Trevor John Hastie 1040 Campus Drive Stanford, CA 94305 Home Phone&FAX: (650) 326-0854
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AMSTATNEWS the Membership Magazine of the American Statistical Association •
May 2021 • Issue #527 AMSTATNEWS The Membership Magazine of the American Statistical Association • http://magazine.amstat.org 2021 COPSS AWARD WINNERS ALSO: ASA, International Community Continue to Decry Georgiou Persecution Birth of an ASA Outreach Group: The Origins of JEDI AMSTATNEWS MAY 2021 • ISSUE #527 Executive Director Ron Wasserstein: [email protected] Associate Executive Director and Director of Operations Stephen Porzio: [email protected] features Senior Advisor for Statistics Communication and Media Innovation 3 President’s Corner Regina Nuzzo: [email protected] 5 ASA, International Community Continue to Decry Director of Science Policy Georgiou Persecution Steve Pierson: [email protected] Director of Strategic Initiatives and Outreach 8 What a Year! Practical Significance Celebrates Resilient Donna LaLonde: [email protected] Class of 2021 Director of Education 9 Significance Launches Data Economy Series with April Issue Rebecca Nichols: [email protected] 10 CHANCE Highlights: Spring Issue Features Economic Managing Editor Impact of COVID-19, Kullback’s Career, Sharing Data Megan Murphy: [email protected] 11 Forget March Madness! Students Test Probability Skills Editor and Content Strategist with March Randomness Val Nirala: [email protected] 12 My ASA Story: James Cochran Advertising Manager Joyce Narine: [email protected] 14 StatFest Back for 21st Year in 2021 Production Coordinators/Graphic Designers 15 Birth of an ASA Outreach Group: The Origins of JEDI Olivia Brown: [email protected] Megan Ruyle: [email protected] 18 2021 COPSS Award Winners Contributing Staff Members 23 A Story of COVID-19, Mentoring, and West Virginia Kim Gilliam Amstat News welcomes news items and letters from readers on matters of interest to the association and the profession. -
Thesis Is in Two Parts
Downloaded from orbit.dtu.dk on: Oct 03, 2021 Statistical Learning with Applications in Biology Nielsen, Agnes Martine Publication date: 2019 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Nielsen, A. M. (2019). Statistical Learning with Applications in Biology. Technical University of Denmark. DTU Compute PHD-2018 Vol. 488 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Statistical Learning with Applications in Biology Agnes Martine Nielsen Kongens Lyngby 2018 PhD-2018-488 Technical University of Denmark Department of Applied Mathematics and Computer Science Richard Petersens Plads, building 324, 2800 Kongens Lyngby, Denmark Phone +45 4525 3031 [email protected] www.compute.dtu.dk PhD-2018-488 Summary (English) Statistical methods are often motivated by real problems. We consider methods inspired by problems in biology and medicine. The thesis is in two parts. -
Raymond J. Carroll
Raymond J. Carroll Young Investigator Award Ceremony Wednesday, March 9, 2016 11:30 am – 12:30 pm Texas A&M Blocker Building Room 149 Daniella M. Witten 2015 Recipient Associate Professor of Biostatistics and Statistics University of Washington Raymond J. Carroll, Distinguished Professor The Raymond J. Carroll Young Investigator Award was established to honor Dr. Raymond J. Carroll, Distinguished Professor of Statistics, Nutrition and Toxicology, for his fundamental contributions in many areas of statistical methodology and practice, such as measurement error models, nonparametric and semiparametric regression, nutritional and genetic epidemiology. Carroll has been instrumental in mentoring and helping young researchers, including his own students and post-doctoral trainees, as well as others in the statistical community. Dr. Carroll is highly regarded as one of the world’s foremost experts on problems of measurement error, functional data analysis, semiparametric methods and more generally on statistical regression modeling. His work, characterized by a combination of deep theoretical effort, innovative methodological development and close contact with science, has impacted a broad variety of fields, including marine biology, laboratory assay methods, econometrics, epidemiology and molecular biology. In 2005, Raymond Carroll became the first statistician ever to receive the prestigious National Cancer Institute Method to Extend Research in Time (MERIT) Award for his pioneering efforts in nutritional epidemiology and biology and the resulting advances in human health. Less than five percent of all National Institutes of Health-funded investigators merit selection for the highly selective award, which includes up to 10 years of grant support. The Carroll Young Investigator Award is awarded biennially on odd numbered years to a statistician who has made important contributions to the area of statistics. -
It Is NOT Junk a Blog About Genomes, DNA, Evolution, Open Science, Baseball and Other Important Things
