Michelle A Ragle

University of Florida | UF · Department of Industrial and Systems Engineering

The selection of probe sets for hybridization experiments directly affects the efficiency and cost of the analysis. We propose the application of the Asynchronous Team (A-Team) technique to determine near-optimal probe sets. An A-Team is comprised of several different heuristic algorithms that communicate with each other via shared memories. The A-...

Keywords Introduction Organization Idiosyncrasies Formulation Methods Review of Solution Approaches Semidefinite Programming Model Conclusion See also References

The non-unique probe selection problem consists of selecting oligonucleotide probes for use in hybridization experiments in which target viruses or bacteria are to be identified in biological samples. The presence or absence of these targets is determined by observing whether selected probes bind to their corresponding sequences. The goal is to sel...

Adverse drug reactions (ADRs) are estimated to be one of the leading causes of death. Many national and international agencies have set up databases of ADR reports for the express purpose of determining the relationship between drugs and adverse reac-tions that they cause. We formulate the drug-reaction relationship problem as a continuous optimiza...

Identification of biological agents in a sample is a relevant problem in medicine. A model to this problem consists of selecting optimal oligonucleotide probe sets for use in hybridization experiments in which target viruses or bacteria are to be identified in biological samples. In such an experiment the presence or absence of these targets is det...

Data analysis often requires the unsupervised partitioning of the data set into clusters. Clustering data is an important but a difficult problem. In the absence of prior knowledge about the shape of the clusters, similarity measures for a clustering technique are hard to specify. In this work, we propose a framework that learns from the structure...