Yuanchun Zhou

Wei Fan, Pengyang Wang, Dongkun Wang et al.

The distribution shift in Time Series Forecasting (TSF), indicating series distribution changes over time, largely hinders the performance of TSF models. Existing works towards distribution shift in time series are mostly limited in the quantification of distribution and, more importantly, overlook the potential shift between lookback and horizon windows. To address above challenges, we systematically summarize the distribution shift in TSF into two categories. Regarding lookback windows as input-space and horizon windows as output-space, there exist (i) intra-space shift, that the distribution within the input-space keeps shifted over time, and (ii) inter-space shift, that the distribution is shifted between input-space and output-space. Then we introduce, Dish-TS, a general neural paradigm for alleviating distribution shift in TSF. Specifically, for better distribution estimation, we propose the coefficient net (CONET), which can be any neural architectures, to map input sequences into learnable distribution coefficients. To relieve intra-space and inter-space shift, we organize Dish-TS as a Dual-CONET framework to separately learn the distribution of input- and output-space, which naturally captures the distribution difference of two spaces. In addition, we introduce a more effective training strategy for intractable CONET learning. Finally, we conduct extensive experiments on several datasets coupled with different state-of-the-art forecasting models. Experimental results show Dish-TS consistently boosts them with a more than 20% average improvement. Code is available.

Meng Xiao, Dongjie Wang, Min Wu et al.

Feature transformation aims to reconstruct an effective representation space by mathematically refining the existing features. It serves as a pivotal approach to combat the curse of dimensionality, enhance model generalization, mitigate data sparsity, and extend the applicability of classical models. Existing research predominantly focuses on domain knowledge-based feature engineering or learning latent representations. However, these methods, while insightful, lack full automation and fail to yield a traceable and optimal representation space. An indispensable question arises: Can we concurrently address these limitations when reconstructing a feature space for a machine-learning task? Our initial work took a pioneering step towards this challenge by introducing a novel self-optimizing framework. This framework leverages the power of three cascading reinforced agents to automatically select candidate features and operations for generating improved feature transformation combinations. Despite the impressive strides made, there was room for enhancing its effectiveness and generalization capability. In this extended journal version, we advance our initial work from two distinct yet interconnected perspectives: 1) We propose a refinement of the original framework, which integrates a graph-based state representation method to capture the feature interactions more effectively and develop different Q-learning strategies to alleviate Q-value overestimation further. 2) We utilize a new optimization technique (actor-critic) to train the entire self-optimizing framework in order to accelerate the model convergence and improve the feature transformation performance. Finally, to validate the improved effectiveness and generalization capability of our framework, we perform extensive experiments and conduct comprehensive analyses.

Meng Xiao, Dongjie Wang, Min Wu et al.

The goal of Feature Selection - comprising filter, wrapper, and embedded approaches - is to find the optimal feature subset for designated downstream tasks. Nevertheless, current feature selection methods are limited by: 1) the selection criteria of these methods are varied for different domains, making them hard to generalize; 2) the selection performance of these approaches drops significantly when processing high-dimensional feature space coupled with small sample size. In light of these challenges, we pose the question: can selected feature subsets be more robust, accurate, and input dimensionality agnostic? In this paper, we reformulate the feature selection problem as a deep differentiable optimization task and propose a new research perspective: conceptualizing discrete feature subsetting as continuous embedding space optimization. We introduce a novel and principled framework that encompasses a sequential encoder, an accuracy evaluator, a sequential decoder, and a gradient ascent optimizer. This comprehensive framework includes four important steps: preparation of features-accuracy training data, deep feature subset embedding, gradient-optimized search, and feature subset reconstruction. Specifically, we utilize reinforcement feature selection learning to generate diverse and high-quality training data and enhance generalization. By optimizing reconstruction and accuracy losses, we embed feature selection knowledge into a continuous space using an encoder-evaluator-decoder model structure. We employ a gradient ascent search algorithm to find better embeddings in the learned embedding space. Furthermore, we reconstruct feature selection solutions using these embeddings and select the feature subset with the highest performance for downstream tasks as the optimal subset.

Dongjie Wang, Meng Xiao, Min Wu et al.

Feature transformation aims to generate new pattern-discriminative feature space from original features to improve downstream machine learning (ML) task performances. However, the discrete search space for the optimal feature explosively grows on the basis of combinations of features and operations from low-order forms to high-order forms. Existing methods, such as exhaustive search, expansion reduction, evolutionary algorithms, reinforcement learning, and iterative greedy, suffer from large search space. Overly emphasizing efficiency in algorithm design usually sacrifices stability or robustness. To fundamentally fill this gap, we reformulate discrete feature transformation as a continuous space optimization task and develop an embedding-optimization-reconstruction framework. This framework includes four steps: 1) reinforcement-enhanced data preparation, aiming to prepare high-quality transformation-accuracy training data; 2) feature transformation operation sequence embedding, intending to encapsulate the knowledge of prepared training data within a continuous space; 3) gradient-steered optimal embedding search, dedicating to uncover potentially superior embeddings within the learned space; 4) transformation operation sequence reconstruction, striving to reproduce the feature transformation solution to pinpoint the optimal feature space.

Meng Xiao, Dongjie Wang, Min Wu et al.

