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arXiv 2019年

作者： Li, Jiangtong Zhao, Hai Li, Zuchao Bi, Wei Liu, Xiaojiang Department of Computer Science and Engineering Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai China MoE Key Lab of Artificial Intelligence AI Institute Shanghai Jiao Tong University Tencent AI Lab Shenzhen China

Embedding from Language Models (ELMo) has shown to be effective for improving many natural language processing (NLP) tasks, and ELMo takes character information to compose word representation to train language models. However, the character is an insufficient and unnatural linguistic unit for word representation. Thus we introduce Embedding from Subword-aware Language Models (ESuLMo) which learns word representation from subwords using unsupervised segmentation over words. We show that ESuLMo can enhance four benchmark NLP tasks more effectively than ELMo, including syntactic dependency parsing, semantic role labeling, implicit discourse relation recognition and textual entailment, which brings a meaningful improvement over ELMo. Copyright © 2019, The Authors. All rights reserved.

关键词： Embeddings

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Phase-Separated Multienzyme Compartmentalization for Terpene Biosynthesis in a Prokaryote

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Angewandte Chemie 2022年第29期134卷

作者： Yue Wang Min Liu Qixin Wei Wanjie Wu Yanping He Jiayang Gao Renjie Zhou Liwen Jiang Jianan Qu Jiang Xia Department of Chemistry and Center for Cell & Developmental Biology The Chinese University of Hong Kong Shatin Hong Kong SAR China Departments of Electronic and Computer Engineering Center of Systems Biology and Human Health School of Science and Institute for Advanced Study Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong SAR China Department of Biomedical Engineering The Chinese University of Hong Kong Shatin Hong Kong SAR China Center for Cell & Developmental Biology School of Life Sciences State Key Laboratory of Agrobiotechnology The Chinese University of Hong Kong Shatin Hong Kong SAR China

Liquid–liquid phase separation (LLPS) forms biomolecular condensates or coacervates in cells. Metabolic enzymes can form phase-separated subcellular compartments that enrich enzymes, cofactors, and substrates. Herein, we report the construction of synthetic multienzyme condensates that catalyze the biosynthesis of a terpene, α-farnesene, in the prokaryote E. coli . RGGRGG derived from LAF-1 was used as the scaffold protein to form the condensates by LLPS. Multienzyme condensates were then formed by assembling two enzymes Idi and IspA through an RIAD/RIDD interaction. Multienzyme condensates constructed inside E. coli cells compartmentalized the cytosolic space into regions of high and low enzyme density and led to a significant enhancement of α-farnesene production. This work demonstrates LLPS-driven compartmentalization of the cytosolic space of prokaryotic cells, condensation of a biosynthetic pathway, and enhancement of the biosynthesis of α-farnesene.

关键词： α-Farnesene Multienzyme Catalysis Multienzyme Compartmentalization Phase Separation Terpene Biosynthesis

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Understanding gender equity in author order assignment

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Proceedings of the ACM on human-computer interaction 2018年第CSCW期2卷 1–21页

作者： Early, Kirstin Hammer, Jessica Hofmann, Megan Rode, Jennifer A. Wong, Anna Mankoff, Jennifer Yahoo Research 701 First Avenue SunnyvaleCA94089 United States Carnegie Mellon University Human-Computer Interaction Institute Entertainment Technology Center 5000 Forbes Avenue PittsburghPA15213 United States University College London Knowledge Lab Gower Street London United Kingdom Carnegie Mellon University Department of Statistics 5000 Forbes Avenue PittsburghPA15213 United States University of Washington Paul G. Allen School of Computer Science and Engineering 185 E Stevens Way NE SeattleWA98195 United States

Academic success and promotion are heavily infuenced by publication record. In many felds, including computer science, multi-author papers are the norm. Evidence from other felds shows that norms for ordering author names can infuence the assignment of credit. We interviewed 38 students and faculty in human-computer interaction (HCI) and machine learning (ML) at two institutions to determine factors related to assignment of author order in collaborative publication in the feld of computer science. Interview outcomes informed metrics for our bibliometric analysis of gender and collaboration in papers published between 1996 and 2016 in three top HCI and ML conferences. Based on our fndings, we make recommendations for assignment of credit in multi-author papers and interpretation of author order, particularly with respect to how these factors afect women. © 2018 Association for Computing Machinery.

