Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

Text Mining Biomedical Literature for Genomic Knowledge Discovery

The last decade has been marked by unprecedented growth in both the production of biomedical data and the amount of published literature discussing it. Almost every known or postulated piece of information pertaining to genes, proteins, and their role in biological processes is reported somewhere in the vast amount of published biomedical literature. We believe the ability to rapidly survey and analyze this literature and extract pertinent information constitutes a necessary step toward both the design and the interpretation of any large-scale experiment. Moreover, automated literature mining offers a yet untapped opportunity to integrate many fragments of information gathered by researchers from multiple fields of expertise into a complete picture exposing the interrelated roles of various genes, proteins, and chemical reactions in cells and organisms. In this thesis, we show that functional keywords in biomedical literature, particularly Medline, represent very valuable information and can be used to discover new genomic knowledge. To validate our claim we present an investigation into text mining biomedical literature to assist microarray data analysis, yeast gene function classification, and biomedical literature categorization. We conduct following studies: 1. We test sets of genes to discover common functional keywords among them and use these keywords to cluster them into groups; 2. We show that it is possible to link genes to diseases by an expert human interpretation of the functional keywords for the genes- none of these diseases are as yet mentioned in public databases; 3. By clustering genes based on commonality of functional keywords it is possible to group genes into meaningful clusters that reveal more information about their functions, link to diseases and roles in metabolism pathways; 4. Using extracted functional keywords, we are able to demonstrate that for yeast genes, we can make a better functional grouping of genes in comparison to available public microarray and phylogenetic databases; 5. We show an application of our approach to literature classification. Using functional keywords as features, we are able to extract epidemiological abstracts automatically from Medline with higher sensitivity and accuracy than a human expert.Ph.D.Committee Chair: Shamkant B. Navathe; Committee Co-Chair: Brian J. Ciliax; Committee Member: Ashwin Ram; Committee Member: Edward Omiecinski; Committee Member: Ray Dingledine; Committee Member: Venu Dasig

A Bayesian Approach to Learning Hidden Markov Model Topology with Applications to Biological Sequence Analysis

Hidden-Markov-Models (HMMs) are a widely and successfully used tool in statistical modeling and statistical pattern recognition. One fundamental problem in the application of HMMs is finding the underlying architecture or topology, particularly when there is no strong evidence from the application domain — e.g., when doing black box modeling. Topology is important with regard to good parameter estimates and with regard to performance: A model with “too many” states — and hence too many parameters — requires too much training data while an model with “not enough” states impedes the HMM from capturing subtle statistical patterns. We have developed a novel algorithm that, given sequence data originating from an ergodic process, infers an HMM, its topology and its parameters. We introduce a Bayesian approach

Faculty Publications and Creative Works 2003

Faculty Publications & Creative Works is an annual compendium of scholarly and creative activities of University of New Mexico faculty during the noted calendar year. It serves to illustrate the robust and active intellectual pursuits conducted by the faculty in support of teaching and research at UNM

Annual Report of the University, 2000-2001, Volumes 1-4

Message from the President Thank you for joining me in this look back over the past year at the University of New Mexico. It was a year filled with activity, accomplishment and challenge, and this is our opportunity to reflect back on that year. In 2000-2001 we engaged in a University-wide strategic planning process that called on the energies and talents of hundreds of individuals- faculty, staff, students and members of our broader community. The plan, which will be completed in Fall 2001, will serve as our roadmap for the future and will guide our efforts to capitalize on the opportunities and to meet the challenges of the next several years. This process has encouraged us to examine closely our mission and our values, who we are and what we aspire to become. It has given us reason to be proud of our past and cause to think seriously about how we must change in the future. While this was a year for looking ahead, it was also a year of significant accomplishment. For example, we launched a comprehensive set of programs designed to enrich the academic and social experiences of our undergraduate students. We began the implementation of Freshman Learning Communities where small cohorts of students study and learn together in a common set of courses under the guidance of a senior faculty scholar. We reorganized our advisement systems, we undertook the construction or renovation of student-centered facilities on campus, and we created new support systems to enhance student academic success. It was a year in which our support of faculty, staff and students was our highest priority. Through the support of the New Mexico Legislature, faculty and staff received significant salary increases. A new health benefits plan for graduate assistants was implemented. Our Staff as Students program enabled more than 40 staff members to obtain UNM degrees. And, a Center for Scholarship in Teaching and Learning was established to assist faculty in their efforts to develop more effective teaching skills. Finally, this was a year in which UNM dramatically expanded its role in the local community and throughout the state. Never before has the University been as active or as visible in meeting its public responsibility as it was in 2000-2001. From its active participation in economic development initiatives, to its involvement in K-12 educational improvement efforts, to its significant leadership role in health care delivery, UNM demonstrated its ability to help the state meet its most pressing social challenges. And, as UNM took on a more visible role in supporting the state\\u27s citizens, the support for UNM was returned in kind. This year, annual giving to the University rose to a record 35.3 million dollars, a 40% increase over just two years ago. All told, it has been a gratifying and successful year. However, we cannot allow our past accomplishments to mask the continued challenges facing this University. Neither will we allow these challenges to dominate our thinking and diminish out pride in what the University has achieved. So we will savor our successes and continue to move forward. As always, we thank you for sharing our dreams and for supporting the University of New Mexico. Sincerely, William C. Gordon, Presiden