Feature transformation for AI is an essential task to boost the effectiveness and interpretability of machine learning (ML). Feature transformation aims to transform original data to identify an optimal feature space that enhances the performances of a downstream ML model. Existing studies either combines preprocessing, feature selection, and generation skills to empirically transform data, or automate feature transformation by machine intelligence, such as reinforcement learning. However, existing studies suffer from: 1) high-dimensional non-discriminative feature space; 2) inability to represent complex situational states; 3) inefficiency in integrating local and global feature information. To fill the research gap, we formulate the feature transformation task as an iterative, nested process of feature generation and selection, where feature generation is to generate and add new features based on original features, and feature selection is to remove redundant features to control the size of feature space. Finally, we present extensive experiments and case studies to illustrate 24.7\% improvements in F1 scores compared with SOTAs and robustness in high-dimensional data.

Hao Dong, Zhiyuan Ning, Pengyang Wang et al.

Temporal knowledge graph (TKG) reasoning aims to predict the future missing facts based on historical information and has gained increasing research interest recently. Lots of works have been made to model the historical structural and temporal characteristics for the reasoning task. Most existing works model the graph structure mainly depending on entity representation. However, the magnitude of TKG entities in real-world scenarios is considerable, and an increasing number of new entities will arise as time goes on. Therefore, we propose a novel architecture modeling with relation feature of TKG, namely aDAptivE path-MemOry Network (DaeMon), which adaptively models the temporal path information between query subject and each object candidate across history time. It models the historical information without depending on entity representation. Specifically, DaeMon uses path memory to record the temporal path information derived from path aggregation unit across timeline considering the memory passing strategy between adjacent timestamps. Extensive experiments conducted on four real-world TKG datasets demonstrate that our proposed model obtains substantial performance improvement and outperforms the state-of-the-art up to 4.8% absolute in MRR.

Meng Xiao, Ziyue Qiao, Yanjie Fu et al.

The peer merit review of research proposals has been the major mechanism for deciding grant awards. However, research proposals have become increasingly interdisciplinary. It has been a longstanding challenge to assign interdisciplinary proposals to appropriate reviewers, so proposals are fairly evaluated. One of the critical steps in reviewer assignment is to generate accurate interdisciplinary topic labels for proposal-reviewer matching. Existing systems mainly collect topic labels manually generated by principal investigators. However, such human-reported labels can be non-accurate, incomplete, labor intensive, and time costly. What role can AI play in developing a fair and precise proposal reviewer assignment system? In this study, we collaborate with the National Science Foundation of China to address the task of automated interdisciplinary topic path detection. For this purpose, we develop a deep Hierarchical Interdisciplinary Research Proposal Classification Network (HIRPCN). Specifically, we first propose a hierarchical transformer to extract the textual semantic information of proposals. We then design an interdisciplinary graph and leverage GNNs for learning representations of each discipline in order to extract interdisciplinary knowledge. After extracting the semantic and interdisciplinary knowledge, we design a level-wise prediction component to fuse the two types of knowledge representations and detect interdisciplinary topic paths for each proposal. We conduct extensive experiments and expert evaluations on three real-world datasets to demonstrate the effectiveness of our proposed model.

Hao Dong, Pengyang Wang, Meng Xiao et al.

Temporal Knowledge Graph (TKG) is an extension of traditional Knowledge Graph (KG) that incorporates the dimension of time. Reasoning on TKGs is a crucial task that aims to predict future facts based on historical occurrences. The key challenge lies in uncovering structural dependencies within historical subgraphs and temporal patterns. Most existing approaches model TKGs relying on entity modeling, as nodes in the graph play a crucial role in knowledge representation. However, the real-world scenario often involves an extensive number of entities, with new entities emerging over time. This makes it challenging for entity-dependent methods to cope with extensive volumes of entities, and effectively handling newly emerging entities also becomes a significant challenge. Therefore, we propose Temporal Inductive Path Neural Network (TiPNN), which models historical information in an entity-independent perspective. Specifically, TiPNN adopts a unified graph, namely history temporal graph, to comprehensively capture and encapsulate information from history. Subsequently, we utilize the defined query-aware temporal paths on a history temporal graph to model historical path information related to queries for reasoning. Extensive experiments illustrate that the proposed model not only attains significant performance enhancements but also handles inductive settings, while additionally facilitating the provision of reasoning evidence through history temporal graphs.

Meng Xiao, Ziyue Qiao, Yanjie Fu et al.

The peer merit review of research proposals has been the major mechanism to decide grant awards. Nowadays, research proposals have become increasingly interdisciplinary. It has been a longstanding challenge to assign proposals to appropriate reviewers. One of the critical steps in reviewer assignment is to generate accurate interdisciplinary topic labels for proposals. Existing systems mainly collect topic labels manually reported by discipline investigators. However, such human-reported labels can be non-accurate and incomplete. What role can AI play in developing a fair and precise proposal review system? In this evidential study, we collaborate with the National Science Foundation of China to address the task of automated interdisciplinary topic path detection. For this purpose, we develop a deep Hierarchical Interdisciplinary Research Proposal Classification Network (HIRPCN). We first propose a hierarchical transformer to extract the textual semantic information of proposals. We then design an interdisciplinary graph and leverage GNNs to learn representations of each discipline in order to extract interdisciplinary knowledge. After extracting the semantic and interdisciplinary knowledge, we design a level-wise prediction component to fuse the two types of knowledge representations and detect interdisciplinary topic paths for each proposal. We conduct extensive experiments and expert evaluations on three real-world datasets to demonstrate the effectiveness of our proposed model.

Meng Xiao, Dongjie Wang, Min Wu et al.

