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IEEE International Conference on Automation, Electronics and Electrical Engineering (AUTEEE)

作者： Yanbin Liu Qidi Hu Kunxian Shu Chongqing Key Laboratory on Big Data for Bio Intelligence CQUPT Chongqing China College of Computer Science and Technology CQUPT Chongqing China

ISBN: (纸本)9781538678626;9781538678619

Pix2code is a framework based on deep learning to transform a graphical user interface screenshot created by the designer into computer coder with 77% of accuracy. The architecture is based on CNN and *** has been broadly applied to natural language processing about language model, which is both general and effective at capturing long-term dependencies. However, the standard LSTM predicting in time sequence ignores the contextual information of the future, but sometimes it is not enough just to look at the previous word. Computer code is a relative spatial relationship and not only needs to recognize token but also fully understands the structure of all sequences. In order to solve the problem, the pix2code model is optimized by Bidirectional LSTM, which allows the output layer to get complete past and future context information for each point in the input sequence. The model's transforming accuracy in the test set has been significantly improved reaching 85%.

关键词： Training Decoding Feature extraction Graphical user interfaces DSL Mathematical model Context modeling

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Bidirectional LSTM-CRF for biomedical named entity recognition 14

Bidirectional LSTM-CRF for biomedical named entity recogniti...

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14th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2018

作者： Yang, Xuemin Gao, Zhihong Li, Yongmin Pan, Chuandi Yang, Ronggen Gong, Lejun Yang, Geng Jiangsu Key Laboratory of Big Data Security Intelligent Processing Nanjing University of Posts and Telecommunications Nanjing210003 China Zhejiang Engineering Research Center of Intelligence Medicine Wenzhou325035 China Faculty Intelligent Science and Control Engineering Jinling Institute of Technology Nanjing211169 China

ISBN: (纸本)9781538680971

Bio-medical entity recognition extracts significant entities, for instance cells, proteins and genes, which is an arduous task in an automatic system that mine knowledge in bioinformatics texts. In this thesis, we utilized a bidirectional long short-term memory (Bi-LSTM) combined with conditional random fields (CRFs) approach to automatically obtain word representation, obliterated the need for a marvelous number of feature engineering tasks. The consequences of this experiment represent the word representation method can effectually acquire potential semantic information. Without relying on any artificial features, the result on the test dataset obtained 76.81 % F-score. Therefore, the proposed method is expected to advance biomedical text mining in bioinformatics entity recognition. © 2018 IEEE.

关键词： Bioinformatics

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Corrigendum to "Commissioning and clinical implementation of an Autoencoder based Classification-Regression model for VMAT patient-specific QA in a multi-institution scenario" [Radiother. Oncol. 161 (2021) 230-240]

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Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 2021年 163卷 119-120页

作者： Ruijie Yang Xueying Yang Le Wang Dingjie Li Yuexin Guo Ying Li Yumin Guan Xiangyang Wu Shouping Xu Shuming Zhang Maria F Chan Lisheng Geng Jing Sui Department of Radiation Oncology Peking University Third Hospital Beijing China. School of Physics Beihang University Beijing China. Brainnetome Center & National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing China School of Artificial Intelligence University of Chinese Academy of Sciences Chinese Academy of Sciences Beijing China. Department of Radiation Therapy Henan Cancer Hospital Zhengzhou China. Department of Radiation Oncology The First Affiliated Hospital of Zhengzhou University Zhengzhou China. Department of Oncology The First Affiliated Hospital of Chongqing Medical University Chongqing China. Department of Radiation Therapy Yantai Yuhuangding Hospital Yantai China. Department of Radiotherapy Shanxi Provincial Cancer Hospital Xi'an China. Department of Radiation Oncology General Hospital of People's Liberation Army Beijing China. Department of Radiation Oncology Peking University Third Hospital Beijing China Department of Ultrasound Beijing Hospital Beijing China. Medical Physics Department Memorial Sloan Kettering Cancer Center New York NY United States. School of Physics Beihang University Beijing China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine and Engineering Beihang University Beijing China. Electronic address: lisheng.geng@***. School of Artificial Intelligence University of Chinese Academy of Sciences Chinese Academy of Sciences Beijing China State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China. Electronic address: jsui@***.

