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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Lu, Mianshuo Wang, Lei Sun, Jinzhu Li, Yang Wei, Mengmeng Wei, Yu Liu, Changchun Li, Zhengwei China University of Mining and Technology School of Computer Science and Technology Xuzhou221116 China Guangxi Academy of Sciences Big Data and Intelligent Computing Research Center Nanning530007 China Zaozhuang Mental Health Center Zaozhuang277100 China Hefei University of Technology School of Computer Science and Information Engineering Hefei230601 China Zaozhuang Univerity College of Information Science and Enginnering 277100 China

ISBN: (纸本)9798350386226

Circular RNA (circRNA) is an RNA molecule that plays an important role in both pathology and physiology. Accurate identification of associations between circRNAs and diseases is crucial for further physiology research. However, verifying the circRNA-disease associations (CDA) through biological experimental methods is time-consuming. Here, we propose a novel method combines Non-negative Matrix Factorization (NMF) and Adversarially Regularized Variational Graph Autoencoder (ARVGA) to accurately predict CDA. Our model first fuses multi-source information in order to build circRNA similarity, disease similarity and circRNA-disease association matrices. Thereby our model constructs graphs for circRNA and disease respectively and optimize them using a K-means clustering algorithm. We obtain linear features using NMF and non-linear features using ARVGA. Finally, an Extremely Randomized Trees classifier is employed to predict CDA. On the gold standard dataset CircR2Disease, our model achieved a prediction accuracy of 94.8% and an AUC of 0.984 under 5-fold cross-validation. In case study, 19 of top 20 predicted circRNAs associated with Hepatocellular Carcinoma were confirmed in relevant literature. Furthermore, ablation experiment, classifier experiment and independent datasets test fully demonstrate the effectiveness and robustness of our model. © 2024 IEEE.

关键词： Non-negative matrix factorization

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An Efficient Graph Accelerator with Distributed On-Chip Memory Hierarchy 22nd

An Efficient Graph Accelerator with Distributed On-Chip Mem...

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22nd International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2022

作者： Zheng, Ran Jiang, Yingxin Wang, Yibo Su, Yongbo Zheng, Long Yao, Pengcheng Liao, Xiaofei Jin, Hai National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China Zhejiang Lab Hangzhou311121 China

ISBN: (纸本)9783031226762

Graph processing has evolved and expanded swiftly with artificial intelligence and big data technology. High-Bandwidth Memory (HBM), which delivers terabyte-level memory bandwidth, has opened up new development possibilities for FPGA-based graph accelerators. However, despite the tremendous expansion of underlying hardware capabilities, existing graph accelerators have not benefited too much. In this paper, we observe that the uniformed on-chip memory hierarchy is the key to the low scalability of existing graph accelerators. We present a novel graph accelerator with a distributed on-chip memory hierarchy called GraphS. The on-chip memory of GraphS is divided into numerous tiny blocks, each of which is assigned to only one Processing Element (PE). Different PEs are connected through a scalable network-on-chip (NoC). For realistic graphs with power-law properties, a degree-aware preprocessing method is designed to balance the workload among different PEs. Our results with various graph algorithms demonstrate that GraphS can outperform state-of-the-art ForeGraph by up to 21.84 ×. © 2023, Springer Nature Switzerland AG.

关键词： Network-on-chip

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MCT-Net: a multi-branch hybrid CNN-transformer model for medical image segmentation

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Pattern Analysis and Applications 2025年第2期28卷 1-21页

作者： Shen, Longfeng Diao, Liangjin Peng, Rui Chen, Jiacong Lu, Zhengtian Ge, Fangzhen Anhui Engineering Research Center for Intelligent Computing and Application on Cognitive Behavior (ICACB) College of Computer Science and Technology Huaibei Normal University Huaibei China Institute of Artificial Intelligence Hefei Comprehensive National Science Center Hefei China Anhui Big-Data Research Center on University Management Huaibei Normal University Huaibei China

