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Consistency label-activated region generating network for weakly supervised medical image segmentation

Computers in Biology and Medicine 2024年 173卷 108380-108380页

作者： Du, Wei Huo, Yongkang Zhou, Rixin Sun, Yu Tang, Shiyi Zhao, Xuan Li, Ying Li, Gaoyang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University Changchun130012 China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East Hospital Shanghai200092 China Bioinformatics Department School of Life Sciences and Technology Tongji University Shanghai200092 China

The current methods of auto-segmenting medical images are limited due to insufficient and ambiguous pathonmorphological labeling. In clinical practice, rough classification labels (such as disease or normal) are more commonly used than precise segmentation masks. However, there is still much to be explored regarding utilizing these weak clinical labels to accurately determine the lesion mask and guide medical image segmentation. In this paper, we proposed a weakly supervised medical image segmentation model to directly generate the lesion mask through a class activation map (CAM) guided cycle-consistency label-activated region transferring network. Cycle-consistency enforces that the mappings between the two domains should be reversible, which ensures that the original image can be reconstructed from the translated image. We developed a complementary branches fusion module to address the issue of blurry boundaries in CAM-guided segmentation. The complementary branch preserves the original semantic information of the non-lesion region and perfectly fuses the transferred feature of the lesion region with a complementary mask-constrained fake image generation process to clear the boundary of the lesion and non-lesion regions. This module allows the class transformation to focus solely on the label-activated region, resulting in more explicit segmentation. This model can accurately identify different region of medical images at the pixel-level while preserving the overall semantic structure semantion. It organizes disease labels and corresponding regions during image synthesis. Our method utilizes a joint discrimination strategy that significantly enhances the precision of the produced lesion mask. Extensive experiments of the proposed method on BraTs, ISIC and COVID-19 datasets demonstrate superior performance over existing state-of-the-art methods. The code and datasets are available at: https://***/mlcb-jlu/MedImgSeg. © 2024 Elsevier Ltd

关键词： Image segmentation

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Sure: Screening Unlabeled Samples for Reliable Negative Samples Based on Reinforcement Learning

SSRN

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SSRN 2022年

作者： Li, Ying Sun, Hang Fang, Wensi Ma, Qin Han, Siyu Wang-Sattler, Rui Du, Wei Yu, Qiong Key Laboratory of Symbolic Computation and Knowledge Engineering College of Computer Science and Technology Jilin University Qianjin Street Jilin Changchun130012 China Department of Biomedical Informatics Ohio State University Lane Ave ColumbusOH43210 United States TUM School of Medicine Technical University of Munich Ismaninger Straße 22 Bavaria Munich81675 Germany Helmholtz Center Munich German Research Center for Environmental Health Ingolstadter Landstraße 1 Bavaria Neuherberg85764 Germany Department of Epidemiology and Biostatistics School of public health Jilin University Qianjin Street Jilin Changchun130012 China

For many classification tasks, only experimentally validated positive samples are available, and experimentally validated negative samples are not recorded. The lack of negative samples poses a great challenge for using supervised machine learning. To address this problem, we propose a novel deep reinforcement learning based model to screen reliable negative samples from unlabeled samples, named SURE. SURE has two modules: sample selector and sample inspector. The sample selector screens reliable negative samples from unlabeled samples by two reinforcement strategies. The sample inspector classifies samples and provides rewards to the sample selector. In this paper, we focus on one popular issue in the field of bioinformatics: the ncRNA-protein interaction (NPI) prediction task, which lacks reliable negative samples. Thirty datasets for NPI prediction are used to test the screening effect of SURE. The Experimental results show that our model has a robust negative sample screening capability and is superior to all outstanding sample screening methods used in the NPI prediction task. In addition, we refine 5 NPI datasets containing reliable negative samples screened by SURE, and a webserver (***/sure) is available offering the NPI prediction refined by SURE. © 2022, The Authors. All rights reserved.

关键词： Reinforcement learning

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A new SAT Encoding Scheme for Exactly-one Constraints

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Journal of Physics: Conference Series 2019年第1期1288卷

作者： Jiatong Cai Yating Su Xixi Yang Jionghao Min Yong Lai College of Software Jilin University Changchun P.R. China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun P.R. China

Exactly-one constraints have comprehensive applications for the fields of artificial intelligence and operations research. For many encoded SAT problems generated by the existing encoding schemes of exactly-one constraints, the state-of-the-art knowledge compilers cannot complete compilation. In this paper, we propose a new encoding scheme of exactly-one constraints. We introduce two-dimensional auxiliary variables (represented as a matrix) to denote the constraint that exactly one of some variables can be assigned as true. The clauses generated by our scheme is significantly less than those generated by three other existing encoding schemes. The experimental results on the exact cover problems show that the encoded CNF formulas generated by our scheme requires less compilation time, compared with the other three coding schemes.

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Ontology Revision based on Pre-trained Language Models

arXiv

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arXiv 2023年

作者： Ji, Qiu Zhang, Xiaoping Ye, Yuxin Qi, Guilin Li, Jiaye Li, Site Ren, Jianjie Lu, Songtao School of Modern Posts Institute of Modern Posts Nanjing University of Posts and Telecommunications Nanjing China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China National Data Center ofTraditional Chinese MedicineChina Academy of ChineseMedical Sciences Beijing100700 China College of Computer Science and Technology Jilin University Changchun130012 China School of Computer Science and Engineering Southeast University Nanjing China Key Laboratory of Computer Network and Information Integration Southeast University Ministry of Education Nanjing China School of Mathematics Southeast University Nanjing China Chien-Shiung Wu College Southeast University Nanjing China

Ontology revision aims to seamlessly incorporate a new ontology into an existing ontology and plays a crucial role in tasks such as ontology evolution, ontology maintenance, and ontology alignment. Similar to repair single ontologies, resolving logical incoherence in the task of ontology revision is also important and meaningful, because incoherence is a main potential factor to cause inconsistency and reasoning with an inconsistent ontology will obtain meaningless answers. To deal with this problem, various ontology revision approaches have been proposed to define revision operators and design ranking strategies for axioms in an ontology. However, they rarely consider axiom semantics which provides important information to differentiate axioms. In addition, pre-trained models can be utilized to encode axiom semantics, and have been widely applied in many natural language processing tasks and ontology-related ones in recent years. Therefore, in this paper, we study how to apply pre-trained models to revise ontologies. We first define four scoring functions to rank axioms based on a pre-trained model by considering various information from an ontology. Based on the functions, an ontology revision algorithm is then proposed to deal with unsatisfiable concepts at once. To improve efficiency, an adapted revision algorithm is designed to deal with unsatisfiable concepts group by group. We conduct experiments over 19 ontology pairs and compare our algorithms and scoring functions with existing ones. According to the experiments, our algorithms could achieve promising performance. The adapted revision algorithm could improve the efficiency largely, and at most about 90% of the time could be saved for some ontology pairs. Some of our scoring functions like reliableOnt cos could help a revision algorithm obtain better results in many cases, especially for those challenging ontology pairs like OM8. We also provide discussion about the overall experimental results and guidelin

关键词： Ontology

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Multimodal Hypothetical Summary for Retrieval-based Multi-image Question Answering

arXiv

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arXiv 2024年

作者： Li, Peize Si, Qingyi Fu, Peng Lin, Zheng Wang, Yan School of Artificial Intelligence Jilin University Changchun China Institute of Information Engineering Chinese Academy of Sciences Beijing China Huawei Technologies Co. Ltd. Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education College of Computer Science and Technology Jilin University Changchun China

Retrieval-based multi-image question answering (QA) task involves retrieving multiple question-related images and synthesizing these images to generate an answer. Conventional "retrieve-then-answer" pipelines often suffer from cascading errors because the training objective of QA fails to optimize the retrieval stage. To address this issue, we propose a novel method to effectively introduce and reference retrieved information into the QA. Given the image set to be retrieved, we employ a multimodal large language model (visual perspective) and a large language model (textual perspective) to obtain multimodal hypothetical summary in question-form and description-form. By combining visual and textual perspectives, MHyS captures image content more specifically and replaces real images in retrieval, which eliminates the modality gap by transforming into text-to-text retrieval and helps improve retrieval. To more advantageously introduce retrieval with QA, we employ contrastive learning to align queries (questions) with MHyS. Moreover, we propose a coarse-to-fine strategy for calculating both sentence-level and word-level similarity scores, to further enhance retrieval and filter out irrelevant details. Our approach achieves a 3.7% absolute improvement over state-of-the-art methods on RETVQA and a 14.5% improvement over CLIP. Comprehensive experiments and detailed ablation studies demonstrate the superiority of our method. Copyright © 2024, The Authors. All rights reserved.

关键词： Question answering

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Multi-Label Classification based on Label-Specific Features

Multi-Label Classification based on Label-Specific Features

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2011年全国理论计算机科学学术年会

作者： QU Huaqiao ZHANG Shichao LIU Huawen ZHAO Jianmin Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China Department of Computer Science Zhejiang Normal University Jinhua 321004 Department of Computer Science Zhejiang Normal University Jinhua 321004 China Department of Computer Science Zhejiang Normal University Jinhua 321004 China

lti-label learning aims at predicting a proper label set for each unseen *** instance in the dataset is associated with a set of predefined ***-label learning approaches frequently used choose identical feature set to...

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Web-based Teamwork: Distributed Software Development Course under Covid-19

Web-based Teamwork: Distributed Software Development Course ...