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The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions

arXiv

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arXiv 2023年

作者： Ma, Jun Xie, Ronald Ayyadhury, Shamini Ge, Cheng Gupta, Anubha Gupta, Ritu Gu, Song Zhang, Yao Lee, Gihun Kim, Joonkee Lou, Wei Li, Haofeng Upschulte, Eric Dickscheid, Timo de Almeida, José Guilherme Wang, Yixin Han, Lin Yang, Xin Labagnara, Marco Gligorovski, Vojislav Scheder, Maxime Rahi, Sahand Jamal Kempster, Carly Pollitt, Alice Espinosa, Leon Mignot, Tâm Middeke, Jan Moritz Eckardt, Jan-Niklas Li, Wangkai Li, Zhaoyang Cai, Xiaochen Bai, Bizhe Greenwald, Noah F. Van Valen, David Weisbart, Erin Cimini, Beth A. Cheung, Trevor Brück, Oscar Bader, Gary D. Wang, Bo Peter Munk Cardiac Centre University Health Network TorontoON Canada Department of Laboratory Medicine and Pathobiology University of Toronto TorontoON Canada Vector Institute TorontoON Canada Department of Molecular Genetics University of Toronto TorontoON Canada Donnelly Centre University of Toronto TorontoON Canada Princess Margaret Cancer Centre University Health Network TorontoON Canada School of Medicine and Pharmacy Ocean University of China Qingdao China New Delhi India Laboratory Oncology Dr. BRA-IRCH All India Institute of Medical Sciences New Delhi India Department of Image Reconstruction Nanjing Anke Medical Technology Co. Ltd. Nanjing China Shanghai Artificial Intelligence Laboratory Shanghai China Graduate School of AI KAIST Seoul Korea Republic of Shenzhen Research Institute of Big Data Shenzhen China Shenzhen China Helmholtz AI Research Center Jülich Jülich Germany Faculty of Mathematics and Natural Sciences Institute of Computer Science Heinrich Heine University Düsseldorf Düsseldorf Germany Hinxton United Kingdom Champalimaud Foundation - Centre for the Unknown Lisbon Portugal Department of Bioengineering Stanford University Palo AltoCA United States Tandon School of Engineering New York University New YorkNY United States School of Biomedical Engineering Health Science Center Shenzhen University Shenzhen China Lausanne Switzerland School of Biological Sciences University of Reading Reading United Kingdom Laboratoire de Chimie Bactérienne CNRS Université Aix Marseille UMR Institut de Microbiologie de la Méditerranée Marseille France Department of Internal Medicine I University Hospital Dresden Technical University Dresden Dresden Germany Else Kroener Fresenius Center for Digital Health Technical University Dresden Dresden Germany Department of Automation University of Science and Technology of China Hefei China Institute of Advanced Technology University of Science and Technology of China Hefei Chi

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging. © 2023, CC BY-NC-ND.

关键词： Deep learning

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Reward Processing in Novelty Seekers: A Transdiagnostic Psychiatric Imaging Biomarker

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BIOLOGICAL PSYCHIATRY 2021年第8期90卷 529-539页