关键词： Paper

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Usability methods for designing programming languages for software engineers

arXiv

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arXiv 2019年

作者： Coblenz, Michael Kambhatla, Gauri Koronkevich, Paulette Wise, Jenna L. Barnaby, Celeste Sunshine, Joshua Aldrich, Jonathan Myers, Brad A. Carnegie Mellon Unversity Computer Science Department Carnegie Mellon University 5000 Forbes Ave. PittsburghPA15213 United States Computer Science Department University of Michigan 500 S. State St. Ann ArborMI48109 United States Computer Science Department University of British Columbia 2329 West Mall VancouverBCV6T 1Z4 Canada Institute for Software Research Carnegie Mellon University 5000 Forbes Ave. PittsburghPA15213 United States Facebook Inc. 1 Hacker Way Menlo ParkCA94025 United States Human-Computer Interaction Institute Carnegie Mellon University 5000 Forbes Ave. PittsburghPA15213 United States

Programming language design requires making many usability-related design decisions. We explored using user-centered methods to make languages more effective for programmers. However, existing HCI methods expect iteration with appropriate users, who must learn to use the language to be evaluated. These methods were impractical to apply to programming languages: they have high iteration costs, programmers require significant learning time, and user performance has high variance. To address these problems, we adapted HCI methods to reduce iteration and training costs and designed tasks and analyses that mitigated the high variance. We evaluated the methods by using them to design two languages for professional developers. Glacier extends Java to enable programmers to express immutability properties effectively and easily. Obsidian is a language for blockchains that includes verification of critical safety properties. Summative usability studies showed that programmers were able to program effectively in both languages after short training periods. Copyright © 2019, The Authors. All rights reserved.

关键词： Usability engineering

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Selfies as social movements: Influences on participation and perceived impact on stereotypes

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Proceedings of the ACM on human-computer interaction 2017年第CSCW期1卷 1-21页

作者： Liu, Fannie Ford, Denae Parnin, Chris Dabbish, Laura Human-Computer Interaction Institute School of Computer Science Carnegie Mellon University 5000 Forbes Ave. PittsburghPA15213 United States Department of Computer Science North Carolina State University Campus Box 8206 890 Oval Dr. RaleighNC27695 United States

A new kind of online movement has emerged on social media: identity hashtag movements, through which individuals share "selfies" and personal stories to elucidate the experiences of marginalized social groups. These movements have the potential to counteract bias and enable social justice, but are enacted in a forum rife with identity and boundary management concerns. To understand this type of movement, we present a qualitative study of #ILookLikeAnEngineer, a hashtag created to challenge engineering stereotypes. We interviewed 32 people, including participants and non-participants of the movement, about their experiences with the hashtag. We found that personally identifiable participation promoted feelings of empowerment and strengthened connections within the marginalized community. At the same time, the personal and professional identity focus raised ambiguity about the boundaries of the collective and the movement's ability to change stereotypes. We discuss implications for online collective action and the use of social media for addressing stereotypes. © 2017 Association for Computing Machinery.

关键词： Social networking (online)

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A framework and resource for global collaboration in non-human primate neuroscience

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Current Research in Neurobiology 2023年 4卷 100079页

