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BERST: An Engine and Tool for Exploring Biomedical Entities and Relationships

Chinese Journal of Electronics 2019年第4期28卷 797-804页

作者： BAI Tian GE Yan YANG Changqing LIU Xiaohua GONG Leiguang WANG Ye HUANG Lan College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Yantai Intelligent Information Technologies Ltd. Department of Computer Science and Technology Zhuhai College of Jilin University

To facilitate the search of rapidly growing biomedical knowledge in literature, we developed a Biomedical entity-relationship search tool(BERST). It is also a biomedical knowledge integration framework, which presently contains six popular databases represented in terms of a network of concepts and relations extracted from these knowledge sources. Users search the integrated knowledge network by entering keywords, and BERST returns a sub-network matching and representing the keywords and their relationships. The resulting graph can be navigated interactively allowing users to explore specific paths between any two nodes representing potentially interesting relationships between them. A graphical UI was developed to provide a more intuitive and overall view of the information being searched and studied. BERST framework can be naturally expanded to integrate other biomedical knowledge sources. BERST is implemented as a Java web application.

关键词： Biomedical ontology Relationship mining Relationship searching tool

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Vertex-Disjoint Paths in BCDC Networks

Vertex-Disjoint Paths in BCDC Networks

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International Symposium on Parallel Architectures, Algorithms and Programming (PAAP)

作者： Xi Wang Jianxi Fan Suzhou Institute of Industrial Technology Suzhou China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun P.R. China School of Computer Science and Technology Soochow University Suzhou China

ISBN: (纸本)9781665496407

For any integer $n\geq 2,\ B_{n}$ , the $n$ -dimensional BCDC network, based on a class of BC networks, crossed cube, is a server-centric and high-performance data center network for mega data centers with manageable cabling complexity. Implementing vertex-disjoint paths has great value of application in fault-tolerance and multi-path routing of data center networks. In this paper, we construct $n$ vertex-disjoint paths joining every two distinct vertices in $B_{n}$ , whose maximum length is limited by $\lceil\frac{n}{2}\rceil+5$ , where the diameter of $B_{n}$ is $\lceil\frac{n+1}{2}\rceil+1$ . Our results are fundamental and essential for fault-tolerance and multi-path routing in BCDC networks.

关键词： Data centers Fault tolerance Fault tolerant systems Programming Routing Parallel architectures Complexity theory

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Msa-Net: A Medical Image Segmentation Network Based on Spatial Pyramid and Attention Mechanism

SSRN

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SSRN 2023年

作者： Feng, Yuncong Zhu, Xiaoyan Li, Yang Zhang, Xiaoli Lu, Huimin College of Computer Science and Engineering Changchun University of Technology Jilin Changchun130012 China Artificial Intelligence Research Institute Changchun University of Technology Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China Academy for Advanced Interdisciplinary Studies Northeast Normal University Jilin Changchun130024 China Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI 3000 North Yuanda Avenue Gaoxin North District Changchun130102 China

Medical image segmentation is an important way to assist doctors to accurately diagnose diseases. However, semantic features are difficult to be fully extracted due to the complexity of medical image lesion tissue features (e.g., size, location, and morphology) and the high similarity between the background and the target region. To tackle these problems, we propose a novel medical image segmentation network MSA-Net based on the spatial pyramid and attention mechanism. This technique facilitates the extraction of multi-scale spatial information and the establishment of channel dependencies within images. By incorporating efficient pyramid attention and channel-spatial dual attention modules, the network autonomously focuses on lesion regions while suppressing background interference. Additionally, the SPCA (Spatial Pyramid-Coordinate Attention) module is integrated at the bottleneck layer, enabling the assimilation of larger receptive field information and prioritizing relevant features. This augmentation improves the network's ability to gather both location and channel-based insights. We proceed to evaluate our model qualitatively and quantitatively across four public datasets: ISIC2018, Lung segmentation, Kvasir-SEG, and ISLES2022. The results substantiate the superior performance of our proposed model. © 2023, The Authors. All rights reserved.

