arXiv subjects

Hui Xiong

Publications and source records attributed to Hui Xiong.

At least 181 records · Page 10Linked to original sources

arXiv2025

HiCMamba: Enhancing Hi-C Resolution and Identifying 3D Genome Structures with State Space Modeling

Hi-C technology measures genome-wide interaction frequencies, providing a powerful tool for studying the 3D genomic structure within the nucleus. However, high sequencing costs and technical challenges often result in Hi-C data with limited coverage, leading to imprecise estimates of chromatin interaction frequencies. To address this issue, we present a novel deep learning-based method HiCMamba to enhance the resolution of Hi-C contact maps using a state space model. We adopt the UNet-based auto-encoder architecture to stack the proposed holistic scan block, enabling the perception of both global and local receptive fields at multiple scales. Experimental results demonstrate that HiCMamba outperforms state-of-the-art methods while significantly reducing computational resources. Furthermore, the 3D genome structures, including topologically associating domains (TADs) and loops, identified in the contact maps recovered by HiCMamba are validated through associated epigenomic features. Our work demonstrates the potential of a state space model as foundational frameworks in the field of Hi-C resolution enhancement.

cs.CV↗

arXiv2025

From Understanding to Excelling: Template-Free Algorithm Design through Structural-Functional Co-Evolution

Large language models (LLMs) have greatly accelerated the automation of algorithm generation and optimization. However, current methods such as EoH and FunSearch mainly rely on predefined templates and expert-specified functions that focus solely on the local evolution of key functionalities. Consequently, they fail to fully leverage the synergistic benefits of the overall architecture and the potential of global optimization. In this paper, we introduce an end-to-end algorithm generation and optimization framework based on LLMs. Our approach utilizes the deep semantic understanding of LLMs to convert natural language requirements or human-authored papers into code solutions, and employs a two-dimensional co-evolution strategy to optimize both functional and structural aspects. This closed-loop process spans problem analysis, code generation, and global optimization, automatically identifying key algorithm modules for multi-level joint optimization and continually enhancing performance and design innovation. Extensive experiments demonstrate that our method outperforms traditional local optimization approaches in both performance and innovation, while also exhibiting strong adaptability to unknown environments and breakthrough potential in structural design. By building on human research, our framework generates and optimizes novel algorithms that surpass those designed by human experts, broadening the applicability of LLMs for algorithm design and providing a novel solution pathway for automated algorithm development.

cs.SE↗

arXiv2025

TimeFound: A Foundation Model for Time Series Forecasting

We present TimeFound, an encoder-decoder transformer-based time series foundation model for out-of-the-box zero-shot forecasting. To handle time series data from various domains, TimeFound employs a multi-resolution patching strategy to capture complex temporal patterns at multiple scales. We pre-train our model with two sizes (200M and 710M parameters) on a large time-series corpus comprising both real-world and synthetic datasets. Over a collection of unseen datasets across diverse domains and forecasting horizons, our empirical evaluations suggest that TimeFound can achieve superior or competitive zero-shot forecasting performance, compared to state-of-the-art time series foundation models.

cs.LG↗

arXiv2025

Can Large Language Models Help Experimental Design for Causal Discovery?

Designing proper experiments and selecting optimal intervention targets is a longstanding problem in scientific or causal discovery. Identifying the underlying causal structure from observational data alone is inherently difficult. Obtaining interventional data, on the other hand, is crucial to causal discovery, yet it is usually expensive and time-consuming to gather sufficient interventional data to facilitate causal discovery. Previous approaches commonly utilize uncertainty or gradient signals to determine the intervention targets. However, numerical-based approaches may yield suboptimal results due to the inaccurate estimation of the guiding signals at the beginning when with limited interventional data. In this work, we investigate a different approach, whether we can leverage Large Language Models (LLMs) to assist with the intervention targeting in causal discovery by making use of the rich world knowledge about the experimental design in LLMs. Specifically, we present Large Language Model Guided Intervention Targeting (LeGIT) -- a robust framework that effectively incorporates LLMs to augment existing numerical approaches for the intervention targeting in causal discovery. Across 4 realistic benchmark scales, LeGIT demonstrates significant improvements and robustness over existing methods and even surpasses humans, which demonstrates the usefulness of LLMs in assisting with experimental design for scientific discovery.

