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Inferring microRNA-disease association by hybrid recommendation algorithm and unbalanced bi-random walk on heterogeneous network

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Scientific reports 2019年第1期9卷 2474页

作者： Dong-Ling Yu Yuan-Lin Ma Zu-Guo Yu Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology Brisbane Q4001 Australia. yuzuguo@***.

More and more research works have indicated that microRNAs (miRNAs) play indispensable roles in exploring the pathogenesis of diseases. Detecting miRNA-disease associations by experimental techniques in biology is expensive and time-consuming. Hence, it is important to propose reliable and accurate computational methods to exploring potential miRNAs related diseases. In our work, we develop a novel method (BRWHNHA) to uncover potential miRNAs associated with diseases based on hybrid recommendation algorithm and unbalanced bi-random walk. We first integrate the Gaussian interaction profile kernel similarity into the miRNA functional similarity network and the disease semantic similarity network. Then we calculate the transition probability matrix of bipartite network by using hybrid recommendation algorithm. Finally, we adopt unbalanced bi-random walk on the heterogeneous network to infer undiscovered miRNA-disease relationships. We tested BRWHNHA on 22 diseases based on five-fold cross-validation and achieves reliable performance with average AUC of 0.857, which an area under the ROC curve ranging from 0.807 to 0.924. As a result, BRWHNHA significantly improves the performance of inferring potential miRNA-disease association compared with previous methods. Moreover, the case studies on lung neoplasms and prostate neoplasms also illustrate that BRWHNHA is superior to previous prediction methods and is more advantageous in exploring potential miRNAs related diseases. All source codes can be downloaded from https://***/myl446/BRWHNHA .

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From social to individuals: A parsimonious path of multi-level models for crowdsourced preference aggregation

arXiv

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arXiv 2018年

作者： Xu, Qianqian Xiong, Jiechao Cao, Xiaochun Huang, Qingming Yao, Yuan Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing1000190 China Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China Tencent AI Lab Shenzhen518057 BICMR-LMAM-LMEQF-LMP School of Mathematical Sciences Peking University Beijing100871 China University of Chinese Academy of Sciences Institute of Computing Technology of Chinese Academy of Sciences Beijing100190 China Department of Mathematics and by courtesy Computer Science and Engineering Hong Kong University of Science and Technology Hong Kong Hong Kong

In crowdsourced preference aggregation, it is often assumed that all the annotators are subject to a common preference or social utility function which generates their comparison behaviors in experiments. However, in reality annotators are subject to variations due to multi-criteria, abnormal, or a mixture of such behaviors. In this paper, we propose a parsimonious mixed-effects model, which takes into account both the fixed effect that the majority of annotators follows a common linear utility model, and the random effect that some annotators might deviate from the common significantly and exhibit strongly personalized preferences. The key algorithm in this paper establishes a dynamic path from the social utility to individual variations, with different levels of sparsity on personalization. The algorithm is based on the Linearized Bregman Iterations, which leads to easy parallel implementations to meet the need of large-scale data analysis. In this unified framework, three kinds of random utility models are presented, including the basic linear model with L2 loss, Bradley-Terry model, and Thurstone-Mosteller model. The validity of these multi-level models are supported by experiments with both simulated and real-world datasets, which shows that the parsimonious multi-level models exhibit improvements in both interpretability and predictive precision compared with traditional HodgeRank. Copyright © 2018, The Authors. All rights reserved.

关键词： Crowdsourcing

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Direct clustering algorithm based on generalized information distance

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Jisuanji Yanjiu yu Fazhan/Computer Research and Development 2007年第4期44卷 674-679页

作者： Ding, Shifei Shi, Zhongzhi Jin, Fengxiang Xia, Shixiong College of Computer Science and Technology China University of Mining and Technology Xuzhou 221008 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100080 China College of Geoinformation Science and Engineering Shandong University of Science and Technology Qingdao 266510 China

In this paper a novel direct clustering algorithm based on generalized information distance (GID) is put forward. Firstly, based on information theory, a basic concept of measure of diversity is given and an inequality about measure of diversity is proved. Based on this inequality, a concept of increment of diversity is discussed and a defined. Secondly, by analyzing distance measure, two new concepts of generalized information distance (GID) and improved generalized information distance (IGID) are proposed, and a new direct clustering algorithm based on GID and IGID is designed. Finally this algorithm is applied to soil fertility data processing, and compared with hierarchical clustering algorithm (HCA). The results of simulation application show that the algorithm presented here is feasible and effective. Because of simplicity of algorithm and robustness. It provides a new research approach for studies of pattern recognition theory.

关键词： Clustering algorithms

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Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction

arXiv

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arXiv 2023年

作者： Lin, Xuan Dai, Lichang Zhou, Yafang Yu, Zu-Guo Zhang, Wen Shi, Jian-Yu Cao, Dong-Sheng Zeng, Li Chen, Haowen Song, Bosheng Yu, Philip S. Zeng, Xiangxiang Xiangtan China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University China College of Informatics Huazhong Agricultural University China The Northwestern Polytechnical University Xi’an China The Xiangya School of Pharmaceutical Sciences Central South University China AIDD Department of Yuyao Biotech Shanghai China Hunan University China The College of Information Science and Engineering Hunan University Changsha China Computer Science The University of Illinois Chicago United States

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction. Copyright © 2023, The Authors. All rights reserved.

