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arXiv 2022年

作者： Callahan, Tiffany J. Stefanski, Adrianne L. Wyrwa, Jordan M. Zeng, Chenjie Ostropolets, Anna Banda, Juan M. Baumgartner, William A. Boyce, Richard D. Casiraghi, Elena Coleman, Ben D. Collins, Janine H. Deakyne-Davies, Sara J. Feinstein, James A. Haendel, Melissa A. Lin, Asiyah Y. Martin, Blake Matentzoglu, Nicolas A. Meeker, Daniella Reese, Justin Sinclair, Jessica Taneja, Sanya B. Trinkley, Katy E. Vasilevsky, Nicole A. Williams, Andrew Zhang, Xingman A. Denny, Joshua C. Robinson, Peter N. Ryan, Patrick Hripcsak, George Bennett, Tellen D. Hunter, Lawrence E. Kahn, Michael G. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States Department of Computer Science Georgia State University AtlantaGA30303 United States Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15260 United States Computer Science Università degli Studi di Milano Milan20122 Italy Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States The Jackson Laboratory for Genomic Medicine FarmingtonCT06032 United States Department of Haematology University of Cambridge Cambridge United Kingdom Department of Research Informatics & Data Science Analytics Resource Center Children’s Hospital Colorado AuroraCO80045 United States University of Colorado Anschutz School of Medicine AuroraCO80045 United States Center for Health AI University of Colorado Anschutz Medical Campus AuroraCO80045 United States Departments of Biomedical Informatics and Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Semanticly Athens Greece Yale School of Medicine New HavenCT06510 United States HealthLinc ValparaisoIN46383 United States Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Family Medicine University of Colorado Anschutz School of Medicine AuroraCO80045 United States Translational and Integrative Sciences Lab University of Colorado Anschutz Medical Campus AuroraCO80045 United States Tufts Institute for Clinical Research and Health Policy Studies Tufts University Bos

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping. © 2022, CC BY.

关键词： Ontology

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

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Genome biology 2025年第1期26卷 31页

作者： Jacob Matthew Schreiber Carles A Boix Jin Wook Lee Hongyang Li Yuanfang Guan Chun-Chieh Chang Jen-Chien Chang Alex Hawkins-Hooker Bernhard Schölkopf Gabriele Schweikert Mateo Rojas Carulla Arif Canakoglu Francesco Guzzo Luca Nanni Marco Masseroli Mark James Carman Pietro Pinoli Chenyang Hong Kevin Y Yip Jefrey P Spence Sanjit Singh Batra Yun S Song Shaun Mahony Zheng Zhang Wuwei Tan Yang Shen Yuanfei Sun Minyi Shi Jessika Adrian Richard S Sandstrom Nina P Farrell Jessica M Halow Kristen Lee Lixia Jiang Xinqiong Yang Charles B Epstein J Seth Strattan Bradley E Bernstein Michael P Snyder Manolis Kellis William S Noble Anshul Bharat Kundaje Department of Genetics Stanford University Stanford CA USA. jmschreiber91@***. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Department of Genetics Stanford University Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Research and Development DeepSeq.AI San Francisco CA USA. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department of Empirical Inference Max Planck Institute for Intelligent Systems Stuttgart Germany. School of Life Sciences University of Dundee Dundee UK. Department of Electronics Information and Bioengineering Politecnico Di Milano Milan Italy. Department of Computational Biology University of Lausanne Lausanne Switzerland. Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong. Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Statistics University of California Berkeley Berkeley CA USA. Department of Biochemistry & Molecular Biology Center for Eukaryotic Gene Regulation Pennsylvania State University University Park PA USA. Department of Statistics Pennsylvania State University University Park PA USA. Department of Electrical and Computer Engineering Texas A&M University College Station TX USA. Altius Institute Seattle WA USA. Epigenomics Program The Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Computer Science Stanford University Stanford CA USA.

