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CircRNAFisher: a systematic computational approach for de novo circular RNA identification

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中国药理学报（英文版） 2019年第1期40卷 55-63页

作者： Guo-yi Jia Duo-lin Wang Meng-zhu Xue Yu-wei Liu Yu-chen Pei Ying-qun Yang Jing-mei Xu Yan-chun Liang Peng Wang School of Life Sciences Shanghai University Shanghai 200444 China Laboratory of Systems Biology Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University Changchun 130012 China Laboratory of Systems Biology Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210 China Laboratory of Systems Biology Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210 China School of Life Science and Technology Shanghai Tech University Shanghai 201210 China

Circular RNAs (circRNAs) are emerging species of mRNA splicing products with largely unknown *** several computational pipelines for circRNA identification have been developed,these methods strictly rely on uniquely mapped reads overlapping back-splice junctions (BSJs) and lack approaches to model the statistical significance of the identified ***,we reported a systematic computational approach to identify circRNAs by simultaneously utilizing BSJ overlapping reads and discordant BSJ spanning reads to identify ***,we developed a novel procedure to estimate the P-values of the identified circRNAs.A computational cross-validation and experimental validations demonstrated that our method performed favorably compared to existing circRNA detection *** created a standalone tool,CircRNAFisher,to implement the method,which might be valuable to computational and experimental scientists studying circRNAs.

关键词： circRNA RNA-Seq alternative splicing pipeline

A Fuzzy Clustering Based Collaborative Filtering Algorithm for Time-aware POI Recommendation

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Journal of Physics: Conference Series 2021年第1期1746卷

作者： Minghao Yin Yanheng Liu Xu Zhou Geng Sun College of Computer Science and Technology Jilin University Changchun Jilin China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun Jilin China Center for Computer Fundamental Education Jilin University Changchun Jilin China

Location based social network develops and gets widely concern along with the population and widespread use of mobile. Point of interest(POI) recommendation become one of the most widely application among location-based service. To get better POI recommendation performance, a fuzzy clustering based collaborative filtering algorithm (FCCF) for time-aware POI recommendation is proposed in this paper. It first constructs the user feature vector from users' check-in behaviours. Individual's check-in behaviour can be under the influence of location region and time slots, so user's feature consists of two parts. One is the vising frequency of each user in different location regions, and the other is the vising frequency of each user in different time slots. Next fuzzy c-means is adopted due to its simplicity to group users according to user feature vector. Then the user similarity computation can be limited in the similar small user groups. In the end, a collaborative filtering algorithm is applied to recommend a number of top-N POIs at a given time for the target user. Some experiments are conducted and the comparative results on Foursquare and Gowalla show that FCCF has higher precision and recall value than the comparative algorithms.

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Learning optimal data augmentation policies via bayesian optimization for image classification tasks

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arXiv 2019年

作者： Zhang, Chunxu Cui, Jiaxu Yang, Bo 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

In recent years, deep learning has achieved remarkable achievements in many fields, including computer vision, natural language processing, speech recognition and others. Adequate training data is the key to ensure the effectiveness of the deep models. However, obtaining valid data requires a lot of time and labor resources. Data augmentation (DA) is an effective alternative, which can generate new labeled data based on existing data using label-preserving transformations. Although we can benefit a lot from DA, designing appropriate DA policies requires a lot of expert experience and time consumption, and the evaluation of searching the optimal policies is costly. So we raise a new question in this paper: how to achieve automated data augmentation at as low cost as possible? We propose a method named BO-Aug for automating the process by finding the optimal DA policies using the Bayesian optimization approach. We validate the BO-Aug on three widely used image classification datasets, including CIFAR-10, CIFAR- 100 and SVHN. Experimental results show that the proposed method can achieve state-of-the-art or near advanced classification accuracy at a relatively low policies search cost, and the searched policies based on a specific dataset are transferable across different neural network architectures or even different datasets. Code to reproduce our experiments is available at https://***/zhangxiaozao/BOAug. Copyright © 2019, The Authors. All rights reserved.

