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IEEE Transactions on computational Biology and Bioinformatics 2025年第1期22卷 203-215页

作者： Ruijie Li Qiao Ning Yaomiao Zhao Shikai Guo Hui Li Department of Information Science and Technology Dalian Maritime University Dalian China DUT Artificial Intelligence Institute Dalian China Dalian Key Laboratory of Artificial Intelligence Dalian China School of Artificial Intelligence and Computer Science Jiangnan University Wuxi China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China School of Computer Science and Engineering Northeastern University Shenyang China

In recent years, microRNA (miRNA) has been recognized as crucial in the progression of human diseases. However, existing computational methods for identifying miRNA-disease associations often overlook the rich association information contained in specific long-distance pathways and lack effective exploration of potential associations. In this study, we propose a biologically interpretable “similarity-association-similarity” metapath and heterogeneous-hyper network (HeteroHyperNet) learning approach for miRNA-disease association prediction (MHMDA). In MHMDA, a “similarity-association-similarity” multi-hop metapaths learning method based on hierarchical attention perception is proposed to explore specific long-distance associated pathway information connecting potentially associated miRNAs and diseases. In addition, a HeteroHyperNet learning approach integrating heterogeneous network and hyper network is designed to progressively learn direct association information and potential association information between miRNA and disease. The “similarity-association-similarity” metapath with hierarchical attention significantly enhances the learning of long-distance biological associations, while the HeteroHyperNet comprehensively learns the known and potential associations of miRNA-disease, greatly improving the richness and accuracy of information. A large number of experimental results show that MHMDA has demonstrated excellent performance in the prediction of miRNA-disease association. In addition, cross independent dataset experiment and cold start experiment on miRNA and disease prove the effectiveness of MHMDA on sparse association points, and its stability and reliability in predicting potential miRNA-disease association are further confirmed.

关键词： Diseases Predictive models Autoencoders Feature extraction Biological system modeling Bioinformatics Kernel computational biology Heterogeneous networks Accuracy

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Generative Classifier for Domain Generalization

arXiv

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arXiv 2025年

作者： Long, Shaocong Zhou, Qianyu Li, Xiangtai Ying, Chenhao Tong, Yunhai Ma, Lizhuang Luo, Yuan Tao, Dacheng Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China Nanyang Technological University Singapore Peking University Beijing China

Domain generalization (DG) aims to improve the generalizability of computer vision models toward distribution shifts. The mainstream DG methods predominantly focus on learning domain invariance across domains, however, such methods overlook the untapped potential inherent in domain-specific information. While the prevailing practice of discriminative linear classifier has been tailored to domain-invariant features, it struggles when confronted with diverse domain-specific information, e.g., intra-class shifts, that exhibits multi-modality. To address these issues, we explore the theoretical implications of relying on domain-invariant features, revealing the crucial role of domain-specific information in mitigating the target risk for DG. Drawing from these insights, we propose Generative Classifier-driven Domain Generalization (GCDG), introducing a generative paradigm for the DG classifier based on Gaussian Mixture Models (GMMs) for each class across domains. GCDG consists of three key modules: Heterogeneity Learning Classifier (HLC), Spurious Correlation Blocking (SCB), and Diverse Component Balancing (DCB). Concretely, HLC attempts to model the feature distributions and thereby capture valuable domain-specific information via GMMs. SCB identifies the neural units containing spurious correlations and perturbs them, mitigating the risk of HLC learning irrelevant spurious patterns. Meanwhile, DCB ensures a balanced contribution of components within HLC, preventing the underestimation or neglect of critical components. In this way, GCDG excels in capturing the nuances of domain-specific information characterized by diverse distributions. GCDG demonstrates the potential to reduce the target risk and encourage flat minima, improving the model’s generalizability. Extensive experiments show GCDG’s comparable performance on five DG benchmarks and one face anti-spoofing dataset, seamlessly integrating into existing DG methods with consistent improvements. Code will be avail

关键词： Discriminant analysis

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Incomplete Graph Learning: A Comprehensive Survey

arXiv

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arXiv 2025年

作者： Xia, Riting Liu, Huibo Li, Anchen Liu, Xueyan Zhang, Yan Zhang, Chunxu Yang, Bo College of Computer Science Inner Mongolia University Hohhot010021 China School of Computer Science and Technology Jilin University Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China

