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.

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.

Zero-shot hashing (ZSH) has shown excellent success owing to its efficiency and generalization in large-scale retrieval scenarios. However, 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. Furthermore, theoretical analysis is provided to show the effectiveness of COMAE. Experimental results demonstrate that COMAE outperforms state-of-the-art hashing models, especially in scenarios with a larger number of unseen label classes.

BACKGROUND: 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, one major challenge for GNN-based methods is their reliance on hard graph constructions derived from similarity matrices. These constructions introduce difficulties when applied to scRNA-seq data due to: (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. RESULTS: 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 designed to effectively handle the sparsity and dropout issues in scRNA-seq data; (ii) a dual-channel cut-informed soft graph embedding module, constructed through deep graph-cut information, capturing continuous similarities between cells while preserving the intrinsic data structures of scRNA-seq; and (iii) an optimal transport-based clustering optimization module, achieving optimal delineation of cell populations while maintaining high biological relevance. CONCLUSION: By integrating dual-channel cut-informed soft graph representation learning, a ZINB-based feature autoencoder, and optimal transport-driven clustering optimization, scSGC effectively overcomes the challenges associated with traditional hard graph constructions in GNN methods. 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.

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 article, 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. To improve the reproducibility of our research, we have released accompanying code by Dropbox. 1

This article studies the problem of semi-supervised learning on graphs, which aims to incorporate ubiquitous unlabeled knowledge (e.g., graph topology, node attributes) with few-available labeled knowledge (e.g., node class) to alleviate the scarcity issue of supervised information on node classification. While promising results are achieved, existing works for this problem usually suffer from the poor balance of generalization and fitting ability due to the heavy reliance on labels or task-agnostic unsupervised information. To address the challenge, we propose a dual-channel framework for semi-supervised learning on G raphs via K nowledge T ransfer between independent supervised and unsupervised embedding spaces, namely, GKT. Specifically, we devise a dual-channel framework including a supervised model for learning the label probability of nodes and an unsupervised model for extracting information from massive unlabeled graph data. A knowledge transfer head is proposed to bridge the gap between the generalization and fitting capability of the two models. We use the unsupervised information to reconstruct batch-graphs to smooth the label probability distribution on the graphs to improve the generalization of prediction. We also adaptively adjust the reconstructed graphs by encouraging the label-related connections to solidify the fitting ability. Since the optimization of the supervised channel with knowledge transfer contains that of the unsupervised channel as a constraint and vice versa, we then propose a meta-learning-based method to solve the bi-level optimization problem, which avoids the negative transfer and further improves the model’s performance. Finally, extensive experiments validate the effectiveness of our proposed framework by comparing state-of-the-art algorithms.

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.

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.

With the development of natural language processing tech- niques(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.

With the growth of the academic engines, the mining and analysis acquisition of massive researcher data, such as collaborator recommendation and researcher retrieval, has become indispensable for improving the quality and intelligence of services. However, most of the existing studies for researcher data mining focus on a single task for a particular application scenario and learning a task-specific model, which is usually unable to transfer to out-of-scope tasks. In this paper, we propose a multi-task self-supervised learning-based researcher data pre-training model named RPT, which is efficient to accomplish multiple researcher data mining tasks. Specifically, we divide the researchers’ data into semantic document sets and community graph. We design the hierarchical Transformer and the local community encoder to capture information from the two categories of data, respectively. Then, we propose three self-supervised learning objectives to train the whole model. For RPT’s main task, we leverage contrastive learning to discriminate whether these captured two kinds of information belong to the same researcher. In addition, two auxiliary tasks, named hierarchical masked language model and community relation prediction for extracting semantic and community information, are integrated to improve pre-training. Finally, we also propose two transfer modes of RPT for fine-tuning in different scenarios. We conduct extensive experiments to evaluate RPT, results on three downstream tasks verify the effectiveness of pre-training for researcher data mining.

Most researches for knowledge graph completion learn representations of entities and relations to predict missing links in incomplete knowledge graphs. However, these methods fail to take full advantage of both the contextual information of entity and relation. Here, we extract contexts of entities and relations from the triplets which they compose. We propose a model named AggrE, which conducts efficient aggregations respectively on entity context and relation context in multi-hops, and learns context-enhanced entity and relation embeddings for knowledge graph completion. The experiment results show that AggrE is competitive to existing models.