In recent years, neural networks have demonstrated substantial progress in medical image segmentation. However, accurately segmenting objects in medical images is often restricted by edge blurring, which complicates the delineation of structures of interest. The purpose of this study is to develop a multi-branch hybrid CNN-transformer model to address the issue of edge blurring in medical image segmentation. This approach enables more precise edge detection and segmentation. Integrating hybrid CNN and transformer decoders facilitates detailed recovery while preserving global structures, thus minimizing errors in regions with blurred edges. Additionally, we incorporate a hybrid attention mechanism at the model’s bottleneck to enhance feature transfer between the encoder and decoder. The model was trained using the ACDC, Synapse, and polyp datasets, with a focus on improving segmentation accuracy in regions with blurry edges. Experimental results reveal that the proposed model surpasses existing state-of-the-art methods on the ACDC, Synapse, and polyp datasets, demonstrating its superior performance and effectiveness. These results suggest that the proposed model offers a significant improvement in handling edge blurring, with potential applications in enhancing medical image analysis and diagnostics.

关键词： Attention mechanism Convolutional neural network Edge information Medical image segmentation Transformer

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Learning from Noisy Crowd Labels with Logics 39

Learning from Noisy Crowd Labels with Logics

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39th IEEE International Conference on data Engineering, ICDE 2023

作者： Chen, Zhijun Sun, Hailong He, Haoqian Chen, Pengpeng Beihang University Sklsde Lab Beijing China Beihang University Beijing Advanced Innovation Center for Big Data and Brain Computing Beijing China China's Aviation System Engineering Research Institute Beijing China

ISBN: (纸本)9798350322279

This paper explores the integration of symbolic logic knowledge into deep neural networks for learning from noisy crowd labels. We introduce Logic-guided Learning from Noisy Crowd Labels (Logic-LNCL), an EM-alike iterative logic knowledge distillation framework that learns from both noisy labeled data and logic rules of interest. Unlike traditional EM methods, our framework contains a "pseudo-E-step"that distills from the logic rules a new type of learning target, which is then used in the "pseudo-M-step"for training the classifier. Extensive evaluations on two real-world datasets for text sentiment classification and named entity recognition demonstrate that the proposed framework improves the state-of-the-art and provides a new solution to learning from noisy crowd labels. © 2023 IEEE.

关键词： Crowdsourcing

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Accumulative Time Based Ranking Method to Reputation Evaluation in Information Networks

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Journal of Computer Science & Technology 2022年第4期37卷 960-974页

作者： Hao Liao Qi-Xin Liu Ze-Cheng Huang Ke-Zhong Lu Chi Ho Yeung Yi-Cheng Zhang National Engineering Laboratory on Big Data System Computing Technology College of Computer Science and SoftwareEngineeringShenzhen UniversityShenzhen 518060China Guangdong Province Key Laboratory of Popular High Performance Computers Shenzhen UniversityShenzhen 518060China Guangdong Province Engineering Center of China-Made High Performance Data Computing System College of ComputerScience and Software EngineeringShenzhen UniversityShenzhen 518060China Institute of Big Data Intelligent Management and Decision Shenzhen UniversityShenzhen 518060China Department of Science and Environmental Studies The Education University of Hong KongHong Kong 999077China Department of Physics University of FribourgFribourg 1700Switzerland

Due to over-abundant information on the Web, information filtering becomes a key task for online users to obtain relevant suggestions and how to extract the most related item is always a key topic for researchers in various fields. In this paper, we adopt tools used to analyze complex networks to evaluate user reputation and item quality. In our proposed Accumulative Time Based Ranking (ATR) algorithm, we take into account the growth record of the network to identify the evolution of the reputation of users and the quality of items, by incorporating two behavior weighting factors which can capture the hidden facts on reputation and quality dynamics for each user and item respectively. Our proposed ATR algorithm mainly combines the iterative approach to rank user reputation and item quality with temporal dependence compared with other reputation evaluation methods. We show that our algorithm outperforms other benchmark ranking algorithms in terms of precision and robustness on empirical datasets from various online retailers and the citation datasets among research publications. Therefore, our proposed method has the capability to effectively evaluate user reputation and item quality.

关键词： temporal network behavior dynamics reputation evaluation ranking algorithm

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Logical Relation Modeling and Mining in Hyperbolic Space for Recommendation 40

Logical Relation Modeling and Mining in Hyperbolic Space for...