关键词： Forecasting

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Real-time Multi-person Eyeblink Detection in the Wild for Untrimmed Video

Real-time Multi-person Eyeblink Detection in the Wild for Un...

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Wenzheng Zeng Yang Xiao Sicheng Wei Jinfang Gan Xintao Zhang Zhiguo Cao Zhiwen Fang Joey Tianyi Zhou Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China School of Biomedical Engineering Southern Medical University Guangzhou China Department of Rehabilitation Medicine Zhujiang Hospital Southern Medical University Guangzhou China Centre for Frontier AI Research Agency for Science Technology and Research (A*STAR) Singapore Institute of High Performance Computing Agency for Science Technology and Research (A*STAR) Singapore

Real-time eyeblink detection in the wild can widely serve for fatigue detection, face anti-spoofing, emotion analysis, etc. The existing research efforts generally focus on single-person cases towards trimmed video. However, multi-person scenario within untrimmed videos is also important for practical applications, which has not been well concerned yet. To address this, we shed light on this research field for the first time with essential contributions on dataset, theory, and practices. In particular, a large-scale dataset termed MPEblink that involves 686 untrimmed videos with 8748 eyeblink events is proposed under multi-person conditions. The samples are captured from uncon-strainedfilms to reveal “in the wild“ characteristics. Meanwhile, a real-time multi-person eyeblink detection method is also proposed. Being different from the existing counter-parts, our proposition runs in a one-stage spatio-temporal way with end-to-end learning capacity. Specifically, it simultaneously addresses the sub-tasks of face detection, face tracking, and human instance-level eyeblink detection. This paradigm holds 2 main advantages: (1) eyeblink features can be facilitated via the face's global context (e.g., head pose and illumination condition) with joint optimization and interaction, and (2) addressing these sub-tasks in parallel instead of sequential manner can save time remarkably to meet the real-time running requirement. Experiments on MPEblink verify the essential challenges of real-time multi-person eyeblink detection in the wild for untrimmed video. Our method also outperforms existing approaches by large margins and with a high inference speed.

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DMNER: Biomedical Named Entity Recognition by Detection and Matching

DMNER: Biomedical Named Entity Recognition by Detection and ...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Junyi Bian Rongze Jiang Weiqi Zhai Tianyang Huang Xiaodi Huang Hong Zhou Shanfeng Zhu School of Computer Science Fudan University Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China School of Computing Mathematics and Engineering Charles Sturt University New South Wales Australia Atypon Systems LLC UK Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science Shanghai Key Lab of Intelligent Information Processing Zhangjiang Fudan International Innovation Center Fudan University Shanghai China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Biomedical Named Entity Recognition (NER) is a crucial task in extracting information from biomedical texts. However, the diversity of professional terminology, semantic complexity, and the widespread presence of synonyms pose significant challenges. Traditional methods that rely on sequence labeling training datasets often struggle to handle these complexities. To address this, we introduce a novel framework for BioNER, termed DMNER, which leverages external knowledge and operates in two steps: entity boundary detection and entity category identification through matching. The core of DMNER is its second step, which determines the entity category by retrieving similar entities and their categories from a knowledge dictionary using semantic similarity matching. Our experiments on 10 biomedical datasets demonstrate that DMNER outperforms baselines across these tasks, proving its effectiveness and adaptability. DMNER is versatile and can be applied to various NER tasks, including supervised NER, distantly supervised NER, and NER on multiple datasets with disjoint label sets. The DMNER code is publicly available 1 .

关键词： Training Dictionaries Codes Semantics Named entity recognition Complexity theory Labeling Data mining Bioinformatics

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Research on high-accuracy gait recognition technique based on parallel genetic algorithm

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Journal of Information Hiding and Multimedia signal processing 2018年第1期9卷 244-255页

作者： Lin, Xiao Jia Zhang, Fu Quan Xu, Lin Department of Computing and Information Technology Fujian Business University No. 19 Huang Pu Road Gulou District Fuzhou350012 China Fujian Provincial Key Laboratory of Information Processing and Intelligent Control Minjiang University School of Software Beijing Institute of Technology Room A9. 301 Juyuan Jinshan Jiyuan Fuzhou350008 China Innovative Information Industry Research Institute Fujian Normal University Fuqing Brunch of Fujian Normal University Campus County 1. Longjiang Road Fuqing Fuzhou350300 China

In the field of sports science, gait recognition has a wide range of applications. However, compared to other biometric technologies, it has the problem of low recognition accuracy. Therefore, a technique combining the parallel genetic algorithm based on hierarchical fair competition with neural network ensemble is proposed to be applied in gait recognition. First, parallel genetic algorithm is adopted to increase individual diversity, and only appropriate features are selected to train each neural network candidate. Then, a set of individual neural networks are selected to complete the neural network ensemble so as to minimize the generalization error and maximize the negative correlation. Experiments on the CASIA gait database demonstrate the effectiveness of the proposed gait recognition method. The results show that the proposed method has a higher recognition rate than the existing methods. © 2018, Ubiquitous International. All rights reserved.