关键词： Deep learning

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An Enhanced Attentive Implicit Relation Embedding for Social Recommendation

SSRN

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SSRN 2022年

作者： Ma, Xintao Dong, Liyan Wang, Yuequn Li, Yongli Liu, Zhen Zhang, Hao 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 School of Information Science and Technology Northeast Normal University Changchun130117 China Graduate School of Engineering Nagasaki Institute of Applied Science 536 Aba-machi Nagasaki851-0193 Japan

Nowadays, recommendation system incorporating social networks has attracted a lot of research attention and is widely used to understand user preferences regarding social relations. Besides, graph neural networks(GNNs) have proven to learn graph-structured data effectively. Thus, integrating GNN into social recommendations has become one challenge. Many approaches encode both the user-item interaction and social relations to learn user preference. However, the implicit relations are also crucial to understanding the features of users and items. Thus, we propose the attentive implicit relation embedding for social recommendation(SR-AIR), which models the user-item interaction and social networks, utilizing a graph attention mechanism on implicit relations of users and items. We evaluate our framework on two real-world datasets and demonstrate that our framework performs the best compared with state-of-the-art baselines © 2022, The Authors. All rights reserved.

关键词： Recommender systems

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A Survey on Fairness in Large Language Models

arXiv

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arXiv 2023年

作者： Li, Yingji Du, Mengnan Song, Rui Wang, Xin Wang, Ying College of Computer Science and Technology Jilin University Changchun130012 China Department of Data Science New Jersey Institute of Technology Newark United States School of Artificial Intelligence Jilin University Changchun130012 China Key Laboratory of Symbol Computation and Knowledge Engineering Jilin University Ministry of Education Changchun130012 China

Large Language Models (LLMs) have shown powerful performance and development prospects and are widely deployed in the real world. However, LLMs can capture social biases from unprocessed training data and propagate the biases to downstream tasks. Unfair LLM systems have undesirable social impacts and potential harms. In this paper, we provide a comprehensive review of related research on fairness in LLMs. Considering the influence of parameter magnitude and training paradigm on research strategy, we divide existing fairness research into oriented to medium-sized LLMs under pre-training and fine-tuning paradigms and oriented to large-sized LLMs under prompting paradigms. First, for medium-sized LLMs, we introduce evaluation metrics and debiasing methods from the perspectives of intrinsic bias and extrinsic bias, respectively. Then, for large-sized LLMs, we introduce recent fairness research, including fairness evaluation, reasons for bias, and debiasing methods. Finally, we discuss and provide insight on the challenges and future directions for the development of fairness in LLMs. Copyright © 2023, The Authors. All rights reserved.

关键词： computational linguistics

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Acupuncture and Tuina knowledge Graph for Ancient Literature of Traditional Chinese Medicine

Acupuncture and Tuina Knowledge Graph for Ancient Literature...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Xiaosong Han Xiaoran Li Yanchun Liang Xinghao Wang Dong Xu Renchu Guan Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Jilin University Changchun China Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Jilin University Changchun China Christopher S. Bond Life Sciences Center University of Missouri Columbia USA

ISBN: (纸本)9781665429825

The Traditional Chinese Medicine’s ancient literature recorded the massive medical theories and abundant medical experiences. To better understand and utilize, the knowledge from the literature, the Acupuncture and Tuina knowledge Graph is proposed in this paper. Meanwhile, a deep learning network is established for acupuncture and tuina-related entity recognition and entity-relationship extraction. Finally, the trained network is able to reach an 82%+ F1-score for NER and 70%+ F1-score for relationship extraction.

关键词： Deep learning Conferences Labeling Bioinformatics

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Revisiting the efficacy of weak consistencies: a study of forward checking

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Science China(Information Sciences) 2021年第7期64卷 233-235页

作者： Zhe LI Zhezhou YU Hongbo LI Jinsong GUO Zhanshan LI Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Jilin University College of Information Science and Technology Northeast Normal University Department of Computer Science University of Oxford

Dear editor,Arc consistency (AC)[1] is currently the most popular local consistency for solving constraint satisfaction problems(CSP). To solve CSPs more efficiently, extensive work [2–4]has been done to find local c... 详细信息

关键词： Information Systems and Communication Service

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Curvature regularization to prevent distortion in graph embedding 34

Curvature regularization to prevent distortion in graph embe...

