A review on machine learning principles for multi-view biological data integration.
TLDR
It is shown that Bayesian models are able to use prior information and model measurements with various distributions, and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.Abstract:
Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.read more
Citations
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
Andrea Cossarizza,Hyun-Dong Chang,Andreas Radbruch,Andreas Acs,Dieter Adam,Sabine Adam-Klages,William W. Agace,William W. Agace,Nima Aghaeepour,Mübeccel Akdis,Matthieu Allez,Larissa Nogueira Almeida,Giorgia Alvisi,Graham Anderson,Immanuel Andrä,Francesco Annunziato,Achille Anselmo,Petra Bacher,Cosima T. Baldari,Sudipto Bari,Vincenzo Barnaba,Vincenzo Barnaba,Joana Barros-Martins,Luca Battistini,Wolfgang Bauer,Sabine Baumgart,Nicole Baumgarth,Dirk Baumjohann,Bianka Baying,Mary Bebawy,Burkhard Becher,Wolfgang Beisker,Vladimir Benes,Rudi Beyaert,Alfonso Blanco,Dominic A. Boardman,Christian Bogdan,Jessica G. Borger,Giovanna Borsellino,Philip E. Boulais,Jolene Bradford,Dirk Brenner,Dirk Brenner,Ryan R. Brinkman,Anna E. S. Brooks,Dirk H. Busch,Martin Büscher,Timothy P. Bushnell,Federica Calzetti,Garth Cameron,Ilenia Cammarata,Xuetao Cao,Susanna Cardell,Stefano Casola,Marco A. Cassatella,Andrea Cavani,Antonio Celada,Lucienne Chatenoud,Pratip K. Chattopadhyay,Sue Chow,Eleni Christakou,Eleni Christakou,Luka Cicin-Sain,Mario Clerici,Federico Colombo,Laura Cook,Anne Cooke,Andrea M. Cooper,Alexandra J. Corbett,Antonio Cosma,Lorenzo Cosmi,Pierre Coulie,Ana Cumano,Ljiljana Cvetkovic,Van Duc Dang,Chantip Dang-Heine,Martin S. Davey,Derek Davies,Sara De Biasi,Genny Del Zotto,Gelo Victoriano Dela Cruz,Michael Delacher,Silvia Della Bella,Paolo Dellabona,Günnur Deniz,Mark C. Dessing,James P. Di Santo,Andreas Diefenbach,Francesco Dieli,Andreas Dolf,Thomas Dörner,Regine J. Dress,Diana Dudziak,Michael L. Dustin,Charles-Antoine Dutertre,Charles-Antoine Dutertre,Friederike Ebner,Sidonia B G Eckle,Matthias Edinger,Pascale Eede,Götz R. A. Ehrhardt,Marcus Eich,Pablo Engel,Britta Engelhardt,Anna Erdei,Charlotte Esser,Bart Everts,Maximilien Evrard,Christine S. Falk,Todd A. Fehniger,Mar Felipo-Benavent,Helen Ferry,Markus Feuerer,Andrew Filby,Kata Filkor,Simon Fillatreau,Marie Follo,Irmgard Förster,John Bellamy Foster,Gemma A. Foulds,Britta Frehse,Paul S. Frenette,Stefan Frischbutter,Wolfgang Fritzsche,David W. Galbraith,David W. Galbraith,Anastasia Gangaev,Natalio Garbi,Brice Gaudilliere,Ricardo T. Gazzinelli,Ricardo T. Gazzinelli,Jens Geginat,Wilhelm Gerner,Nicholas A Gherardin,Kamran Ghoreschi,Lara Gibellini,Florent Ginhoux,Florent Ginhoux,Florent Ginhoux,Keisuke Goda,Keisuke Goda,Keisuke Goda,Dale I. Godfrey,Christoph Goettlinger,José M. González-Navajas,Carl S. Goodyear,Andrea Gori,Jane L. Grogan,Daryl Grummitt,Andreas Grützkau,Claudia Haftmann,Jonas Hahn,Hamida Hammad,Günter J. Hämmerling,Leo Hansmann,Göran K. Hansson,Christopher M. Harpur,Susanne