Modelling and Performance analysis of a Network of Chemical Sensors with Dynamic Collaboration

The problem of environmental monitoring using a wireless network of chemical sensors with a limited energy supply is considered. Since the conventional chemical sensors in active mode consume vast amounts of energy, an optimisation problem arises in the context of a balance between the energy consumption and the detection capabilities of such a network. A protocol based on "dynamic sensor collaboration" is employed: in the absence of any pollutant, majority of sensors are in the sleep (passive) mode; a sensor is invoked (activated) by wake-up messages from its neighbors only when more information is required. The paper proposes a mathematical model of a network of chemical sensors using this protocol. The model provides valuable insights into the network behavior and near optimal capacity design (energy consumption against detection). An analytical model of the environment, using turbulent mixing to capture chaotic fluctuations, intermittency and non-homogeneity of the pollutant distribution, is employed in the study. A binary model of a chemical sensor is assumed (a device with threshold detection). The outcome of the study is a set of simple analytical tools for sensor network design, optimisation, and performance analysis.Comment: 21 pages and 7 figure

A Large Scale Analysis of Information-Theoretic Network Complexity Measures Using Chemical Structures

This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based) complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University

Improving classification performance of microarray analysis by feature selection and feature extraction methods

In this study, we compared two feature extraction methods (PCA, PLS) and seven feature selection methods (mRMR and its variations, MaxRel, QPFS) on four different classifiers (SVM, RF, KNN, NN). We use ratio comparison validation for PCA method and 10-folds cross validation method for both the feature extraction and feature selection methods. We use Leukemia data set and Colon data set to apply the combinations and measured accuracy as well as area under ROC. The results illustrated that feature selection and extraction methods can both somehow improve the performance of classification tasks on microarray data sets. Some combinations of classifier and feature preprocessing method can greatly improve the accuracy as well as the AUC value are given in this study.Master of Science (MSc) in Computational Science