Feature transformation aims to extract a good representation (feature) space by mathematically transforming existing features. It is crucial to address the curse of dimensionality, enhance model generalization, overcome data sparsity, and expand the availability of classic models. Current research focuses on domain knowledge-based feature engineering or learning latent representations; nevertheless, these methods are not entirely automated and cannot produce a traceable and optimal representation space. When rebuilding a feature space for a machine learning task, can these limitations be addressed concurrently? In this extension study, we present a self-optimizing framework for feature transformation. To achieve a better performance, we improved the preliminary work by (1) obtaining an advanced state representation for enabling reinforced agents to comprehend the current feature set better; and (2) resolving Q-value overestimation in reinforced agents for learning unbiased and effective policies. Finally, to make experiments more convincing than the preliminary work, we conclude by adding the outlier detection task with five datasets, evaluating various state representation approaches, and comparing different training strategies. Extensive experiments and case studies show that our work is more effective and superior.

Guojiao Lin, Zhen Meng, Dongjie Wang et al.

Multimodal recommendation systems (MMRS) have received considerable attention from the research community due to their ability to jointly utilize information from user behavior and product images and text. Previous research has two main issues. First, many long-tail items in recommendation systems have limited interaction data, making it difficult to learn comprehensive and informative representations. However, past MMRS studies have overlooked this issue. Secondly, users' modality preferences are crucial to their behavior. However, previous research has primarily focused on learning item modality representations, while user modality representations have remained relatively simplistic.To address these challenges, we propose a novel Graphs and User Modalities Enhancement (GUME) for long-tail multimodal recommendation. Specifically, we first enhance the user-item graph using multimodal similarity between items. This improves the connectivity of long-tail items and helps them learn high-quality representations through graph propagation. Then, we construct two types of user modalities: explicit interaction features and extended interest features. By using the user modality enhancement strategy to maximize mutual information between these two features, we improve the generalization ability of user modality representations. Additionally, we design an alignment strategy for modality data to remove noise from both internal and external perspectives. Extensive experiments on four publicly available datasets demonstrate the effectiveness of our approach.

Ziyue Qiao, Xiao Luo, Meng Xiao et al.

As a specific case of graph transfer learning, unsupervised domain adaptation on graphs aims for knowledge transfer from label-rich source graphs to unlabeled target graphs. However, graphs with topology and attributes usually have considerable cross-domain disparity and there are numerous real-world scenarios where merely a subset of nodes are labeled in the source graph. This imposes critical challenges on graph transfer learning due to serious domain shifts and label scarcity. To address these challenges, we propose a method named Semi-supervised Graph Domain Adaptation (SGDA). To deal with the domain shift, we add adaptive shift parameters to each of the source nodes, which are trained in an adversarial manner to align the cross-domain distributions of node embedding, thus the node classifier trained on labeled source nodes can be transferred to the target nodes. Moreover, to address the label scarcity, we propose pseudo-labeling on unlabeled nodes, which improves classification on the target graph via measuring the posterior influence of nodes based on their relative position to the class centroids. Finally, extensive experiments on a range of publicly accessible datasets validate the effectiveness of our proposed SGDA in different experimental settings.

Meng Xiao, Min Wu, Ziyue Qiao et al.

Funding agencies are largely relied on a topic matching between domain experts and research proposals to assign proposal reviewers. As proposals are increasingly interdisciplinary, it is challenging to profile the interdisciplinary nature of a proposal, and, thereafter, find expert reviewers with an appropriate set of expertise. An essential step in solving this challenge is to accurately model and classify the interdisciplinary labels of a proposal. Existing methodological and application-related literature, such as textual classification and proposal classification, are insufficient in jointly addressing the three key unique issues introduced by interdisciplinary proposal data: 1) the hierarchical structure of discipline labels of a proposal from coarse-grain to fine-grain, e.g., from information science to AI to fundamentals of AI. 2) the heterogeneous semantics of various main textual parts that play different roles in a proposal; 3) the number of proposals is imbalanced between non-interdisciplinary and interdisciplinary research. Can we simultaneously address the three issues in understanding the proposal's interdisciplinary nature? In response to this question, we propose a hierarchical mixup multiple-label classification framework, which we called H-MixUp. H-MixUp leverages a transformer-based semantic information extractor and a GCN-based interdisciplinary knowledge extractor for the first and second issues. H-MixUp develops a fused training method of Wold-level MixUp, Word-level CutMix, Manifold MixUp, and Document-level MixUp to address the third issue.

Zhiyuan Ning, Pengfei Wang, Pengyang Wang et al.

Graph Contrastive Learning (GCL) has emerged as a promising approach in the realm of graph self-supervised learning. Prevailing GCL methods mainly derive from the principles of contrastive learning in the field of computer vision: modeling invariance by specifying absolutely similar pairs. However, when applied to graph data, this paradigm encounters two significant limitations: (1) the validity of the generated views cannot be guaranteed: graph perturbation may produce invalid views against semantics and intrinsic topology of graph data; (2) specifying absolutely similar pairs in the graph views is unreliable: for abstract and non-Euclidean graph data, it is difficult for humans to decide the absolute similarity and dissimilarity intuitively. Despite the notable performance of current GCL methods, these challenges necessitate a reevaluation: Could GCL be more effectively tailored to the intrinsic properties of graphs, rather than merely adopting principles from computer vision? In response to this query, we propose a novel paradigm, Graph Soft-Contrastive Learning (GSCL). This approach facilitates GCL via neighborhood ranking, avoiding the need to specify absolutely similar pairs. GSCL leverages the underlying graph characteristic of diminishing label consistency, asserting that nodes that are closer in the graph are overall more similar than far-distant nodes. Within the GSCL framework, we introduce pairwise and listwise gated ranking InfoNCE loss functions to effectively preserve the relative similarity ranking within neighborhoods. Moreover, as the neighborhood size exponentially expands with more hops considered, we propose neighborhood sampling strategies to improve learning efficiency. Our extensive empirical results across 11 commonly used graph datasets-including 8 homophily graphs and 3 heterophily graphs-demonstrate GSCL's superior performance compared to 20 SOTA GCL methods.