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International Conference on Computer Science & Education (ICCSE)

作者： Rui ZHANG Pedro Mestre Carlos Serodio Marília Prada Wenjuan GAO College of Computer Science and Technology Jilin University Key Lab of Symbolic Computation and Knowledge Engineering Chinese Ministry of Education Changchun China Centro Algoritmi University of Minho Guimaraes Portugal CITAB University of Tras-os-Montes and Alto Douro Vila Real Portugal Department of Social and Organizational Psychology Instituto Universitário de Lisboa (ISCTE-IUL) Lisboa Portugal Library of Changchun University Changchun China

ISBN: (数字)9781728172675

ISBN: (纸本)9781728172682

In a increasingly globalized world, it is very important to help students to acquire the hard and soft skills needed to cope with the challenges they will face when working in such environments. However, even though students find this subject interesting and volunteer for it, it is hard, even impossible to teach college students such a distributed fashion of teamwork. In this paper, a case study is provided to illustrate the methodology and experiences of a joint course, distributed software development, of multiple universities from Asia, Europe, North and South Americas. The results show that student can get the spirit, effective communication for such web-based teamwork environment and achieve software project development. The recent developments because of the Covid-19 pandemic are the facts that now students have to cooperate remotely with each other not only across continents but also inside their own city or country. It has increased the awareness of the need for this kind of training and effectively improved the interactions between team elements in different countries and improved the students' feeling of belonging to their team.

关键词： Software Software engineering Games Faces Teamwork Electronic mail Tools

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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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UAV Virtual Antenna Array Deployment for Uplink Interference Mitigation in Data Collection Networks

arXiv

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arXiv 2024年

作者： Li, Hongjuan Kang, Hui Sun, Geng Li, Jiahui Wang, Jiacheng Wang, Xue Niyato, Dusit Leung, Victor C.M. 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 Computing and Data Science Nanyang Technological University Singapore639798 Singapore College of Computing and Data Science Nanyang Technological University Singapore Department of Communication Engineering Jilin University Changchun130012 China Artificial Intelligence Research Institute Shenzhen MSU-BIT University Shenzhen518115 China College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China Department of Electrical and Computer Engineering The University of British Columbia VancouverV6T 1Z4 Canada

Unmanned aerial vehicles (UAVs) have gained considerable attention as a platform for establishing aerial wireless networks and communications. However, the line-of-sight dominance in air-to-ground communications often leads to significant interference with terrestrial networks, reducing communication efficiency among terrestrial terminals. This paper explores a novel uplink interference mitigation approach based on the collaborative beamforming (CB) method in multi-UAV network systems. Specifically, the UAV swarm forms a UAV-enabled virtual antenna array (VAA) to achieve the transmissions of gathered data to multiple base stations (BSs) for data backup and distributed processing. However, there is a trade-off between the effectiveness of CB-based interference mitigation and the energy conservation of UAVs. Thus, by jointly optimizing the excitation current weights and hover position of UAVs as well as the sequence of data transmission to various BSs, we formulate an uplink interference mitigation multi-objective optimization problem (MOOP) to decrease interference affection, enhance transmission efficiency, and improve energy efficiency, simultaneously. In response to the computational demands of the formulated problem, we introduce an evolutionary computation method, namely chaotic non-dominated sorting genetic algorithm II (CNSGA-II) with multiple improved operators. The proposed CNSGA-II efficiently addresses the formulated MOOP, outperforming several other comparative algorithms, as evidenced by the outcomes of the simulations. Moreover, the proposed CB-based uplink interference mitigation approach can significantly reduce the interference caused by UAVs to non-receiving BSs. Copyright © 2024, The Authors. All rights reserved.

关键词： Multiobjective optimization

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CellMirror: Deciphering Cell Populations from Spatial Transcriptomics Data by Interpretable Contrastive Learning

CellMirror: Deciphering Cell Populations from Spatial Transc...

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Medical Artificial Intelligence (MedAI), IEEE International Conference on

作者： Junjie Xia Jiangnan Cui Zhenyu Huang Shuangquan Zhang Fang Yao Yijian Zhang Chunman Zuo Department of Applied Mathematics Institute of Artificial Intelligence Donghua University Shanghai China Institute of Artificial Institute Donghua University Shanghai China College of Computer Science and Technology Jilin University Changchun China School of Cyber Science and Engineering Nanjing University of Science and Technology Nanjing China Affiliated Shenzhen Maternity and Child Healthcare Hospital Institute of Maternal and Child Medicine Southern Medical University Shenzhen China Department of General Surgery Xinhua Hospital Affiliated to Shanghai Jiao Tong University of Medicine Shanghai China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China

Spatial transcriptomics (ST) has enabled us elucidating tumor microenvironments, however, the technological limitations without single-cell resolution severely hinder its application. Here, we propose CellMirror, an interpretable contrastive learning model to decipher heterogeneous cell populations in ST data by single-cell RNA-sequencing (scRNA-seq) data. Specifically, CellMirror learns the disentangled shared (representing biological variations in both data) and salient features (specific to ST data) by two contrastive variational encoders, while constructing the relations between genes and features by a shared linear decoder. In various cancer samples, CellMirror outperforms other tools in learning common features for label transfer, and interpretation of features. Particularly, in breast cancer studies, CellMirror detects finer domains in ST data missed by other methods, and is robust to dissect cell populations in ST data using independent scRNA-seq data. These results demonstrate applications of CellMirror in interpreting the complex tumor structure in ST data by integrating scRNA-seq data.

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