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MBC-DTA: A Multi-Scale Bilinear Attention with Contrastive Learning Framework for Drug-Target Binding Affinity Prediction

MBC-DTA: A Multi-Scale Bilinear Attention with Contrastive L...

引用

2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Li, Huiting Zhang, Weiyu Shang, Yong Lu, Wenpeng Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center Jinan China Shandong Fundamental Research Center for Computer Science Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Jinan China

ISBN: (纸本)9798350386226

Drug-target binding affinity prediction is critical to drug design. Some existing computational methods rely on single-scale data and cannot fully integrate the rich information of multi-scale data, such as molecular structures and network information. In this paper, we propose the MBC-DTA model, which effectively integrates multi-scale data, and models the complex interactions between atoms and amino acids. We introduce GCN and GAT, which effectively extract the feature representation of molecular structure scale and network scale. Afterwards, the features obtained from the molecular structure scale are fed into a bilinear attention network, which captures the intricate interaction information between drug-target pairs. Additionally, a cross-scale graph contrastive learning strategy is applied, optimizing the feature representations across different scales. Extensive experimental results on two benchmark datasets demonstrate that the MBC-DTA model outperforms existing state-of-the-art methods. © 2024 IEEE.

关键词： Contrastive Learning

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Generating Personalized Imputations for Patient Health Status Prediction in Electronic Health Records

Generating Personalized Imputations for Patient Health Statu...

引用

2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Liu, Yang Zhang, Weiyu Si, Jiasheng Li, Zhao Peng, Xueping Lu, Wenpeng Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center Jinan China Evay Info Jinan China Shandong Fundamental Research Center for Computer Science Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Jinan China University of Technology Sydney Australian Artificial Intelligence Institute Sydney Australia

ISBN: (纸本)9798350386226

Electronic health records (EHRs) play a crucial role in the development of personalized treatment plans for patients. However, EHRs are often highly incomplete, posing significant challenges for predictive modeling. While existing deep learning models employ various imputation techniques to reconstruct missing values, they often fail to represent missing data in a personalized manner and do not learn from the missingness patterns in EHRs data. This limitation reduces their effectiveness in practical personalized healthcare applications. To address this issue, we propose SPIME, a self-supervised model that generates personalized imputations in EHRs data for patient health status prediction. We introduce a personalized missing mask (PMM) based on the frequency of feature measurements. Additionally, we incorporate a masked imputation task (MIT) loss that minimizes the loss of artificially introduced missing values, thereby enhancing the model's capability to handle missing data. SPIME adopts self-supervised pretraining to learn representations from personalized missing patterns and reconstructs missing data in the latent space. To further enhance representation learning, two independent attention mechanisms are applied separately across the feature and temporal dimensions. Experimental results on two real-world EHRs datasets show that SPIME outperforms existing state-of-the-art methods in predicting in-hospital mortality and decompensation, demonstrating its effectiveness in reconstructing missing data and predicting patient health status. The code will be published at https://***/cling6666/SPIME. © 2024 IEEE.

关键词： Electronic health record

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HiRes: Hierarchical Feature Optimization and Rescorer for Automatic ICD Coding

HiRes: Hierarchical Feature Optimization and Rescorer for Au...

引用

2025 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2025

作者： Liang, Zhenpeng Guan, Hongjiao Lu, Wenpeng Peng, Xueping Xu, Bing Yang, Muyun Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center National Supercomputer Center in Jinan Qilu University of Technology Shandong Academy of Sciences Jinan China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China Australian Artificial Intelligence Institute University of Technology Sydney Sydney Australia Faculty of Computing Harbin Institute of Technology Harbin China

ISBN: (纸本)9798350368741

The International Classification of Diseases (ICD) coding assigns standardized codes to diseases. Automating this process enhances the efficiency and accuracy of clinical records processing. However, current methods struggle with noisy and lengthy clinical texts, making it difficult to ensure the reliability of feature extraction. Furthermore, they typically make separate binary predictions for each code, overlooking the dependencies between them. To address these issues, we propose a novel model called Hierarchical Feature Optimization and Rescorer (HiRes). We employ a cascaded convolution architecture to mitigate noise and enhance feature representation. Additionally, a masked autoencoder-based rescorer is introduced to capture ICD code interdependencies, refining initial predictions for improved accuracy. The model also considers the inconsistencies in code representations. Experiments on the MIMIC datasets demonstrate the effectiveness of our model. © 2025 IEEE.

关键词： automatic ICD coding cascaded convolutional network multi-label classification

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BPTTD: Block-Parallel Singular Value Decomposition(SVD) Based Tensor Train Decomposition 26

BPTTD: Block-Parallel Singular Value Decomposition(SVD) Base...

