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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Modeling the homophily effect between links and communities for overlapping community detection 25

Modeling the homophily effect between links and communities ...

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25th International Joint Conference on Artificial Intelligence, IJCai 2016

作者： Zhang, Hongyi Zhao, Tong King, Irwin Lyu, Michael R. Shenzhen Key Laboratory of Rich Media Big Data Analytics and Applications Shenzhen Research Institute Chinese University of Hong Kong Shenzhen China Department of Computer Science and Engineering Chinese University of Hong Kong Shatin N.T. Hong Kong

Overlapping community detection has drawn much attention recently since it allows nodes in a network to have multiple community memberships. A standard framework to deal with overlapping community detection is Matrix Factorization (MF). Although all existing MF-based approaches use links as input to identify communities, the relationship between links and communities is still under-investigated. Most of the approaches only view links as consequences of communities (community-to-link) but fail to explore how nodes' community memberships can be represented by their linked neighbors (link-to-community). In this paper, we propose a Homophily-based Nonnegative Matrix Factorization (HNMF) to model both-sided relationships between links and communities. From the community-to-link perspective, we apply a preference-based pairwise function by assuming that nodes with common communities have a higher probability to build links than those without common communities. From the link-to-community perspective, we propose a new community representation learning with network embedding by assuming that linked nodes have similar community representations. We conduct experiments on several real-world networks and the results show that our HNMF model is able to find communities with better quality compared with state-of-the-art baselines.

关键词： Matrix factorization

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Exploring articulatory characteristics of Cantonese dysarthric speech using distinctive features

Exploring articulatory characteristics of Cantonese dysarthr...

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Ka Ho Wong Wing Sum Yeung Yu Ting Yeung Helen Meng Department of Systems Engineering and Engineering Management Human-Computer Communications Laboratory Stanley Ho Big Data Decision Analytics Research Centre Chinese University of Hong Kong Hong Kong SAR China

ISBN: (纸本)9781479999897

Dysarthria is a kind of motor speech disorder due to neurological deficits. Understanding the articulatory problems of dysarthric speakers may help to design suitable intervention strategies to improve their speech intelligibility. We have developed an automatic articulatory characteristics analysis framework based on a distinctive feature (DF) recognition. We recruited 16 Cantonese dysarthric subjects with spinocerebellar ataxia (SCA) or cerebral palsy (CP) to support our research. To the best of our knowledge, this is among the first efforts in collecting and automatically analyzing Cantonese dysarthric speech. The framework shows a close Pearson correlation to manual annotation of the subjects in most DFs and also in the average DF error rates. It indicates a potential way to describe articulatory characteristics of dysarthric speech and automatically assess it.

关键词： Speech Tongue Speech recognition Lips Training Error analysis Acoustics

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Exploratory data analysis on nuclei in cantonese dysarthric speech

Exploratory data analysis on nuclei in cantonese dysarthric ...

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International Symposium on Chinese Spoken Language Processing

作者： Ka Ho Wong Hoi Kiu Kristy Mok Helen Meng Department of Systems Engineering and Engineering Management Human–Computer Communications Laboratory Stanley Ho Big Data Decision Analytics Research Centre The Chinese University of Hong Kong Hong Kong SAR China

ISBN: (纸本)9781509042951

Phone substitutions, distortions, deletions, and insertions are some of the main problems in dysarthric speech. This work aims to explore the articulatory error patterns in dysarthric speech, which provides insights for the improvement of automatic dysarthric speech analysis technologies. A set of dysarthric speech is collected and phonetically transcribed manually by different transcribers. Transcriptions are mapped into distinctive feature values. Error rates for each value are extracted. Substitutions and distortions are found to be the major errors in dysarthric speech. Their error patterns are analyzed in this paper. The analysis may provide guidance for labelling dysarthric speech errors, which will be useful to future development of technologies to achieve automated analysis of dysarthric speech.

关键词： Speech Distortion Error analysis data analysis Muscles Image analysis Labeling

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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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Improving automatic forced alignment for dysarthric speech transcription 16

Improving automatic forced alignment for dysarthric speech t...

