Workshop Mathematical Models for Prediction and Control of Epidemics (Virtual Workshop)

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Aug 13, 2020
Thursday

10:45 AM - 11:15 AM

Bayesian Approaches to the heterogeneity in the Covid-19 original R_0 coefficient
Susan Holmes (Stanford University)

October 24, 2007 - October 26, 2007

Workshop Mathematical Systems Biology of Cancer II

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Oct 24, 2007
Wednesday

04:15 PM - 05:00 PM		New in situ data for the analysis of interactions between cancer and the immune system in auxillary lymph nodes Susan Holmes (Stanford University)
Location -- Video -- Abstract Recent work (Kohrt et al, 2005) has shown that T cell profiles in lymph nodes are much more accurate predictors of cancer survival in breast cancer than tumor size. In order to extend this preliminary staudy on 76 patients to a very large cohort, we needed to collect large amount of data on stained images. We have built {GemIdent: http://www.gemident.com}} a novel object identification algorithm in Java to locate immune and cancer cells in images of immunohistochemically-stained lymph node tissue from the Kohrt study and also shows promise in other domains. Our method leans heavily on the use of color and the relative homogeneity of object appearance. As is often the case in segmentation, an algorithm specifically tailored to the application works better than using broader methods that work passably well on any problem. Our main innovation is interactive feature extraction from color images. We also enable the user to improve the classification with an interactive visualization system. This is then oupled with the statistical learning algorithms and intensive interaction with the user over many classification-correction iterations, resulting in a highly accurate and user-friendly solution. At the web site we have made available both a detailed manual, movies showing the various stages of analyses and the code as well as the documented source code available to academics. Kohrt, H.~E., N.~Nouri, K.~Nowels, D.~Johnson, S.~Holmes, and P.~P. Lee, 2005: Profile of immune cells in axillary lymph nodes predicts disease-free survival in breast cancer. {\em PLoS Med\/}, {\bf 2(9)}, e284. Kapelner, A., P.~Lee, and S.~Holmes, 2007: An interactive statistical image segmentation and visualization system. {\em Medivis\/}, {\bf 00}, 81--86. Supplements -- Show Detail

September 18, 2006 - September 22, 2006

Workshop Workshop on Application of Topology in Science and Engineering

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Sep 19, 2006
Tuesday

09:00 AM - 10:00 AM		Genes in Codon Space Susan Holmes (Stanford University)
Location MSRI: Simons Auditorium Video Abstract -- Supplements -- Show Detail

September 05, 2006 - September 08, 2006

Workshop Introductory Workshop on Computational Application of Algebraic Topology

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Sep 06, 2006
Wednesday

04:00 PM - 05:00 PM		Horseshoes and Spectral Methods for Detecting Hidden Variables Susan Holmes (Stanford University)
Location MSRI: Simons Auditorium Video Abstract -- Supplements -- Show Detail

April 18, 2005 - April 22, 2005

Workshop Models of Real-World Random Networks

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Apr 18, 2005
Monday

02:50 PM - 03:20 PM		Multivariate Techniques for using Graph Structure and Covariates. Susan Holmes (Stanford University)
Location MSRI: Simons Auditorium Video Abstract -- Supplements -- Show Detail

December 09, 2004 - December 13, 2004

Workshop HOT TOPICS: Mathematical and Statistical Methods for Visualization and Analysis of High Dimensional Data

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Dec 09, 2004
Thursday

11:30 AM - 12:30 PM		Eigenspace Decompositions for Graphs. Susan Holmes (Stanford University)
Location MSRI: Simons Auditorium Video Abstract -- Supplements -- Show Detail