Local search for the generalized tree alignment problem

Monte-Carlo Tree Search for the Multiple Sequence Alignment Problem

The paper considers solving the multiple sequence alignment, a combinatorial challenge in computational biology, where several DNA RNA, or protein sequences are to be arranged for high similarity. The proposal applies randomized MonteCarlo tree search with nested rollouts and is able to improve the solution quality over time. Instead of learning the position of the letters, the approach learns ...

Approximation algorithms for constrained generalized tree alignment problem

In generalized tree alignment problem, we are given a set S of k biologically related sequences and we are interested in a minimum cost evolutionary tree for S. In many instances of this problem partial topology of the phylogenetic tree for S is known. In such instances, we would like to make use of this knowledge to restrict the tree topologies that we consider and construct a biologically rel...

Local Search Algorithms for the k-cardinality Tree Problem

the algorithm for solving the inverse numerical range problem

برد عددی ماتریس مربعی a را با w(a) نشان داده و به این صورت تعریف می کنیم w(a)={x8ax:x ?s1} ، که در آن s1 گوی واحد است. در سال 2009، راسل کاردن مساله برد عددی معکوس را به این صورت مطرح کرده است : برای نقطه z?w(a)، بردار x?s1 را به گونه ای می یابیم که z=x*ax، در این پایان نامه ، الگوریتمی برای حل مساله برد عددی معکوس ارانه می دهیم.

On local search for the generalized graph coloring problem

Given an edge-weighted graph and an integer k, the generalized graph coloring problem is the problem of partitioning the vertex set into k subsets so as to minimize the total weight of the edges that are included in a single subset. We recall a result on the equivalence between Karush–Kuhn–Tucker points for a quadratic programming formulation and local optima for the simple 5ip-neighborhood. We...