crafted to train and evaluate GPICL functionalities. Each benchmark encompasses a vast number of tasks characterized by significant task variance. These tasks are also crafted to promote long-horizon in-context learning through continuous generation and interaction, covering domains such as language modeling, decision-making, and world modeling. The benchmarks necessitate the models to leverage contexts and history interactions to enhance their capabilities, which we believe to be the key characteristics of GPICL. Our experiments indicate that the diversity of training tasks is positively correlated with the ability to generalize with ICL, but inversely correlated with zero-shot capabilities. Additionally, our findings indicate that the scale of parameters alone may not be crucial for ICL or GPICL, suggesting alternative approaches such as increasing the scale of contexts and memory states.

cs.AI↗