Algorithmic approaches for the single individual haplotyping problem

Since its introduction in 2001, the Single Individual Haplotyping problem has received an ever-increasing attention from the scientific community. In this paper we survey, in the form of an annotated bibliography, the developments in the study of the problem from its origin until our days

Finding the Best 3-{OPT} Move in Subcubic Time

Given a Traveling Salesman Problem solution, the best 3-OPT move requires us to remove three edges and replace them with three new ones so as to shorten the tour as much as possible. No worst-case algorithm better than the \u398(n3 ) enumeration of all triples is likely to exist for this problem, but algorithms with average case O(n3 12\u25b ) are not ruled out. In this paper we describe a strategy for 3-OPT optimization which can find the best move by looking only at a fraction of all possible moves. We extend our approach also to some other types of cubic moves, such as some special 6-OPT and 5-OPT moves. Empirical evidence shows that our algorithm runs in average subcubic time (upper bounded by O(n2.5 )) on a wide class of random graphs as well as Traveling Salesman Problem Library (TSPLIB) instances

FASTSET: A Fast Data Structure for the Representation of Sets of Integers

We describe a simple data structure for storing subsets of { 0 ,..., N - 1 } , with N a given integer, which has optimal time performance for all the main set operations, whereas previous data structures are non-optimal for at least one such operation. We report on the comparison of a Java implementation of our structure with other structures of the standard Java Collections

Finding the largest triangle in a graph in expected quadratic time

Finding the largest triangle in an n-nodes edge-weighted graph belongs to a set of problems all equivalent under subcubic reductions. Namely, a truly subcubic algorithm for any one of them would imply that they are all subcubic. A recent strong conjecture states that none of them can be solved in less than \u398(n3) time, but this negative result does not rule out the possibility of algorithms with average, rather than worst-case, subcubic running time. Indeed, in this work we describe the first truly-subcubic average complexity procedure for this problem for graphs whose edge lengths are uniformly distributed in [0,1]. Our procedure finds the largest triangle in average quadratic time, which is the best possible complexity of any algorithm for this problem. We also give empirical evidence that the quadratic average complexity holds for many other random distributions of the edge lengths. A notable exception is when the lengths are distances between random points in Euclidean space, for which the algorithm takes average cubic time

The approximability of the String Barcoding problem

The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight