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SYNAPSE: An international roadmap to large brain imaging

Physics Reports 2023年 999卷 1-60页

作者： Stampfl, Anton P.J. Liu, Zhongdong Hu, Jun Sawada, Kei Takano, H. Kohmura, Yoshiki Ishikawa, Tetsuya Lim, Jae-Hong Je, Jung-Ho Low, Chian-Ming Teo, Alvin Tok, Eng Soon Tan, Tin Wee Ban, Kenneth Libedinsky, Camilo Tan, Francis Chee Kuan Chen, Kuan-Peng Yang, An-Cheng Chuang, Chao-Chun Chen, Nan-Yow Shih, Chi-Tin Lee, Ting-Kuo Yang, De-Nian Lai, Hsu-Chao Shuai, Hong-Han Cheng, Chang-Chieh Ching, Yu-Tai Li, Chia-Wei Charng, Ching-Che Lo, Chung-Chuan Chiang, Ann-Shyn Recur, Benoit Petibois, Cyril Cheng, Chia-Liang Chen, Hsiang-Hsin Yang, Shun-Min Hwu, Yeukuang Rojviriya, Catleya Rugmai, Supagorn Rujirawat, Saroj Margaritondo, Giorgio Australian Nuclear Science and Technology Organization Lucas Heights 2234 NSW Australia Henan university of Technology Zhengzhou China Shanghai Institute of Applied Physics Chinese Academy of Science Shanghai China RIKEN SPring-8 Center Hyogo 679-5148 Japan Pohang Accelerator Laboratory Pohang University of Science and Technology Pohang Gyeongbuk 37673 South Korea Department of Materials Science and Engineering Pohang University of Science and Technology Gyeongbuk Pohang 37673 South Korea Department of Pharmacology Department of Anaesthesia and Healthy Longevity Research Programme Yong Loo Lin School of Medicine National University of Singapore Singapore School of Chemical and Life Sciences Nanyang Polytechnic Singapore eMaGIC-Lab Department of Physics National University of Singapore Singapore National Supercomputing Center Singapore Department of Psychology The N1 Institute for Health National University of Singapore Singapore Institute of Molecular and Cell Biology A*STAR Singapore Department of Anaesthesia National University Hospital National University Health System Singapore National Center for High-Performance Computing Hsinchu Taiwan Department of Physics Tunghai University Taichung Taiwan Department of Physics National Tsing Hua University Hsinchu Taiwan Institute of Information Science Academia Sinica Taipei Taiwan Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Electronics and Electrical Engineering National Yang Ming Chiao Tung University Hsinchu Taiwan Information Technology Service Center National Yang Ming Chiao Tung University Hsinchu Taiwan National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Life Science National Tsing Hua University Hsinchu Taiwan Institute of Systems Neuroscience and Brain Research Center National Tsing Hua University Hsinchu Taiwan Institute of Physics Academia Sinica Taipei Taiwan Department of Physics National Dong Hwa University

Since 2020, synchrotron radiation facilities in several Asia-Pacific countries have been collaborating in a major project called “SYNAPSE” (Synchrotrons for Neuroscience: an Asia-Pacific Scientific Enterprise). They use x-ray imaging to attack in a coordinated fashion one of the major issues in modern science: the structure of animal and human brains, including neurons and connections. The objective is to develop Google-like maps also including detailed structural and functional information for selected regions of interest. The sheer mass of data needed for the objective poses huge problems for the acquisition, processing, storage and use of images. In order to complete the task within a reasonable time, the key element of the SYNAPSE strategy is the parallel and coordinated work of several facilities on the same specimens. This article reviews different aspects of the enterprise, including the foundations of synchrotron radiation, coherence and of its role in advanced imaging, electron accelerators, x-ray optics and detectors. This will provide the foundation for an extensive presentation of the different components of SYNAPSE, with an overview of results already obtained within the consortium. © 2022

