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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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Novel alignment approach of dna sequences 1st

Novel alignment approach of dna sequences

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1st International Conference on Smart Information and Communication Technologies, SmartICT 2019

作者： Rhalem, Wajih Mhamdi, Jamel El Raji, Mourad Hammouch, Ahmed Kharmoum, Nassim Raoui, Sanae Amzazi, Saaid Hamdi, Salsabil Ghazal, Hassan LRGE Laboratory ENSET Mohammed V University Rabat Morocco Direction of Scientific Research and Innovation at the Ministry of Higher Education in Rabat Rabat Morocco Rabat Morocco Laboratory of Environemental Health l’Institut Pasteur du Maroc Casablanca Morocco Laboratory of Biology of Human Pathologies Faculty of Sciences Mohammed V University Rabat Morocco Department of Computer Science Intelligent Processing Systems and Security Team Faculty of Sciences Mohammed V University Rabat Morocco

ISBN: (纸本)9783030531867

In recent decades, researchers have proposed a number of string matching algorithms, searching for instances of one model string in another string or body of text. Channel matching is usually deployed in plagiarism, text mining, network intrusion detection, form recognition, information security, application in bioinformatics and other areas of expertise. In this study, a new algorithm will be programmed, adapted and applied in the field of DNA sequence analysis based on the approach of the transition from discrete to continuous unlike most algorithms, which are based on the matching channels concept. Experimental results, revealed that our approach ensures an efficient pairing of DNA sequences. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2020.

关键词： String searching algorithms

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Binary neural networks for speech recognition

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Frontiers of Information Technology & Electronic Engineering 2019年第5期20卷 701-715页

作者： Yan-min QIAN Xu XIANG Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai 200240 China SpeechLab Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

Recently, deep neural networks(DNNs) significantly outperform Gaussian mixture models in acoustic modeling for speech recognition. However, the substantial increase in computational load during the inference stage makes deep models difficult to directly deploy on low-power embedded devices. To alleviate this issue,structure sparseness and low precision fixed-point quantization have been applied widely. In this work, binary neural networks for speech recognition are developed to reduce the computational cost during the inference stage.A fast implementation of binary matrix multiplication is introduced. On modern central processing unit(CPU)and graphics processing unit(GPU) architectures, a 5–7 times speedup compared with full precision floatingpoint matrix multiplication can be achieved in real applications. Several kinds of binary neural networks and related model optimization algorithms are developed for large vocabulary continuous speech recognition acoustic modeling. In addition, to improve the accuracy of binary models, knowledge distillation from the normal full precision floating-point model to the compressed binary model is explored. Experiments on the standard Switchboard speech recognition task show that the proposed binary neural networks can deliver 3–4 times speedup over the normal full precision deep models. With the knowledge distillation from the normal floating-point models, the binary DNNs or binary convolutional neural networks(CNNs) can restrict the word error rate(WER) degradation to within 15.0%,compared to the normal full precision floating-point DNNs or CNNs, respectively. Particularly for the binary CNN with binarization only on the convolutional layers, the WER degradation is very small and is almost negligible with the proposed approach.

关键词： Speech recognition Binary neural net works Binary matrix multiplication Knowledge distillation Population count

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Retraction Note: Minimal key set of binary key-derivation tree in cloud storage

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Soft Computing 2024年第2期28卷 1007-1007页

作者： Ren, Zhengwei Li, Xiaojuan Wang, Lina Xu, Shiwei Tong, Yan Tang, Jinshan School of Computer Science and Technology Wuhan University of Science and Technology Wuhan China Hubei Province Key Laboratory of Intelligent Information Processing and Real-Time Industrial System Wuhan China School of Cyber Science and Engineering Wuhan University Wuhan China Huazhong Agricultural University Wuhan China Department of Health Administration and Policy College of Health and Human Services George Mason University Fairfax USA

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Pre-Chirper Free Nonlinear Fiber Amplifier Generating Tunable Picosecond Pulses for Coherent Anti-Stokes Raman Imaging

Pre-Chirper Free Nonlinear Fiber Amplifier Generating Tunabl...