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The application of an extracellular vesicle-based biosensor in early diagnosis and prediction of chemoresponsiveness in ovarian cancer

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Cancer Letters 2024年 581卷 216533-216533页

作者： Tsang, Benjamin K. Asare-Werehene, Meshach Hunter, Rob Gerber, Emma Reunov, Arkadiy Brine, Isaiah Chang, Chia-Yu Chang, Chia-Ching Shieh, Dar-Bin Burger, Dylan Anis, Hanan Departments of Obstetrics & Gynecology and Cellular & Molecular Medicine Centre for Infection Immunity and Inflammation Interdisciplinary School of Health Sciences University of Ottawa Ottawa ON K1N 6N5 Canada Chronic Disease Program Ottawa Hospital Research Institute The Ottawa Hospital Ottawa ON K1Y 4E9 Canada Department of Biology St. Francis Xavier University 2320 Notre Dame Avenue Antigonish NS B2G 2W5 Canada School of Electrical Engineering and Computer Science Ottawa-Carleton Institute for Biomedical Engineering University of Ottawa Ottawa ON K1N 6N5 Canada Department of Biological Science and Department of Electrophysics Technology Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu 30068 Taiwan Institute of Basic Medical Science Institute of Oral Medicine and Department of Stomatology Advanced Optoelectronic Technology Center and Center for Micro/Nano Science and Technology National Cheng Kung University Hospital National Cheng Kung University Tainan 704 Taiwan Institute of Physics Academia Sinica Taipei 10529 Taiwan

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Speech Emotion Recognition using Convolutional Neural Network with Audio Word-based Embedding

Speech Emotion Recognition using Convolutional Neural Networ...

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International Symposium on Chinese Spoken Language Processing

作者： Kun-Yi Huang Chung-Hsien Wu Qian-Bei Hong Ming-Hsiang Su Yuan-Rong Zeng Department of Computer Science and Information Engineering National Cheng Kung University Taiwan PhD Program for Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Taiwan

ISBN: (纸本)9781538656280;9781538656273

A complete emotional expression typically contains a complex temporal course in a natural conversation. Related research on utterance-level, segment-level and multi-level processing lacks understanding of the underlying relation of emotional speech. In this work, a convolutional neural network (CNN) with audio word-based embedding is proposed for emotion modeling. In this study, vector quantization is first applied to convert the low level features of each speech frame into audio words using k-means algorithm. Word2vec is adopted to convert an input speech utterance into the corresponding audio word vector sequence. Finally, the audio word vector sequences of the training emotional speech data with emotion annotation are used to construct the CNN- based emotion model. The NCKU-ES database, containing seven emotion categories: happiness, boredom, anger, anxiety, sadness, surprise and disgust, was collected and five-fold cross validation was used to evaluate the performance of the proposed CNN-based method for speech emotion recognition. Experimental results show that the proposed method achieved an emotion recognition accuracy of 82.34%, improving by 8.7% compared to the Long Short Term Memory (LSTM)- based method, which faced the challenging issue of long input sequence. Comparing with raw features, the audio word-based embedding achieved an improvement of 3.4% for speech emotion recognition.

关键词： Emotion recognition Feature extraction Speech recognition Acoustics Training Databases Neural networks

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The association for the advancement of artificial intelligence 2020 workshop program

The association for the advancement of artificial intelligen...

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作者： Bang, Grace Barash, Guy Bea, Ryan Cali, Jacques Castillo-Effen, Mauricio Chen, Xin Cynthia Chhaya, Niyati Dhoopar, Rohan Dumancic, Sebastijan Espinoza, Huáscar Farchi, Eitan Fioretto, Ferdinando Fuentetaja, Raquel Galley, Michel Geib, Christopher Hernández-Orallo, José Huang, Xiaowei Keren, Sarah Kim, Seokhwan Jaidka, Kokil Liu, Xiaomo Lu, Tyler Ma, Zhiqiang Mallah, Richard McDermid, John Michalowski, Martin Mirsky, Reuth Héigeartaigh, Seán Ó. Ramachandran, Deepak Segovia-Aguas, Javier Shaban-Nejad, Arash Shehory, Onn Shwartz, Vered Srivastava, Siddharth Talamadupula, Kartik Tang, Jian Zhang, Dell Zhang, Jian S&P Global. Western Digital University of Southampton United Kingdom Blue Prism Group PLC Lockheed Martin's Advanced Technology Laboratories ArlingtonVA United States University of Hong Kong Hong Kong Adobe Research Google Research Katholieke Universiteit Leuven Belgium Commissariat à ĺÉnergie Atomique France IBM Research Department of Electrical Engineering and Computer Science Syracuse University United States Universidad Carlos III de Madrid Spain Microsoft Research AI SIFT LLC Universitat Politècnica de València Spain Leverhulme Centre for the Future of Intelligence United Kingdom Department of Computer Science University of Liverpool United Kingdom National University of Singapore Singapore Harvard School of Engineering and Applied Sciences in the of Fields of Multiagent Environment Design and Goal Recognition Design Amazon Alexa AI Future of Life Institute United States University of York Assuring Autonomy International Program United Kingdom University of Minnesota School of Nursing MinneapolisMN United States University of Texas at Austin AustinTX United States Institut de Robòtica i Informàtica Industrial Spanish Council for Scientific Research Technical University of Catalonia Spain Oak Ridge National Laboratory Center for Biomedical Informatics Department of Pediatrics University of Tennessee Health Science Center United States Bar Ilan University Israel University of Washington SeattleWA United States Autonomous Agents and Intelligent Robots lab of the School of Computing Informatics Decision Systems Arizona State University United States DiDi AI Labs School of Industrial and System Engineering Georgia Institute of Technology United States University of London United Kingdom Microsoft Azure

