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189 results on '"Winkler, Jonathan"'

4. Effective Resistance-based Germination of Seed Sets for Community Detection

Author

Eskreis-Winkler, Jonathan and Kondor, Risi

Subjects
Computer Science - Social and Information Networks, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Community detection is, at its core, an attempt to attach an interpretable function to an otherwise indecipherable form. The importance of labeling communities has obvious implications for identifying clusters in social networks, but it has a number of equally relevant applications in product recommendations, biological systems, and many forms of classification. The local variety of community detection starts with a small set of labeled seed nodes, and aims to estimate the community containing these nodes. One of the most ubiquitous methods - due to its simplicity and efficiency - is personalized PageRank. The most obvious bottleneck for deploying this form of PageRank successfully is the quality of the seeds. We introduce a "germination" stage for these seeds, where an effective resistance-based approach is used to increase the quality and number of seeds from which a community is detected. By breaking seed set expansion into a two-step process, we aim to utilize two distinct random walk-based approaches in the regimes in which they excel. In synthetic and real network data, a simple, greedy algorithm which minimizes the effective resistance diameter combined with PageRank achieves clear improvements in precision and recall over a standalone PageRank procedure., Comment: 10 pages, 4 figures, currently under review for conference submission

Published
2018

5. Multiresolution Kernel Approximation for Gaussian Process Regression

Author

Ding, Yi, Kondor, Risi, and Eskreis-Winkler, Jonathan

Subjects
Statistics - Machine Learning
Abstract

Gaussian process regression generally does not scale to beyond a few thousands data points without applying some sort of kernel approximation method. Most approximations focus on the high eigenvalue part of the spectrum of the kernel matrix, $K$, which leads to bad performance when the length scale of the kernel is small. In this paper we introduce Multiresolution Kernel Approximation (MKA), the first true broad bandwidth kernel approximation algorithm. Important points about MKA are that it is memory efficient, and it is a direct method, which means that it also makes it easy to approximate $K^{-1}$ and $\mathop{\textrm{det}}(K)$.

Published
2017

15. SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection

Author

Feuerstadt, Paul, primary, Louie, Thomas J., additional, Lashner, Bret, additional, Wang, Elaine E.L., additional, Diao, Liyang, additional, Bryant, Jessica A., additional, Sims, Matthew, additional, Kraft, Colleen S., additional, Cohen, Stuart H., additional, Berenson, Charles S., additional, Korman, Louis Y., additional, Ford, Christopher B., additional, Litcofsky, Kevin D., additional, Lombardo, Mary-Jane, additional, Wortman, Jennifer R., additional, Wu, Henry, additional, Auniņš, John G., additional, McChalicher, Christopher W.J., additional, Winkler, Jonathan A., additional, McGovern, Barbara H., additional, Trucksis, Michele, additional, Henn, Matthew R., additional, and von Moltke, Lisa, additional

Published
2022
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18. 1035. Manufacturing Processes of SER-109, a Purified Investigational Microbiome Therapeutic, Reduce Risk of Transmission of Emerging and Undetected Infections in Donor Stool

Author

McChalicher, Christopher, primary, Abdulaziz, Ahmad, additional, Halvorsen, Elizabeth, additional, Lombardo, Mary-Jane, additional, Winkler, Jonathan, additional, Almomani, Sanabel, additional, McGovern, Barbara, additional, McKenzie, Gregory, additional, Ege, David, additional, and Aunins, John, additional

Published
2021
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19. Efficacy and Safety of Investigational Microbiome Drug SER-109 for Treatment of Recurrent Clostridioides difficile Infection

Author

McGovern, Barbara, primary, Sims, Mathew, additional, Kraft, Colleen, additional, Wang, Elaine, additional, Brady, Kelly, additional, Ford, Christopher, additional, Edward, O’Brien, additional, Lombardo, Mary-Jane, additional, Wortman, Jennifer, additional, Litcofsky, Kevin, additional, Mahoney, Jennifer, additional, McChalicher, Christopher, additional, Winkler, Jonathan, additional, Garant, Sarah, additional, Aunins, John, additional, Henn, Matthew, additional, and von Moltke, Lisa, additional

Published
2021
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23. Fr572 24-WEEK EFFICACY AND SAFETY DATA FROM ECOSPOR-III, A PHASE 3 DOUBLE-BLIND, PLACEBO-CONTROLLED RANDOMIZED TRIAL OF SER-109, AN INVESTIGATIONAL MICROBIOME THERAPEUTIC FOR TREATMENT OF RECURRENT CLOSTRIDIOIDES DIFFICILE INFECTION