cs.AI↗

arXiv2025

MR-EIT: Multi-Resolution Reconstruction for Electrical Impedance Tomography via Data-Driven and Unsupervised Dual-Mode Neural Networks

This paper presents a multi-resolution reconstruction method for Electrical Impedance Tomography (EIT), referred to as MR-EIT, which is capable of operating in both supervised and unsupervised learning modes. MR-EIT integrates an ordered feature extraction module and an unordered coordinate feature expression module. The former achieves the mapping from voltage to two-dimensional conductivity features through pre-training, while the latter realizes multi-resolution reconstruction independent of the order and size of the input sequence by utilizing symmetric functions and local feature extraction mechanisms. In the data-driven mode, MR-EIT reconstructs high-resolution images from low-resolution data of finite element meshes through two stages of pre-training and joint training, and demonstrates excellent performance in simulation experiments. In the unsupervised learning mode, MR-EIT does not require pre-training data and performs iterative optimization solely based on measured voltages to rapidly achieve image reconstruction from low to high resolution. It shows robustness to noise and efficient super-resolution reconstruction capabilities in both simulation and real water tank experiments. Experimental results indicate that MR-EIT outperforms the comparison methods in terms of Structural Similarity (SSIM) and Relative Image Error (RIE), especially in the unsupervised learning mode, where it can significantly reduce the number of iterations and improve image reconstruction quality.

cs.CV↗

arXiv2025

Towards Continuous Reuse of Graph Models via Holistic Memory Diversification

This paper addresses the challenge of incremental learning in growing graphs with increasingly complex tasks. The goal is to continuously train a graph model to handle new tasks while retaining proficiency in previous tasks via memory replay. Existing methods usually overlook the importance of memory diversity, limiting in selecting high-quality memory from previous tasks and remembering broad previous knowledge within the scarce memory on graphs. To address that, we introduce a novel holistic Diversified Memory Selection and Generation (DMSG) framework for incremental learning in graphs, which first introduces a buffer selection strategy that considers both intra-class and inter-class diversities, employing an efficient greedy algorithm for sampling representative training nodes from graphs into memory buffers after learning each new task. Then, to adequately rememorize the knowledge preserved in the memory buffer when learning new tasks, a diversified memory generation replay method is introduced. This method utilizes a variational layer to generate the distribution of buffer node embeddings and sample synthesized ones for replaying. Furthermore, an adversarial variational embedding learning method and a reconstruction-based decoder are proposed to maintain the integrity and consolidate the generalization of the synthesized node embeddings, respectively. Extensive experimental results on publicly accessible datasets demonstrate the superiority of \method{} over state-of-the-art methods.

cs.LG↗

arXiv2025

EXCLAIM: An Explainable Cross-Modal Agentic System for Misinformation Detection with Hierarchical Retrieval

Misinformation continues to pose a significant challenge in today's information ecosystem, profoundly shaping public perception and behavior. Among its various manifestations, Out-of-Context (OOC) misinformation is particularly obscure, as it distorts meaning by pairing authentic images with misleading textual narratives. Existing methods for detecting OOC misinformation predominantly rely on coarse-grained similarity metrics between image-text pairs, which often fail to capture subtle inconsistencies or provide meaningful explainability. While multi-modal large language models (MLLMs) demonstrate remarkable capabilities in visual reasoning and explanation generation, they have not yet demonstrated the capacity to address complex, fine-grained, and cross-modal distinctions necessary for robust OOC detection. To overcome these limitations, we introduce EXCLAIM, a retrieval-based framework designed to leverage external knowledge through multi-granularity index of multi-modal events and entities. Our approach integrates multi-granularity contextual analysis with a multi-agent reasoning architecture to systematically evaluate the consistency and integrity of multi-modal news content. Comprehensive experiments validate the effectiveness and resilience of EXCLAIM, demonstrating its ability to detect OOC misinformation with 4.3% higher accuracy compared to state-of-the-art approaches, while offering explainable and actionable insights.

cs.IR↗

arXiv2025

SCA3D: Enhancing Cross-modal 3D Retrieval via 3D Shape and Caption Paired Data Augmentation

