arXiv subjects

Yuanchun Zhou

Publications and source records attributed to Yuanchun Zhou.

At least 37 records · Page 2Linked to original sources

arXiv2025

scUnified: An AI-Ready Standardized Resource for Single-Cell RNA Sequencing Analysis

Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have been developed for tasks such as cell clustering, cell type annotation, and marker gene identification. To fully assess and compare these methods, standardized, analysis-ready datasets are essential. However, such datasets remain scarce, and variations in data formats, preprocessing workflows, and annotation strategies hinder reproducibility and complicate systematic evaluation of existing methods. To address these challenges, we present scUnified, an AI-ready standardized resource for single-cell RNA sequencing data that consolidates 13 high-quality datasets spanning two species (human and mouse) and nine tissue types. All datasets undergo standardized quality control and preprocessing and are stored in a uniform format to enable direct application in diverse computational analyses without additional data cleaning. We further demonstrate the utility of scUnified through experimental analyses of representative biological tasks, providing a reproducible foundation for the standardized evaluation of computational methods on a unified dataset.

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arXiv2025

SciTopic: Enhancing Topic Discovery in Scientific Literature through Advanced LLM

Topic discovery in scientific literature provides valuable insights for researchers to identify emerging trends and explore new avenues for investigation, facilitating easier scientific information retrieval. Many machine learning methods, particularly deep embedding techniques, have been applied to discover research topics. However, most existing topic discovery methods rely on word embedding to capture the semantics and lack a comprehensive understanding of scientific publications, struggling with complex, high-dimensional text relationships. Inspired by the exceptional comprehension of textual information by large language models (LLMs), we propose an advanced topic discovery method enhanced by LLMs to improve scientific topic identification, namely SciTopic. Specifically, we first build a textual encoder to capture the content from scientific publications, including metadata, title, and abstract. Next, we construct a space optimization module that integrates entropy-based sampling and triplet tasks guided by LLMs, enhancing the focus on thematic relevance and contextual intricacies between ambiguous instances. Then, we propose to fine-tune the textual encoder based on the guidance from the LLMs by optimizing the contrastive loss of the triplets, forcing the text encoder to better discriminate instances of different topics. Finally, extensive experiments conducted on three real-world datasets of scientific publications demonstrate that SciTopic outperforms the state-of-the-art (SOTA) scientific topic discovery methods, enabling researchers to gain deeper and faster insights.

cs.CL↗

arXiv2025

A Comprehensive Survey on Data Augmentation

Data augmentation is a series of techniques that generate high-quality artificial data by manipulating existing data samples. By leveraging data augmentation techniques, AI models can achieve significantly improved applicability in tasks involving scarce or imbalanced datasets, thereby substantially enhancing AI models' generalization capabilities. Existing literature surveys only focus on a certain type of specific modality data and categorize these methods from modality-specific and operation-centric perspectives, which lacks a consistent summary of data augmentation methods across multiple modalities and limits the comprehension of how existing data samples serve the data augmentation process. To bridge this gap, this survey proposes a more enlightening taxonomy that encompasses data augmentation techniques for different common data modalities by investigating how to take advantage of the intrinsic relationship between and within instances. Additionally, it categorizes data augmentation methods across five data modalities through a unified inductive approach.

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arXiv2025

scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data

Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have significantly improved clustering performance. However, the analysis of scRNA-seq data remains challenging due to noise, sparsity, and high dimensionality. Compounding these challenges, GNNs often suffer from over-smoothing, limiting their ability to capture complex biological information. In response, we propose scSiameseClu, a novel Siamese Clustering framework for interpreting single-cell RNA-seq data, comprising of 3 key steps: (1) Dual Augmentation Module, which applies biologically informed perturbations to the gene expression matrix and cell graph relationships to enhance representation robustness; (2) Siamese Fusion Module, which combines cross-correlation refinement and adaptive information fusion to capture complex cellular relationships while mitigating over-smoothing; and (3) Optimal Transport Clustering, which utilizes Sinkhorn distance to efficiently align cluster assignments with predefined proportions while maintaining balance. Comprehensive evaluations on seven real-world datasets demonstrate that scSiameseClu outperforms state-of-the-art methods in single-cell clustering, cell type annotation, and cell type classification, providing a powerful tool for scRNA-seq data interpretation.

