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Variational Wasserstein Barycenters with c-Cyclical Monotonicity Regularization

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arXiv 2021年

作者： Chi, Jinjin Yang, Zhiyao Li, Ximing Ouyang, Jihong Guan, Renchu College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China

Wasserstein barycenter, built on the theory of Optimal Transport (OT), provides a powerful framework to aggregate probability distributions, and it has increasingly attracted great attention within the machine learning community. However, it is often intractable to precisely compute, especially for high dimensional and continuous settings. To alleviate this problem, we develop a novel regularization by using the fact that c-cyclical monotonicity is often necessary and sufficient conditions for optimality in OT problems, and incorporate it into the dual formulation of Wasserstein barycenters. For efficient computations, we adopt a variational distribution as the approximation of the true continuous barycenter, so as to frame the Wasserstein barycenters problem as an optimization problem with respect to variational parameters. Upon those ideas, we propose a novel end-to-end continuous approximation method, namely Variational Wasserstein Barycenters with c-Cyclical Monotonicity Regularization (VWB-CMR), given sample access to the input distributions. We show theoretical convergence analysis and demonstrate the superior performance of VWB-CMR on synthetic data and real applications of subset posterior aggregation. Copyright © 2021, The Authors. All rights reserved.

关键词： Probability distributions

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

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arXiv 2024年

作者： Li, Kewei Wu, Yuqian Li, Yinheng Guo, Yutong Wang, Yan Liang, Yiyang Fan, Yusi Huang, Lan Zhang, Ruochi Zhou, Fengfeng College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Software Jilin University Jilin Changchun130012 China School of Life Sciences Jilin University Jilin Changchun130012 China Department of Computer Science Columbia University 116th and Broadway New York CityNY10027 United States School of Artificial Intelligence Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Biology and Engineering Guizhou Medical University Guizhou Guiyang550025 China School of Computer Engineering Changchun University of Engineering Jilin Changchun130103 China Changchun Wenli High School Jilin Changchun130062 China

Since the mechanism of action of drug molecules in the human body is difficult to reproduce in the in vitro environment, it becomes difficult to reveal the causes of the activity cliff phenomenon of drug molecules. We found out the AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in peptides with canonical amino acids. Understanding the mechanism of AC in canonical amino acids might help understand the one in drug molecules. This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the MIC, and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the MIC values on the benchmark dataset. Source code and additional resources are available at https://***/supp/or https://***/Kewei2023/AMPCliff-generation. © 2024, CC BY-NC-SA.

关键词： Deep learning

S3map: Semi-Supervised Aspect-Based Sentiment Analysis with Masked Aspect Prediction

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SSRN

SSRN 2022年

作者： Yang, Zhiyao Wang, Bing Li, Ximing Wang, Wenting Ouyang, Jihong College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China Department of Computer Science University of Texas Dallas United States

Aspect-Based Sentiment Analysis (ABSA) refers to a fine-grained task of detecting the sentiment polarities of sentences at the aspect level. To resolve this task, training samples of ABSA must be annotated with aspect words and the corresponding sentiment polarities. However, collecting such fine-grained training samples is expensive and time consuming. Therefore the available ABSA training samples are often scarce. To break the data scarcity challenge of ABSA, we investigate Semi-supervised Aspect-Based Sentiment Analysis (SemiABSA), which trains ABSA models by using a limited amount of expensive labeled sentences and more unlabeled-yet-cheaper ones. We propose a novel SemiABSA framework, namely Semi-supervised aspect-based Sentiment analysis with Masked aspect prediction (S3MAP), built on the self-training paradigm. For unlabeled sentences, we form pseudo-aspect words and pseudo-sentiment polarities and improve model training. Specifically, a BERT-Encoder-based Masked Aspect Prediction (MAP) task achieves the pseudo-aspect words generation. Based on S3MAP, we thoroughly investigate the potential of SemiABSA from various perspectives. Empirical results show that S3MAP can consistently improve the performance by leveraging unlabeled sentences even with those from different domains. © 2022, The Authors. All rights reserved.