Chengrui Wang, Qingqing Long, Meng Xiao et al.

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

Xunxin Cai, Meng Xiao, Zhiyuan Ning et al.

In addressing the imbalanced issue of data within the realm of Natural Language Processing, text data augmentation methods have emerged as pivotal solutions. This data imbalance is prevalent in the research proposals submitted during the funding application process. Such imbalances, resulting from the varying popularity of disciplines or the emergence of interdisciplinary studies, significantly impede the precision of downstream topic models that deduce the affiliated disciplines of these proposals. At the data level, proposals penned by experts and scientists are inherently complex technological texts, replete with intricate terminologies, which augmenting such specialized text data poses unique challenges. At the system level, this, in turn, compromises the fairness of AI-assisted reviewer assignment systems, which raises a spotlight on solving this issue. This study leverages large language models (Llama V1) as data generators to augment research proposals categorized within intricate disciplinary hierarchies, aiming to rectify data imbalances and enhance the equity of expert assignments. We first sample within the hierarchical structure to find the under-represented class. Then we designed a prompt for keyword-based research proposal generation. Our experiments attests to the efficacy of the generated data, demonstrating that research proposals produced using the prompts can effectively address the aforementioned issues and generate high quality scientific text data, thus help the model overcome the imbalanced issue.

Meng Xiao, Min Wu, Ziyue Qiao et al.

The objective of topic inference in research proposals aims to obtain the most suitable disciplinary division from the discipline system defined by a funding agency. The agency will subsequently find appropriate peer review experts from their database based on this division. Automated topic inference can reduce human errors caused by manual topic filling, bridge the knowledge gap between funding agencies and project applicants, and improve system efficiency. Existing methods focus on modeling this as a hierarchical multi-label classification problem, using generative models to iteratively infer the most appropriate topic information. However, these methods overlook the gap in scale between interdisciplinary research proposals and non-interdisciplinary ones, leading to an unjust phenomenon where the automated inference system categorizes interdisciplinary proposals as non-interdisciplinary, causing unfairness during the expert assignment. How can we address this data imbalance issue under a complex discipline system and hence resolve this unfairness? In this paper, we implement a topic label inference system based on a Transformer encoder-decoder architecture. Furthermore, we utilize interpolation techniques to create a series of pseudo-interdisciplinary proposals from non-interdisciplinary ones during training based on non-parametric indicators such as cross-topic probabilities and topic occurrence probabilities. This approach aims to reduce the bias of the system during model training. Finally, we conduct extensive experiments on a real-world dataset to verify the effectiveness of the proposed method. The experimental results demonstrate that our training strategy can significantly mitigate the unfairness generated in the topic inference task.

Xu Ye, Meng Xiao, Zhiyuan Ning et al.

With the development of natural language processing techniques(NLP), automatic diagnosis of eye diseases using ophthalmology electronic medical records (OEMR) has become possible. It aims to evaluate the condition of both eyes of a patient respectively, and we formulate it as a particular multi-label classification task in this paper. Although there are a few related studies in other diseases, automatic diagnosis of eye diseases exhibits unique characteristics. First, descriptions of both eyes are mixed up in OEMR documents, with both free text and templated asymptomatic descriptions, resulting in sparsity and clutter of information. Second, OEMR documents contain multiple parts of descriptions and have long document lengths. Third, it is critical to provide explainability to the disease diagnosis model. To overcome those challenges, we present an effective automatic eye disease diagnosis framework, NEEDED. In this framework, a preprocessing module is integrated to improve the density and quality of information. Then, we design a hierarchical transformer structure for learning the contextualized representations of each sentence in the OEMR document. For the diagnosis part, we propose an attention-based predictor that enables traceable diagnosis by obtaining disease-specific information. Experiments on the real dataset and comparison with several baseline models show the advantage and explainability of our framework.

Le Ma, Ran Zhang, Yikun Han et al.

Vector databases (VDBs) have emerged to manage high-dimensional data that exceed the capabilities of traditional database management systems, and are now tightly integrated with large language models as well as widely applied in modern artificial intelligence systems. Although relatively few studies describe existing or introduce new vector database architectures, the core technologies underlying VDBs, such as approximate nearest neighbor search, have been extensively studied and are well documented in the literature. In this work, we present a comprehensive review of the relevant algorithms to provide a general understanding of this booming research area. Specifically, we first provide a review of storage and retrieval techniques in VDBs, with detailed design principles and technological evolution. Then, we conduct an in-depth comparison of several advanced VDB solutions with their strengths, limitations, and typical application scenarios. Finally, we also outline emerging opportunities for coupling VDBs with large language models, including open research problems and trends, such as novel indexing strategies. This survey aims to serve as a practical resource, enabling readers to quickly gain an overall understanding of the current knowledge landscape in this rapidly developing area.

Qinlong Wang, Tingfeng Lan, Yinghao Tang et al.