关键词： Brain mapping Phase contrast Radiology Supercomputing Synchrotron X-rays

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An embedded estimating equation for the additive risk model with biased-sampling data

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Science China Mathematics 2018年第8期61卷 1495-1518页

作者： Feipeng Zhang Xingqiu Zhao Yong Zhou School of Mathematics and Statistics Key Laboratory of High Performance Computing and Stochastic Information Processing (Ministry of Education)Hunan Normal University Department of Applied Mathematics The Hong Kong Polytechnic University School of Statistics East China Normal University Academy of Mathematics and Systems Science Chinese Academy of Sciences

This paper presents a novel class of semiparametric estimating functions for the additive model with right-censored data that are obtained from general biased-sampling. The new estimator can be obtained using a weighted estimating equation for the covariate coefficients, by embedding the biased-sampling data into left-truncated and right-censored data. The asymptotic properties(consistency and asymptotic normality) of the proposed estimator are derived via the modern empirical processes theory. Based on the cumulative residual processes, we also propose graphical and numerical methods to assess the adequacy of the additive risk *** good finite-sample performance of the proposed estimator is demonstrated by simulation studies and two applications of real datasets.

关键词： additive risk model biased-sampling data missing covariates estimating equation model checking

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Motif Discovery via Convolutional Networks with K-mer Embedding 15th

Motif Discovery via Convolutional Networks with K-mer Embedd...

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15th International Conference on Intelligent computing, ICIC 2019

作者： Wang, Dailun Zhang, Qinhu Yuan, Chang-An Qin, Xiao Huang, Zhi-Kai Shang, Li Institute of Machine Learning and Systems Biology School of Electronics and Information Engineering Tongji University Shanghai China Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory Nanning Normal University NanningGuangxi China College of Mechanical and Electrical Engineering Nanchang Institute of Technology NanchangJiangxi330099 China Department of Communication Technology College of Electronic Information Engineering Suzhou Vocational University SuzhouJiangsu215104 China

ISBN: (纸本)9783030269685

With the rapid development of deep learning, some discriminative motif discovery methods based on deep neural network are gradually becoming the mainstream, which also bringing huge improvement of prediction accuracy. In this paper, we propose a convolutional neural network based architecture (eCNN), combining embedding layer with GloVe. Firstly, eCNN divides each single sequence of ChIP-seq datasets into multiple subsequences called k-mers by a sliding window, and then encoding k-mers into a relatively low dimension vectors by GloVe, and finally scores each vector using multiple convolutional networks. The experiment shows that our architecture can get good results on the task of motif discovery. © 2019, Springer Nature Switzerland AG.

关键词： Embeddings

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Leaf Recognition Based on Capsule Network 15th

Leaf Recognition Based on Capsule Network

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15th International Conference on Intelligent computing, ICIC 2019

作者： Zheng, Yang Yuan, Chang-An Shang, Li Huang, Zhi-Kai Institute of Machine Learning and Systems Biology School of Electronics and Information Engineering Tongji University Shanghai China Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory Nanning Normal University NanningGuangxi China Department of Communication Technology College of Electronic Information Engineering Suzhou Vocational University SuzhouJiangsu215104 China College of Mechanical and Electrical Engineering Nanchang Institute of Technology NanchangJiangxi330099 China

ISBN: (纸本)9783030267629

Plant is an indispensable part of human life, so it is very important to identify and protect plants. Convolutional neural network is a commonly used neural network for image recognition. However, convolutional neural network has huge defects. In order to avoid the defects of convolutional neural network, this paper adopts a new type of neural network: capsule neural network to complete plant leaf recognition. The experiment shows that the capsule neural network has a more effective recognition rate than the common neural network in plant leaf recognition. © 2019, Springer Nature Switzerland AG.

关键词： Convolution

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Hierarchical Attention Network for Predicting DNA-Protein Binding Sites 15th

Hierarchical Attention Network for Predicting DNA-Protein Bi...

