**DESCRIPTION OF COURSES**

**BI 524 TOOLS AND TECHNIQUES FOR BIOLOGICAL DATA MINING (2L+1P) I**

**Objective**

To understand various algorithms of machine learning approaches.

**Theory**

UNIT I

Quality of Biological Data & Data Accuracy; General issues regarding Biological Databases: Representation of errors due to (machines, 3D structural and sequence data of proteins and nucleic acid, Proteomics and Micro array data).

UNIT II

Optimization Techniques: Steepest Descent, Conjugate Gradient, Newton-Raphson, Simulated annealing in Biomolecular Structure Optimization; Genetic Algorithms: *Ab initio *methods for structure prediction; Lattice, SOM, etc., Information theory, entropy and relative entropy, Stochastic Grammars & natural languages processing techniques.

UNIT III

Clustering and Classification Algorithms: Hierarchical and non-hierarchical Clustering, K-Means clustering, Grid based clustering, Analysis of MD trajectories, Protein Array data Analysis.

UNIT IV

Dynamic Programming and application in bioinformatics: Sequence Alignments, Structure Alignments; Foundations for Machine learning Techniques: Hidden Markov Model, Neural Network, Bayesian modeling, The Cox-Jaynes Axiomes; Support Vector machine & Ant colony optimization: Multiple Sequence Alignments, Biomolecular Structure Prediction; Fuzzy logic system & application in bioinformatics; Introduction to WEKA package; Clustering and classifications, Protein Array data Analysis.

**Suggested Readings**

- Amaratunga, D. & Cabrera, J. 2004.
*Exploration and Analysis of DNA Microarray and Protein Array*. John Wiley. - Gupta, G. K. 2006.
*Introduction to Data Mining with Case Studies.*Prentice Hall of India, New Delhi. Han, J. and Kamber, M. 2006.*Data Mining: Concepts and Techniques.*Morgan Kaufman. - Hand, D., H. Mannila, P. Smyth. 2001.
*Principles of Data Mining.*Prentice Hall of India, New Delhi. - Klir, G. J. and Yuan Bo. 2002.
*Fuzzy sets and Fuzzy logic: Theory and Applications*Prentice Hall of India, New Delhi. - Lee, K. H. 2005.
*First Course on Fuzzy Theory and Applications.*Springer. - Mitra, S., Acharya, T. 2004.
*Data Mining: Multimedia, Soft Computing, and Bioinformatics.*John Wiley.