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arXiv2025

scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data analysis often neglect the structural information embedded in gene expression profiles, crucial for understanding cellular correlations and dependencies. Existing strategies, including graph neural networks, face challenges in handling the inefficiency due to scRNA-seq data's intrinsic high-dimension and high-sparsity. Addressing these limitations, we introduce scCDCG (single-cell RNA-seq Clustering via Deep Cut-informed Graph), a novel framework designed for efficient and accurate clustering of scRNA-seq data that simultaneously utilizes intercellular high-order structural information. scCDCG comprises three main components: (i) A graph embedding module utilizing deep cut-informed techniques, which effectively captures intercellular high-order structural information, overcoming the over-smoothing and inefficiency issues prevalent in prior graph neural network methods. (ii) A self-supervised learning module guided by optimal transport, tailored to accommodate the unique complexities of scRNA-seq data, specifically its high-dimension and high-sparsity. (iii) An autoencoder-based feature learning module that simplifies model complexity through effective dimension reduction and feature extraction. Our extensive experiments on 6 datasets demonstrate scCDCG's superior performance and efficiency compared to 7 established models, underscoring scCDCG's potential as a transformative tool in scRNA-seq data analysis. Our code is available at: https://github.com/XPgogogo/scCDCG.

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arXiv2025

FedGCS: A Generative Framework for Efficient Client Selection in Federated Learning via Gradient-based Optimization

Federated Learning faces significant challenges in statistical and system heterogeneity, along with high energy consumption, necessitating efficient client selection strategies. Traditional approaches, including heuristic and learning-based methods, fall short of addressing these complexities holistically. In response, we propose FedGCS, a novel generative client selection framework that innovatively recasts the client selection process as a generative task. Drawing inspiration from the methodologies used in large language models, FedGCS efficiently encodes abundant decision-making knowledge within a continuous representation space, enabling efficient gradient-based optimization to search for optimal client selection that will be finally output via generation. The framework comprises four steps: (1) automatic collection of diverse "selection-score" pair data using classical client selection methods; (2) training an encoder-evaluator-decoder framework on this data to construct a continuous representation space; (3) employing gradient-based optimization in this space for optimal client selection; (4) generating the final optimal client selection via using beam search for the well-trained decoder. FedGCS outperforms traditional methods by being more comprehensive, generalizable, and efficient, simultaneously optimizing for model performance, latency, and energy consumption. The effectiveness of FedGCS is proven through extensive experimental analyses.

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arXiv2025

Zero-Shot Human Mobility Forecasting via Large Language Model with Hierarchical Reasoning

Human mobility forecasting is important for applications such as transportation planning, urban management, and personalized recommendations. However, existing methods often fail to generalize to unseen users or locations and struggle to capture dynamic intent due to limited labeled data and the complexity of mobility patterns. We propose ZHMF, a framework for zero-shot human mobility forecasting that combines a semantic enhanced retrieval and reflection mechanism with a hierarchical language model based reasoning system. The task is reformulated as a natural language question answering paradigm. Leveraging LLMs semantic understanding of user histories and context, our approach handles previously unseen prediction scenarios. We further introduce a hierarchical reflection mechanism for iterative reasoning and refinement by decomposing forecasting into an activity level planner and a location level selector, enabling collaborative modeling of long term user intentions and short term contextual preferences. Experiments on standard human mobility datasets show that our approach outperforms existing models. Ablation studies reveal the contribution of each module, and case studies illustrate how the method captures user intentions and adapts to diverse contextual scenarios.

cs.AI↗

arXiv2025

Knowledge-Guided Biomarker Identification for Label-Free Single-Cell RNA-Seq Data: A Reinforcement Learning Perspective

Gene panel selection aims to identify the most informative genomic biomarkers in label-free genomic datasets. Traditional approaches, which rely on domain expertise, embedded machine learning models, or heuristic-based iterative optimization, often introduce biases and inefficiencies, potentially obscuring critical biological signals. To address these challenges, we present an iterative gene panel selection strategy that harnesses ensemble knowledge from existing gene selection algorithms to establish preliminary boundaries or prior knowledge, which guide the initial search space. Subsequently, we incorporate reinforcement learning through a reward function shaped by expert behavior, enabling dynamic refinement and targeted selection of gene panels. This integration mitigates biases stemming from initial boundaries while capitalizing on RL's stochastic adaptability. Comprehensive comparative experiments, case studies, and downstream analyses demonstrate the effectiveness of our method, highlighting its improved precision and efficiency for label-free biomarker discovery. Our results underscore the potential of this approach to advance single-cell genomics data analysis.