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Pacific Rim Conference on Lasers and Electro-Optics (CLEO/Pacific Rim)

作者： Jiaying Li Jiamei Wu Kangwen Yang Qiang Hao Minbiao Ji Ming Yan Kun Huang Heping Zeng Shanghai Key Laboratory of Modern Optical System and Engineering Research Center of Optical Instrument and System Ministry of Education School of Optical Electrical and Computer Engineering University of Shanghai for Science and Technology Shanghai China State Key Laboratory of Surface Physics and Department of Physics Human Phenome Institute Multiscale Research Institute of Complex Systems Academy for Engineering and Technology Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education) Fudan University Shanghai China State Key Laboratory of Precision Spectroscopy East China Normal University Shanghai China Chongqing Institute of East China Normal University Chongqing China Jinan Institute of Quantum Technology Jinan China

A pre-chirper free, core-pumped nonlinear fiber amplifier was demonstrated to generate parabolic pulse with spectral bandwidth of 53 nm, these pulses were filtered and passively synchronized for conducting coherent an...

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Longitudinal Complex Dynamics of Labour Markets Reveal Increasing Polarisation

arXiv

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arXiv 2022年

作者： Althobaiti, Shahad Alabdulkareem, Ahmad Shen, Judy Hanwen Rahwan, Iyad Frank, Morgan Moro, Esteban Rutherford, Alex Riyadh Saudi Arabia Intelmatix Intelligent Informatics Technologies CambridgeMA United States Computer Science Department Stanford University CA United States Center for Humans and Machines Max Planck Institute for Human Development Berlin Germany Department of Informatics and Networked Systems University of Pittsburgh PittsburghPA United States Digital Economy Lab Institute for Human-Centered Artificial Intelligence Stanford University StanfordCA United States Media Laboratory Massachusetts Institute of Technology CambridgeMA United States Department of Mathematics & GISC Universidad Carlos III de Madrid Leganes Spain Institute for Data Systems and Society Massachusetts Institute of Technology CambridgeMA United States

In this paper we conduct a longitudinal analysis of the structure of labour markets in the US over 7 decades of technological, economic and policy change. We make use of network science, natural language processing and machine learning to uncover structural changes in the labour market over time. We find a steady rate of both disappearance of jobs and a shift in the required work tasks, despite much technological and economic change over this time period. Machine learning is used to classify jobs as being predominantly cognitive or physical based on the textual description of the workplace tasks. We also measure increasing polarisation between these two classes of jobs, linked by the similarity of tasks, over time that could constrain workers wishing to move to different jobs. © 2022, CC BY.

关键词： Employment

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Disability in space - What ESA should have aimed for

arXiv

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arXiv 2021年

作者： Heinicke, Christiane Kaczmarzyk, Marcin Tannert, Benjamin Wasniowski, Aleksander Perycz, Malgorzata Schöning, Johannes Am Fallturm 2 Bremen28359 Germany Rzeszow University of Technology The Faculty of Civil and Environmental Engineering and Architecture Department of Building Engineering Poznańska Street 2 Rzeszow35-084 Poland Hochschule Bremen - City University of Applied Science Applied Media Informatics Flughafenallee 10 Bremen28199 Germany Space Is More ul. Mikulskiego 17 Wroclaw52-420 Poland Institute of Computer Science Polish Academy of Sciences Department of Artificial Intelligence Lab of Computational Biology Jana Kazimierza 5 st. Warsaw01-248 Poland University of Bremen Human-Computer Interaction Bibliothekstraße 5 Bremen28359 Germany

With announcing their "Parastronaut Feasibility Project", the European Space Agency ESA promises to make every reasonable effort to send astronauts with disability to space. This could spark hope in the 15% of all people who live with some form of disability. However, the fine-print of the announcement sets overly tight boundaries to "acceptable" disabilities, allowing only malformations that are expected to have a positive impact on the parastronaut's performance in space. By doing so, ESA is following decade-old traditions in space flight, with some inclusion for the sake of inclusion and public opinion. Instead of accommodating people with disabilities, ESA should send a strong signal for inclusion and truly challenge people with disabilities so they can and will tease out the best of their qualities. © 2021, CC BY.

