J. Redstone. Algorithms for ordering DNA probes on chromosomes, 1996. Ph.D. Qualifying Exam paper. Department of Computer Science, University of Washington. 16 Home/Search Document Details and Download
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Probe Location in the Presence of Errors: A Problem from DNA Mapping - Mumey (1999) (Correct)
....on separation distance intervals estimated from fluorescence in situ hybridization (FISH) experiments 1 . As the problem is too big to solve by hand, some previous algorithmic approaches include: a seriation algorithm [2] a simulated annealing approach [6] and a branch and bound algorithm [7]. Due to their exhaustive nature, these methods are limited to problems with about 20 1 A FISH experiment measures the physical distance (on a microscope slide) between pairs of fluorescently marked probes hybridized to an interphase chromosome [9,8] For genomic distances of up to about 1 2 ....
J. Redstone. Algorithms for ordering DNA probes on chromosomes, 1996. Ph.D. Qualifying Exam paper. Department of Computer Science, University of Washington. 16
Algorithms for a Simple Point Placement Problem - Redstone, Ruzzo Self-citation (Redstone Ruzzo) (Correct)
....desirable properties, like being unbiased maximum likelihood estimators. Even though the error distribution in our motivating problem violated these assumptions, choosing weights inversely proportional to the variances substantially improved the solution quality (and speed) of our algorithms; see [9]. 3.1 Finding Least Squares Solutions for a Fixed Ordering One standard approach to solving a least squares problem is to take the partial derivatives of the cost with respect to each of the x i s, set them equal to 0, and solve. Unfortunately, our cost function is not differentiable due to the ....
....solution is encountered. Instead we first run the local search algorithm from a few random starting orderings. Empirically, this will quickly locate a good solution, facilitating good pruning from the beginning. In our experiments, branch and bound removes 100 1000 times as many nodes as a result [9]. There is one remaining detail to be specified we need to modify the construction of the M of Equation 5. As it stands, the linear system Mx = r of Section 3.1 is underconstrained (the rank of the null space of M is non zero) Because the system is constructed from relative orderings between ....
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Joshua Redstone and Walter L. Ruzzo. Algorithms for ordering DNA probes on chromosomes. Technical Report UW-CSE-98-12-04, Department of Computer Science and Engineering, University of Washington, December 1998.
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