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arXiv2025

Are Your LLM-based Text-to-SQL Models Secure? Exploring SQL Injection via Backdoor Attacks

Large language models (LLMs) have shown state-of-the-art results in translating natural language questions into SQL queries (Text-to-SQL), a long-standing challenge within the database community. However, security concerns remain largely unexplored, particularly the threat of backdoor attacks, which can introduce malicious behaviors into models through fine-tuning with poisoned datasets. In this work, we systematically investigate the vulnerabilities of LLM-based Text-to-SQL models and present ToxicSQL, a novel backdoor attack framework. Our approach leverages stealthy {semantic and character-level triggers} to make backdoors difficult to detect and remove, ensuring that malicious behaviors remain covert while maintaining high model accuracy on benign inputs. Furthermore, we propose leveraging SQL injection payloads as backdoor targets, enabling the generation of malicious yet executable SQL queries, which pose severe security and privacy risks in language model-based SQL development. We demonstrate that injecting only 0.44% of poisoned data can result in an attack success rate of 79.41%, posing a significant risk to database security. Additionally, we propose detection and mitigation strategies to enhance model reliability. Our findings highlight the urgent need for security-aware Text-to-SQL development, emphasizing the importance of robust defenses against backdoor threats.

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arXiv2025

Soft Graph Clustering for single-cell RNA Sequencing Data

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs), have significantly improved in tackling the challenges of high-dimension, high-sparsity, and frequent dropout events that lead to ambiguous cell population boundaries. However, their reliance on hard graph constructions derived from thresholded similarity matrices presents challenges:(i) The simplification of intercellular relationships into binary edges (0 or 1) by applying thresholds, which restricts the capture of continuous similarity features among cells and leads to significant information loss.(ii) The presence of significant inter-cluster connections within hard graphs, which can confuse GNN methods that rely heavily on graph structures, potentially causing erroneous message propagation and biased clustering outcomes. To tackle these challenges, we introduce scSGC, a Soft Graph Clustering for single-cell RNA sequencing data, which aims to more accurately characterize continuous similarities among cells through non-binary edge weights, thereby mitigating the limitations of rigid data structures. The scSGC framework comprises three core components: (i) a zero-inflated negative binomial (ZINB)-based feature autoencoder; (ii) a dual-channel cut-informed soft graph embedding module; and (iii) an optimal transport-based clustering optimization module. Extensive experiments across ten datasets demonstrate that scSGC outperforms 13 state-of-the-art clustering models in clustering accuracy, cell type annotation, and computational efficiency. These results highlight its substantial potential to advance scRNA-seq data analysis and deepen our understanding of cellular heterogeneity.

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arXiv2025

Reinforcement Learning-based Feature Generation Algorithm for Scientific Data

Feature generation (FG) aims to enhance the prediction potential of original data by constructing high-order feature combinations and removing redundant features. It is a key preprocessing step for tabular scientific data to improve downstream machine-learning model performance. Traditional methods face the following two challenges when dealing with the feature generation of scientific data: First, the effective construction of high-order feature combinations in scientific data necessitates profound and extensive domain-specific expertise. Secondly, as the order of feature combinations increases, the search space expands exponentially, imposing prohibitive human labor consumption. Advancements in the Data-Centric Artificial Intelligence (DCAI) paradigm have opened novel avenues for automating feature generation processes. Inspired by that, this paper revisits the conventional feature generation workflow and proposes the Multi-agent Feature Generation (MAFG) framework. Specifically, in the iterative exploration stage, multi-agents will construct mathematical transformation equations collaboratively, synthesize and identify feature combinations ex-hibiting high information content, and leverage a reinforcement learning mechanism to evolve their strategies. Upon completing the exploration phase, MAFG integrates the large language models (LLMs) to interpreta-tively evaluate the generated features of each significant model performance breakthrough. Experimental results and case studies consistently demonstrate that the MAFG framework effectively automates the feature generation process and significantly enhances various downstream scientific data mining tasks.