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40th IEEE International Conference on data Engineering, ICDE 2024

作者： Tan, Yanchao Lv, Hang Zhou, Zihao Guo, Wenzhong Xiong, Bo Liu, Weiming Chen, Chaochao Wang, Shiping Yang, Carl College of Computer and Data Science Fuzhou University Fuzhou China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou China Institute for Artificial Intelligence University of Stuttgart Stuttgart Germany College of Computer Science Zhejiang University Hangzhou China Emory University Department of Computer Science Atlanta United States

ISBN: (纸本)9798350317152

The sparse interactions between users and items have aggravated the difficulty of their representations in recommender systems. Existing methods leverage tags to alleviate the sparsity problem but ignore prevalent logical relations among items and tags (e.g., membership, hierarchy, and exclusion), which can be leveraged to enhance the accuracy of modeling user preferences and conducting recommendations. To this end, we propose to extract logical relations among item tags from existing tag taxonomies and exploit the individual strengths of the Poincaré and the Lorentz models in hyperbolic space for logical relation modeling towards enhanced recommendations. Moreover, we find that the logical relations directly extracted from existing tag taxonomies can be inaccurate and coarse. Therefore, we further devise innovative consistency-based and granularity-based weighting mechanisms based on user behavior patterns for data-driven logical relation mining that can be jointly optimized along with recommendations in an end-to-end fashion. Extensive experiments on four real-world benchmark datasets show drastic performance gains brought by our proposed framework, which constantly achieves an average of 8.25% improvement over state-of-the-art competitors regarding both Recall and NDCG metrics. Insightful case studies further demonstrate that our automatically refined logical relations are highly accurate and interpretable. © 2024 IEEE.

关键词： Recommender systems

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MedX-Net: Hierarchical Transformer with Large Kernel Convolutions for 3D Medical Image Segmentation

MedX-Net: Hierarchical Transformer with Large Kernel Convolu...

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2024 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2024

作者： Lu, Lin Zou, Qingzhi Key Laboratory of Computing Power Network and Information Se-curity Ministry of Education Shandong Computer Science Center Jinan China Shandong Engineering Research Center of Big Data Applied Technology Faculty of Computer Science and Technology Jinan China Shandong Provincial Key Laboratory of Computer Networks Shandong Fundamental Research Center for Computer Science Jinan China

ISBN: (纸本)9781665410205

Due to the exceptional performance of Transform-ers in 2D medical image segmentation, recent work has also introduced them into 3D medical segmentation tasks. For instance, Swin UNETR and other hierarchical Transformers have reintroduced prior knowledge from several convolutional networks, further enhancing the volume segmentation capabilities of models. The efficacy of these hybrid methodologies is primarily attributed to the substantial quantity of parameters and the nonlocal self-attention mechanism with a large receptive field. We argue that the behavior of these methods' large receptive fields can be simulated by employing fewer parameters through the utilization of depth-wise convolutions with large kernel. Within this manuscript, we introduce a lightweight volume segmentation model called MedX-Net, which uses convolutional network modules to simulate hierarchical Transformers for robust volume segmentation. Firstly, inspired by the hierarchical Transformer module of Swin UNETR, we investigate large-kernel depth-wise convolutions with different sizes to achieve a reduced model parameter count while maintaining a large global receptive field. Secondly, we replace the multilayer perceptron (MLP) in the hierarchical Transformer module with Inverted Bottleneck with Depthwise Convolution Enhancement(DWCE) to improve model performance with fewer activation and normalization layers, further reducing the parameter count. We validate the effectiveness and efficiency of our model for volume segmentation on three public datasets: Synapse, BTCV and ACDC. On the Synapse dataset, compared to Swin UNETR, our model achieves an improvement from 83.48% to 87.21% in Dice score. Compared to the result of 86.57% achieved by nnFormer, our model achieves superior performance while reducing the model parameter count by 64%. © 2024 IEEE.