Hartmann,Andrea Hauser,Anja E. Hauser,David L. Haviland,David W. Hedley,Daniela C. Hernández,Guadalupe Herrera,Martin Herrmann,Christoph Hess,Christoph Hess,Thomas Höfer,Petra Hoffmann,Kristin A. Hogquist,Tristan Holland,Thomas Höllt,Thomas Höllt,Rikard Holmdahl,Pleun Hombrink,Jessica P. Houston,Bimba F. Hoyer,Bo Huang,Fang-Ping Huang,Johanna Huber,Jochen Huehn,Michael Hundemer,Christopher A. Hunter,William Hwang,William Hwang,Anna Iannone,Florian Ingelfinger,Sabine Ivison,Hans-Martin Jäck,Peter K. Jani,Beatriz Jávega,Stipan Jonjić,Toralf Kaiser,Tomas Kalina,Thomas Kamradt,Stefan H. E. Kaufmann,Baerbel Keller,Steven L. C. Ketelaars,Ahad Khalilnezhad,Ahad Khalilnezhad,Srijit Khan,Jan Kisielow,Paul Klenerman,Jasmin Knopf,Hui-Fern Koay,Katja Kobow,Jay K. Kolls,Wan Ting Kong,Manfred Kopf,Thomas Korn,Katharina Kriegsmann,Hendy Kristyanto,Thomas Kroneis,Andreas Krueger,J. Kühne,Christian Kukat,Désirée Kunkel,Heike Kunze-Schumacher,Tomohiro Kurosaki,Christian Kurts,Pia Kvistborg,Immanuel Kwok,Immanuel Kwok,Jonathan J M Landry,Olivier Lantz,Paola Lanuti,Francesca LaRosa,Agnès Lehuen,Salomé LeibundGut-Landmann,Michael D. Leipold,Leslie Y. T. Leung,Megan K. Levings,Andreia C. 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Oja,Diana Ordonez,Alberto Orfao,Eva Orlowski-Oliver,Wenjun Ouyang,Annette Oxenius,Raghavendra Palankar,Isabel Panse,Kovit Pattanapanyasat,Malte Paulsen,Dinko Pavlinic,Livius Penter,Pärt Peterson,Christian Peth,Jordi Petriz,Federica Piancone,Winfried F. Pickl,Silvia Piconese,Marcello Pinti,A. Graham Pockley,Malgorzata J. Podolska,Zhiyong Poon,Katharina Pracht,Immo Prinz,Carlo Pucillo,Sally A. Quataert,Linda Quatrini,Kylie M. Quinn,Kylie M. Quinn,Helena Radbruch,Tim R. Radstake,Susann Rahmig,Hans-Peter Rahn,Bartek Rajwa,Gevitha Ravichandran,Yotam Raz,Jonathan Rebhahn,Diether J. Recktenwald,Dorothea Reimer,Caetano Reis e Sousa,Ester B. M. Remmerswaal,Lisa Richter,Laura G. Rico,Andy Riddell,Aja M. Rieger,J. 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Wing,Rieke Winkelmann,Thomas Winkler,Oliver F. Wirz,Alicia Wong,Peter Wurst,Jennie H M Yang,Jennie H M Yang,Juhao Yang,Maria Yazdanbakhsh,Liping Yu,Alice Yue,Hanlin Zhang,Yi Zhao,Susanne Ziegler,Christina E. Zielinski,Jakob Zimmermann,Arturo Zychlinsky +462 more
TL;DR: These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community providing the theory and key practical aspects offlow cytometry enabling immunologists to avoid the common errors that often undermine immunological data.
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Current Applications and Future Impact of Machine Learning in Radiology.
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TL;DR: Examples of current applications of machine learning and artificial intelligence techniques in diagnostic radiology and the future impact and natural extension of these techniques in radiology practice are discussed.
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