Graph learning is a prevalent field that operates on ubiquitous graph data. Effective graph learning methods can extract valuable information from graphs. However, these methods are non-robust and affected by missing attributes in graphs, resulting in sub-optimal outcomes. This has led to the emergence of incomplete graph learning, which aims to process and learn from incomplete graphs to achieve more accurate and representative results. In this paper, we conducted a comprehensive review of the literature on incomplete graph learning. Initially, we categorize incomplete graphs and provide precise definitions of relevant concepts, terminologies, and techniques, thereby establishing a solid understanding for readers. Subsequently, we classify incomplete graph learning methods according to the types of incompleteness: (1) attribute-incomplete graph learning methods, (2) attribute-missing graph learning methods, and (3) hybrid-absent graph learning methods. By systematically classifying and summarizing incomplete graph learning methods, we highlight the commonalities and differences among existing approaches, aiding readers in selecting methods and laying the groundwork for further advancements. In addition, we summarize the datasets, incomplete processing modes, evaluation metrics, and application domains used by the current methods. Lastly, we discuss the current challenges and propose future directions for incomplete graph learning, with the aim of stimulating further innovations in this crucial field. To our knowledge, this is the first review dedicated to incomplete graph learning, aiming to offer valuable insights for researchers in related fields.1 Copyright © 2025, The Authors. All rights reserved.

关键词： knowledge graph

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WGAN-GP_Glu: A semi-supervised model based on double generator-Wasserstein GAN with gradient penalty algorithm for glutarylation site identification

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Computers in Biology and Medicine 2025年 184卷 109328-109328页

作者： Ning, Qiao Qi, Zedong Information Science and Technology Dalian Maritime University Liaoning Dalian China The School of Artificial Intelligence and Computer Science Jiangnan University Wuxi China Neusoft Education Technology Group Dalian China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China

As an important post-translational modification, glutarylation plays a crucial role in a variety of cellular functions. Recently, diverse computational methods for glutarylation site identification have been proposed. However, the class imbalance problem due to data noise and uncertainty of non-glutarylation sites remains a great challenge. In this article, we propose a novel semi-supervised learning algorithm, called WGAN-GP_Glu, for identifying reliable non-glutarylation lysine sites from those without glutarylation annotation. WGAN-GP_Glu method is a multi-module framework algorithm, which mainly includes a reliable negative sample selection module, a deep feature extraction module, and a glutarylation site prediction module. In reliable negative sample selection module, we design an improved method of Wasserstein GAN with Gradient Penalty (WGAN-GP), named ReliableWGAN-GP, including three parts, two generators G1, G2 and a discriminator D, which can select reliable non-glutarylation samples from a great number of unlabeled samples. Generator G1 is utilized to generate noise data from unlabeled samples. For generator G2, both the positive sample and the noise data are used as inputs to improve the discriminant capability of discriminator D. Then, convolutional neural network and bidirectional long short-term memory network combined with attention mechanism are utilized to extract deep features for glutarylation samples and reliable non-glutarylation samples. Finally, a glutarylation site prediction module based on the three-layer fully connected layer is designed to make class predictions for samples. The sensitivity, specificity, accuracy and Matthew correlation coefficient of WGAN-GP_Glu on the independent test data set reach 90.58 %, 95.82 %, 94.44 % and 0.8645, respectively, which surpassed the existing methods for glutarylation sites prediction. Therefore, WGAN-GP_Glu can serve as a powerful tool in identifying glutarylation sites and the ReliableWGAN-GP algo

关键词： Gallium nitride

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Scalable Precise computation of Shannon Entropy

arXiv

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arXiv 2025年

作者： Lai, Yong Tong, Haolong Xu, Zhenghang Yin, Minghao College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China School of Computer Science and Information Technology Northeast Normal University Changchun130017 China