作者： Hartig, Renée Klink, P. Christiaan Polyakova, Zlata Dehaqani, Mohammad-Reza A. Bondar, Igor Merchant, Hugo Vanduffel, Wim Roe, Anna Wang Nambu, Atsushi Thirumala, M. Shmuel, Amir Kapoor, Vishal Gothard, Katalin M. Evrard, Henry C. Basso, Michele A. Petkov, Christopher I. Mitchell, Anna S. Max Planck Institute for Biological Cybernetics Max-Planck-Ring 11 Tübingen 72076 Germany Functional and Comparative Neuroanatomy Laboratory Werner Reichardt Centre for Integrative Neuroscience Eberhard Karls University of Tübingen Otfried-Müller-Straße 25 Tübingen 72076 Germany Department of Psychiatry and Psychotherapy University Medical Center Johannes Gutenberg-University Mainz 55131 Germany Nathan S. Kline Institute for Psychiatric Research Center for Biomedical Imaging and Neuromodulation Orangeburg New York 10962 United States Department of Vision and Cognition Netherlands Institute for Neuroscience Royal Netherlands Academy of Arts and Sciences Meibergdreef 47 Amsterdam 1105 BA Netherlands Laboratory of Visual Brain Therapy Sorbonne Université Institut National de la Santé et de la Recherche Médicale Centre National de la Recherche Scientifique Institut de la Vision Paris F-75012 France Experimental Psychology Helmholtz institute Utrecht University Heidelberglaan 1 Utrecht 3584 CS Netherlands Center for Human Nature Artificial Intelligence and Neuroscience Hokkaido University Sapporo 060-0812 Japan School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran School of Cognitive Sciences Institute for Research in Fundamental Sciences (IPM) Tehran Iran Department of Brain and Cognitive Sciences Cell Science Research Center Royan Institute for Stem Cell Biology and Technology ACECR Tehran Iran Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences Moscow Russian Federation Institute of Neurobiology Universidad Nacional Autónoma de México Campus Juriquilla Department of Neurophysiology Querétaro 76230 Mexico Laboratory for Neuro- and Psychophysiology Department of Neurosciences KU Leuven Medical School Leuven 3000 Belgium Leuven Brain Institute KU Leuven Leuven 3000 Belgium Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlest

As science and technology evolve, there is an increasing need for promotion of international scientific exchange. Collaborations, while offering substantial opportunities for scientists and benefit to society, also present challenges for those working with animal models, such as non-human primates (NHPs). Diversity in regulation of animal research is sometimes mistaken for the absence of common international welfare standards. Here, the ethical and regulatory protocols for 13 countries that have guidelines in place for biomedical research involving NHPs were assessed with a focus on neuroscience. Review of the variability and similarity in trans-national NHP welfare regulations extended to countries in Asia, Europe and North America. A tabulated resource was established to advance solution-oriented discussions and scientific collaborations across borders. Our aim is to better inform the public and other stakeholders. Through cooperative efforts to identify and analyze information with reference to evidence-based discussion, the proposed key ingredients may help to shape and support a more informed, open framework. This framework and resource can be expanded further for biomedical research in other countries. © 2023

关键词： Ethics Macaque Marmoset Regulations Requirements Welfare

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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

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四川生理科学杂志 2022年第6期44卷 1118-1118页

作者： Smruthi Karthikeyan Department of Pediatrics University of California San Diego La Jolla CA USA Department of Biomedical Informatics University of California San Diego La Jolla California USA Department of Computer Science and Engineering University of California San Diego La Jolla CA USA Department of Bioengineering University of California San Diego La Jolla CA USA Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA Expedited COVID Identification Environment (EXCITE) Laboratory Department of Pediatrics University of California San Diego La Jolla CA USA Department of Obstetrics Gynecology and Reproductive Sciences University of California San Diego La Jolla CA USA COVID-19 Detection Investigation Surveillance Clinical and Outbreak Response California Department of Public Health Richmond CA USA Sanford Consortium of Regenerative Medicine University of California San Diego La Jolla CA USA Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA Student Health and Well-Being University of California San Diego La Jolla CA USA Center for Computational Biology and Bioinformatics University of California San Diego La Jolla CA USA Institute for Genomic Medicine University of California San Diego La Jolla CA USA Operational Strategic Initiatives University of California San Diego La Jolla CA USA Return to Learn University of California San Diego La Jolla CA USA Student Affairs University of California San Diego La Jolla CA USA Academic Affairs University of California San Diego La Jolla CA USA Department of Pathology University of California San Diego La Jolla CA USA Scripps Health San Diego La Jolla CA USA Rady Children’s Institute for Genomic Medicine San Diego CA USA Sharp Healthcare San Diego CA USA Helix San Mateo CA USA County of San Diego Health and Human Services Agency San Diego CA USA Herbert Wertheim School of Public Health and Human Longevity Science Univers