作者： Qi, Shile Schumann, Gunter Bustillo, Juan Turner, Jessica A. Jiang, Rongtao Zhi, Dongmei Fu, Zening Mayer, Andrew R. Vergara, Victor M. Silva, Rogers F. Iraji, Armin Chen, Jiayu Damaraju, Eswar Ma, Xiaohong Yang, Xiao Stevens, Michael Mathalon, Daniel H. Ford, Judith M. Voyvodic, James Mueller, Bryon A. Belger, Aysenil Potkin, Steven G. Preda, Adrian Zhuo, Chuanjun Xu, Yong Chu, Congying Banaschewski, Tobias Barker, Gareth J. Bokde, Arun L. W. Quinlan, Erin Burke Desrivieres, Sylvane Flor, Herta Grigis, Antoine Garavan, Hugh Gowland, Penny Heinz, Andreas Martinot, Jean-Luc Martinot, Marie-Laure Paillere Artiges, Eric Nees, Frauke Orfanos, Dimitri Papadopoulos Paus, Tomas Poustka, Luise Hohmann, Sarah Frohner, Juliane H. Smolka, Michael N. Walter, Henrik Whelan, Robert Calhoun, Vince D. Sui, Jing [a]Tri-institutional Center for Translational Research in Neuroimaging and Data Science Georgia State University Georgia Institute Technology and Emory University Atlanta Georgia [b]Department of Psychiatry University of New Mexico Albuquerque New Mexico [c]Department of Psychology Georgia State University Atlanta Georgia [d]Olin Neuropsychiatry Research Center Hartford Connecticut [e]Department of Psychiatry University of California San Francisco San Francisco California [f]Department of Radiology Duke University Durham North Carolina [g]Department of Psychiatry University of North Carolina at Chapel Hill Chapel Hill North Carolina [h]Department of Psychiatry University of Minnesota Minneapolis Minnesota [i]Department of Psychiatry University of California Irvine Irvine California [j]Departments of Psychiatry and Psychology University of Vermont Burlington Vermont [k]Centre for Population Neuroscience and Stratified Medicine Institute for Science and Technology of Brain-Inspired Intelligence Fudan University Shanghai China [l]University of Chinese Academy of Sciences Beijing China [dd]Department of Computer Science and Engineering Nanjing University of Aeronautics and Astronautics Nanjing China [m]Brainnetome Center and National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing China [ee]State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China [n]Psychiatric Laboratory and Mental Health Center the State Key Laboratory of Biotherapy West China Hospital of Sichuan University Chengdu China [o]Department of Psychiatric-Neuroimaging-Genetics and Morbidity Laboratory Nankai University Affiliated Anding Hospital Tianjin China [p]Department of Humanities and Social Science Shanxi Medical University Taiyuan China [q]Department of Psychiatry and Psychotherapy Charité – Universitätsmedizin Berlin Campus Charité Mitte corporate member of Freie Universität Berlin Humboldt-Univers

BACKGROUND: Dysfunctional reward processing is implicated in multiple mental disorders. Novelty seeking (NS) assesses preference for seeking novel experiences, which is linked to sensitivity to reward environmental cues. METHODS: A subset of 14-year-old adolescents (IMAGEN) with the top 20% ranked high-NS scores was used to identify high-NS-associated multimodal components by supervised fusion. These features were then used to longitudinally predict five different risk scales for the same and unseen subjects (an independent dataset of subjects at 19 years of age that was not used in predictive modeling training at 14 years of age) (within IMAGEN, n z 1100) and even for the corresponding symptom scores of five types of patient cohorts (non-IMAGEN), including drinking (n = 313), smoking (n = 104), attention-deficit/hyperactivity disorder (n = 320), major depressive disorder (n = 81), and schizophrenia (n = 147), as well as to classify different patient groups with diagnostic labels. RESULTS: Multimodal biomarkers, including the prefrontal cortex, striatum, amygdala, and hippocampus, associated with high NS in 14-year-old adolescents were identified. The prediction models built on these features are able to longitudinally predict five different risk scales, including alcohol drinking, smoking, hyperactivity, depression, and psychosis for the same and unseen 19-year-old adolescents and even predict the corresponding symptom scores of five types of patient cohorts. Furthermore, the identified reward-related multimodal features can classify among attention-deficit/hyperactivity disorder, major depressive disorder, and schizophrenia with an accuracy of 87.2%. CONCLUSIONS: Adolescents with higher NS scores can be used to reveal brain alterations in the reward-related system, implicating potential higher risk for subsequent development of multiple disorders. The identified high-NS- associated multimodal reward-related signatures may serve as a transdiagnostic neuroimaging bi