it is NOT junk a blog about genomes, DNA, evolution, open science, baseball and other important things The Past, Present and Future of Scholarly Publishing By MIC H A EL EISEN | Published: MA RC H 2 8 , 2 0 1 3 Search To search, type and hit enter I gave a talk last night at the Commonwealth Club in San Francisco about science publishing and PLoS. There will be an audio link soon, but, for the first time in my life, Michael Eisen I actually gave the talk (largely) from prepared remarks, so I thought I’d post it here. I'm a biologist at UC An audio recording of the talk with Q&A is available here. Berkeley and an Investigator of the —— Howard Hughes Medical Institute. I work primarily On January 6, 2011, 24 year old hacker and activist Aaron Swartz was arrested by on flies, and my research encompases police at the Massachusetts Institute of Technology for downloading several million evolution, development, genetics, articles from an online archive of research journals called JSTOR. genomics, chemical ecology and behavior. I am a strong proponent of After Swartz committed suicide earlier this year in the face of legal troubles arising open science, and a co-founder of the from this incident, questions were raised about why MIT, whose access to JSTOR he Public Library of Science. And most exploited, chose to pursue charges, and what motivated the US Department of Justice importantly, I am a Red Sox fan. (More to demand jail time for his transgression. about me here). -
Gene Co-Expression Network Mining Using Graph Sparsification
Gene Co-expression Network Mining Using Graph Sparsification THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Jinchao Di Graduate Program in Electrical and Computer Engineering The Ohio State University 2013 Master’s Examination Committee: Dr. Kun Huang, Advisor Dr. Raghu Machiraju Dr. Yuejie Chi ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Copyright by Jinchao Di 2013 ! ! Abstract Identifying and analyzing gene modules is important since it can help understand gene function globally and reveal the underlying molecular mechanism. In this thesis, we propose a method combining local graph sparsification and a gene similarity measurement method TOM. This method can detect gene modules from a weighted gene co-expression network more e↵ectively since we set a local threshold which can detect clusters with di↵erent densities. In our algorithm, we only retain one edge for each gene, which can generate more balanced gene clusters. To estimate the e↵ectiveness of our algorithm we use DAVID to functionally evaluate the gene list for each module we detect and compare our results with some well known algorithms. The result of our algorithm shows better biological relevance than the compared methods and the number of the meaningful biological clusters is much larger than other methods, implying we discover some previously missed gene clusters. Moreover, we carry out a robustness test by adding Gaussian noise with di↵erent variance to the expression data. We find that our algorithm is robust to noise. We also find that some hub genes considered as important genes could be artifacts. -
Ddawson2012.Pdf (700.6Kb)
Open Science and Crowd Science: Selected Sites and Resources Diane (DeDe) Dawson Natural Sciences Liaison Librarian University of Saskatchewan Saskatoon, Saskatchewan, Canada [email protected] Table of Contents Introduction Open Science Crowd Science Methods and Scope Open Science – Definitions and Principles Open Science – Open Lab Notebooks of Individuals and Lab Groups Open Science – Blogs Crowd Science – Projects for Individuals or Small Teams Crowd Science – Volunteer Distributed Computing Projects The Main Software Organizations Selected Projects Further Sources for Projects Selected Examples of Collaborative Science Sites for Specialists Main Software & Online Tools for Open Science Open Science Conferences and Community Conferences Further Reading/Viewing Videos Reports and White Papers Open e-Books Selected Essays, Articles, and Interviews References Introduction “To take full advantage of modern tools for the production of knowledge, we need to create an open scientific culture where as much information as possible is moved out of people’s heads and laboratories, and onto the network” (Nielsen 2011, p.183). New Internet technologies are radically enhancing the speed and ease of scholarly communications, and are providing opportunities for conducting and sharing research in new ways. This webliography explores the emerging “open science” and “crowd science” movements which are making use of these new opportunities to increase collaboration and openness in scientific research. The collaboration of many researchers on a project can enhance the rate of data-collection and analysis, and ignite new ideas. In addition, since there are more eyes to spot any inaccuracies or errors, collaborative research is likely to produce better quality results. Openness early in the research process alerts others to the work resulting in less duplication of efforts. -
Trevor Hastie Robert Tibshirani Jerome Friedman
