A sequence based genetic algorithm with local search for the travelling salesman problem

The standard Genetic Algorithm often suffers from slow convergence for solving combinatorial optimization problems. In this study, we present a sequence based genetic algorithm (SBGA) for the symmetric travelling salesman problem (TSP). In our proposed method, a set of sequences are extracted from the best individuals, which are used to guide the search of SBGA. Additionally, some procedures are applied to maintain the diversity by breaking the selected sequences into sub tours if the best individual of the population does not improve. SBGA is compared with the inver-over operator, a state-of-the-art algorithm for the TSP, on a set of benchmark TSPs. Experimental results show that the convergence speed of SBGA is very promising and much faster than that of the inver-over algorithm and that SBGA achieves a similar solution quality on all test TSPs

Learning to Prune: Speeding up Repeated Computations

It is common to encounter situations where one must solve a sequence of similar computational problems. Running a standard algorithm with worst-case runtime guarantees on each instance will fail to take advantage of valuable structure shared across the problem instances. For example, when a commuter drives from work to home, there are typically only a handful of routes that will ever be the shortest path. A naive algorithm that does not exploit this common structure may spend most of its time checking roads that will never be in the shortest path. More generally, we can often ignore large swaths of the search space that will likely never contain an optimal solution. We present an algorithm that learns to maximally prune the search space on repeated computations, thereby reducing runtime while provably outputting the correct solution each period with high probability. Our algorithm employs a simple explore-exploit technique resembling those used in online algorithms, though our setting is quite different. We prove that, with respect to our model of pruning search spaces, our approach is optimal up to constant factors. Finally, we illustrate the applicability of our model and algorithm to three classic problems: shortest-path routing, string search, and linear programming. We present experiments confirming that our simple algorithm is effective at significantly reducing the runtime of solving repeated computations

A hybrid genetic algorithm and inver over approach for the travelling salesman problem

This article posted here with permission of the IEEE - Copyright @ 2010 IEEEThis paper proposes a two-phase hybrid approach for the travelling salesman problem (TSP). The first phase is based on a sequence based genetic algorithm (SBGA) with an embedded local search scheme. Within the SBGA, a memory is introduced to store good sequences (sub-tours) extracted from previous good solutions and the stored sequences are used to guide the generation of offspring via local search during the evolution of the population. Additionally, we also apply some techniques to adapt the key parameters based on whether the best individual of the population improves or not and maintain the diversity. After SBGA finishes, the hybrid approach enters the second phase, where the inver over (IO) operator, which is a state-of-the-art algorithm for the TSP, is used to further improve the solution quality of the population. Experiments are carried out to investigate the performance of the proposed hybrid approach in comparison with several relevant algorithms on a set of benchmark TSP instances. The experimental results show that the proposed hybrid approach is efficient in finding good quality solutions for the test TSPs.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of the United Kingdom under Grant EP/E060722/1

On the Greedy Algorithm for the Shortest Common Superstring Problem with Reversals

We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem Shortest Common Superstring with Reversals (SCS-R). This problem has been introduced by Jiang et al., who designed a greedy-like algorithm with length approximation ratio $4$. In this paper, we show that a natural adaptation of the classical greedy algorithm for SCS has (optimal) compression ratio $\frac12$, i.e., the sum of the overlaps in the output string is at least half the sum of the overlaps in an optimal solution. We also provide a linear-time implementation of our algorithm.Comment: Published in Information Processing Letter

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs. Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the unitigs against a reference genome. By applying the method on 35-fold human resequencing data, we showed that in comparison to the standard pipeline, our approach yields similar accuracy for SNP calling and better results for INDEL calling. It has higher sensitivity than other de novo assembly based methods for variant calling. Our work suggests that variant calling with de novo assembly be a beneficial complement to the standard variant calling pipeline for whole-genome resequencing. In the methodological aspects, we proposed FMD-index for forward-backward extension of DNA sequences, a fast algorithm for finding all super-maximal exact matches and one-pass construction of unitigs from an FMD-index. Availability: http://github.com/lh3/fermi Contact: [email protected]: Rev2: submitted version with minor improvements; 7 page

Optimal Assembly for High Throughput Shotgun Sequencing

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the shotgun sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.Comment: 26 pages, 18 figure