Quantitative information flow analyses (QIF) are a class of techniques for measuring the amount of confidential information leaked by a program to its public outputs. Shannon entropy is an important method to quantify the amount of leakage in QIF. This paper focuses on the programs modeled in Boolean constraints and optimizes the two stages of the Shannon entropy computation to implement a scalable precise tool PSE. In the first stage, we design a knowledge compilation language called ADD[∧] that combines Algebraic Decision Diagrams and conjunctive decomposition. ADD[∧] avoids enumerating possible outputs of a program and supports tractable entropy computation. In the second stage, we optimize the model counting queries that are used to compute the probabilities of outputs. We compare PSE with the state-of-the-art probably approximately correct tool EntropyEstimation, which was shown to significantly outperform the existing precise tools. The experimental results demonstrate that PSE solved 55 more benchmarks compared to EntropyEstimation in a total of 441. For 98% of the benchmarks that both PSE and EntropyEstimation solved, PSE is at least 10× as efficient as EntropyEstimation. Copyright © 2025, The Authors. All rights reserved.

关键词： Information leakage

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Rethinking Polyp Segmentation from the Perspectives of Matching Views and Seeking Camouflage

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Multimedia Systems 2025年第3期31卷 1-17页

作者： Jiang, Zhengfang Chen, Haipeng Yang, Yongping Liu, Xianzhu Lyu, Yingda College of Software Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China College of Computer Science and Technology Jilin University Changchun130012 China Department of Colorectal Anal Surgery The Second Hospital of Jilin University Changchun130022 China National and Local Joint Engineering Research Center of Space Optoelectronics Technology Changchun University of Science and Technology Changchun130022 China College of Opto-Electronic Engineering Changchun University of Science and Technology Changchun130022 China Public Computer Education and Research Center Jilin University Changchun130012 China

Accurate segmentation of polyps from colonoscopy images is of great significance for the prevention of colorectal cancer. Despite notable progress, polyp segmentation remains a challenging task due to the diversity of polyp size and shape, as well as the camouflage property of polyps caused by their high similarity to surrounding tissues. To address these challenges, inspired by human perceptual experience in finding objects, we propose a multi-perspective collaborative network (MPCNet), innovatively identifying the potential polyps from the perspectives of matching views and seeking camouflage. Firstly, from the former perspective, a global–local aware module is proposed to provide various feature receptive fields to match suitable views for polyps of different sizes and shapes. Then, from the latter perspective, a texture enhancement module (TEM) and an interaction refinement module (IRM) are proposed to mine and complement clues essential for breaking the camouflage. Specifically, TEM mines texture-related clues and amplifies the subtle texture differences between polyps and their background, while IRM complements boundary clues and further optimizes feature representation through the interaction between boundaries and regions, thereby generating accurate segmentation results with complete regions and fine boundaries. Extensive experiments on five benchmark polyp datasets show that our MPCNet outperforms other state-of-the-art methods. In particular, we achieve a mean Dice of 81.7% and 82.4% on the most challenging datasets CVC-ColonDB and ETIS, respectively, which are significantly higher than competing methods. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Image segmentation

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Supervised topic models with weighted words:multi-label document classification

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Frontiers of Information Technology & Electronic engineering 2018年第4期19卷 513-523页

作者： Yue-peng ZOU Ji-hong OUYANG Xi-ming LI College of Computer Science and Technology Jilin University MOE Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University

Supervised topic modeling algorithms have been successfully applied to multi-label document classification *** models include labeled latent Dirichlet allocation(L-LDA)and ***,these models neglect the class frequency information of words(i.e.,the number of classes where a word has occurred in the training data),which is significant for *** address this,we propose a method,namely the class frequency weight(CF-weight),to weight words by considering the class frequency *** CF-weight is based on the intuition that a word with higher(lower)class frequency will be less(more)*** this study,the CF-weight is used to improve L-LDA and dependency-LDA.A number of experiments have been conducted on real-world multi-label *** results demonstrate that CF-weight based algorithms are competitive with the existing supervised topic models.