关键词： Genetic algorithms

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Cavity-Quantum Electrodynamics with Moiré Flatband Photonic Crystals

arXiv

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arXiv 2024年

作者： Wang, Yu-Tong Ye, Qi-Hang Yan, Jun-Yong Qiao, Yufei Chen, Chen Cheng, Xiao-Tian Li, Chen-Hui Zhang, Zi-Jian Huang, Cheng-Nian Meng, Yun Zou, Kai Zhan, Wen-Kang Zhao, Chao Hu, Xiaolong Tee, Clarence Augustine T.H. Sha, Wei E.I. Huang, Zhixiang Liu, Huiyun Jin, Chao-Yuan Ying, Lei Liu, Feng State Key Laboratory of Extreme Photonics and Instrumentation College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China School of Physics Zhejiang Key Laboratory of Micro-nano Quantum Chips and Quantum Control Zhejiang University Hangzhou310027 China School of Precision Instrument and Optoelectronic Engineering Tianjin University Tianjin300072 China Key Laboratory of Optoelectronic Information Science and Technology Ministry of Education Tianjin300072 China Laboratory of Solid State Optoelectronics Information Technology Institute of Semiconductors Chinese Academy of Sciences Beijing100083 China College of Materials Science and Opto-Electronic Technology University of Chinese Academy of Science Beijing101804 China College of Physics and Electrical Information Engineering Zhejiang Normal University Hangzhou310058 China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei230039 China Department of Electronic and Electrical Engineering University College London LondonWC1E 7JE United Kingdom International Joint Innovation Center Zhejiang University Haining314400 China

Quantum emitters are a key component in photonic quantum technologies. Enhancing their single-photon emission by engineering the photonic environment using cavities can improve the overall efficiency in quantum information processing. However, this enhancement is often limited by the need for precise nanoscale control over emitter’s position within micro/nano-cavities. Inspired by the fascinated physics of moiré pattern, we present an approach to strongly modify the spontaneous emission rate of a quantum emitter using fine-designed multilayer moiré photonic crystal with a robust isolate-flatband dispersion. Theoretical analysis reveals that due to its nearly infinite photonic density of states, the moiré cavity can simultaneously possess high Purcell factor and large tolerance over emitter’s position. We experimentally demonstrate the coupling between this moiré cavity and a quantum dot via the cavity-determined polarization of the dot’s emission. The radiative lifetime of the quantum dot can be tuned by a factor of 40 from 42 ps to 1692 ps, attributed to strong Purcell enhancement and Purcell inhibition effects. Our findings pave the way for moiré flatband cavity-enhanced quantum light sources, quantum optical switches and quantum nodes for quantum internet. Copyright © 2024, The Authors. All rights reserved.

关键词： Particle beams

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MaxMatch: Semi-Supervised Learning with Worst-Case Consistency

arXiv

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arXiv 2022年

作者： Jiang, Yangbangyan Li, Xiaodan Chen, Yuefeng He, Yuan Xu, Qianqian Yang, Zhiyong Cao, Xiaochun Huang, Qingming State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China School of Cyber Security University of Chinese Academy of Sciences Beijing100049 China Security Department of Alibaba Group Hangzhou311121 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing101408 China School of Cyber Science and Technology Shenzhen Campus Sun Yat-sen University Shenzhen518107 China University of Chinese Academy of Sciences Beijing101408 China Peng Cheng Laboratory Shenzhen518055 China

In recent years, great progress has been made to incorporate unlabeled data to overcome the inefficiently supervised problem via semi-supervised learning (SSL). Most state-of-the-art models are based on the idea of pursuing consistent model predictions over unlabeled data toward the input noise, which is called consistency regularization. Nonetheless, there is a lack of theoretical insights into the reason behind its success. To bridge the gap between theoretical and practical results, we propose a worst-case consistency regularization technique for SSL in this paper. Specifically, we first present a generalization bound for SSL consisting of the empirical loss terms observed on labeled and unlabeled training data separately. Motivated by this bound, we derive an SSL objective that minimizes the largest inconsistency between an original unlabeled sample and its multiple augmented variants. We then provide a simple but effective algorithm to solve the proposed minimax problem, and theoretically prove that it converges to a stationary point. Experiments on five popular benchmark datasets validate the effectiveness of our proposed method. Copyright © 2022, The Authors. All rights reserved.

关键词： Image classification

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Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2003年 2773卷 V页

作者： Palade, Vasile Howlett, Bob Jain, Lalthmi Oxford University Computing Laboratory Parks Road Oxford United Kingdom University of Blighton Intelligent Systems and Signal Processing Labs Moulsecoomb Brighton United Kingdom University of South Australia Knowledge-Based Intelligent Engineering Systems Centre Mawson Lakes AdelaideSA Australia

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