引用

26th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2023

作者： Meng, Fanshuo Li, Peng Fan, Weibei Zhang, Hongjun Xue, Zhuangzhuang Cheng, Haitao Nanjing University of Posts and Telecommunications School of Computer Science Nanjing210023 China Institute of Network Security and Trusted Computing Nanjing210023 China Nanjing University of Posts and Telecommunications School of Internet of Things Nanjing210023 China Advanced Cryptography and System Security Key Laboratory of Sichuan Province Chengdu610054 China

ISBN: (纸本)9798350331684

Tensors are naturally suitable for representing high-dimensional data. Tensor train decomposition is an effective data processing method to cope with high-dimensional tensors. It is widely used in many fields, such as recommendation system, data completion and dimension reduction. However, experiments show that the traditional tensor decomposition method is only suitable for processing small-scale data. With the increase of the amount of data, the traditional algorithm will not be able to meet the efficiency of processing data. Therefore, this paper improves the traditional tensor train decomposition algorithm. Based on the most crucial step - SVD in the algorithm process, we first divide the matrix into column blocks, and then, considering the storage characteristics of cache, we call multiple threads to process different submatrix blocks. Each thread calls the one-sided Jacobi algorithm respectively to parallelize the SVD process of the matrix. In this paper, performance comparison experiments are carried out on simulated tensor data. The experimental results demonstrate that this method shows good scalability and can greatly improve the speed of tensor train decomposition. © 2023 IEEE.

关键词： Singular value decomposition

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MBC-DTA: A Multi-Scale Bilinear Attention with Contrastive Learning Framework for Drug-Target Binding Affinity Prediction

MBC-DTA: A Multi-Scale Bilinear Attention with Contrastive L...

引用

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Huiting Li Weiyu Zhang Yong Shang Wenpeng Lu Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center Qilu University of Technology (Shandong Academy of Sciences) Jinan China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

关键词： Drugs Computational modeling Biological system modeling Contrastive learning Benchmark testing Feature extraction Data models Bipartite graph Bioinformatics Periodic structures

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FedSimRep: A Federated Learning Method Based on Data Representation Selection 25

FedSimRep: A Federated Learning Method Based on Data Represe...

引用

Proceedings of the 2025 3rd International Conference on Communication networks and Machine Learning

作者： Falu Zhai Lu Wu Chunxiao Wang Tongyang Hao Shucang Zang Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan Shandong China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan Shandong China

ISBN: (纸本)9798400713231

As an emerging distributed technology, Federated learning enables model training while protecting privacy without sharing local data. However, the heterogeneity of geographic locations and devices leads to response delays from stragglers. Client grouping in federated learning can tolerate stragglers from a global perspective, but differences in data distribution within groups may result in local performance bias. To address this issue, we propose a federated learning method called FedSimRep, which selects representative clients based on data distribution similarity. FedSimRep performs group training by collecting readiness signals from topological communications and maintains synchronization tables and graphs to track training progress. Additionally, it selects representative clients by leveraging the relationship between local optimization similarity and data distribution similarity to optimize the global model. Experiments and theoretical analyses on public datasets such as MNIST, CIFAR-10, and UEU-Fed demonstrate that FedSimRep achieves significant advantages in terms of accuracy and efficiency.

关键词： Client Grouping

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Machine Learning-Based Prediction of MPI Communication Time in High-Performance computing Applications

Machine Learning-Based Prediction of MPI Communication Time ...

引用

Frontiers Technology of Information and Computer (ICFTIC), IEEE International Conference on

作者： Zhuang Wang Yuan Zhuang Yunhui Zeng Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China

ISBN: (数字)9798331541750

ISBN: (纸本)9798331541767

The rapid advancements in high-performance computing (HPC) have made large-scale parallel computing feasible. As a commonly used parallel programming model, Message Passing Interface (MPI) plays a crucial role in HPC systems and directly affects the performance and efficiency of these applications. Therefore, modeling and predicting the performance of MPI communication is critically important. This paper utilizes a machine learning-based approach to predict MPI communication time. It uses performance analysis tools to collect real-time communication data and select critical features related to execution time. The data is categorized, then, for each type of MPI communication, a dedicated regression model is trained. Firstly, XGBoost and Artificial Neural networks (ANN) are employed for function level modeling. Then, fusion techniques are used to combine XGBoost and ANN models to improve prediction accuracy. Finally, these function level models are integrated into an application level model to predict the overall communication time. This model is evaluated using CG, FT, and CPMD. Experimental results show that the average prediction errors of the model are 12.6%, 13.2%, and 13.5%, with a minimum error of 7%.

关键词： Accuracy Computational modeling High performance computing Message passing Artificial neural networks Machine learning Predictive models Data models Supercomputers Tuning

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DAC-UNet: Dual Attention CNN-Enhanced CswinUnet for Gastric Cancer Pathological Image Segmentation

DAC-UNet: Dual Attention CNN-Enhanced CswinUnet for Gastric ...