关键词： Supervised topic model Multi-label classification Class frequency Labeled latent Dirichlet allocation (L-LDA) Dependency-LDA

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Sfmfold: A Multi-Modal Contrast Learning Model for Rna Secondary Structure Prediction

SSRN

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SSRN 2025年

作者： Li, Ang Liu, Yuanning Zhang, Zhaoyang Li, Shuwang Dong, Hao Lv, Meng College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China College of Software Jilin University Changchun130012 China College of Information Engineering Chang’an University Xi’an710064 China

The secondary structure of RNA can regulate the interaction between RNA and protein and perform various biological tasks through specific folding shapes, which plays an important role in revealing biomolecular mechanisms and developing new vaccines and therapeutic drugs. However, existing RNA secondary structure prediction methods based on thermodynamics and traditional neural network models usually lack the ability to model long-distance dependencies of RNA molecules and cannot handle complex non-nested structures in RNA molecules. In this paper, we propose a multi-modal contrastive learning method SFMFold based on state space model, which captures long-distance interactions in RNA sequences through RNA sequence representation learning part, and models the structure of RNA molecules through RNA structure representation learning part. Finally, the features of the two modalities are aligned and deeply fused to obtain the final RNA molecule prediction map. We test SFMFold on several datasets, and the experiments show that our proposed model shows excellent performance in cross-family prediction and long sequence prediction tasks. In addition, SFMFold can also effectively predict non-nested structures such as pseudoknot with better accuracy than the SOTA methods. © 2025, The Authors. All rights reserved.

关键词： Prediction models

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DeepSelective: Feature Gating and Representation Matching for Interpretable Clinical Prediction

arXiv

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arXiv 2025年

作者： Zhang, Ruochi Yang, Qian Wang, Xiaoyang Wu, Haoran Zhou, Qiong Wang, Yu Li, Kewei Wang, Yueying Fan, Yusi Zhang, Jiale Huang, Lan Liu, Chang Zhou, Fengfeng College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China Beijing Life Science Academy Beijing102209 China Syneron Technology Guangzhou510700 China

The rapid accumulation of Electronic Health Records (EHRs) has transformed healthcare by providing valuable data that enhance clinical predictions and diagnoses. While conventional machine learning models have proven effective, they often lack robust representation learning and depend heavily on expert-crafted features. Although deep learning offers powerful solutions, it is often criticized for its lack of interpretability. To address these challenges, we propose DeepSelective, a novel end to end deep learning framework for predicting patient prognosis using EHR data, with a strong emphasis on enhancing model interpretability. DeepSelective combines data compression techniques with an innovative feature selection approach, integrating custom-designed modules that work together to improve both accuracy and interpretability. Our experiments demonstrate that DeepSelective not only enhances predictive accuracy but also significantly improves interpretability, making it a valuable tool for clinical decision-making. The source code is freely available at http://***/supp/*** . © 2025, CC BY-NC-ND.

关键词： Electronic health record

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Causality-inspired Unsupervised Domain Adaptation with Target Style Imitation for Medical Image Segmentation

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IEEE Transactions on Circuits and Systems for Video Technology 2025年

作者： Song, Jincai Chen, Haipeng Lyu, Yingda Nie, Weizhi Liu, An-An Jilin University College of Computer Science and Technology Jilin Changchun130012 China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin Changchun130012 China Jilin University Public Computer Education and Research Center Jilin Changchun130012 China Tianjin University School of Electrical and Information Engineering Tianjin300072 China

Deep learning performance may decrease substantially with unseen heterogeneous data. While most unsupervised domain adaptation (UDA) methods seek to address this through image alignment, they often ignore uncertainty style fluctuations within the target domain. When testing image styles vary in both direction and intensity, such models may fail to adapt. Furthermore, existing UDA methods tend to over-reliance on domain-level entire feature alignment, resulting in potentially over-exploiting semantic content-independent cues (e.g., intensity) as shortcut features. To address these limitations, this paper introduces an innovative and model-agnostic Causality-inspired Representation Learning Based on Target Style Imitation method for UDA. Specifically, we propose a novel Target Style Imitation (TSI) data augmentation approach to diversify the training data and align training and unseen target testing image styles. TSI constructs a Gaussian distribution for the target domain style and simulates unseen testing style variations through random sampling. Additionally, inspired by the stable and generalizable causal mechanism, we propose Causality-inspired Representation Learning (CRL) based on TSI method to enforce feature representations to adhere to causal properties (i.e., Separation and Independence) essential for robust UDA, thus fostering the model to focus on the domain-invariant semantic features. Our method surpasses state-of-the-art methods on two cross-modality medical image segmentation datasets. © 1991-2012 IEEE.

关键词： Semantic Segmentation

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