The Association for the Advancement of Artificial Intelligence 2020 Workshop program included twenty-three workshops covering a wide range of topics in artificial intelligence. This report contains the required reports, which were submitted by most, but not all, of the workshop chairs. Copyright © 2020, Association for the Advancement of Artificial Intelligence. All rights reserved.

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LSTM-based Text Emotion Recognition Using Semantic and Emotional Word Vectors

LSTM-based Text Emotion Recognition Using Semantic and Emoti...

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Asian Conference on Affective Computing and intelligent Interaction (ACII Asia)

作者： Ming-Hsiang Su Chung-Hsien Wu Kun-Yi Huang Qian-Bei Hong Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Tainan Taiwan

ISBN: (纸本)9781538653128

This study proposes a long-short term memory (LSTM)-based approach to text emotion recognition based on semantic word vector and emotional word vector of the input text. For each word in an input text, the semantic word vector is extracted from the word 2vec model. Besides, each lexical word is projected to all the emotional words defined in an affective lexicon to derive an emotional word vector. An autoencoder is then adopted to obtain the bottleneck features from the emotional word vector for dimensionality reduction. The autoencoder bottleneck features are then concatenated with the features in the semantic word vector to form the final textual features for emotion recognition. Finally, given the textual feature sequence of the entire sentence, the LSTM is used for emotion recognition by modeling the contextual emotion evolution of the input text. For evaluation, the NLPCC-MHMC-TE database containing seven emotion categories: anger, boredom, disgust, anxiety, happiness, sadness, and surprise was constructed and used. Five-fold cross-validation was employed to evaluate the performance of the proposed method. Experimental results show that the proposed LSTM-based method achieved a recognition accuracy of 70.66%, improving 5.33% compared with the CNN-based method. Besides, the proposed method based on integration of the semantic word vector and emotional word vector of the input text outperformed that using the individual feature vector.

关键词： Emotion recognition Databases Logic gates Feature extraction Semantics Speech recognition computer science

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Exploring Macroscopic Fluctuation of Facial Expression for Mood Disorder Classification

Exploring Macroscopic Fluctuation of Facial Expression for M...

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Asian Conference on Affective Computing and intelligent Interaction (ACII Asia)

作者： Qian-Bei Hong Chung-Hsien Wu Ming-Hsiang Su Kun-Yi Huang Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Tainan Taiwan Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan

ISBN: (纸本)9781538653128

In clinical diagnosis of mood disorder, a large portion of bipolar disorder patients (BDs) are misdiagnosed as unipolar depression (UDs). Clinicians have confirmed that BDs generally show "reduced affect'' during clinical treatment. Thus, it is expected to build an objective and one-time diagnosis system for diagnosis assistance by using machine-learning techniques. In this study, facial expressions of BD, UD and control group (C) elicited by emotional video clips are collected for exploring temporal fluctuation characteristics of intensities of facial muscles expression among the three groups. The differences of facial expressions among mood disorders are investigated by observing macroscopic fluctuations. To deal with these problems, the corresponding methods for feature extraction and modeling are proposed. From the viewpoint of macroscopic facial expression, action unit (AU) is applied for describing the temporal transformation of muscles. Then, modulation spectrum is used for extracting short-term variation of AU. The multilayer perceptron (MLP)-based disorder prediction model is then applied to obtain the prediction results. For evaluation of the proposed method, 12 subjects for three group are included in the K-fold (K=12) cross validation experiments. The experiment results reached 61.1% classification accuracy, and outperformed the other baseline methods.