Deep learning recommendation models (DLRM) rely on large embedding tables to manage categorical sparse features. Expanding such embedding tables can significantly enhance model performance, but at the cost of increased GPU/CPU/memory usage. Meanwhile, tech companies have built extensive cloud-based services to accelerate training DLRM models at scale. In this paper, we conduct a deep investigation of the DLRM training platforms at AntGroup and reveal two critical challenges: low resource utilization due to suboptimal configurations by users and the tendency to encounter abnormalities due to an unstable cloud environment. To overcome them, we introduce DLRover-RM, an elastic training framework for DLRMs designed to increase resource utilization and handle the instability of a cloud environment. DLRover-RM develops a resource-performance model by considering the unique characteristics of DLRMs and a three-stage heuristic strategy to automatically allocate and dynamically adjust resources for DLRM training jobs for higher resource utilization. Further, DLRover-RM develops multiple mechanisms to ensure efficient and reliable execution of DLRM training jobs. Our extensive evaluation shows that DLRover-RM reduces job completion times by 31%, increases the job completion rate by 6%, enhances CPU usage by 15%, and improves memory utilization by 20%, compared to state-of-the-art resource scheduling frameworks. DLRover-RM has been widely deployed at AntGroup and processes thousands of DLRM training jobs on a daily basis. DLRover-RM is open-sourced and has been adopted by 10+ companies.

Siyu Pu, Qingqing Long, Xiaohan Huang et al.

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points as unpaired snapshot populations, leaving substantial temporal gaps. This motivates trajectory inference at unmeasured time points. Existing methods mainly follow two directions, optimal-transport (OT) alignment provides distribution-level matching between observed snapshots, while continuous-time generative models support forecasting via learned dynamics. However, two challenges remain: (i) unpaired snapshots render local transitions between adjacent time points ambiguous, leading to unstable supervision; and (ii) long-horizon prediction relies on repeated integration, where small modeling errors compound and cause distribution drift. To address these challenges, we propose single-cell Flow Matching (scFM), a latent generative framework based on coupling-conditioned flow matching. First, we compute entropically regularized OT couplings between adjacent snapshots and use them to construct soft, weighted flow-matching targets for learning time-dependent velocity fields. Second, we learn bidirectional velocity fields and leverage their consistency to refine couplings and improve temporal coherence under sparse supervision. Third, we introduce distribution-level alignment and latent dynamic regularization to anchor long rollouts and mitigate drift. Experiments on real-world time-series scRNA-seq datasets show that scFM consistently improves distributional prediction performance for both temporal interpolation and extrapolation. Moreover, scFM yields more accurate trajectory reconstruction and temporally coherent visualizations where intermediate time points are absent, indicating a more faithful recovery of underlying temporal gene expression dynamics.

Ping Xu, Zaitian Wang, Zhirui Wang et al.

Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain fragmented, often lacking standardized protocols and failing to incorporate recent advances in artificial intelligence. To fill these gaps, we present scCluBench, a comprehensive benchmark of clustering algorithms for scRNA-seq data. First, scCluBench provides 36 scRNA-seq datasets collected from diverse public sources, covering multiple tissues, which are uniformly processed and standardized to ensure consistency for systematic evaluation and downstream analyses. To evaluate performance, we collect and reproduce a range of scRNA-seq clustering methods, including traditional, deep learning-based, graph-based, and biological foundation models. We comprehensively evaluate each method both quantitatively and qualitatively, using core performance metrics as well as visualization analyses. Furthermore, we construct representative downstream biological tasks, such as marker gene identification and cell type annotation, to further assess the practical utility. scCluBench then investigates the performance differences and applicability boundaries of various clustering models across diverse analytical tasks, systematically assessing their robustness and scalability in real-world scenarios. Overall, scCluBench offers a standardized and user-friendly benchmark for scRNA-seq clustering, with curated datasets, unified evaluation protocols, and transparent analyses, facilitating informed method selection and providing valuable insights into model generalizability and application scope.

Ludi Wang, Xueqing Chen, Yi Du et al.

The field of catalysis holds paramount importance in shaping the trajectory of sustainable development, prompting intensive research efforts to leverage artificial intelligence (AI) in catalyst design. Presently, the fine-tuning of open-source large language models (LLMs) has yielded significant breakthroughs across various domains such as biology and healthcare. Drawing inspiration from these advancements, we introduce CataLM Cata}lytic Language Model), a large language model tailored to the domain of electrocatalytic materials. Our findings demonstrate that CataLM exhibits remarkable potential for facilitating human-AI collaboration in catalyst knowledge exploration and design. To the best of our knowledge, CataLM stands as the pioneering LLM dedicated to the catalyst domain, offering novel avenues for catalyst discovery and development.

Ping Xu, Zhiyuan Ning, Meng Xiao et al.

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.

Qingqing Long, Yuchen Yan, Peiyan Zhang et al.

Large-scale "pre-train and prompt learning" paradigms have demonstrated remarkable adaptability, enabling broad applications across diverse domains such as question answering, image recognition, and multimodal retrieval. This approach fully leverages the potential of large-scale pre-trained models, reducing downstream data requirements and computational costs while enhancing model applicability across various tasks. Graphs, as versatile data structures that capture relationships between entities, play pivotal roles in fields such as social network analysis, recommender systems, and biological graphs. Despite the success of pre-train and prompt learning paradigms in Natural Language Processing (NLP) and Computer Vision (CV), their application in graph domains remains nascent. In graph-structured data, not only do the node and edge features often have disparate distributions, but the topological structures also differ significantly. This diversity in graph data can lead to incompatible patterns or gaps between pre-training and fine-tuning on downstream graphs. We aim to bridge this gap by summarizing methods for alleviating these disparities. This includes exploring prompt design methodologies, comparing related techniques, assessing application scenarios and datasets, and identifying unresolved problems and challenges. This survey categorizes over 100 relevant works in this field, summarizing general design principles and the latest applications, including text-attributed graphs, molecules, proteins, and recommendation systems. Through this extensive review, we provide a foundational understanding of graph prompt learning, aiming to impact not only the graph mining community but also the broader Artificial General Intelligence (AGI) community.