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15th International Conference on Intelligent computing, ICIC 2019

作者： Yu, Wenbo Yuan, Chang-An Qin, Xiao Huang, Zhi-Kai Shang, Li Institute of Machine Learning and Systems Biology School of Electronics and Information Engineering Tongji University Shanghai China Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory Nanning Normal University NanningGuangxi China College of Mechanical and Electrical Engineering Nanchang Institute of Technology NanchangJiangxi330099 China Department of Communication Technology College of Electronic Information Engineering Suzhou Vocational University SuzhouJiangsu215104 China

ISBN: (纸本)9783030269685

Discovering DNA-protein binding sites, also known as motif discovery, is the foundation for further analyses of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) and recurrent neural networks (RNN) are introduced to motif discovery task and have achieved state-of–art performance. However, these methods still have limitations such as neglecting the context information in large-scale sequencing data. Thus, inspired by the similarity between DNA sequence and human language, in this paper we propose a hierarchical attention network for predicting DNA-protein binding sites which is based on a natural language processing method for document classification. The proposed method is tested on real ChIP-seq datasets and the experimental results show a considerable improvement compared with two well-tested deep learning-based sequence model, DeepBind and Deepsea. © 2019, Springer Nature Switzerland AG.

关键词： Transcription factors

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Solution-based phase saving and MaxSAT for employee scheduling: A computational study 12

Solution-based phase saving and MaxSAT for employee scheduli...

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12th International Conference on the Practice and Theory of Automated Timetabling, PATAT 2018

作者： Demirovic, Emir Winter, Felix Musliu, Nysret Stuckey, Peter J. School of Computing and Information Systems University of Melbourne Australia Chrstn.Doppler Laboratory for Artificial Intelligence and Optimization for Planning and Scheduling DBAI TU Wien Austria

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Towards a Formal Approach to Defining and computing the Complexity of Component Based Software

Towards a Formal Approach to Defining and Computing the Comp...

引用

Asia-Pacific Conference on Software Engineering

作者： Yongxin Zhao Xiujuan Zhang Ling Shi Gan Zeng Feng Sheng Shuang Liu Shanghai Key Laboratory of Trustworthy Computing East China Normal University Shanghai China School of Information Systems Singapore Management University Singapore School of Computer Software Tianjin University Tianjin China

With the rapid development of software engineering and the widely adoption of software systems in various domains, the requirement for software systems is becoming more and more complex, which results in very complex software systems. Motivated by the principle of divide and conquer, component based software development is an effective way of managing the complexity in software development. In this paper, we propose a calculus to formally describe the functional and performance specification of component based software and provide formal semantics for the proposed calculus. Then we provide a method to measure the dynamic complexity of software compositions based on the proposed calculus. Finally, we define a set of algebraic laws to manifest the complexity relations between different functionally equivalent components. We conduct a case study with a real software system and the results show that our method is able to calculate the dynamic complexity of component based systems, and the complexity can be reduced based on our algebraic laws.

关键词： Complexity theory Software systems Calculus Software measurement Semantics Aerodynamics

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Multiple workflows scheduling in multi-tenant distributed systems: A taxonomy and future directions

arXiv

引用

arXiv 2018年

作者： HILMAN, MUHAMMAD H. RODRIGUEZ, MARIA A. BUYYA, RAJKUMAR Laboratory School of Computing and Information Systems the University of Melbourne

The *** is a general notion representing the automated processes along with the flow of data. The automation ensures the processes being executed in the order. Therefore, this feature attracts users from various background to build the workflow. However, the computational requirements are enormous and investing for a dedicated infrastructure for these *** is not always feasible. To cater to the broader needs, multi-tenant platforms for executing *** were began to be built. In this paper, we identify the problems and challenges in the multiple workflows scheduling that adhere to the platforms. We present a detailed taxonomy from the existing solutions on scheduling and resource provisioning aspects followed by the survey of relevant works in this area. We open up the problems and challenges to shove up the research on multiple *** scheduling in multi-tenant distributed systems. Copyright © 2018, The Authors. All rights reserved.

