Jonas Almeida, PhD, Professor and Chief Technology Officer, Department of Biomedical Informatics, Stony Brook University (SUNY), “Data Science for Biomedical Informatics in the Planet of the Apps” at 11:00 am on Thursday, November 30, 2017, in Rooms 407A/B BAUM, 5607 Baum Blvd., at the Offices at Baum.
Abstract: As in all new fields of academic inquiry, Data Science starts with an identity crisis. So, what’s new about the way Data Science derives from Computer Science, Biostatistics and Genomic Atlases? Does the deployment of interoperable Data Spaces from Genomic Data Commons to HL7 FHIR, the commoditization of Cloud Computing, or the optimized classification with Machine Learning, fundamentally contribute to answering important questions? What about Precision Medicine, does Data Science even play a role in that translation beyond being a toolbox? This discussion will be illustrated with examples* of how Data Science already contributes to some of these endeavors, and how it could for many others, as it matures into a quantitative framework that is both pervasive and participated. It will be argued, and illustrated with published work, that Data Science opens a number of novel avenues in quantitative research that go beyond its immediate applications to the delivery of HealthCare. Bring your laptop if you want to try the examples as they are presented.
Biography: In January 2015, Dr. Almeida accepted the new position of Professor and Chief Technology Officer at the Biomedical Informatics Department of Stony Brook University (State University of NY, Long Island). This follows 4 years as the inaugural director of a new Division in Informatics in the Department of Pathology of the University of Alabama at Birmingham (UAB), and 5 years as Professor of Bioinformatics in the Division of Applied Mathematics of the University of Texas MDAnderson Cancer Center (2005-2010).
His current research interests are at the intersection of Semantic Web abstractions and distributed Cloud Computing approaches to Bioinformatics application development in the pervasive Web Platform. The use of computational statistics at the intersection of those two fields now gets a fancy new name, Big Data Science, which is also the focus of his educational and service activities. This research pulls together threads from past, and ongoing, work on mathematical modeling and machine learning for Medical Genomics, at a time when these fields are challenged by the increasingly data driven nature of modern Biomedical research. In his own work this has often focused on The Cancer Genome Atlas (TCGA), a Biomedical Big Data resource that enables, and requires, this new synthesis for the development of Personalized Medicine applications. As Population Health data becomes available in real-time (see for example http://bit.ly/pqiSuffolk), the opportunities for pursuing Machine Learning as a pervasive Web Computing exercise are emerging, with a new avenues for research in Artificial Intelligence applications embedded in the increasingly patient-facing Health-Care enterprise.
Professor and Willett Faculty Scholar, Department of Computer Science, University of Illinois, “Statistical Approaches to Analysis of Traditional Chinese Medicine Practice Records” at 11:00 am on Thursday, May 18, 2017, in Rooms 407A/B BAUM, 5607 Baum Blvd., The Offices at Baum.
Abstract: Traditional Chinese Medicine (TCM) can provide important complementary medical care to modern medicine, and is widely practiced in China and many other countries. Recently, TCM patient records have been digitalized, leading to a large number of online patient records. The data contains potentially valuable knowledge about diagnosis and treatment of various diseases using the TCM methodology and thus creates an interesting opportunity to apply data mining techniques to extract such knowledge. In this talk, I will present some of our recent work on using statistical approaches to analyze TCM patient records for disease profiling, disease subcategorization, and survival analysis. In disease profiling, we propose a new probabilistic model for the joint analysis of symptoms, diagnoses, and herbs in patient records to discover the typical symptoms and typical herbs associated with different diseases. In disease subcategorization, we study how to cluster patient records to discover subcategories of diseases and show that we can use machine learning to leverage the knowledge in a TCM dictionary of herb functions for improving the accuracy of subcategorization. In survival analysis, we cluster lung cancer patients and compare the survival time of different clusters of patients and show that integration of medical records with molecular interaction networks and TCM knowledge graph is effective for addressing the problem of missing data in the medical records. The experimental results on multiple TCM patient data sets show the benefit of integrating medical records with other biomedical knowledge bases and the promise of leveraging TCM patient records for improving precision medicine.
Biography: ChengXiang Zhai is a Professor of Computer Science and a Willett Faculty Scholar at the University of Illinois at Urbana-Champaign (UIUC), where he is also affiliated with the Institute for Genomic Biology, Department of Statistics, and School of Information Sciences. He received a Ph.D. in Computer Science from Nanjing University in 1990, and a Ph.D. in Language and Information Technologies from Carnegie Mellon University in 2002. He worked at Clairvoyance Corp. as a Research Scientist and a Senior Research Scientist from 1997 to 2000. His research interests are in the general area of intelligent information systems, including specifically information retrieval, data mining, and their applications in biomedical and health informatics, and intelligent education systems. He has published over 200 papers in these areas with high citations, and a textbook on text data management and analysis. He is an Editor-in-Chief of Springer’s Information Retrieval Book Series and an Associate Editor of BMC Medical Informatics and Decision Making, and previously served as an Associate Editor of ACM Transactions on Information Systems, Associate Editor of Elsevier’s Information Processing and Management. He is an ACM Distinguished Scientist, and received a number of awards, including Association for Computing Machinery SIGIR Test of Time Paper Award (three times), the 2004 Presidential Early Career Award for Scientists and Engineers (PECASE), an Alfred P. Sloan Research Fellowship, IBM Faculty Award, HP Innovation Research Award, and UIUC Campus Award for Excellence in Graduate Student Mentoring.
Professor and Chair, Department of Statistics, University of Washington, “Nested Markov Models” at 11:00 am on Thursday, April 20, 2017, in Rooms 407A/B BAUM, 5607 Baum Blvd., The Offices at Baum.
Abstract: Directed acyclic graph (DAG) models may be characterized in several different ways: via a factorization, via d-separation or a local Markov property. It has been known for a long time that marginals of DAG models also imply equality constraints that are not conditional independences. The well-known ‘Verma constraint’ is an example.
In this talk, we will show that equality constraints of this type can be viewed as conditional independences in kernel objects obtained from joint distributions via a fixing operation that generalizes conditioning and marginalization. We use these constraints to define, a graphical model, called the “nested Markov model”, that is associated with acyclic directed mixed graphs (ADMGs).
Naturally associated with a DAG with latent variables, is an ADMG known as the “latent projection”. The nested Markov model associated with an ADMG is a (smooth) supermodel of the model associated with the original latent variable model. Nested Markov models thus constitute a natural class in which to perform causal model search.
This is joint work with Robin Evans (Oxford), James Robins (Harvard) and Ilya Shpitser (Johns Hopkins).
Biography: Dr. Richardson is Professor and Chair of the Department of Statistics. He is also an Adjunct Professor in the Departments of Economics and Electrical Engineering and a member of the eScience Steering Committee. He received his BA in Mathematics & Philosophy from the University of Oxford and his MS and PhD in Logic, Computation & Methodology from Carnegie Mellon University. He is a Fellow of the Center for Advanced Studies in the Behavioral Sciences at Stanford University. His research interests include Graphical Models and Causality.