关键词： ADHD Attention-deficit/hyperactivity disorder Major depressive disorders MDD Novelty seeking Reward processing Schizophrenia Substance use

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Correction to: Path-based estimation for link prediction

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International Journal of Machine Learning and Cybernetics 2021年第9期12卷 2459-2459页

作者： Ma, Guoshuai Yan, Hongren Qian, Yuhua Wang, Lingfeng Dang, Chuangyin Zhao, Zhongying Institute of Big Data Science and Industry Shanxi University Taiyuan China School of Computer and Information Technology Shanxi University Taiyuan China Key Laboratory of Computational Intelligence and Chinese Information Processing of Ministry of Education Shanxi University Taiyuan China Department of Electrical Engineering and Computer Science University of Wisconsin-Milwaukee Milwaukee USA Department of Manufacture Engineering and Engineering Management City University of Hong Kong Kowloon Tong Hong Kong The School of Computer Science and Engineering Shandong University of Science and Technology Qingdao China

A correction to this paper has been published: https://***/10.1007/s13042-021-01350-4

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Erratum to: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins

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Briefings in bioinformatics 2021年第6期22卷 bbab287页

作者： Hideki Yamaguchi Yutaka Saito Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Chiba 277-8561 Japan. Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku Tokyo 135-0064 Japan. AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL) Shinjuku-ku Tokyo 169-8555 Japan.

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Logic could be learned from images

arXiv

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arXiv 2019年

作者： Guo, Qian Qian, Yuhua Liang, Xinyan She, Yanhong Li, Deyu Liang, Jiye Institute of Big Data Science and Industry Shanxi University Shanxi Taiyuan030006 China Key Laboratory of Computational Intelligence Chinese Information Processing of Ministry of Education Shanxi University Shanxi Taiyuan030006 China School of Computer and Information Technology Shanxi University Shanxi Taiyuan030006 China College of Science Xi’an Shiyou University Shanxi Xi'an710065 China

Logic reasoning is a significant ability of human intelligence and also an important task in artificial intelligence. The existing logic reasoning methods, quite often, need to design some reasoning patterns beforehand. This has led to an interesting question: can logic reasoning patterns be directly learned from given data? The problem is termed as a data concept logic. In this study, a learning logic task from images, called a LiLi task, first is proposed. This task is to learn and reason the logic relation from images, without presetting any reasoning patterns. As a preliminary exploration, we design six LiLi data sets (Bitwise And, Bitwise Or, Bitwise Xor, Addition, Subtraction and Multiplication), in which each image is embedded with a n-digit number. It is worth noting that a learning model beforehand does not know the meaning of the n-digit numbers embedded in images and the relation between the input images and the output image. In order to tackle the task, in this work we use many typical neural network models and produce fruitful results. However, these models have the poor performances on the difficult logic task. For furthermore addressing this task, a novel network framework called a divide and conquer model by adding some label information is designed, achieving a high testing accuracy. Copyright © 2019, The Authors. All rights reserved.

关键词： Computer circuits

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Feature extraction for hyperspectral imagery: The evolution from shallow to deep