Haotian Chen, Qingqing Long, Siyu Pu et al.

With the rapid growth of scientific literature, scientific question answering (SciQA) has become increasingly critical for exploring and utilizing scientific knowledge. Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating knowledge from external sources, thereby providing credible evidence for scientific question answering. But existing retrieval and reranking methods remain vulnerable to passages that are semantically similar but logically irrelevant, often reducing factual reliability and amplifying hallucinations.To address this challenge, we propose a Deep Evidence Reranking Agent (DeepEra) that integrates step-by-step reasoning, enabling more precise evaluation of candidate passages beyond surface-level semantics. To support systematic evaluation, we construct SciRAG-SSLI (Scientific RAG - Semantically Similar but Logically Irrelevant), a large-scale dataset comprising about 300K SciQA instances across 10 subjects, constructed from 10M scientific corpus. The dataset combines naturally retrieved contexts with systematically generated distractors to test logical robustness and factual grounding. Comprehensive evaluations confirm that our approach achieves superior retrieval performance compared to leading rerankers. To our knowledge, this work is the first to comprehensively study and empirically validate innegligible SSLI issues in two-stage RAG frameworks.

Chuan Qin, Xin Chen, Chengrui Wang et al.

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.

Xunxin Cai, Chengrui Wang, Qingqing Long et al.

The rapid advancement of large language models (LLMs) in biological-medical applications has highlighted a gap between their potential and the limited scale and often low quality of available open-source annotated textual datasets. In addition, the inherent complexity of the biomedical knowledge hierarchy significantly hampers efforts to bridge this gap.Can LLMs themselves play a pivotal role in overcoming this limitation? Motivated by this question, we investigate this challenge in the present study.We propose a framework that automates the distillation of high-quality textual training data from the extensive scientific literature. Our approach self-evaluates and generates questions that are more closely aligned with the biomedical domain, guided by the biomedical knowledge hierarchy through medical subject headings (MeSH). This comprehensive framework establishes an automated workflow, thereby eliminating the need for manual intervention. Furthermore, we conducted comprehensive experiments to evaluate the impact of our framework-generated data on downstream language models of varying sizes. Our approach substantially improves question-answering tasks compared to pre-trained models from the life sciences domain and powerful close-source models represented by GPT-4. Notably, the generated AI-Ready dataset enabled the Llama3-70B base model to outperform GPT-4 using MedPrompt with multiple times the number of parameters. Detailed case studies and ablation experiments underscore the significance of each component within our framework

Meng Xiao, Xunxin Cai, Qingqing Long et al.

Corpus distillation for biomedical large language models (LLMs) seeks to address the pressing challenge of insufficient quantity and quality in open-source annotated scientific corpora, which remains a bottleneck for effective LLM training in biomedical research. This paper proposes a knowledge-driven, agentic framework for scientific corpus distillation, tailored explicitly for LLM training in the biomedical domain, addressing the challenge posed by the complex hierarchy of biomedical knowledge. Central to our approach is a collaborative multi-agent architecture, where specialized agents, each guided by the Medical Subject Headings (MeSH) hierarchy, work in concert to autonomously extract, synthesize, and self-evaluate high-quality textual data from vast scientific literature. This agentic framework collectively generates and refines domain-specific question-answer pairs, ensuring comprehensive coverage and consistency with biomedical ontologies while minimizing manual involvement. Extensive experimental results show that language models trained on our multi-agent distilled datasets achieve notable improvements in biomedical question-answering tasks, outperforming both strong life sciences LLM baselines and advanced proprietary models. Notably, our AI-Ready dataset enables Llama3-70B to surpass GPT-4 with MedPrompt and Med-PaLM-2, despite their larger scale. Detailed ablation studies and case analyses further validate the effectiveness and synergy of each agent within the framework, highlighting the potential of multi-agent collaboration in biomedical LLM training.

Zaitian Wang, Pengfei Wang, Kunpeng Liu et al.

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.

Qingqing Long, Zheng Fang, Chen Fang et al.

Traffic flow forecasting is a fundamental research issue for transportation planning and management, which serves as a canonical and typical example of spatial-temporal predictions. In recent years, Graph Neural Networks (GNNs) and Recurrent Neural Networks (RNNs) have achieved great success in capturing spatial-temporal correlations for traffic flow forecasting. Yet, two non-ignorable issues haven't been well solved: 1) The message passing in GNNs is immediate, while in reality the spatial message interactions among neighboring nodes can be delayed. The change of traffic flow at one node will take several minutes, i.e., time delay, to influence its connected neighbors. 2) Traffic conditions undergo continuous changes. The prediction frequency for traffic flow forecasting may vary based on specific scenario requirements. Most existing discretized models require retraining for each prediction horizon, restricting their applicability. To tackle the above issues, we propose a neural Spatial-Temporal Delay Differential Equation model, namely STDDE. It includes both delay effects and continuity into a unified delay differential equation framework, which explicitly models the time delay in spatial information propagation. Furthermore, theoretical proofs are provided to show its stability. Then we design a learnable traffic-graph time-delay estimator, which utilizes the continuity of the hidden states to achieve the gradient backward process. Finally, we propose a continuous output module, allowing us to accurately predict traffic flow at various frequencies, which provides more flexibility and adaptability to different scenarios. Extensive experiments show the superiority of the proposed STDDE along with competitive computational efficiency.

