PPT-CSC 589 Lecture 22 Image Alignment and least square methods

Bei Xiao American University April 13 Final project Due May 4 th The final websites will be shared among students Presentations will be recorded as a 5 mins youtube video We will learn how to do this . Image from http://graphics.cs.cmu.edu/courses/15-463/2010_fall/. A look into the past. http://blog.flickr.net/en/2010/01/27/a-look-into-the-past/. A look into the past. Leningrad during the blockade. CS/. BioE. 598. Tandy Warnow. Alignment Error/Accuracy. SP-FN: percentage of homologies in the true alignment that are *not* recovered. SP-FP: percentage of homologies in the estimated alignment that are false. Image from http://graphics.cs.cmu.edu/courses/15-463/2010_fall/. Robust feature-based alignment. So far, we’ve assumed that we are given a set of “ground-truth” correspondences between the two images we want to align. Undersampled. Dithered Stars. Guoliang Li & Lei Wang. Purple Mountain . Observatoy. Classic Methods. 1.Interlace. 2.shift-and-add. 3.Drizzle. Convolution effects. The original image is a Gaussian profile with sigma=1.5, i.e., FWHM~4 pixels (black line).. Dilip. . Krishnan. Depth Qualifying Examination Presentation . Sep 13, 2010. TexPoint fonts used in EMF. . Read the TexPoint manual before you delete this box.: . A. A. A. A. A. A. A. A. Overview of Talk. Image from http://graphics.cs.cmu.edu/courses/15-463/2010_fall/. A look into the past. http://blog.flickr.net/en/2010/01/27/a-look-into-the-past/. A look into the past. Leningrad during the blockade. Tandy . Warnow. Multiple Sequence Alignment (MSA): . another grand challenge. 1. S1 = -AGGCTATCACCTGACCTCCA. S2 = TAG-CTATCAC--GACCGC--. S3 = TAG-CT-------GACCGC--. …. Sn. = -------TCAC--GACCGACA. Guoliang Li & Lei Wang. Purple Mountain . Observatoy. Classic Methods. 1.Interlace. 2.shift-and-add. 3.Drizzle. Convolution effects. The original image is a Gaussian profile with sigma=1.5, i.e., FWHM~4 pixels (black line).. Tandy . Warnow. Studies we will discuss. Katoh. and . Standley. , MBE 2013 (about MAFFT). Nelesen. et al., PSB 2008 (Impact of guide tree). Liu and Warnow, . PLoS. ONE 2012 (about treelength criteria). Tandy . Warnow. Joint with Mike . Nute. and Ehsan Saleh. https://. www.biorxiv.org. /content/early/2018/04/20/304659. Performance Study on bioRxiv . Goal: Evaluate . Bali-Phy. (Redelings and Suchard) on both biological and simulated datasets, in comparison to leading alignment methods on small protein sequence datasets . Andrea . Bertozzi. University of California, Los Angeles. Diffuse interface methods. Ginzburg-Landau functional. Total variation. W is a double well potential with two minima. Total variation measures length of boundary between two constant regions.. Applications. Genome sequencing on the rise. Whole genome comparison provides a deeper understanding of biology. Evolutionary history. Non-coding regions. Variant detection. Methods. General two-fold approach. 1. Today we will.... Learn how combinations of lenses form images. Thin lens equation & magnification. Learn about the compound microscope. Eyepiece & objective . Total magnification. Learn about limits to resolution. and . Metagenomics. Tandy Warnow. The Department of Computer Science. The University of Texas at Austin. The “Tree of Life”. Applications of phylogenies to:. . protein structure and function. .