CS395T (Spring, 2008)

start

Bill Press — 2008-05-07T12:39:42-04:00

Course Wiki from Spring, 2008, Semester CS 395T Computational Statistics with Application to Bioinformatics Course Information Department: The University of Texas at Austin, Department of Computer Sciences Instructor: Professor William H. Press Term: Spring, 2008 Unique#: 55899 Meets: MW 1:30 - 3:00 PM in PAR 201

lecturenotes:15:4

MEKA; RAGHU VARDHA REDDY — 2008-05-04T11:04:23-04:00

Lecture 15 Slide 4 More on Four Point Test top previous next

exam_times

Bill Press — 2008-04-30T16:33:26-04:00

Sign-up Page for Final Exams (Oral Interviews Sign up for your exam by editing this page and adding your name on the same line as the time of your choice. The interview should take between 20 and 30 minutes. Sample questions are “What can you tell me about X?” where “X” is one of the items listed under concepts here; or, “Tell me about your project.”

roc - created

RAMAKRISHNAN; SMRITI R. — 2008-04-30T00:27:45-04:00

A good introductory paper with considerations on generating ROC curves, from Tom Fawcett's ROC Convex Hull page. Note: There's a typo in his AUC algorithm, while computing the area of the last trapezoid (TPR = FPR = 1) --- RAMAKRISHNAN; SMRITI R. 2008/04/30 00:22

contributed

RAMAKRISHNAN; SMRITI R. — 2008-04-30T00:22:02-04:00

Contributed Pages This is where to link-in a new page on any topic related to the course. Group or individual term projects should link from projects rather than this page. If your contribution is directly related to a top page, then you should link from there instead of here.

datafiles

Bill Press — 2008-04-16T13:51:28-04:00

Here are links to data and code files used in examples in the lectures: Code Files (1 KB) MATLAB code for reading genestats.dat (1 KB) C++ code (NR3 style) for using IQagent from MATLAB (mex file) (15 KB) enhanced version of NR3's psplot.h (creates simple PostScript plots)

lecturenotes:top

Bill Press — 2008-04-14T17:21:18-04:00

Course Lecture Notes Lecture notes for individual lectures are linked from here. A “lecture” is not necessarily one class session, but is a logically linked set of slides. Class members are encouraged to edit the wiki pages of the individual slides to fill in missing steps, add explanation, add useful web links or references, etc. The results will become part of the “permanent” course web site.

lecturenotes:21:5

MEKA; RAGHU VARDHA REDDY — 2008-04-13T11:14:19-04:00

Lecture 21 Slide 5 top previous next

lecturenotes:20:more_on_sequence_alignment - created

Vijaya Raghavan Sindhu — 2008-04-11T19:37:51-04:00

Sequence Alignment We have seen Needleman-Wunsch algorithm to obtain sequence alignment of two sequences in class. This algorithm attempts to align every nucleotide in the given sequences, i.e it is achieves global alignment of the two input sequences.

lecturenotes:20:17

Vijaya Raghavan Sindhu — 2008-04-11T19:27:11-04:00

Lecture 20 Slide 17 More on sequence alignment top previous next

lecturenotes:15:more_tools_to_perform_cluster_analysis_of_microarray_data - created

Vijaya Raghavan Sindhu — 2008-04-11T11:41:18-04:00

Here are some tools that can used to perform clustering on micro array data Machaon Clustering and Validation Environment- Cluster - Maple Tree - A java based program to view the results of clustering

lecturenotes:15:16

Vijaya Raghavan Sindhu — 2008-04-11T11:37:58-04:00

Lecture 15 Slide 16 More tools to perform cluster analysis of microarray data top previous next

lecturenotes:15:more_on_four_point_test - created

Vijaya Raghavan Sindhu — 2008-04-11T11:31:41-04:00

Four Point Test Consider the following tree. It is an unrooted tree. A matrix D is additive if and only if for every four indices i,j,k,l, the maximum and median of the three pairwise sums are identical: Dij+Dkl < Dik+Djl = Dil+Djk Let us find the pairwise distances between the four leaf nodes in the tree above.