引用

Medical Artificial Intelligence (MedAI), IEEE International Conference on

作者： Tao Hu Jingshan Pan Na Li Tangbin Tian Shengyu Liu Lu Zhang Yujiao Han Jiwei Xu Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center(National Supercomputer Center in Jinan) Qilu University of Technology(Shandong Academy of Sciences) Jinan China Shandong Fundamental Research Center for Computer Science Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Jinan China

ISBN: (数字)9798350377613

ISBN: (纸本)9798350377620

Gastric cancer is one of the most lethal cancers. Currently, clinical diagnosis primarily relies on gastroscopic biopsies and the manual experience of doctors to assess the development of lesions in tissue sections. However, pathological screening requires a significant amount of time from specialized pathologists. Due to variations in clinical experience and limitations in medical resources, the detection of gastric cancer still faces challenges. Traditional methods for segmenting gastric cancer images often overlook the hierarchical structure of features and the spatial details, both local and global, in the lesion images. To address the above issues, this paper proposes a hybrid and efficient pathological image segmentation network named DAC-UNet, designed for precise pathological image segmentation tasks. DAC-UNet uses Cswin Transformer blocks to build a hierarchical structure, allowing it to capture global information with less computational complexity. The network also includes multi-scale dual attention skip connections between the encoder and decoder to preserve local spatial details and improve global interactions across different scales. We conducted a thorough theoretical analysis of this method and validated it on a gastric slice dataset. The experimental results demonstrate that our proposed method achieves outstanding performance on both our gastric slice dataset and the MoNuSeg dataset. Specifically, on our gastric slice dataset, we obtained a Dice similarity coefficient (DSC) of 89.42% and an HD95 of 47.24, while on the MoNuSeg dataset, we achieved a DSC of 79.28% and a 95th percentile Hausdorff distance (HD95) of 19.38.

关键词： Image segmentation Pathology Semantics Manuals Transformers Decoding Lesions Medical diagnostic imaging Faces Cancer

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STAD: Joint Spatial-Temporal Dimension and Channel Correlation for Time Series Anomaly Detection

STAD: Joint Spatial-Temporal Dimension and Channel Correlati...

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Mingle Zhou Xingli Wang Delong Han Jin Wan Jiachen Li Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China SHANDONG SCICOM Information and Economy Research Institute Co. Ltd

ISBN: (数字)9798350368741

ISBN: (纸本)9798350368758

Accurately identifying real anomalies and pseudo-anomalies in complex multi-dimensional time series data has been a difficult problem in time series anomaly detection. To solve this problem, this paper proposes a new framework, STAD, that joint temporal and spatial dimensions. This framework guides the model to capture the correlation information between channels It also aims to learn the deep feature representation of sequences by mining potential information in the spatialtemporal dimension. It can effectively distinguish between true and false anomalies by comparing information from spatial and temporal dimensions. STAD identifies and integrates correlated channels by using a correlation aggregation mechanism to join multiple channels and detect *** addition, the KAN mixer designed in this paper can effectively extract features from different spatial locations in the spatial-temporal dimension. Through extensive experiments on several public datasets, STAD demonstrates its superiority in terms of accuracy and robustness.

关键词： Correlation Accuracy Time series analysis Signal processing Feature extraction Robustness Acoustics Speech processing Mixers Anomaly detection

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Comprehensive Feature Processing Based on Attention Mechanism for Co-Salient Object Detection

Comprehensive Feature Processing Based on Attention Mechanis...

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Guohua Lv Mao Yuan Zengbin Zhang Zhengyang Zhang Zhenhui Ding Guangxiao Ma Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center (National Supercomputer Center in Jinan) Qilu University of Technology (Shandong Academy of Sciences) Jinan China Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China Shandong Key Laboratory of Ubiquitous Intelligent Computing Jinan China College of Computer Science and Engineering Shandong University of Science and Technology Qingdao China

ISBN: (数字)9798350368741

ISBN: (纸本)9798350368758

Co-salient object detection (CoSOD) aims to detect common salient objects across multiple related images. However, existing methods often struggle with limited attention coverage, missing some co-salient objects. To address this, we propose a two-stage feature processing module (FPM) comprising comprehensive feature extraction module (CFE) and feature enhancement module (FEM). CFE extracts comprehensive cosalient features while reducing background noise, and FEM enhances feature representation and adjusts attention weights for full object coverage. Additionally, we introduce an adversarial learning module (ALM) to improve prediction quality by reducing noise in the co-salient regions. Extensive experiments on three benchmark datasets—CoCA, CoSOD3k, and CoSal2015—demonstrate that our model significantly outperforms state-of-the-art methods. The source code is available at https://***/yaobaimiao/CFPAM.

关键词： Attention mechanisms Source coding Noise Object detection Benchmark testing Feature extraction Adversarial machine learning Finite element analysis Background noise Speech processing

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