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34th Conference on Neural Information Processing Systems, NeurIPS 2020

作者： Pei, Hongbin Wei, Bingzhe Chang, Kevin Chen-Chuan Zhang, Chunxu Yang, Bo College of Computer Science and Technology Jilin University China Department of Electrical and Computer Engineering University of Illinois Urbana-Champaign United States Department of Computer Science University of Illinois Urbana-Champaign United States Key Laboratory of Symbolic Computation Knowledge Engineering of Ministry of Education China

Recent research on graph embedding has achieved success in various applications. Most graph embedding methods preserve the proximity in a graph into a manifold in an embedding space. We argue an important but neglected problem about this proximity-preserving strategy: Graph topology patterns, while preserved well into an embedding manifold by preserving proximity, may distort in the ambient embedding Euclidean space, and hence to detect them becomes difficult for machine learning models. To address the problem, we propose curvature regularization, to enforce flatness for embedding manifolds, thereby preventing the distortion. We present a novel angle-based sectional curvature, termed ABS curvature, and accordingly three kinds of curvature regularization to induce flat embedding manifolds during graph embedding. We integrate curvature regularization into five popular proximity-preserving embedding methods, and empirical results in two applications show significant improvements on a wide range of open graph datasets. © 2020 Neural information processing systems foundation. All rights reserved.

关键词： Topology

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A two-stage HV-driven adaptive multi-objective evolutionary algorithm and its application in fixed polarity reed-muller circuits

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Expert Systems with Applications 2025年 288卷

作者： Lu Yang Shengsheng Wang Ruyi Dong Zihao Fu College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China College of Information and Control Engineering Jilin Institute of Chemical Technology Changchun 130012 China

To achieve a balance between convergence and diversity, we proposed a two-stage HV-driven adaptive multi-objective evolutionary algorithm (TSAMEA). TSAMEA employs a sinusoidal decreasing parameter adjustment method to enhance exploration pace in the first stage. An adaptive parameter control mechanism utilizes historical memory pools and an HV-driven degree adjustment strategy to achieve better exploitation in the second stage. Extensive experimental data demonstrate that TSAMEA outperforms nine other compared MOEAs. The component analysis illustrates the efficacy of each component of TSAMEA. In addition, area and power optimization are now the main limitations in chip design, TSAMEA is applied to area and power optimization for Fixed Polarity Reed-Muller (FPRM) logic circuits and perform well, which further verifies the ability of the TSAMEA to solve practical problems.

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Multi-objective Optimization for Multi-UAV-assisted Mobile Edge Computing

arXiv

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arXiv 2024年

作者： Sun, Geng Wang, Yixian Sun, Zemin Wu, Qingqing Kang, Jiawen Niyato, Dusit Leung, Victor C.M. 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 College of Computing and Data Science Nanyang Technological University Singapore639798 Singapore Department of Electronic Engineering Shanghai Jiao Tong University Shanghai China School of Automation Guangdong University of Technology Guangzhou510006 China College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China Department of Electrical and Computer Engineering University of British Columbia VancouverBCV6T 1Z4 Canada

Recent developments in unmanned aerial vehicles (UAVs) and mobile edge computing (MEC) have provided users with flexible and resilient computing services. However, meeting the computing-intensive and latency-sensitive demands of users poses a significant challenge due to the limited resources of UAVs. To address this challenge, we present a multi-objective optimization approach for multi-UAV-assisted MEC systems. First, we formulate a multi-objective optimization problem aiming at minimizing the total task completion delay, reducing the total UAV energy consumption, and maximizing the total amount of offloaded tasks by jointly optimizing task offloading, computation resource allocation, and UAV trajectory control. Since the problem is a mixed-integer non-linear programming (MINLP) and NP-hard problem which is challenging, we propose a joint task offloading, computation resource allocation, and UAV trajectory control (JTORATC) approach to solve the problem. However, since the decision variables of task offloading, computation resource allocation, and UAV trajectory control are coupled with each other, the original problem is split into three sub-problems, i.e., task offloading, computation resource allocation, and UAV trajectory control, which are solved individually to obtain the corresponding decisions. Moreover, the sub-problem of task offloading is solved by using distributed splitting and threshold rounding methods, the sub-problem of computation resource allocation is solved by adopting the Karush-Kuhn-Tucker (KKT) method, and the sub-problem of UAV trajectory control is solved by employing the successive convex approximation (SCA) method. Simulation results show that the proposed JTORATC has superior performance compared to the other benchmark methods. Copyright © 2024, The Authors. All rights reserved.

关键词： Unmanned aerial vehicles (UAV)

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