arXiv

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arXiv 2020年

作者： Rasti, Behnood Hong, Danfeng Hang, Renlong Ghamisi, Pedram Kang, Xudong Chanussot, Jocelyn Benediktsson, Jon Atli Machine Learning Group Exploration Division Helmholtz Institute Freiberg for Resource Technology Helmholtz-Zentrum Dresden-Rossendorf Freiberg09599 Germany Univ. Grenoble Alpes CNRS Grenoble INP GIPSAlab Grenoble38000 France Jiangsu Key Laboratory of Big Data Analysis Technology School of Automation Nanjing University of Information Science and Technology Nanjing210044 China Machine Learning Group Exploration Division Helmholtz Institute Freiberg for Resource Technology Helmholtz-Zentrum Dresden-Rossendorf Freiberg09599 Germany College of Electrical and Information Engineering Hunan University Changsha410082 China Key Laboratory of Visual Perception and Artificial Intelligence of Hunan Province Changsha410082 China Univ. Grenoble Alpes Inria CNRS Grenoble INP LJK GrenobleF-38000 France Faculty of Electrical and Computer Engineering University of Iceland Reykjavik101 Iceland Faculty of Electrical and Computer Engineering University of Iceland Reykjavik107 Iceland

The final version of the paper can be found in IEEE Geoscience and Remote Sensing Magazine. Hyperspectral images provide detailed spectral information through hundreds of (narrow) spectral channels (also known as dimensionality or bands) with continuous spectral information that can accurately classify diverse materials of interest. The increased dimensionality of such data makes it possible to significantly improve data information content but provides a challenge to the conventional techniques (the so-called curse of dimensionality) for accurate analysis of hyperspectral images. Feature extraction, as a vibrant field of research in the hyperspectral community, evolved through decades of research to address this issue and extract informative features suitable for data representation and classification. The advances in feature extraction have been inspired by two fields of research, including the popularization of image and signal processing as well as machine (deep) learning, leading to two types of feature extraction approaches named shallow and deep techniques. This article outlines the advances in feature extraction approaches for hyperspectral imagery by providing a technical overview of the state-of-the-art techniques, providing useful entry points for researchers at different levels, including students, researchers, and senior researchers, willing to explore novel investigations on this challenging topic. In more detail, this paper provides a bird's eye view over shallow (both supervised and unsupervised) and deep feature extraction approaches specifically dedicated to the topic of hyperspectral feature extraction and its application on hyperspectral image classification. Additionally, this paper compares 15 advanced techniques with an emphasis on their methodological foundations in terms of classification accuracies. Furthermore, to push this vibrant field of research forward an impressive amount of codes and libraries is shared at: https://***/Behnoo

关键词： Feature extraction

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Controllability analysis of transcriptional regulatory networks for Saccharomyces cerevisiae 44

Controllability analysis of transcriptional regulatory netwo...

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44th Annual Conference of the IEEE Industrial Electronics Society, IECON 2018

作者： Liu, Suling Wang, Pei Xu, Qiong Chen, Aimin Lü, Jinhu School of Mathematics and Statistics Henan University Kaifeng China School of Mathematics and Statistics Institute of Applied Mathematics Laboratory of Data Analysis Technology Henan University Kaifeng China School of Mathematics and Statistics Institute of Applied Mathematics Henan University Kaifeng China School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment Beijing Advanced Innovation Center for Big Data Brain Machine Intelligence Beihang University Beijing China

ISBN: (纸本)9781509066841

Structural controllability of complex networks has been a research focus in recent years. However, few works considered the structural controllability of biological networks, especially for dynamic biological networks. In this paper, structural controllability of one static and five dynamic transcriptional regulatory networks (TRNs) for Saccharomyces cerevisiae (S. cerevisiae) have been investigated. The five dynamic networks included two endogenous and three exogenous ones. We clarified the controllability properties of these networks, as well as explored the differences among different types of networks. Our results revealed that the structural properties of different types of networks are significantly different. We found that the TRNs are rather difficult to be fully controlled. However, the dynamic TRNs were relatively easier to be controlled than the static one, and one needs relatively more external inputs to control the exogenous TRNs than the endogenous ones. Based on the structural controllability analysis of subnetworks with the same sizes, as well as randomly perturbed networks by preserving degree distributions, we further illustrated that the structural controllability of the six networks may be mainly dominated by their degree distributions. Our investigations clarify the control properties of TRNs in S. cerevisiae, it provides some insights on real-world control of biological networks. © 2018 IEEE.

关键词： Complex networks

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