关键词： Image classification

Correction to: MRI enhancement based on visual-attention by adaptive contrast adjustment and image fusion

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Multimedia Tools and Applications 2021年第9期80卷 13019-13019页

作者： Rui Zhu Xiongfei Li Xiaoli Zhang Xiaowei Xu Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China College of Computer Science and Technology Jilin University Changchun China Department of Information Sciences University of Arkansas at Little Rock Little Rock USA

A Correction to this paper has been published: https://***/10.1007/s11042-021-10782-7

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Recruitment-imitation mechanism for evolutionary reinforcement learning

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arXiv 2019年

作者： Lü, Shuai Han, Shuai Zhou, Wenbo Zhang, Junwei Key Laboratory of Symbolic Computation and Knowledge Engineering Jilin University Ministry of Education Changchun130012 China College of Computer Science and Technology Jilin University Changchun130012 China

Reinforcement learning, evolutionary algorithms and imitation learning are three principal methods to deal with continuous control tasks. Reinforcement learning is sample efficient, yet sensitive to hyper-parameters setting and needs efficient exploration;Evolutionary algorithms are stable, but with low sample efficiency;Imitation learning is both sample efficient and stable, however it requires the guidance of expert data. In this paper, we propose Recruitment-imitation Mechanism (RIM) for evolutionary reinforcement learning, a scalable framework that combines advantages of the three methods mentioned above. The core of this framework is a dual-actors and single critic reinforcement learning agent. This agent can recruit high-fitness actors from the population of evolutionary algorithms, which instructs itself to learn from experience replay buffer. At the same time, low-fitness actors in the evolutionary population can imitate behavior patterns of the reinforcement learning agent and improve their adaptability. Reinforcement and imitation learners in this framework can be replaced with any off-policy actor-critic reinforcement learner or data-driven imitation learner. We evaluate RIM on a series of benchmarks for continuous control tasks in Mujoco. The experimental results show that RIM outperforms prior evolutionary or reinforcement learning methods. The performance of RIM's components is significantly better than components of previous evolutionary reinforcement learning algorithm, and the recruitment using soft update enables reinforcement learning agent to learn faster than that using hard update. Copyright © 2019, The Authors. All rights reserved.

关键词： Evolutionary algorithms

Prior-guided dual-stage diabetic retinopathy grading model based on feature collaboration of lesion and vascular structure

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Expert Systems with Applications 2025年 285卷

作者： Guo, Xiaoxin Yang, Guangqi Xu, Chenfangqian Dong, Hongliang Hu, Xiaoying Che, Songtian Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Jilin University 2699 Qianjin Street Changchun130012 China College of Computer Science and Technology Jilin University 2699 Qianjin Street Changchun130012 China Ophthalmology Department Bethune First Hospital of Jilin University Changchun Jilin130021 China Ophthalmology Department Bethune Second Hospital of Jilin University Changchun Jilin130041 China

In order to fully utilize lesion features and vascular structure and solve the problem of class imbalance, diabetes retinopathy (DR) grading is modeled as a dual-stage task, and the prior-guided dual-stage diabetes retinopathy grading model is proposed by designing an end-to-end hierarchical framework, consisting of XE-Net and MFC-Net. The former uses vascular structure from color fundus images as prior knowledge to guide the classification of proliferative diabetic retinopathy (PDR) and non-PDR;the latter further classifies non-PDR images using color fundus images with four types of segmented lesions. The core of MFC-Net is the feature collaboration block (FCB) for multi-classification tasks, which is proposed to facilitate effective collaboration between global and local features. In addition, a class-balanced (CB) loss weight is also introduced to address the common class imbalance problem in DR datasets. The experimental results on two publicly available datasets, DDR and IDRiD show that the proposed model has significant advantages. © 2025 Elsevier Ltd

关键词： Image segmentation

Applications of Game Theory in Vehicular Networks: A Survey

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arXiv 2021年

作者： Sun, Zemin Liu, Yanheng Wang, Jian Li, Guofa Anil, Carie Li, Keqiang Guo, Xinyu Sun, Geng Tian, Daxin Cao, Dongpu 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 Institute of Human Factors and Ergonomics College of Mechatronics and Control Engineering Shenzhen University Guangdong Shenzhen518060 China School of Computer Science and Engineering VIT-AP Andhra Pradesh Amaravati522237 India College of Engineering Nanjing Agricultural University Nanjing210031 China State Key Laboratory of Automotive Safety and Energy Department of Automotive Engineering Tsinghua University Beijing100084 China Beijing Advanced Innovation Center for Big Data and Brain Computing Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control School of Transportation Science and Engineering Beihang University Beijing100191 China Waterloo Cognitive Autonomous Driving Lab University of Waterloo N2L 3G1 Canada