关键词： Forecasting

Toward Moiré-Free and Detail-Preserving Demosaicking

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arXiv 2023年

作者： Li, Xuanchen Niu, Yan Zhao, Bo Shi, Haoyuan An, Zitong State Key Laboratory of Symbol Computation and Knowledge Engineering College of Computer Science and Technology Ministry of Education Jilin University Changchun China The College of Software Jilin University Changchun130012 China

3D convolutions are commonly employed by demosaicking neural models, in the same way as solving other image restoration problems. Counter-intuitively, we show that 3D convolutions implicitly impede the RGB color spectra from exchanging complementary information, resulting in spectral-inconsistent inference of the local spatial high frequency components. As a consequence, shallow 3D convolution networks suffer the Moiré artifacts, but deep 3D convolutions cause over-smoothness. We analyze the fundamental difference between demosaicking and other problems that predict lost pixels between available ones (e.g., super-resolution reconstruction), and present the underlying reasons for the confliction between Moiré-free and detail-preserving. From the new perspective, our work decouples the common standard convolution procedure to spectral and spatial feature aggregations, which allow strengthening global communication in the spectral dimension while respecting local contrast in the spatial dimension. We apply our demosaicking model to two tasks: Joint Demosaicking-Denoising and Independently Demosaicking. In both applications, our model substantially alleviates artifacts such as Moiré and over-smoothness at similar or lower computational cost to currently top-performing models, as validated by diverse evaluations. Source code will be released along with paper publication. Copyright © 2023, The Authors. All rights reserved.

关键词： Convolution

Self-Ensembling Semi-Supervised Model for Bone X-ray Images Landmark Detection

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Self-Ensembling Semi-Supervised Model for Bone X-ray Images ...

2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Bai, Tian Liu, Shenyao Wang, Yuzhao Wang, Yu Dong, Dong Jilin University College of Computer Science and Technology Changchun China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun China College of Software Jilin University Changchun China Department of Radiology First Hospital of Jilin University Changchun China

ISBN: (纸本)9781665401265

Bone image landmark detection plays a vital role in orthopedic diseases diagnosis and analysis. As a promising approach, the data-driven convolutional neural network has been widely applied in landmarks detection. However, the model's performance relies heavily on numerous high-quality labeled data, which are difficult to access. A practical solution for this issue in bone images landmark detection has not been provided, so we propose a framework of semi-supervised bone images landmark detection encouraged by the recent success of the self-ensembling method. The student and teacher networks share the same structure in our framework, where unlabeled data are utilized by enforcing the prediction consistency of two networks under different perturbations to enhance the network's performance. The two networks use a mutual learning approach to improve the efficiency of using unlabeled data. In addition, we also propose a transformative perturbation scheme to prevent model overfitting during training and enhance the generalization capability of the model on unseen data. Experimental results on an in-house hip dataset collected from the actual process of clinical diagnosis and a publicly available dataset demonstrate that our framework has excellent performance compared with other semi-supervised methods. © 2021 IEEE.

关键词： Convolutional neural networks

Machine learning in diagnosis of coronary artery disease

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Chinese Medical Journal 2021年第4期134卷 401-403页

作者： Hao Ling Zi-Yuan Guo Un-Lin Tan Ren-Chu Guan Jing-Bo Chen Chun-Li Department of Cardiology the Second Hospital of Jilin UniversityChangchunJilin 130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education College of Computer Science and TechnologyJilin UniversityChangchunJilin 130012China

Cardiovascular diseases continue to be the foremost cause of death among both males and females worldwide.[1]Coronary artery disease(CAD)represents a major subtype of cardiovascular *** evidence has highlighted a worldwide increase in incidence of CAD clinical manifestations regardless of geographical region.[2]Despite a steady decline in CAD mortality in western countries over the past few decades,approximately one-third of the population suffering from CAD will succumb to the *** and accurate diagnostic decisions are crucial for patients with CAD and aid in guidance for effective treatment.

关键词： CAD diagnosis continue

A Novel Distributed Differential Privacy Preserving Based on Random Forest in Data Centers 9th

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A Novel Distributed Differential Privacy Preserving Based on...