As SARS-CoV-2 continues to spread and evolve,detecting emerging variants early is critical for public health *** lineage prevalence by clinical testing is infeasible at scale,especially in areas with limited resources,participation,or testing/sequencing capacity,which can also introduce ***-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,*** virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants.

关键词： wastewater Wastewater testing

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Dual co-matching network for multi-choice reading comprehension

arXiv

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arXiv 2019年

作者： Zhang, Shuailiang Zhao, Hai Wu, Yuwei Zhang, Zhuosheng Zhou, Xi Zhou, Xiang Department of Computer Science and Engineering Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai China MoE Key Lab of Artificial Intelligence AI Institute Shanghai Jiao Tong University Shanghai China CloudWalk Technology Shanghai China

Multi-choice reading comprehension is a challenging task to select an answer from a set of candidates when given passage and question. This work proposes dual co-matching network which models the relationship among passage, question and answer bidirectionally. The experimental results on RACE, ROCStories and COIN Shared Task 1 show that our model obtains state-of-the-art results and even the single model outperforms the human performance on RACE dataset. Copyright © 2019, The Authors. All rights reserved.

关键词： Machine learning

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A unified syntax-aware framework for semantic role labeling

A unified syntax-aware framework for semantic role labeling

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2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018

作者： Li, Zuchao He, Shexia Cai, Jiaxun Zhang, Zhuosheng Zhao, Hai Liu, Gongshen Li, Linlin Si, Luo Department of Computer Science and Engineering Shanghai Jiao Tong University China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai China School of Cyber Security Shanghai Jiao Tong University China Alibaba Group Hangzhou China

ISBN: (纸本)9781948087841

Semantic role labeling (SRL) aims to recognize the predicate-argument structure of a sentence. Syntactic information has been paid a great attention over the role of enhancing SRL. However, the latest advance shows that syntax would not be so important for SRL with the emerging much smaller gap between syntax-aware and syntax-agnostic SRL. To comprehensively explore the role of syntax for SRL task, we extend existing models and propose a unified framework to investigate more effective and more diverse ways of incorporating syntax into sequential neural networks. Exploring the effect of syntactic input quality on SRL performance, we confirm that high-quality syntactic parse could still effectively enhance syntactically-driven SRL. Using empirically optimized integration strategy, we even enlarge the gap between syntax-aware and syntax-agnostic SRL. Our framework achieves state-of-the-art results on CoNLL-2009 benchmarks both for English and Chinese, substantially outperforming all previous models. © 2018 Association for Computational Linguistics

关键词： Syntactics

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DCMN+: Dual Co-matching network for multi-choice reading comprehension

arXiv

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arXiv 2019年

Multi-choice reading comprehension is a challenging task to select an answer from a set of candidate options when given passage and question. Previous approaches usually only calculate question-aware passage representation and ignore passage-aware question representation when modeling the relationship between passage and question, which obviously cannot take the best of information between passage and question. In this work, we propose dual co-matching network (DCMN) which models the relationship among passage, question and answer options bidirectionally. Besides, inspired by how human solve multi-choice questions, we integrate two reading strategies into our model: (i) passage sentence selection that finds the most salient supporting sentences to answer the question, (ii) answer option interaction that encodes the comparison information between answer options. DCMN integrated with the two strategies (DCMN+) obtains state-of-the-art results on five multi-choice reading comprehension datasets which are from different domains: RACE, SemEval-2018 Task 11, ROCStories, COIN, MCTest. Copyright © 2019, The Authors. All rights reserved.

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