Yuqi Li, Qingqing Long, Yihang Zhou et al.

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.

Dianyu Liu, Chuan Qin, Xi Chen et al.

AI-for-Science (AI4Science) is increasingly transforming scientific discovery by embedding machine learning models into prediction, simulation, and hypothesis generation workflows across domains. However, the effectiveness of these models is fundamentally constrained by the AI-readiness of scientific data, for which no scalable and systematic evaluation mechanism currently exists. In this work, we propose SciHorizon-DataEVA, a novel agentic system to scalable AI-readiness evaluation of heterogeneous scientific data. At the evaluation-criteria level, we introduce the Sci-TQA2 principles, which organize AI-readiness into four complementary dimensions: Governance Trustworthiness, Data Quality, AI Compatibility, and Scientific Adaptability. Each dimension is decomposed into measurable atomic elements that enable fine-grained and executable assessment. To operationalize these principles at scale, we develop Sci-TQA2-Eval, a hierarchical multi-agent evaluation approach orchestrated through a directed, cyclic workflow. Our Sci-TQA2-Eval dynamically constructs dataset-aware evaluation specifications by combining lightweight dataset profiling, applicability-aware metric activation, and knowledge-augmented planning grounded in domain constraints and dataset-paper signals. These specifications are executed through an adaptive, tool-centric evaluation mechanism with built-in verification and self-correction, enabling scalable and reliable assessment across heterogeneous scientific data. Extensive experiments on scientific datasets spanning multiple domains demonstrate the effectiveness and generality of SciHorizon-DataEVA for principled AI-readiness evaluation.

Zhiyuan Ning, Chunlin Tian, Meng Xiao et al.

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.

Zhiyuan Ning, Zaitian Wang, Ran Zhang et al.

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.

Zhengmao Ye, Dengchun Li, Zetao Hu et al.

Transformer-based, pre-trained large language models (LLMs) have demonstrated outstanding performance across diverse domains, particularly in the emerging {\em pretrain-then-finetune} paradigm. Low-Rank Adaptation (LoRA), a parameter-efficient fine-tuning method, is commonly used to adapt a base LLM to multiple downstream tasks. Further, LLM platforms enable developers to fine-tune multiple models and develop various domain-specific applications simultaneously. However, existing model parallelism schemes suffer from high communication overhead and inefficient GPU utilization when training multiple LoRA tasks across GPUs and machines. In this paper, we present mLoRA, a parallelism-efficient fine-tuning system designed for training multiple LoRA across GPUs and machines. mLoRA introduces a novel LoRA-aware pipeline parallelism scheme that efficiently pipelines independent LoRA adapters and their distinct fine-tuning stages across GPUs and machines, along with a new LoRA-efficient operator to enhance GPU utilization during pipelined LoRA training. Our extensive evaluation shows that mLoRA can significantly reduce average fine-tuning task completion time, e.g., by 30\%, compared to state-of-the-art methods like FSDP. More importantly, mLoRA enables simultaneous fine-tuning of larger models, e.g., two Llama-2-13B models on four NVIDIA RTX A6000 48GB GPUs, which is not feasible for FSDP due to high memory requirements. Hence, mLoRA not only increases fine-tuning efficiency but also makes it more accessible on cost-effective GPUs. mLoRA has been deployed in AntGroup's production environment.

Cong Li, Meng Xiao, Pengfei Wang et al.

Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to train and adapt the Large Language Model with the capability to interpret and distinguish cell types in single-cell RNA sequencing data. Our preliminary research results indicate that these foundational models excel in accurately categorizing known cell types, demonstrating the potential of the Large Language Models as effective tools for uncovering new biological insights.

Ping Xu, Zhiyuan Ning, Pengjiang Li et al.

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.

Zhiyuan Ning, Pengfei Wang, Ziyue Qiao et al.

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.

Zaitian Wang, Jinghan Zhang, Xinhao Zhang et al.

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.

Tianqi He, Xiaohan Huang, Yi Du et al.

Feature Transformation is crucial for classic machine learning that aims to generate feature combinations to enhance the performance of downstream tasks from a data-centric perspective. Current methodologies, such as manual expert-driven processes, iterative-feedback techniques, and exploration-generative tactics, have shown promise in automating such data engineering workflow by minimizing human involvement. However, three challenges remain in those frameworks: (1) It predominantly depends on downstream task performance metrics, as assessment is time-consuming, especially for large datasets. (2) The diversity of feature combinations will hardly be guaranteed after random exploration ends. (3) Rare significant transformations lead to sparse valuable feedback that hinders the learning processes or leads to less effective results. In response to these challenges, we introduce FastFT, an innovative framework that leverages a trio of advanced strategies.We first decouple the feature transformation evaluation from the outcomes of the generated datasets via the performance predictor. To address the issue of reward sparsity, we developed a method to evaluate the novelty of generated transformation sequences. Incorporating this novelty into the reward function accelerates the model's exploration of effective transformations, thereby improving the search productivity. Additionally, we combine novelty and performance to create a prioritized memory buffer, ensuring that essential experiences are effectively revisited during exploration. Our extensive experimental evaluations validate the performance, efficiency, and traceability of our proposed framework, showcasing its superiority in handling complex feature transformation tasks.

Yuyang Song, Hanxu Yan, Jiale Lao et al.