The cross-modal 3D retrieval task aims to achieve mutual matching between text descriptions and 3D shapes. This has the potential to enhance the interaction between natural language and the 3D environment, especially within the realms of robotics and embodied artificial intelligence (AI) applications. However, the scarcity and expensiveness of 3D data constrain the performance of existing cross-modal 3D retrieval methods. These methods heavily rely on features derived from the limited number of 3D shapes, resulting in poor generalization ability across diverse scenarios. To address this challenge, we introduce SCA3D, a novel 3D shape and caption online data augmentation method for cross-modal 3D retrieval. Our approach uses the LLaVA model to create a component library, captioning each segmented part of every 3D shape within the dataset. Notably, it facilitates the generation of extensive new 3D-text pairs containing new semantic features. We employ both inter and intra distances to align various components into a new 3D shape, ensuring that the components do not overlap and are closely fitted. Further, text templates are utilized to process the captions of each component and generate new text descriptions. Besides, we use unimodal encoders to extract embeddings for 3D shapes and texts based on the enriched dataset. We then calculate fine-grained cross-modal similarity using Earth Mover's Distance (EMD) and enhance cross-modal matching with contrastive learning, enabling bidirectional retrieval between texts and 3D shapes. Extensive experiments show our SCA3D outperforms previous works on the Text2Shape dataset, raising the Shape-to-Text RR@1 score from 20.03 to 27.22 and the Text-to-Shape RR@1 score from 13.12 to 16.67. Codes can be found in https://github.com/3DAgentWorld/SCA3D.

cs.CV↗

arXiv2025

A Survey of fMRI to Image Reconstruction

Functional magnetic resonance imaging (fMRI) based image reconstruction plays a pivotal role in decoding human perception, with applications in neuroscience and brain-computer interfaces. While recent advancements in deep learning and large-scale datasets have driven progress, challenges such as data scarcity, cross-subject variability, and low semantic consistency persist. To address these issues, we introduce the concept of fMRI-to-Image Learning (fMRI2Image) and present the first systematic review in this field. This review highlights key challenges, categorizes methodologies such as fMRI signal encoding, feature mapping, and image generator. Finally, promising research directions are proposed to advance this emerging frontier, providing a reference for future studies.

cs.CV↗

arXiv2025

Continual Test-Time Adaptation for Single Image Defocus Deblurring via Causal Siamese Networks

Single image defocus deblurring (SIDD) aims to restore an all-in-focus image from a defocused one. Distribution shifts in defocused images generally lead to performance degradation of existing methods during out-of-distribution inferences. In this work, we gauge the intrinsic reason behind the performance degradation, which is identified as the heterogeneity of lens-specific point spread functions. Empirical evidence supports this finding, motivating us to employ a continual test-time adaptation (CTTA) paradigm for SIDD. However, traditional CTTA methods, which primarily rely on entropy minimization, cannot sufficiently explore task-dependent information for pixel-level regression tasks like SIDD. To address this issue, we propose a novel Siamese networks-based continual test-time adaptation framework, which adapts source models to continuously changing target domains only requiring unlabeled target data in an online manner. To further mitigate semantically erroneous textures introduced by source SIDD models under severe degradation, we revisit the learning paradigm through a structural causal model and propose Causal Siamese networks (CauSiam). Our method leverages large-scale pre-trained vision-language models to derive discriminative universal semantic priors and integrates these priors into Siamese networks, ensuring causal identifiability between blurry inputs and restored images. Extensive experiments demonstrate that CauSiam effectively improves the generalization performance of existing SIDD methods in continuously changing domains.

eess.IV↗

arXiv2025

AnimAlte:Designing AI-Infused Cartoon Videos to Improve Preschoolers' Language Learning with Family Engagement at Home

Cartoon videos have proven to be effective in learning vocabulary to preschool children.However, we have little knowledge about integrating AI into cartoon videos to provide systematic, multimodal vocabulary learning support. This late-breaking work present \name{}, an AI-powered cartoon video system that enables real-time Q\&A, vocabulary review, and contextual learning. Preliminary findings contextualized how families interact with \name{} to support vocabulary learning. Parents appreciated the system for its personalized, engaging experiences, fostering collaboration, and encouraging self-reflection on parenting. This study offers valuable design implications for informing future video systems to support vocabulary learning.