关键词： Image segmentation

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RAGRAPH: A General Retrieval-Augmented Graph Learning Framework 38

RAGRAPH: A General Retrieval-Augmented Graph Learning Framew...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Jiang, Xinke Qiu, Rihong Xu, Yongxin Zhang, Wentao Zhu, Yichen Zhang, Ruizhe Fang, Yuchen Chu, Xu Zhao, Junfeng Wang, Yasha School of Computer Science Peking University China University of Electronic Science and Technology of China China Center on Frontiers of Computing Studies Peking University Beijing China Big Data Technology Research Center Nanhu Laboratory Jiaxing China Peking University Information Technology Institute Binhai Tianjin China

Graph Neural Networks (GNNs) have become essential in interpreting relational data across various domains, yet, they often struggle to generalize to unseen graph data that differs markedly from training instances. In this paper, we introduce a novel framework called General Retrieval-Augmented Graph Learning (RAGRAPH), which brings external graph data into the general graph foundation model to improve model generalization on unseen scenarios. On the top of our framework is a toy graph vector library that we established, which captures key attributes, such as features and task-specific label information. During inference, the RAGRAPH adeptly retrieves similar toy graphs based on key similarities in downstream tasks, integrating the retrieved data to enrich the learning context via the message-passing prompting mechanism. Our extensive experimental evaluations demonstrate that RAGRAPH significantly outperforms state-of-the-art graph learning methods in multiple tasks such as node classification, link prediction, and graph classification across both dynamic and static datasets. Furthermore, extensive testing confirms that RAGRAPH consistently maintains high performance without the need for task-specific fine-tuning, highlighting its adaptability, robustness, and broad applicability. © 2024 Neural information processing systems foundation. All rights reserved.

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bigRU-DA: Based on Improved bigRU Multi-Target data Association Method

BiGRU-DA: Based on Improved BiGRU Multi-Target Data Associat...

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International Conference on Computers, Communications, and Systems (ICCCS)

作者： Guangsheng Wu Licai Wang Xun Hu Qibin Luo Dongliang Guo Big data research and development center North China Institute of Computing Technology Beijing China

Trajectory data association algorithm is an important part of multi-target tracking method. Traditional association methods require priori information such as target motion model and clutter density to conduct association, and the association accuracy is low in complex scenes such as trajectory accompaniments and crosses. Based on the sensitivity of bigRU to time series, this paper proposes an improved trajectory data association algorithm of bigRU network: bigRU-DA. In this paper, an output gate structure is added on the basis of the existing bigRU model, which can optimize the output results of the model and extract the influence of trajectory timing sequence on trajectory data association. In order to verify the data association effect of bigRU-DA method, the experiment conducted comparison experiments in four datasets under the condition of clutter interference. Experimental results show that bigRU-DA is superior to other methods in all datasets.

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A Time-Efficient Distributed Constant Conditional Functional Dependency Discovery Algorithm for data Consistency

A Time-Efficient Distributed Constant Conditional Functional...

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IEEE Annual International Computer Software and Applications Conference (COMPSAC)

作者： Junchao Chen Jian-tao Zhou Xinyu Hao Inner Mongolia Engineering Laboratory for Cloud Computing and Service Software Inner Mongolia Key Laboratory of Social Computing and Data Processing Inner Mongolia Engineering Laboratory for Big Data Analysis Technology College of Computer Science Inner Mongolia University Engineering Research Center of Ecological Big Data Ministry of Education National & Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian Hohhot China

ISBN: (数字)9798350376968

ISBN: (纸本)9798350376975

The accuracy of data analysis depends on data quality, and addressing data consistency issues is a key challenge to improve it. Constant Conditional Functional Dependency (CCFD) is an effective approach that ensures data consistency by enforcing bindings of semantically related values, thus providing quality assurance for data analysis and decision-making processes. However, with the growth of data scale, especially the increasing number of data tuples and attributes, existing single-machine CCFD discovery algorithms face issues of low computational efficiency and lengthy computation time. This paper proposes a time-efficient distributed CCFD discovery algorithm (DCCFD). Through the optimization of data preprocessing and index mapping, the data organization structure is enhanced, laying the foundation for the discovery of CCFDs under distributed conditions. The Spark parallel computing framework is used to partition the dataset, which accelerates the parallel loading and processing of data. Additionally, this algorithm ensures accuracy and processing speed when discovering dependencies by efficiently generating frequent itemsets and verifying CCFDs in parallel. Experiments on multiple real datasets show that, especially with the complex Airline dataset, the DCCFD algorithm not only accurately discovers CCFDs, but also reduces the average running time by 75.64% compared with the preCFDMiner algorithm.

关键词： Accuracy data preprocessing Software algorithms Distributed databases Parallel processing Software Partitioning algorithms

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