关键词： Scheduling

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Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations

arXiv

引用

arXiv 2022年

作者： Chen, Qingyu Allot, Alexis Leaman, Robert Islamaj, Rezarta Du, Jingcheng Fang, Li Wang, Kai Xu, Shuo Zhang, Yuefu Bagherzadeh, Parsa Bergler, Sabine Bhatnagar, Aakash Bhavsar, Nidhir Chang, Yung-Chun Lin, Sheng-Jie Tang, Wentai Zhang, Hongtong Tavchioski, Ilija Pollak, Senja Tian, Shubo Zhang, Jinfeng Otmakhova, Yulia Yepes, Antonio Jimeno Dong, Hang Wu, Honghan Dufour, Richard Labrak, Yanis Chatterjee, Niladri Tandon, Kushagri Laleye, Fréjus A.A. Rakotoson, Loïc Chersoni, Emmanuele Gu, Jinghang Friedrich, Annemarie Pujari, Subhash Chandra Chizhikova, Mariia Sivadasan, Naveen Saipradeep, V.G. Lu, Zhiyong National Center for Biotechnology Information National Library of Medicine National Institutes of Health MD United States School of Biomedical Informatics UT Health Texas United States Raymond G. Perelman Center for Cellular and Molecular Therapeutics Children's Hospital of Philadelphia Philadelphia United States Department of Pathology Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia United States College of Economics and Management Beijing University of Technology Beijing China CLaC Labs Concordia University Montreal Canada Navrachana University Vadodara India Graduate Institute of Data Science Taipei Medical University Taipei Taiwan College of Computer Science and Technology Dalian University of Technology Dalian China Computer and Information Science University of Ljubljana Ljubljana Slovenia Jožef Stefan Institute Ljubljana Slovenia Department of Statistics Florida State University Tallahassee United States School of Computing and Information Systems University of Melbourne Melbourne Australia School of Computing Technologies RMIT University Melbourne Australia Centre for Medical Informatics Usher Institute University of Edinburgh Edinburgh United Kingdom Institute of Health Informatics University College London London United Kingdom LS2N Nantes University Nantes France LIA Avignon University Avignon France Department of Mathematics Indian Institute of Technology Delhi New Delhi India Opscidia Paris France Department of Chinese and Bilingual Studies The Hong Kong Polytechnic University Hong Kong Heidelberg University Heidelberg Germany Bosch Center for Artificial Intelligence Renningen Germany Universidad de Jaén Jaén Spain TCS Research Life Sciences Hyderabad India

The COVID-19 pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature - at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest, and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset - consisting of over 30,000 articles with manually reviewed topics - was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g., 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is pub

关键词： COVID-19

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Contextualization of morphological inflection

arXiv

引用

arXiv 2019年

作者： Vylomova, Ekaterina Cotterell, Ryan Baldwin, Timothy Cohn, Trevor Eisner, Jason School of Computing and Information Systems University of Melbourne Melbourne Australia Computer Laboratory University of Cambridge Cambridge United Kingdom Department of Computer Science Johns Hopkins University Baltimore United States

Critical to natural language generation is the production of correctly inflected text. In this paper, we isolate the task of predicting a fully inflected sentence from its partially lemmatized version. Unlike traditional morphological inflection or surface realization, our task input does not provide "gold" tags that specify what morphological features to realize on each lemmatized word;rather, such features must be inferred from sentential context. We develop a neural hybrid graphical model that explicitly reconstructs morphological features before predicting the inflected forms, and compare this to a system that directly predicts the inflected forms without relying on any morphological annotation. We experiment on several typologically diverse languages from the Universal Dependencies treebanks, showing the utility of incorporating linguisticallymotivated latent variables into NLP models. Copyright © 2019, The Authors. All rights reserved.

关键词： Natural language processing systems

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