Job#: 325659p Date: 11-03-22 16:24:06 Springer Series in Statistics Hastie Springer Series in Statistics • Tibshirani • Friedman Trevor Hastie Trevor Hastie • Robert Tibshirani • Jerome Friedman The Elements of Statistical Learning Robert Tibshirani Jerome Friedman During the past decade there has been an explosion in computation and information tech- nology. With it have come vast amounts of data in a variety of fields such as medicine, biolo- gy, finance, and marketing. The challenge of understanding these data has led to the devel- opment of new tools in the field of statistics, and spawned new areas such as data mining, The Elements of machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in The these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It should be a valuable resource for statisticians and anyone interested Elements Statistical Learning in data mining in science or industry. The book’s coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting—the first comprehensive treatment of this topic in any book. Data Mining,Inference,and Prediction This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression and path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on of methods for “wide” data (p bigger than n), including multiple testing and false discovery rates. -
Big Data Fazekas 2020.Pdf
Using Big Data for social science research Mihály Fazekas School of Public Policy Central European University Winter semester 2019-20 (2 credits) Class times : Fridays on a bi-weekly bases (6 blocks) Office hours: By appointment (Quellenstrasse building) Teaching Assistant: Daniel Kovarek Version: 9/12/2019 Introduction The course is an introduction to state-of-the-art methods to use Big Data in social sciences research. It is a hands-on course requiring students to bring their own research problems and ideas for independent research. The course will review three main topics making Big Data research unique: 1. New and emerging data sources such social media or government administrative data; 2. Innovative data collection techniques such as web scraping; and 3. Data analysis techniques typical of Big Data analysis such as machine learning. Big Data means that both the speed and frequency of data created are increasing at an accelerating pace virtually covering the full spectrum of social life in ever greater detail. Moreover, much of this data is more and more readily available making real-time data analysis feasible. During the course students will acquaint themselves with different concepts, methodological approaches, and empirical results revolving around the use of Big Data in social sciences. As this domain of knowledge is rapidly evolving and already vast, the course can only engender basic literacy skills for understanding Big Data and its novel uses. Students will be encouraged to use acquired skills in their own research throughout the course and continue engaging with new methods. Learning outcomes Students will be acquainted with basic concepts and methods of Big Data and their use for social sciences research. -
Ali Shojaie, Ph.D
Ali Shojaie, Ph.D. University of Washington Department of Biostatistics Phone: (206) 616-5323 334 Hans Rosling Center Email: [email protected] 3980 15th Avenue NE, Box 351617 Homepage: faculty.washington.edu/ashojaie/ Seattle, WA 98195 Education • Iran University of Science & Technology, Tehran, Iran, B.Sc in Industrial and Systems Engineering, 09/1993-02/1998 • Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran, M.Sc in Industrial Engineering, 09/1998-02/2001 • Michigan State University, East Lansing, MI, M.S. Statistics, 01/2003-05/2005 • University of Michigan, Ann Arbor, MI, M.S. in Human Genetics, 09/2006-12/2009 • University of Michigan, Ann Arbor, MI, M.S. in Applied Mathematics, 09/2007-04/2010 • University of Michigan, Ann Arbor, MI, PhD in Statistics, 09/2005- 04/2010 Professional Positions • Postdoctoral Research Fellow, Dept. of Statistics, University of Michigan, 05/2010-06/2011 • Visiting Scholar, Statistical & Applied Mathematical Sciences Institute (SAMSI), 09/2010-05/2010 • Professor of Biostatistics and Adjunct Professor of Statistics, University of Washington, 07/2020- present – Associate Professor of Biostatistics and Adjunct Associate Professor of Statistics, University of Washington, 07/2016-06/2020 – Assistant Professor of Biostatistics and Adjunct Assistant Professor of Statistics, University of Washington, 07/2011-06/2016 • Associate Chair for Strategic Research Affairs, Department of Biostatistics, University of Washington, 09/2020-present • Founding Director, Summer Institute for Statistics in Big Data (SISBID), 05/2014-present • Affiliate Member, Center for Statistics in Social Sciences (CSSS), University of Washington, 03/2012- present • Affiliate Member, Biostatistics and Biomathematics Program, Fred Hutchinson Cancer Research Center (FHCRC), 09/2012-present • Affiliate Faculty, eSciences Institute, University of Washington, 03/2014-present • Affiliate Member, Algorithmic Foundations of Data Science (ADSI) Institute, University of Washington, 2018-present Ali Shojaie, Ph.D. -
Converting Scholarly Journals to Open Access: a Review of Approaches and Experiences David J
