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Events for February 14, 2014
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AI Seminar-Fabio Rinaldi:
Fri, Feb 14, 2014 @ 11:00 AM - 12:00 PM
Information Sciences Institute
Conferences, Lectures, & Seminars
Speaker: Fabio Rinaldi, Senior Researcher, Lecturer, and PI at the University of Zurich, Switzerland
Talk Title: OntoGene & SASEBio: biomedical text mining research at UZH
Series: AISeminar
Abstract: There are vast amounts of knowledge encoded in the scientific literature which could be made more easily accessible and useful to a broader range of users through the application of more effective software tools. Text mining is a new discipline which seeks to provide ways to find, extract and manipulate the knowledge which still remains to a large extent hidden in the literature.
Text mining tools can already provide a very effective way to extract some specific types of information, but are not yet so advanced that their results can be used without human verification by domain experts. Therefore one very promising area of application of text mining technologies is within the process of database curation.
The need to efficiently retrieve key information derived from experimental results, and published in the scientific literature, is of fundamental importance in biology. In order to help biologists, as well as in some cases medical practitioners, to efficiently find such
information in the enormous quantity of published articles, several public and private institutions fund the construction and maintenance of specialized databases, which have the role to collect specific knowledge items and provide them in an easily accessible format. There are several dozens of such databases, each specializing in a
particular domain of the life sciences [1].
In this talk I will describe text mining activities conducted by my research group at the University of Zurich (OntoGene: www.ontogene.org). The OntoGene group is supported by the Swiss National Science Foundation (project SASEBIO: Semi-Automated Semantic
Enrichment of the Biomedical Literature) and by Roche Pharmaceuticals. The SASEBio project focuses in particular on applications of text mining technologies to the process of biomedical database curation.
The OntoGene team has participated in several competitive evaluations of biomedical text mining technologies, obtaining competitive results in all of them. Some of these results will be discussed in the talk. Additionally, I will present ODIN (OntoGene Document Inspector), an interactive tool which allows database curators to leverage upon the results of the OntoGene text mining system and use them in their
curation tasks.
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[1] Xose M. Fernandez-Suarez, Daniel J. Rigden, and Michael Y. Galperin. The 2014 nucleic acids research database issue and an updated NAR online molecular biology database collection. Nucleic Acids Research, 42(D1):D1-D6, 2014
The OntoGene text mining system is based on a scalable entity recognition component with a semi-automated organism-based disambiguation module, an in-house dependency parser, and a flexible relation mining approach. The OntoGene team has participated in several biomedical text mining challenges (BioCreative, BioNLP,
CALBC), obtaining competitive results in all of them. Some of these results will be discussed in the talk.
The OntoGene Document Inspector (ODIN) is an interactive tool which allows database curators to leverage upon the results of the OntoGene text mining system and use them in their curation tasks. One recent version of the system has been tested in the curation process of the Pharmacogenomics Knowledge Base (PharmGKB), and another version
adapted for the Comparative Toxicogenomics Database in the context of
a BioCreative challenge.
Biography: Fabio Rinaldi is the leader of the OntoGene research group at the University of Zurich and the principal investigator of the SASEBio project. He holds an MSc in Computer Science (University of Udine, Italy) and a PhD in Computational Linguistics (University of Zurich, Switzerland). He is author of more than 100 scientific publications (including 19 journal papers) dealing with topics such as Ontologies, Text Mining, Text Classification, Document and Knowledge Management, Language Resources and Terminology.