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arXiv2025

Diversity-oriented Data Augmentation with Large Language Models

Data augmentation is an essential technique in natural language processing (NLP) for enriching training datasets by generating diverse samples. This process is crucial for improving the robustness and generalization capabilities of NLP models. However, a significant challenge remains: \textit{Insufficient Attention to Sample Distribution Diversity}. Most existing methods focus on increasing the sample numbers while neglecting the sample distribution diversity, which can lead to model overfitting. In response, we explore data augmentation's impact on dataset diversity and propose a \textbf{\underline{D}}iversity-\textbf{\underline{o}}riented data \textbf{\underline{Aug}}mentation framework (\textbf{DoAug}). % \(\mathscr{DoAug}\) Specifically, we utilize a diversity-oriented fine-tuning approach to train an LLM as a diverse paraphraser, which is capable of augmenting textual datasets by generating diversified paraphrases. Then, we apply the LLM paraphraser to a selected coreset of highly informative samples and integrate the paraphrases with the original data to create a more diverse augmented dataset. Finally, we conduct extensive experiments on 12 real-world textual datasets. The results show that our fine-tuned LLM augmenter improves diversity while preserving label consistency, thereby enhancing the robustness and performance of downstream tasks. Specifically, it achieves an average performance gain of \(10.52\%\), surpassing the runner-up baseline with more than three percentage points.

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arXiv2025

SciHorizon: Benchmarking AI-for-Science Readiness from Scientific Data to Large Language Models

In recent years, the rapid advancement of Artificial Intelligence (AI) technologies, particularly Large Language Models (LLMs), has revolutionized the paradigm of scientific discovery, establishing AI-for-Science (AI4Science) as a dynamic and evolving field. However, there is still a lack of an effective framework for the overall assessment of AI4Science, particularly from a holistic perspective on data quality and model capability. Therefore, in this study, we propose SciHorizon, a comprehensive assessment framework designed to benchmark the readiness of AI4Science from both scientific data and LLM perspectives. First, we introduce a generalizable framework for assessing AI-ready scientific data, encompassing four key dimensions: Quality, FAIRness, Explainability, and Compliance-which are subdivided into 15 sub-dimensions. Drawing on data resource papers published between 2018 and 2023 in peer-reviewed journals, we present recommendation lists of AI-ready datasets for Earth, Life, and Materials Sciences, making a novel and original contribution to the field. Concurrently, to assess the capabilities of LLMs across multiple scientific disciplines, we establish 16 assessment dimensions based on five core indicators Knowledge, Understanding, Reasoning, Multimodality, and Values spanning Mathematics, Physics, Chemistry, Life Sciences, and Earth and Space Sciences. Using the developed benchmark datasets, we have conducted a comprehensive evaluation of over 50 representative open-source and closed source LLMs. All the results are publicly available and can be accessed online at www.scihorizon.cn/en.

cs.LG↗

arXiv2025

Disentangled Multi-span Evolutionary Network against Temporal Knowledge Graph Reasoning

Temporal Knowledge Graphs (TKGs), as an extension of static Knowledge Graphs (KGs), incorporate the temporal feature to express the transience of knowledge by describing when facts occur. TKG extrapolation aims to infer possible future facts based on known history, which has garnered significant attention in recent years. Some existing methods treat TKG as a sequence of independent subgraphs to model temporal evolution patterns, demonstrating impressive reasoning performance. However, they still have limitations: 1) In modeling subgraph semantic evolution, they usually neglect the internal structural interactions between subgraphs, which are actually crucial for encoding TKGs. 2) They overlook the potential smooth features that do not lead to semantic changes, which should be distinguished from the semantic evolution process. Therefore, we propose a novel Disentangled Multi-span Evolutionary Network (DiMNet) for TKG reasoning. Specifically, we design a multi-span evolution strategy that captures local neighbor features while perceiving historical neighbor semantic information, thus enabling internal interactions between subgraphs during the evolution process. To maximize the capture of semantic change patterns, we design a disentangle component that adaptively separates nodes' active and stable features, used to dynamically control the influence of historical semantics on future evolution. Extensive experiments conducted on four real-world TKG datasets show that DiMNet demonstrates substantial performance in TKG reasoning, and outperforms the state-of-the-art up to 22.7% in MRR.

cs.AI↗

arXiv2025

Distilling Closed-Source LLM's Knowledge for Locally Stable and Economic Biomedical Entity Linking