Author

Korman, Louis, primary, Lashner, Bret, additional, Kraft, Colleen, additional, Sims, Matthew, additional, Wang, Elaine E., additional, Brady, Kelly, additional, Ford, Christopher B., additional, Lombardo, Mary-Jane, additional, Litcofsky, Kevin D., additional, Mahoney, Jennifer C., additional, McChalicher, Christopher W., additional, Winkler, Jonathan, additional, Garant, Sarah, additional, Mcgovern, Babara, additional, McMullen, Erin, additional, Henn, Matthew R., additional, Trucksis, Michele, additional, and von Moltke, Lisa, additional

Published
2021
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26. Communication and Empire: Media, Markets and Globalization, 1860-1930

Author

Winkler, Jonathan Reed

Subjects
Communication and Empire: Media, Markets and Globalization, 1860-1930 (Book) -- Winseck, Dwayne R. -- Pike, Robert M., Books -- Book reviews, International relations
Abstract

COMMUNICATION AND EMPIRE Media, Markets and Globalization, 1860-1930 Dwayne R. Winseck and Robert M. Pike Durham, NC: Duke University Press, 2007. xx, 429pp, US $24.95 (ISBN 978-0-8223-3928-1) Globalization is a [...]

Published
2008

27. Multiresolution Analysis on Discrete Spaces

Author

Eskreis-Winkler, Jonathan Mark

Subjects
Statistics, FOS: Mathematics, Computer science
Abstract

It continues to be much cheaper to store data than to analyze it. This state of data analysis motivates methods that make minimal assumptions in order to reduce the complexity of data. In order to address scalability in certain applied, network-based problems, we bring together three distinct fields: multiresolution analysis (MRA), hyperbolic embeddings, and community detection. Together, the work in these fields provides a path forward for certain difficult problems in large-scale data analysis. We provide a theoretical background, a description of our contributions, and a number of applications to show the viability of our ideas in a real-world setting. The primary contributions of this dissertation are threefold. First, we draw a connection between a class of currently-used methods in computational MRA to hyperbolic representations of data. This connection allows us to suggest a rationale for when different MRA methods are appropriate, and to define related tree-based kernels for wavelet construction. Second, we broaden the existing work describing the mechanics of how the multiresolution matrix factorization (MMF) summarizes data. We look at this MRA framework from two perspectives. First, we consider how MMF may be viewed as a hyperbolic embedding. Second, we consider the way MMF may be seen as a regularization operator. We show that for certain graphs, the regularization imposed by MMF enables methods to perform more accurate inference than when no regularization is used. This work fits within the existing field of high dimensional statistics where regularization may turn a massive problem into a manageable one. Third, we show the way that MMF, and other similar multiresolution methods, may be used efficiently in unsupervised and semisupervised settings. By taking advantage of the localization of wavelets in time and frequency space of graphs, we are able to detect complex, multiscale, overlapping community structures, as well as combine network structure with the small amounts of labeling for semisupervised learning.

Published
2020
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33. SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial

Author

McGovern, Barbara H, primary, Ford, Christopher B, additional, Henn, Matthew R, additional, Pardi, Darrell S, additional, Khanna, Sahil, additional, Hohmann, Elizabeth L, additional, O’Brien, Edward J, additional, Desjardins, Christopher A, additional, Bernardo, Patricia, additional, Wortman, Jennifer R, additional, Lombardo, Mary-Jane, additional, Litcofsky, Kevin D, additional, Winkler, Jonathan A, additional, McChalicher, Christopher W J, additional, Li, Sunny S, additional, Tomlinson, Amelia D, additional, Nandakumar, Madhumitha, additional, Cook, David N, additional, Pomerantz, Roger J, additional, Auninš, John G, additional, and Trucksis, Michele, additional

Published
2020
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35. SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial.