9th International Conference on Information Technology and Quantitative Management, ITQM 2022

作者： Wang, Xi Fan, Weibei He, Jing Chi, Chi-Hung Suzhou Institute of Industrial Technology Suzhou215006 China College of Computer Nanjing University of Posts and Telecommunications Nanjing210003 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China Department of Neuroscience University of Oxford OxfordOX1 3QR United Kingdom School of Computer Nanyang Technological University Nanyang Avenue 639798 Singapore

Traditional privacy-preserving technologies have been unable to provide adequate protection and are vulnerable to background knowledge. MapReduce is parallel distributed computing model which has the advantages of good scalability and high fault tolerance. In this paper, we design a differential privacy protection based on MapReduce for the security problems faced in the distributed environment. Firstly, we propose a random forest algorithm DPMRRF that satisfies differential privacy under the MapReduce framework. Secondly, we use the MapReduce framework in the Hadoop platform to make the classification results satisfy differential privacy by adding random noise values to the leaf nodes. Finally, through the design of the feature selection scheme combined with the index mechanism, three different privacy budget allocation methods are adopted, namely, equal distribution, equal distribution and equal distribution. Experiments show that the algorithm has better classification accuracy while ensuring data availability. The proposed algorithm effectively improves the classification accuracy and operating efficiency, and greatly reduces the amount of computation. © 2022 The Authors. Published by Elsevier B.V.

关键词： MapReduce

Heterogeneous Graph Reinforcement Learning for Dependency-aware Multi-task Allocation in Spatial Crowdsourcing

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arXiv 2024年

作者： Zhao, Yong Zhu, Zhengqiu Gao, Chen Wang, En Huang, Jincai Wang, Fei-Yue College of Systems Engineering National University of Defense Technology Hunan Province Changsha410073 China BNRist Tsinghua University Beijing100084 China 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 State Key Laboratory for Management and Control of Complex Systems Institute of Automation Chinese Academy of Sciences Beijing100190 China

Spatial Crowdsourcing (SC) is gaining traction in both academia and industry, with tasks on SC platforms becoming increasingly complex and requiring collaboration among workers with diverse skills. Recent research works address complex tasks by dividing them into subtasks with dependencies and assigning them to suitable workers. However, the dependencies among subtasks and their heterogeneous skill requirements, as well as the need for efficient utilization of workers’ limited work time in the multi-task allocation mode, pose challenges in achieving an optimal task allocation scheme. Therefore, this paper formally investigates the problem of Dependency-aware Multi-task Allocation (DMA) and presents a well-designed framework to solve it, known as Heterogeneous Graph Reinforcement Learning-based Task Allocation (HGRL-TA). To address the challenges associated with representing and embedding diverse problem instances to ensure robust generalization, we propose a multi-relation graph model and a Compound-path-based Heterogeneous Graph Attention Network (CHANet) for effectively representing and capturing intricate relations among tasks and workers, as well as providing embedding of problem state. The task allocation decision is determined sequentially by a policy network, which undergoes simultaneous training with CHANet using the proximal policy optimization algorithm. Extensive experiment results demonstrate the effectiveness and generality of the proposed HGRL-TA in solving the DMA problem, leading to average profits that is 21.78% higher than those achieved using the metaheuristic methods. © 2024, CC BY-NC-ND.

关键词： Reinforcement learning

U-HRMLP: Refining Segmentation Boundaries in Histopathology Images

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U-HRMLP: Refining Segmentation Boundaries in Histopathology ...

IEEE International Symposium on Biomedical Imaging

作者： Tao Wang Kai Zhang Weijie Wang Mingrui Ma Ye Zhang He Zhao Guixia Liu College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China School of Information Science and Engineering Shandong Normal University China Department of Information Engineering and Computer Science University of Trento Italy Faculty of Information Engineering and Automation Kunming University of Science and Technology China School of Information Science and Technology Northeast Normal University China

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

Segmenting regions of interest in histopathology images is a critical prerequisite for biomedical applications. CNN-based models have advanced medical image segmentation, yet accurately delineating boundaries is still challenging. This challenge arises from the loss of spatial resolution due to downsampling and the complexity of capturing contextual information when upsampling to the original resolution. To address these issues, we design U-HRMLP, a U-shaped network based on a hybrid combination of HRNet and Multi-Layer Perceptron (MLP). Specifically, we propose a multi-scale feature fusion module to avoid the loss of image resolution in the encoding stage as much as possible. Simultaneously, we propose an MLP-based decoding block to recover image details and resolution progressively, alleviating the issues related to the inadequate segmentation of smaller objects and the blurring of tissue boundaries. Results on the MoNuSeg and GlaS datasets demonstrate that U-HRMLP outperforms conventional or transformer-based methods and achieves state-of- the-art performance.

关键词： Measurement Image segmentation Histopathology Biological system modeling Semantics Refining Transformers