Biomedical entity linking aims to map nonstandard entities to standard entities in a knowledge base. Traditional supervised methods perform well but require extensive annotated data to transfer, limiting their usage in low-resource scenarios. Large language models (LLMs), especially closed-source LLMs, can address these but risk stability issues and high economic costs: using these models is restricted by commercial companies and brings significant economic costs when dealing with large amounts of data. To address this, we propose ``RPDR'', a framework combining closed-source LLMs and open-source LLMs for re-ranking candidates retrieved by a retriever fine-tuned with a small amount of data. By prompting a closed-source LLM to generate training data from unannotated data and fine-tuning an open-source LLM for re-ranking, we effectively distill the knowledge to the open-source LLM that can be deployed locally, thus avoiding the stability issues and the problem of high economic costs. We evaluate RPDR on two datasets, including one real-world dataset and one publicly available dataset involving two languages: Chinese and English. RPDR achieves 0.019 Acc@1 improvement and 0.036 Acc@1 improvement on the Aier dataset and the Ask A Patient dataset when the amount of training data is not enough. The results demonstrate the superiority and generalizability of the proposed framework.

cs.CL↗

arXiv2025

COMAE: COMprehensive Attribute Exploration for Zero-shot Hashing

Zero-shot hashing (ZSH) has shown excellent success owing to its efficiency and generalization in large-scale retrieval scenarios. While considerable success has been achieved, there still exist urgent limitations. Existing works ignore the locality relationships of representations and attributes, which have effective transferability between seeable classes and unseeable classes. Also, the continuous-value attributes are not fully harnessed. In response, we conduct a COMprehensive Attribute Exploration for ZSH, named COMAE, which depicts the relationships from seen classes to unseen ones through three meticulously designed explorations, i.e., point-wise, pair-wise and class-wise consistency constraints. By regressing attributes from the proposed attribute prototype network, COMAE learns the local features that are relevant to the visual attributes. Then COMAE utilizes contrastive learning to comprehensively depict the context of attributes, rather than instance-independent optimization. Finally, the class-wise constraint is designed to cohesively learn the hash code, image representation, and visual attributes more effectively. Experimental results on the popular ZSH datasets demonstrate that COMAE outperforms state-of-the-art hashing techniques, especially in scenarios with a larger number of unseen label classes.

cs.CV↗

arXiv2025

Rethinking Graph Contrastive Learning through Relative Similarity Preservation

Graph contrastive learning (GCL) has achieved remarkable success by following the computer vision paradigm of preserving absolute similarity between augmented views. However, this approach faces fundamental challenges in graphs due to their discrete, non-Euclidean nature -- view generation often breaks semantic validity and similarity verification becomes unreliable. Through analyzing 11 real-world graphs, we discover a universal pattern transcending the homophily-heterophily dichotomy: label consistency systematically diminishes as structural distance increases, manifesting as smooth decay in homophily graphs and oscillatory decay in heterophily graphs. We establish theoretical guarantees for this pattern through random walk theory, proving label distribution convergence and characterizing the mechanisms behind different decay behaviors. This discovery reveals that graphs naturally encode relative similarity patterns, where structurally closer nodes exhibit collectively stronger semantic relationships. Leveraging this insight, we propose RELGCL, a novel GCL framework with complementary pairwise and listwise implementations that preserve these inherent patterns through collective similarity objectives. Extensive experiments demonstrate that our method consistently outperforms 20 existing approaches across both homophily and heterophily graphs, validating the effectiveness of leveraging natural relative similarity over artificial absolute similarity.

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arXiv2025

Deep Cut-informed Graph Embedding and Clustering

Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a common issue of representation collapse in existing GNN-based deep graph clustering algorithms. We attribute two main reasons for such issues: (i) the inductive bias of GNN models: GNNs tend to generate similar representations for proximal nodes. Since graphs often contain a non-negligible amount of inter-cluster links, the bias results in error message passing and leads to biased clustering; (ii) the clustering guided loss function: most traditional approaches strive to make all samples closer to pre-learned cluster centers, which causes a degenerate solution assigning all data points to a single label thus making all samples similar and less discriminative. To address these challenges, we investigate graph clustering from a graph cut perspective and propose an innovative and non-GNN-based Deep Cut-informed Graph embedding and Clustering framework, namely DCGC. This framework includes two modules: (i) cut-informed graph encoding; (ii) self-supervised graph clustering via optimal transport. For the encoding module, we derive a cut-informed graph embedding objective to fuse graph structure and attributes by minimizing their joint normalized cut. For the clustering module, we utilize the optimal transport theory to obtain the clustering assignments, which can balance the guidance of "proximity to the pre-learned cluster center". With the above two tailored designs, DCGC is more suitable for the graph clustering task, which can effectively alleviate the problem of representation collapse and achieve better performance. We conduct extensive experiments to demonstrate that our method is simple but effective compared with benchmarks.

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