关键词： Mood Gold Fluctuations Databases Feature extraction Modulation Predictive models

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Syncgan: Synchronize the Latent Spaces of Cross-Modal Generative Adversarial Networks

Syncgan: Synchronize the Latent Spaces of Cross-Modal Genera...

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IEEE International Conference on Multimedia and Expo (ICME)

作者： Wen-Cheng Chen Chien-Wen Chen Min-Chun Hu Dept. of Computer Science and Information Engineering National Cheng Kung University Taiwan Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Taiwan

Generative adversarial network (GAN) has achieved impressive success on cross-domain generation, but it faces difficulty in cross-modal generation due to the lack of a common distribution between heterogeneous data. Most existing methods of conditional based cross-modal GANs adopt the strategy of one-directional transfer and have achieved preliminary success on text-to-image transfer. Instead of learning the transfer between different modalities, we aim to learn a synchronous latent space representing the cross-modal common concept. A novel network component named synchronizer is proposed in this work to judge whether the paired data is synchronous/corresponding or not, which can constrain the latent space of generators in the GANs. Our GAN model, named as SyncGAN, can successfully generate synchronous data (e.g., a pair of image and sound) from identical random noise. For transforming data from one modality to another, we recover the latent code by inverting the mappings of a generator and use it to generate data of different modality. In addition, the proposed model can achieve semi-supervised learning, which makes our model more flexible for practical applications.

关键词： Synchronization Gallium nitride Generators Data models Training Generative adversarial networks Training data

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An interactive tool for natural language processing on clinical text

arXiv

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arXiv 2017年

作者： Trivedi, Gaurav Pham, Phuong Chapman, Wendy Hwa, Rebecca Wiebe, Janyce Hochheiser, Harry Intelligent Systems Program University of Pittsburgh Dept. of Computer Science University of Pittsburgh Dept. of Biomed. Informatics University of Utah Dept. of Computer Science and Intelligent Systems Program University of Pittsburgh

Natural Language Processing (NLP) systems often make use of machine learning techniques that are unfamiliar to endusers who are interested in analyzing clinical records. Although NLP has been widely used in extracting information from clinical text, current systems generally do not support model revision based on feedback from domain experts. We present a prototype tool that allows end users to visualize and review the outputs of an NLP system that extracts binary variables from clinical text. Our tool combines multiple visualizations to help the users understand these results and make any necessary corrections, thus forming a feedback loop and helping improve the accuracy of the NLP models. We have tested our prototype in a formative think-aloud user study with clinicians and researchers involved in colonoscopy research. Results from semi-structured interviews and a System Usability Scale (SUS) analysis show that the users are able to quickly start refining NLP models, despite having very little or no experience with machine learning. Observations from these sessions suggest revisions to the interface to better support review workflow and interpretation of results. Copyright © 2017, The Authors. All rights reserved.

关键词： Visualization

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How can NLP tasks mutually benefit sentiment analysis? A holistic approach to sentiment analysis 7

How can NLP tasks mutually benefit sentiment analysis? A hol...

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7th Workshop on Computational Approaches to Subjectivity, Sentiment and Social Media Analysis, WASSA 2016 at the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL-HLT 2016

作者： Deng, Lingjia Wiebe, Janyce Intelligent Systems Program University of Pittsburgh Intelligent Systems Program Department of Computer Science University of Pittsburgh

ISBN: (纸本)9781941643822

Existing opinion analysis techniques rely on the clues within the sentence that focus on the sentiment analysis task itself. However, the sentiment analysis task is not isolated from other NLP tasks (co-reference resolution, entity linking, etc) but they can benefit each other. In this paper, we define dependencies between sentiment analysis and other tasks, and express the dependencies in first order logic rules regardless of the representations of different tasks. The conceptual framework proposed in this paper using such dependency rules as constraints aims at exploiting information outside the sentence and outside the document to improve sentiment analysis. Further, the framework allows exception to the rules. © 2016 Association for Computational Linguistics

关键词： Sentiment analysis

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