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16th Annual Conference of the International Speech Communication Association, INTERSPEECH 2015

作者： Yeung, Yu Ting Wong, Ka Ho Meng, Helen Human-Computer Communications Laboratory Department of Systems Engineering and Engineering Management Hong Kong Stanley Ho Big Data Decision Analytics Research Centre Chinese University of Hong Kong Hong Kong

Dysarthria is a motor speech disorder due to neurologic deficits. The impaired movement of muscles for speech production leads to disordered speech where utterances have prolonged pause intervals, slow speaking rates, poor articulation of phonemes, syllable deletions, etc. These present challenges towards the use of speech technologies for automatic processing of dysarthric speech data. In order to address these challenges, this work begins by addressing the performance degradation faced in forced alignment. We perform initial alignments to locate long pauses in dysarthric speech and make use of the pause intervals as anchor points. We apply speech recognition for word lattice outputs for recovering the time-stamps of the words in disordered or incomplete pronunciations. By verifying the initial alignments with word lattices, we obtain the reliably aligned segments. These segments provide constraints for new alignment grammars, that can improve alignment and transcription quality. We have applied the proposed strategy to the TORGO corpus and obtained improved alignments for most dysarthric speech data, while maintaining good alignments for non-dysarthric speech data. Copyright © 2015 ISCA.

关键词： Alignment

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AUTOMATIC SPEECH RECOGNITION FOR ACOUSTICAL ANALYSIS AND ASSESSMENT OF CANTONESE PATHOLOGICAL VOICE AND SPEECH

AUTOMATIC SPEECH RECOGNITION FOR ACOUSTICAL ANALYSIS AND ASS...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Tan Lee Yuanyuan Liu Pei-Wen Huang Jen-Tzung Chien Wang Kong Lam Yu Ting Yeung Thomas K.T. Law Kathy Y.S. Lee Anthony Pak-Hin Kong Sam-Po Law Department of Electronic Engineering The Chinese University of Hong Kong Department of Electrical and Computer Engineering National Chiao Tung University Stanley Ho Big Data Decision Analytics Research Centre The Chinese University of Hong Kong Department of Otorhinolaryngology Head and Neck Surgery The Chinese University of Hong Kong Department of Communication Sciences and Disorders University of Central Florida Division of Speech and Hearing Sciences University of Hong Kong

ISBN: (纸本)9781479999897

This paper describes the application of state-of-the-art automatic speech recognition (ASR) systems to objective assessment of voice and speech disorders. Acoustical analysis of speech has long been considered a promising approach to non-invasive and objective assessment of people. In the past the types and amount of speech materials used for acoustical assessment were very limited. With the ASR technology, we are able to perform acoustical and linguistic analyses with a large amount of natural speech from impaired speakers. The present study is focused on Cantonese, which is a major Chinese dialect. Two representative disorders of speech production are investigated: dysphonia and aphasia. ASR experiments are carried out with continuous and spontaneous speech utterances from Cantonese-speaking patients. The results confirm the feasibility and potential of using natural speech for acoustical assessment of voice and speech disorders, and reveal the challenging issues in acoustic modeling and language modeling of pathological speech.

关键词： Pathological speech automatic speech recognition acoustical analysis objective assessment

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MODULAR SENSOR SYSTEM (MSS) FOR URBAN aiR POLLUTION MONITORING

MODULAR SENSOR SYSTEM (MSS) FOR URBAN AIR POLLUTION MONITORI...

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IEEE Sensors

作者： Wei-Ying Yi Kwong-Sak Leung Yee Leung Mei-Ling Meng Terrence Mak Institute of Future Cities Department of Computer Science and Engineering Stanley Ho Big Data Decision Analytics Research Center The Chinese University of Hong Kong China Department of Systems Engineering and Engineering Management Department of Electronics and Computer Science University of Southampton UK

air pollution attracts extensive attention globally due to its critical impacts on human life. Monitoring systems providing real-time micro-level pollution information have been developed to provide authorities with data to mitigate these impacts. However, current systems are usually application-specific with fixed hardware and software configurations. They are inconvenient in maintenance, infeasible in reconfiguration, and unexpandable in sensing capabilities. This paper proposes a novel Modular Sensor System (MSS), which aims at tackling these issues by adopting the proposed Universal Sensor Interface (USI) and modular design in a sensor node. A compact MSS senor node with expandable plug-and-play sensor modules and multiple Wireless Sensor Networks (WSNs) compatibility is implemented and evaluated. Results indicate that MSS sensor node can be deployed in different scenarios while dynamically adapting to reconfigurations and monitoring air pollution at low concentration levels with high energy efficiency. We anticipate that MSS is able to relax the efforts on system maintenance, adaptation, and evolution in real-life large-scale deployment situation.