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Copyright, Fair Use, Scholarly Communication, etc. Libraries at University of Nebraska-Lincoln 2016 Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences David J. Solomon Michigan State University Mikael Laakso Hanken School of Economics Bo-Christer Björk Hanken School of Economics Peter Suber editor Harvard University Follow this and additional works at: http://digitalcommons.unl.edu/scholcom Part of the Intellectual Property Law Commons, Scholarly Communication Commons, and the Scholarly Publishing Commons Solomon, David J.; Laakso, Mikael; Björk, Bo-Christer; and Suber, Peter editor, "Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences" (2016). Copyright, Fair Use, Scholarly Communication, etc.. 27. http://digitalcommons.unl.edu/scholcom/27 This Article is brought to you for free and open access by the Libraries at University of Nebraska-Lincoln at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Copyright, Fair Use, Scholarly Communication, etc. by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences By David J. Solomon, Mikael Laakso, and Bo-Christer Björk With interpolated comments from the public and a panel of experts Edited by Peter Suber Published by the Harvard Library August 2016 This entire report, including the main text by David Solomon, Bo-Christer Björk, and Mikael Laakso, the preface by Peter Suber, and the comments by multiple authors is licensed under a Creative Commons Attribution 4.0 International License. https://creativecommons.org/licenses/by/4.0/ 1 Preface Subscription journals have been converting or “flipping” to open access (OA) for about as long as OA has been an option. -
In Memoriam: PNAS Editor-In-Chief Nicholas R. Cozzarelli (1938 –2006)
In Memoriam: PNAS Editor-in-Chief Nicholas R. Cozzarelli (1938–2006) hen Nicholas R. Cozzarelli possessed a sharp, analytical memory, became Editor-in-Chief of which perhaps explains why he initially the Proceedings of the Na- chose to study pre-law at Princeton. tional Academy of Sciences However, after some undergraduate Wof the United States of America (PNAS) research, he began falling in love with in 1995, he inherited a journal that in science, and he graduated magna cum many ways had remained unchanged laude in 1960 with a bachelor’s degree since its inception in 1914. Yet in just in biology. Afterward, he attended Yale over a decade, he had—through a com- University School of Medicine (New bination of visionary leadership and Haven, CT) but soon realized that, de- sheer force of will—transformed PNAS spite his talents, he did not want to be a and raised it to a higher level. That physician. After a year, he transferred to transformation can be seen throughout Harvard Medical School (Boston, MA) the journal, from cover to last page. to embark on a journey of research, Since 1995, PNAS has experienced a which began with his graduate studies in marked rise in the number of submis- the laboratory of E. C. C. Lin, examin- sions and published papers, an improve- ing the genes and pathways regulating ment in the quality and variety of Escherichia coli glycerol metabolism. published material, and the introduction After receiving his Ph.D. from Har- of an innovative hybrid open access vard in 1966, Cozzarelli moved to Stan- model. -
IN BRIEF Accounted For
RESEARCH HIGHLIGHTS content or isochore location are IN BRIEF accounted for. The dovetailing of the authors’ experimental and bioinformatic data EVOLUTION provides extremely strong circumstan- tial evidence that L1 insertions Noise minimization in eukaryotic gene expression. decrease gene expression in vivo. Fraser, H. B. et al. PloS Biol. 27 Apr 2004 (doi:10.1371/journal.pbio.0020137) Moreover, this new work tallies with previous findings that gene expression Until now, the functional and evolutionary significance of stochastic is suppressed when full-length L1 (‘noisy’) fluctuations in the rates of protein production was a mys- sequences are inserted into introns. tery.Michael Eisen and colleagues have developed a model of sto- The authors also raise the intrigu- chastic gene expression in yeast to test their hypothesis that genes ing possibility that the mammalian that encode subunits of multiprotein complexes or that cause lethal- genome might have co-opted tran- ity when deleted would be sensitive to such variation. Their estimates scriptional suppression of L1 (which of the noise in protein production for most yeast genes confirm this probably first evolved to prevent hypothesis and indicate that natural selection minimizes noise in excessive mutagenic retrotransposi- gene expression. tion) as a mechanism for fine-tuning the relative levels of expression of dif- CANCER GENETICS ferent genes. If this model is correct, perhaps L1 is better viewed as more Impact of the KU80 pathway on NHEJ-induced of a genomic classroom assistant than genome rearrangements on mammalian cells. Han and colleagues followed up a problematic pupil? Guirouilh-Barbat, J. et al. Mol. Cell 14, 611–623 (2004) their experiments with a neat bit of Nick Campbell bioinformatics.