cs.HC↗

arXiv2025

Unleashing the Power of Large Language Model for Denoising Recommendation

Recommender systems are crucial for personalizing user experiences but often depend on implicit feedback data, which can be noisy and misleading. Existing denoising studies involve incorporating auxiliary information or learning strategies from interaction data. However, they struggle with the inherent limitations of external knowledge and interaction data, as well as the non-universality of certain predefined assumptions, hindering accurate noise identification. Recently, large language models (LLMs) have gained attention for their extensive world knowledge and reasoning abilities, yet their potential in enhancing denoising in recommendations remains underexplored. In this paper, we introduce LLaRD, a framework leveraging LLMs to improve denoising in recommender systems, thereby boosting overall recommendation performance. Specifically, LLaRD generates denoising-related knowledge by first enriching semantic insights from observational data via LLMs and inferring user-item preference knowledge. It then employs a novel Chain-of-Thought (CoT) technique over user-item interaction graphs to reveal relation knowledge for denoising. Finally, it applies the Information Bottleneck (IB) principle to align LLM-generated denoising knowledge with recommendation targets, filtering out noise and irrelevant LLM knowledge. Empirical results demonstrate LLaRD's effectiveness in enhancing denoising and recommendation accuracy.

cs.IR↗

arXiv2025

Talk2Radar: Bridging Natural Language with 4D mmWave Radar for 3D Referring Expression Comprehension

Embodied perception is essential for intelligent vehicles and robots in interactive environmental understanding. However, these advancements primarily focus on vision, with limited attention given to using 3D modeling sensors, restricting a comprehensive understanding of objects in response to prompts containing qualitative and quantitative queries. Recently, as a promising automotive sensor with affordable cost, 4D millimeter-wave radars provide denser point clouds than conventional radars and perceive both semantic and physical characteristics of objects, thereby enhancing the reliability of perception systems. To foster the development of natural language-driven context understanding in radar scenes for 3D visual grounding, we construct the first dataset, Talk2Radar, which bridges these two modalities for 3D Referring Expression Comprehension (REC). Talk2Radar contains 8,682 referring prompt samples with 20,558 referred objects. Moreover, we propose a novel model, T-RadarNet, for 3D REC on point clouds, achieving State-Of-The-Art (SOTA) performance on the Talk2Radar dataset compared to counterparts. Deformable-FPN and Gated Graph Fusion are meticulously designed for efficient point cloud feature modeling and cross-modal fusion between radar and text features, respectively. Comprehensive experiments provide deep insights into radar-based 3D REC. We release our project at https://github.com/GuanRunwei/Talk2Radar.

cs.RO↗

arXiv2025

Boosting Knowledge Graph-based Recommendations through Confidence-Aware Augmentation with Large Language Models

Knowledge Graph-based recommendations have gained significant attention due to their ability to leverage rich semantic relationships. However, constructing and maintaining Knowledge Graphs (KGs) is resource-intensive, and the accuracy of KGs can suffer from noisy, outdated, or irrelevant triplets. Recent advancements in Large Language Models (LLMs) offer a promising way to improve the quality and relevance of KGs for recommendation tasks. Despite this, integrating LLMs into KG-based systems presents challenges, such as efficiently augmenting KGs, addressing hallucinations, and developing effective joint learning methods. In this paper, we propose the Confidence-aware KG-based Recommendation Framework with LLM Augmentation (CKG-LLMA), a novel framework that combines KGs and LLMs for recommendation task. The framework includes: (1) an LLM-based subgraph augmenter for enriching KGs with high-quality information, (2) a confidence-aware message propagation mechanism to filter noisy triplets, and (3) a dual-view contrastive learning method to integrate user-item interactions and KG data. Additionally, we employ a confidence-aware explanation generation process to guide LLMs in producing realistic explanations for recommendations. Finally, extensive experiments demonstrate the effectiveness of CKG-LLMA across multiple public datasets.

cs.IR↗

arXiv2025

Editable Concept Bottleneck Models

Concept Bottleneck Models (CBMs) have garnered much attention for their ability to elucidate the prediction process through a humanunderstandable concept layer. However, most previous studies focused on cases where the data, including concepts, are clean. In many scenarios, we often need to remove/insert some training data or new concepts from trained CBMs for reasons such as privacy concerns, data mislabelling, spurious concepts, and concept annotation errors. Thus, deriving efficient editable CBMs without retraining from scratch remains a challenge, particularly in large-scale applications. To address these challenges, we propose Editable Concept Bottleneck Models (ECBMs). Specifically, ECBMs support three different levels of data removal: concept-label-level, concept-level, and data-level. ECBMs enjoy mathematically rigorous closed-form approximations derived from influence functions that obviate the need for retraining. Experimental results demonstrate the efficiency and adaptability of our ECBMs, affirming their practical value in CBMs.