关键词： Manned space flight

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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

arXiv

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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Calculation of likelihood ratios for inference of biological sex from human skeletal remains

Forensic Science International: Synergy

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Forensic science International: Synergy 2021年 3卷 100202页

作者： Morrison, Geoffrey Stewart Weber, Philip Basu, Nabanita Puch-Solis, Roberto Randolph-Quinney, Patrick S. Forensic Data Science Laboratory Computer Science Department & Aston Institute for Forensic Linguistics Aston University Birmingham United Kingdom Forensic Evaluation Ltd Birmingham United Kingdom Leverhulme Research Centre for Forensic Science University of Dundee Dundee United Kingdom Forensic Science Research Group Department of Applied Sciences Northumbria University Newcastle upon Tyne United Kingdom Department of Human Anatomy and Physiology University of Johannesburg South Africa

It is common in forensic anthropology to draw inferences (e.g., inferences with respect to biological sex of human remains) using statistical models applied to anthropometric data. Commonly used models can output posterior probabilities, but a threshold is usually applied in order to obtain a classification. In the forensic-anthropology literature, there is some unease with this “fall-off-the-cliff” approach. Proposals have been made to exclude results that fall within a “zone of uncertainty”, e.g., if the posterior probability for “male” is greater than 0.95 then the remains are classified as male, and if the posterior probability for “male” is less than 0.05 then the remains are classified as female, but if the posterior probability for “male” is between 0.05 and 0.95 the remains are not classified as either male or female. In the present paper, we propose what we believe is a simpler solution that is in line with interpretation of evidence in other branches of forensic science: implementation of the likelihood-ratio framework using relevant data, quantitative measurements, and statistical models. Statistical models that can implement this approach are already widely used in forensic anthropology. All that is required are minor modifications in the way those models are used and a change in the way practitioners and researchers think about the meaning of the output of those models. We explain how to calculate likelihood ratios using osteometric data and linear discriminant analysis, quadratic discriminant analysis, and logistic regression models. We also explain how to empirically validate likelihood-ratio models. © 2021 The Authors

关键词： Forensic anthropology Forensic inference and statistics Likelihood ratio Osteometry Sex assessment

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An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

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Signal Transduction and Targeted Therapy 2021年第5期6卷 1585-1600页

作者： Yiyue Ge Tingzhong Tian Suling Huang Fangping Wan Jingxin Li Shuya Li Xiaoting Wang Hui Yang Lixiang Hong Nian Wu Enming Yuan Yunan Luo Lili Cheng Chengliang Hu Yipin Lei Hantao Shu Xiaolong Feng Ziyuan Jiang Yunfu Wu Ying Chi Xiling Guo Lunbiao Cui Liang Xiao Zeng Li Chunhao Yang Zehong Miao Ligong Chen Haitao Li Hainian Zeng Dan Zhao Fengcai Zhu Xiaokun Shen Jianyang Zeng Institute for Interdisciplinary Information Sciences Tsinghua UniversityBeijingChina NHC Key laboratory of Emeric Pathogenic Microbiology Jiangsu Provincial Center for Diseases Control and PreventionNanjingJiangsu ProvinceChina Shanghai Institute of Materia Medica Chinese Academy of SciencesShanghaiChina Silexon Al Technology Co. Ltd.NanjingJiangsu ProvinceChina Department of Computer Science University of Illinois at Urbana-ChampaignIllinoisILUSA School of Pharmaceutical Sciences Tsinghua UniversityBeijingChina School of Electronic Information and Communications Huazhong University of Science and TechnologyWuhanHubei ProvinceChina Institute of Pathology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceChina Department of Automation Tsinghua UniversityBeijingChina Inner Mongolia Alashan League Organization Establishment Committee Office Electronic Support Center AlashanInner MongoliaChina Convalife(Shanghai)Co. Ltd.ShanghaiChina Advanced Innovation Center for Human Brain Protection Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Beijing Advanced Innovation Center for Structural Biology Tsinghua-Peking Joint Center for Life SciencesDepartment of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingChina Center for Global Health Nanjing Medical UniversityNanjingJiangsu ProvinceChina

The global spread of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019(COVID-19).In this study,we developed an integrative drug repositioning framework,which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph,literature and transcriptome data to discover the potential drug candidates against *** in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1(PARP1)inhibitor,CVL218,currently in Phase I clinical trial,may be repurposed to treat *** in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic *** addition,we showed that CVL218 can interact with the nucleocapsid(N)protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.

关键词： prevention respiratory acute

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