Author

McGovern, Barbara H, Ford, Christopher B, Henn, Matthew R, Pardi, Darrell S, Khanna, Sahil, Hohmann, Elizabeth L, O'Brien, Edward J, Desjardins, Christopher A, Bernardo, Patricia, Wortman, Jennifer R, Lombardo, Mary-Jane, Litcofsky, Kevin D, Winkler, Jonathan A, McChalicher, Christopher W J, Li, Sunny S, Tomlinson, Amelia D, Nandakumar, Madhumitha, Cook, David N, Pomerantz, Roger J, and Auninš, John G

Subjects
CONFIDENCE intervals, INVESTIGATIONAL drugs, CLOSTRIDIUM diseases, DISEASE relapse, RANDOMIZED controlled trials, HUMAN microbiota, DESCRIPTIVE statistics, GENOMICS, POLYMERASE chain reaction, FECAL microbiota transplantation, SPORES, PHARMACODYNAMICS
Abstract

Background Recurrent Clostridioides difficile infection (rCDI) is associated with loss of microbial diversity and microbe-derived secondary bile acids, which inhibit C. difficile germination and growth. SER-109, an investigational microbiome drug of donor-derived, purified spores, reduced recurrence in a dose-ranging, phase (P) 1 study in subjects with multiple rCDIs. Methods In a P2 double-blind trial, subjects with clinical resolution on standard-of-care antibiotics were stratified by age (< or ≥65 years) and randomized 2:1 to single-dose SER-109 or placebo. Subjects were diagnosed at study entry by PCR or toxin testing. Safety, C. difficile–positive diarrhea through week 8, SER-109 engraftment, and bile acid changes were assessed. Results 89 subjects enrolled (67% female; 80.9% diagnosed by PCR). rCDI rates were lower in the SER-109 arm than placebo (44.1% vs 53.3%) but did not meet statistical significance. In a preplanned analysis, rates were reduced among subjects ≥65 years (45.2% vs 80%, respectively; RR, 1.77; 95% CI, 1.11–2.81), while the <65 group showed no benefit. Early engraftment of SER-109 was associated with nonrecurrence (P <.05) and increased secondary bile acid concentrations (P <.0001). Whole-metagenomic sequencing from this study and the P1 study revealed previously unappreciated dose-dependent engraftment kinetics and confirmed an association between early engraftment and nonrecurrence. Engraftment kinetics suggest that P2 dosing was suboptimal. Adverse events were generally mild to moderate in severity. Conclusions Early SER-109 engraftment was associated with reduced CDI recurrence and favorable safety was observed. A higher dose of SER-109 and requirements for toxin testing were implemented in the current P3 trial. Clinical Trials Registration NCT02437487, https://clinicaltrials.gov/ct2/show/NCT02437487?term=SER-109&draw= 2&rank=4. [ABSTRACT FROM AUTHOR]

Published
2021
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37. War made new

Author

Winkler, Jonathan

Subjects
Technology, Warfare and the Course of History, 1500 to Today (Nonfiction work) -- Boot, Max -- Book reviews, Books -- Book reviews, International relations
Abstract

Technology, Warfare and the Course of History, 1500 to Today Max Boot New York: Gotham Books, 2006. 640pp, US$35.00 cloth ISBN 1-592-40222-4 This is a sweeping and ambitious book that [...]

Published
2009

39. Information Warfare in World War I.

Author

Winkler, Jonathan Reed

Subjects
*INFORMATION warfare, *MILITARY communications, *MILITARY intelligence, *MILITARY strategy, *WORLD War I, 20TH century British military history, 20TH century German military history
Abstract

Traditional narratives of World War I generally overlook a misunderstood but important part of the conflict: information warfare. Both Great Britain and Germany understood the significance of information as a force multiplier and as a valuable financial and diplomatic tool in the larger geostrategic environment. Britain's systematic wartime destruction of Germany's prewar network occurred on a much larger level than historians have recognized. Germany's simultaneous but hidden campaign against Allied communications has escaped historical notice. Greater understanding of this missing element, both in World War I and beyond, will deepen our understanding of the larger economic, political, intelligence, and military dimensions of modern conflict. [ABSTRACT FROM AUTHOR]

Published
2009
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43. Nexus

Author

Winkler, Jonathan Reed and Winkler, Jonathan Reed

Published
2009

46. A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents RecurrentClostridium difficileInfection

Author

Khanna, Sahil, primary, Pardi, Darrell S., additional, Kelly, Colleen R., additional, Kraft, Colleen S., additional, Dhere, Tanvi, additional, Henn, Matthew R., additional, Lombardo, Mary-Jane, additional, Vulic, Marin, additional, Ohsumi, Toshiro, additional, Winkler, Jonathan, additional, Pindar, Christina, additional, McGovern, Barbara H., additional, Pomerantz, Roger J., additional, Aunins, John G., additional, Cook, David N., additional, and Hohmann, Elizabeth L., additional

Published
2016
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