Query rewrite transforms SQL queries into semantically equivalent forms that run more efficiently. Existing approaches mainly rely on predefined rewrite rules, but they handle a limited subset of queries and can cause performance regressions. This limitation stems from three challenges of rule-based query rewrite: (1) it is hard to discover and verify new rules, (2) fixed rewrite rules do not generalize to new query patterns, and (3) some rewrite techniques cannot be expressed as fixed rules. Motivated by the fact that human experts exhibit significantly better rewrite ability but suffer from scalability, and Large Language Models (LLMs) have demonstrated nearly human-level semantic and reasoning abilities, we propose a new approach of using LLMs to rewrite SQL queries beyond rules. Due to the hallucination problems in LLMs, directly applying LLMs often leads to nonequivalent and suboptimal queries. To address this issue, we propose QUITE (query rewrite), a training-free and feedback-aware system based on LLM agents that rewrites SQL queries into semantically equivalent forms with significantly better performance, covering a broader range of query patterns and rewrite strategies compared to rule-based methods. Firstly, we design a multi-agent framework controlled by a finite state machine (FSM) to equip LLMs with the ability to use external tools and enhance the rewrite process with real-time database feedback. Secondly, we develop a rewrite middleware to enhance the ability of LLMs to generate optimized query equivalents. Finally, we employ a novel hint injection technique to improve execution plans for rewritten queries. Extensive experiments show that QUITE reduces query execution time by up to 35.8% over state-of-the-art approaches and produces 24.1% more rewrites than prior methods, covering query cases that earlier systems did not handle.

Meng Xiao, Weiliang Zhang, Xiaohan Huang et al.

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.

Ping Xu, Pengfei Wang, Zhiyuan Ning et al.

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.

Xiaohan Huang, Dongjie Wang, Zhiyuan Ning et al.

Feature transformation methods aim to find an optimal mathematical feature-feature crossing process that generates high-value features and improves the performance of downstream machine learning tasks. Existing frameworks, though designed to mitigate manual costs, often treat feature transformations as isolated operations, ignoring dynamic dependencies between transformation steps. To address the limitations, we propose TCTO, a collaborative multi-agent reinforcement learning framework that automates feature engineering through graph-driven path optimization. The framework's core innovation lies in an evolving interaction graph that models features as nodes and transformations as edges. Through graph pruning and backtracking, it dynamically eliminates low-impact edges, reduces redundant operations, and enhances exploration stability. This graph also provides full traceability to empower TCTO to reuse high-utility subgraphs from historical transformations. To demonstrate the efficacy and adaptability of our approach, we conduct comprehensive experiments and case studies, which show superior performance across a range of datasets.

Cong Li, Qingqing Long, Yuanchun Zhou et al.

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life sciences, where vast collections of single-cell omics data from multiple species provide a foundation for training foundational models. However, the challenge lies in the disparity of data scales across different species, hindering the development of a comprehensive model for interpreting genetic data across diverse organisms. In this study, we propose an innovative hybrid approach that integrates the general knowledge capabilities of LLMs with domain-specific representation models for single-cell omics data interpretation. We begin by focusing on genes as the fundamental unit of representation. Gene representations are initialized using functional descriptions, leveraging the strengths of mature language models such as LLaMA-2. By inputting single-cell gene-level expression data with prompts, we effectively model cellular representations based on the differential expression levels of genes across various species and cell types. In the experiments, we constructed developmental cells from humans and mice, specifically targeting cells that are challenging to annotate. We evaluated our methodology through basic tasks such as cell annotation and visualization analysis. The results demonstrate the efficacy of our approach compared to other methods using LLMs, highlighting significant improvements in accuracy and interoperability. Our hybrid approach enhances the representation of single-cell data and offers a robust framework for future research in cross-species genetic analysis.

Zhijian Chen, Chuan Hu, Min Wu et al.

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and formidable challenges for researchers striving to keep abreast of the latest advancements. One significant challenge is navigating the vast corpus of literature to extract vital gene-related information, a time-consuming and cumbersome task. To enhance the efficiency of this process, it is crucial to address several key challenges: (1) the overwhelming volume of literature, (2) the complexity of gene functions, and (3) the automated integration and generation. In response, we propose GeneSUM, a two-stage automated gene summary extractor utilizing a large language model (LLM). Our approach retrieves and eliminates redundancy of target gene literature and then fine-tunes the LLM to refine and streamline the summarization process. We conducted extensive experiments to validate the efficacy of our proposed framework. The results demonstrate that LLM significantly enhances the integration of gene-specific information, allowing more efficient decision-making in ongoing research.

Xiaohan Huang, Meng Xiao, Chuan Qin et al.

Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap, we introduce SciHorizon-GENE, a large-scale gene-centric benchmark constructed from authoritative biological databases. The benchmark integrates curated knowledge for over 190K human genes and comprises more than 540K questions covering diverse gene-to-function reasoning scenarios relevant to cell type annotation, functional interpretation, and mechanism-oriented analysis. Motivated by behavioral patterns observed in preliminary examinations, SciHorizon-GENE evaluates LLMs along four biologically critical perspectives: research attention sensitivity, hallucination tendency, answer completeness, and literature influence, explicitly targeting failure modes that limit the safe adoption of LLMs in biological interpretation pipelines. We systematically evaluate a wide range of state-of-the-art general-purpose and biomedical LLMs, revealing substantial heterogeneity in gene-level reasoning capabilities and persistent challenges in generating faithful, complete, and literature-grounded functional interpretations. Our benchmark establishes a systematic foundation for analyzing LLM behavior at the gene scale and offers insights for model selection and development, with direct relevance to knowledge-enhanced biological interpretation.

Ping Xu, Zaitian Wang, Zhirui Wang et al.

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.

Wenyao Li, Ran Zhang, Pengyang Wang et al.

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.