cs.LG↗

arXiv2025

RGB-Event ISP: The Dataset and Benchmark

Event-guided imaging has received significant attention due to its potential to revolutionize instant imaging systems. However, the prior methods primarily focus on enhancing RGB images in a post-processing manner, neglecting the challenges of image signal processor (ISP) dealing with event sensor and the benefits events provide for reforming the ISP process. To achieve this, we conduct the first research on event-guided ISP. First, we present a new event-RAW paired dataset, collected with a novel but still confidential sensor that records pixel-level aligned events and RAW images. This dataset includes 3373 RAW images with 2248 x 3264 resolution and their corresponding events, spanning 24 scenes with 3 exposure modes and 3 lenses. Second, we propose a conventional ISP pipeline to generate good RGB frames as reference. This conventional ISP pipleline performs basic ISP operations, e.g.demosaicing, white balancing, denoising and color space transforming, with a ColorChecker as reference. Third, we classify the existing learnable ISP methods into 3 classes, and select multiple methods to train and evaluate on our new dataset. Lastly, since there is no prior work for reference, we propose a simple event-guided ISP method and test it on our dataset. We further put forward key technical challenges and future directions in RGB-Event ISP. In summary, to the best of our knowledge, this is the very first research focusing on event-guided ISP, and we hope it will inspire the community. The code and dataset are available at: https://github.com/yunfanLu/RGB-Event-ISP.

cs.CV↗

arXiv2025

Hierarchical Time-Aware Mixture of Experts for Multi-Modal Sequential Recommendation

Multi-modal sequential recommendation (SR) leverages multi-modal data to learn more comprehensive item features and user preferences than traditional SR methods, which has become a critical topic in both academia and industry. Existing methods typically focus on enhancing multi-modal information utility through adaptive modality fusion to capture the evolving of user preference from user-item interaction sequences. However, most of them overlook the interference caused by redundant interest-irrelevant information contained in rich multi-modal data. Additionally, they primarily rely on implicit temporal information based solely on chronological ordering, neglecting explicit temporal signals that could more effectively represent dynamic user interest over time. To address these limitations, we propose a Hierarchical time-aware Mixture of experts for multi-modal Sequential Recommendation (HM4SR) with a two-level Mixture of Experts (MoE) and a multi-task learning strategy. Specifically, the first MoE, named Interactive MoE, extracts essential user interest-related information from the multi-modal data of each item. Then, the second MoE, termed Temporal MoE, captures user dynamic interests by introducing explicit temporal embeddings from timestamps in modality encoding. To further address data sparsity, we propose three auxiliary supervision tasks: sequence-level category prediction (CP) for item feature understanding, contrastive learning on ID (IDCL) to align sequence context with user interests, and placeholder contrastive learning (PCL) to integrate temporal information with modalities for dynamic interest modeling. Extensive experiments on four public datasets verify the effectiveness of HM4SR compared to several state-of-the-art approaches.

cs.IR↗

arXiv2025

LLM-powered Multi-agent Framework for Goal-oriented Learning in Intelligent Tutoring System

Intelligent Tutoring Systems (ITSs) have revolutionized education by offering personalized learning experiences. However, as goal-oriented learning, which emphasizes efficiently achieving specific objectives, becomes increasingly important in professional contexts, existing ITSs often struggle to deliver this type of targeted learning experience. In this paper, we propose GenMentor, an LLM-powered multi-agent framework designed to deliver goal-oriented, personalized learning within ITS. GenMentor begins by accurately mapping learners' goals to required skills using a fine-tuned LLM trained on a custom goal-to-skill dataset. After identifying the skill gap, it schedules an efficient learning path using an evolving optimization approach, driven by a comprehensive and dynamic profile of learners' multifaceted status. Additionally, GenMentor tailors learning content with an exploration-drafting-integration mechanism to align with individual learner needs. Extensive automated and human evaluations demonstrate GenMentor's effectiveness in learning guidance and content quality. Furthermore, we have deployed it in practice and also implemented it as an application. Practical human study with professional learners further highlights its effectiveness in goal alignment and resource targeting, leading to enhanced personalization. Supplementary resources are available at https://github.com/GeminiLight/gen-mentor.

cs.AI↗