关键词： plug-and-play air pollution monitoring wireless sensor network modular sensor node

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Exploiting game theoretic analysis for link recommendation in social networks 15

Exploiting game theoretic analysis for link recommendation i...

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24th ACM International Conference on Information and Knowledge Management, CIKM 2015

作者： Zhao, Tong Zhao, H. Vicky King, Irwin Shenzhen Key Laboratory of Rich Media Big Data Analytics and Applications Shenzhen Research Institute Chinese University of Hong Kong Shenzhen China Department of Computer Science and Engineering Chinese University of Hong Kong Shatin N.T. Hong Kong Electrical and Computer Engineering Department University of Alberta EdmontonAB Canada

ISBN: (纸本)9781450337946

The popularity of Online Social Networks (OSNs) has attracted great research interests in different fields. In Economics, researchers use game theory to analyze the mechanism of network formation, which is called Network Formation Game. While in computer Science, much effort has been done in building machine learning models to predict future or missing links. However, there are few works considering how to combine game theoretic analysis and machine learning models. Therefore, in this paper, we study the problem of Exploiting Game Theoretic Analysis for Link Recommendation in Social Networks. Our goal is to improve link recommendation accuracy via leveraging the power of Network Formation Games into machine learning models. We present two different approaches to solve this problem. First, we propose a three-phase method that straightforwardly combines game theoretic analysis with machine learning models. Second, we develop a unified model, BPRLGT, that incorporates Network Formation Game into a Bayesian ranking framework for link recommendation. Specifically, BPRLGT takes advantage of network topology and we design a game theoretic sampling approach to improve its training process. The experiments are conducted on four real world datasets and the results on all datasets demonstrate that both our proposed three-phase method and the unified ranking model outperform the baseline methods. © 2015 ACM.

关键词： Game theory

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Improving latent factor models via personalized feature projection for one class recommendation 15

Improving latent factor models via personalized feature proj...

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24th ACM International Conference on Information and Knowledge Management, CIKM 2015

作者： Zhao, Tong McAuley, Julian King, Irwin Shenzhen Key Laboratory of Rich Media Big Data Analytics and Applications Shenzhen Research Institute Chinese University of Hong Kong Shenzhen China Department of Computer Science and Engineering Chinese University of Hong Kong Shatin N.T. Hong Kong Department of Computer Science and Engineering UC San Diego San DiegoCA United States

ISBN: (纸本)9781450337946

Latent Factor models, which transform both users and items into the same latent feature space, are one of the most successful and ubiquitous models in recommender systems. Most existing models in this paradigm define both users' and items' latent factors to be of the same size and use an inner product to represent a user's 'compatibility' with an item. Intuitively, users' factors encode 'preferences' while item factors encode 'properties', so that the inner product encodes how well an item matches a user's preferences. However, a user's opinion of an item may be more complex, for example each dimension of each user's opinion may depend on a combination of multiple item factors simultaneously. Thus it may be better to view each dimension of a user's preference as a personalized projection of an item's properties so that the preference model can capture complex relationships between items' properties and users' preferences. Therefore, in this paper we propose a novel personalized feature projection method to model users' preferences over items. Specifically, for each user, we define a personalized projection matrix, which takes the place of user-specific factors from existing models. This matrix describes a mapping between items' factors and users' preferences in order to build personalized preference models for each user and item. The proposed personalized feature projection method is quite general and existing latent factor models, for example, can be cast as a special case. We present three objective functions to optimize predictions in the form of ranked lists of users' preferences over items, and demonstrate how each can be used to improve one-class recommendation performance. Experiments are conducted on four real-world datasets and our results show that our personalized feature projection method outperforms several state-of-the-art methods on various evaluation metrics. © 2015 ACM.

关键词： Collaborative filtering

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