Host: David Chiang
Webcast: http://webcasterms1.isi.edu/mediasite/Viewer/?peid=7bf4d5a5d7404d249254a2b96006ea6e1dLocation: Information Science Institute (ISI) - 11th fl Large CR
WebCast Link: http://webcasterms1.isi.edu/mediasite/Viewer/?peid=7bf4d5a5d7404d249254a2b96006ea6e1d
Audiences: Everyone Is Invited
Contact: Alma Nava / Information Sciences Institute
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PhD Social Lunch
Fri, Feb 14, 2014 @ 12:00 PM - 01:30 PM
Thomas Lord Department of Computer Science
Receptions & Special Events
Location: Seaver Science Library (SSL) - 150
Audiences: Department Only
Contact: Assistant to CS chair
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Seminars in Biomedical Engineering
Fri, Feb 14, 2014 @ 12:30 PM - 01:50 PM
Alfred E. Mann Department of Biomedical Engineering
Conferences, Lectures, & Seminars
Speaker: Jungwoo Lee, Ph.D., Postdoctoral Research Fellow, Massachusetts General Hospital, Harvard Medical School
Talk Title: Enabling 3D Microenvironments for Bone Marrow Bioengineering
Abstract: Bone marrow, a sponge-like gelatinous and vascular tissue located at the inside of bone matrix is a vital part of human body as a major reservoir of adult stem cells, an exclusive site for hematopoiesis, and a key regulator of body homeostasis via continuous cellular trafficking. Bone marrow is also deeply involved in metastasis of many prominent tumors e.g. breast and prostate tumors as a direct metastatic target for disseminated circulating tumor cells and/or a potent instigator of their metastatic spread to other peripheral tissue sites. Therefore, in depth understanding of bone marrow biology is critical to advance many fields of modern medicine. However, probing the bone marrow microenvironments has been challenging because of its anatomical inaccessibility, tissue complexity and lack of relevant preclinical models. In this talk, I will introduce bioengineering strategies to develop functional and standardized bone marrow models based on 3D hydrogel scaffolds that closely emulate physical and anatomical features of the bone marrow in a controlled and reproducible manner. Specifically I will discuss development of in vitro and in vivo human bone marrow tissue analogues combining the 3D hydrogel scaffolds with primary human bone marrow stromal cells that recapitulate essential bone marrow functions with high analytical power. In the last part of my talk, I will introduce an exciting application of our in vivo bone marrow model for studying human prostate tumor metastasis with several enabling features. Biomimetic design of 3D hydrogel scaffolds coupled with a powerful set of material, microfluidic, imaging and cellular engineering tools offer unique opportunity to build functional and analytical preclinical bone marrow models for studying many complex, dynamic physiological and pathological processes in the bone marrow.
Biography: Jungwoo Lee received his Ph.D in Biomedical Engineering from the University of Michigan in 2009 under Prof. Nicholas Kotov. He then joined the Center for Engineering in Medicine at Harvard Medical School and Massachusetts General Hospital as a postdoctoral research fellow. Currently Jungwoo is a NIH Pathway to Independence (K99/R00) fellow from National Cancer Institute. He has authored and co-authored over 24 papers in PNAS, Nature Materials, Biomaterials, Small and other major research journals, and has won several honors and awards including Postdoctoral Fellowship from Shriners Hospital for Children, Poster Distinction Award from Annual MGH Research Symposium, Selection of "Cell Biology 2010" from ASCB Annual meeting, 1st Place in Entrepreneurial Challenging from MRS meeting, Distinguished Achievement Award from Univ. Michigan, and Horace H. Rackham Predoctoral Fellowship. His research has focused on developing preclinical in vitro and in vivo human bone marrow models that can be used in a diverse range of bone marrow related fundamental and translational studies.
Host: David D'Argenio
Location: Olin Hall of Engineering (OHE) - 100C
Audiences: Everyone Is Invited
Contact: Mischalgrace Diasanta
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The W.V.T. Rusch Engineering Honors Colloquim
Fri, Feb 14, 2014 @ 01:00 PM - 01:50 PM
USC Viterbi School of Engineering, Viterbi School of Engineering Student Affairs
Conferences, Lectures, & Seminars
Speaker: Dr. Andrea M. Armani, Assistant Professor and Fluor Early Career Chair of Engineering, USC
Talk Title: Maximizing Sensitivity While Miniaturizing Sensors: The Future of Integrated Devices
Host: W.V.T. Rusch Engineering Honors Program
Location: Seeley G. Mudd Building (SGM) - 101
Audiences: Everyone Is Invited
Contact: Christine Viterbi Admission & Student Affairs
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NL Seminar- Hal Daume: "Predicting Linguistic Structures Accurately and Efficiently"
Fri, Feb 14, 2014 @ 03:00 PM - 04:00 PM
Information Sciences Institute
Conferences, Lectures, & Seminars
Speaker: Hal Daume, University of Maryland
Talk Title: "Predicting Linguistic Structures Accurately and Efficiently"
Series: Natural Language Seminar
Abstract: Many classic problems in natural language processing can be cast as building mapping from a complex input (e.g., a sequence of words) to a complex output (e.g., a syntax tree or semantic graph). This task is challenging both because language is ambiguous (learning difficulties) and represented with discrete combinatorial structures (computational difficulties). Often these are at odds: the features you want to add to decrease learning difficulties cause nontrivial additional structure yielding worse computational difficulties.
I will begin by discussing algorithms that side-step the issue of combinatorial blowup and aim to predict an output structure directly. I will then present approaches that explicitly learn to trade-off accuracy and efficiency, applied to a variety of linguistic phenomena. Moreover, I will show that in some cases, we can actually obtain a model that is faster and more accurate by exploiting smarter learning algorithms.
Biography: http://www.umiacs.umd.edu/~hal/
Host: Yang Gao
More Info: http://nlg.isi.edu/nl-seminar/
Location: Information Science Institute (ISI) - 11th Flr Conf Rm # 1135, Marina Del Rey
Audiences: Everyone Is Invited
Contact: Peter Zamar
Event Link: http://nlg.isi.edu/nl-seminar/