In the Internet of things (IoT) era, vehicles and other intelligent components in an intelligent transportation system (ITS) are connected, forming vehicular networks (VNs) that provide efficient and safe traffic and ubiquitous access to various applications. However, as the number of nodes in an ITS increases, it is challenging to satisfy a varied and large number of service requests with different quality of service (QoS) and security requirements in highly dynamic VNs. Intelligent nodes in VNs can compete or cooperate for limited network resources to achieve the objective for either an individual or a group. Game theory (GT), a theoretical framework designed for strategic interactions among rational decision makers sharing scarce resources, can be used to model and analyze individual or group behaviors of communicating entities in VNs. This paper primarily surveys the recent developments of GT in solving various challenges of VNs. This survey starts with an introduction to the background of VNs. A review of GT models studied in the VNs is then introduced, including the basic concepts, classifications, and applicable vehicular issues. After discussing the requirements of VNs and the motivation of using GT, a comprehensive literature review on GT applications in dealing with the challenges of current VNs is provided. Furthermore, recent contributions of GT to VNs that are integrated with diverse emerging 5G technologies are surveyed. Finally, the lessons learned are given, and several key research challenges and possible solutions of applying GT in VNs are outlined. Copyright © 2021, The Authors. All rights reserved.

关键词： Quality of service

Game Theoretic Approaches in Vehicular Networks: A Survey

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arXiv 2020年

作者： Sun, Zemin Liu, Yanheng Wang, Jian Anil, Carie Cao, Dongpu College of Computer Science and Technology Key Laboratory of Symbolic Computation Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China Engineering VIT-AP AmaravatiAndhra Pradesh522237 India College of Engineering Nanjing Agricultural University Nanjing210031 China Waterloo Cognitive Autonomous Driving Lab University of Waterloo N2L 3G1 Canada

—In the era of the Internet of Things (IoT), vehicles and other intelligent components in Intelligent Transportation System (ITS) are connected, forming the Vehicular Networks (VNs) that provide efficient and secure traffic, ubiquitous access to information, and various applications. However, as the number of connected nodes keeps increasing, it is challenging to satisfy various and large amounts of service requests with different Quality of Service (QoS) and security requirements in the highly dynamic VNs. Intelligent nodes in VNs can compete or cooperate for limited network resources so that either an individual or a group objectives can be achieved. Game theory, a theoretical framework designed for strategic interactions among rational decision-makers who faced with scarce resources, can be used to model and analyze individual or group behaviors of communication entities in VNs. This paper primarily surveys the recent advantages of GT used in solving various challenges in VNs. As VNs and GT have been extensively investigate34d, this survey starts with a brief introduction of the basic concept and classification of GT used in VNs. Then, a comprehensive review of applications of GT in VNs is presented, which primarily covers the aspects of QoS and security. Moreover, with the development of fifth-generation (5G) wireless communication, recent contributions of GT to diverse emerging technologies of 5G integrated into VNs are surveyed in this paper. Finally, several key research challenges and possible solutions for applying GT in VNs are outlined. Copyright © 2020, The Authors. All rights reserved.

关键词： Game theory

BAENET: A Brain Age Estimation Network with 3D Skipping and Outlier Constraint Loss

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BAENET: A Brain Age Estimation Network with 3D Skipping and ...

IEEE International Symposium on Biomedical Imaging

作者： Taiping Qu Yangming Yue Qirui Zhang Cheng Wang Zhiqiang Zhang Guangming Lu Wei Du Xiuli Li Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Changchun China Deepwise AI Lab Beijing China Jinling Hospital Medical School of Nanjing University Nanjing Jiangsu China

ISBN: (数字)9781538693308

ISBN: (纸本)9781538693315

The potential pattern changes in brain micro-structure can be used for the brain development assessment in children and adolescents by MRI scans. In this paper, we propose a highly accurate and efficient end-to-end brain age estimation network (BAENET) on T1-weighted MRI images. On the network, 3D skipping and outlier constraint loss are designed to accommodate deeper network and increase the robustness. Besides, we incorporate the neuroimaging domain knowledge into stratified sampling for better generalization ability for datasets with different age distributions, and gender learning for more gender-specific features during modeling. We verify the effectiveness of the proposed method on the public ABIDE2 and ADHD200 benchmark, consisting of 382 and 378 normal children scans respectively. Our BAENET achieves MAE of 1.11 and 1.16, significantly outperforming the best reported methods by 5.1 % and 9.4%.

关键词： Three-dimensional displays Brain modeling Estimation Solid modeling Feature extraction Magnetic resonance imaging Task analysis