Heuristics for the inversion median problem

Background: The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three gene arrangements, find a fourth that minimizes the sum of the evolutionary distances between itself and the given three. Many exact algorithms and heuristics have been developped for the inversion median problem, of which the best known is MGR. Results: We present a unifying framework for median heuristics, which enables us to clarify existing strategies and to place them in a partial ordering. Analysis of this framework leads to a new insight: the best strategies continue to refer to the input data rather than just to updated estimates. Using this insight, we develop a new heuristic for inversion medians that uses input data to the end of its computation and leverages our previous work with DCJ medians. Finally, we present the results of extensive experimentation showing that our new heuristic outperforms all others in accuracy and, especially, in running time: the heuristic typically returns solutions within 1 % of optimal and runs in seconds to minutes even on genomes with 25’000 genes—in contrast, MGR can take days on instances of 200 genes and cannot be used beyond 1’000 genes. Conclusions: Finding good rearrangement medians, in particular inversion medians, had long been regarded as the computational bottleneck in whole-genome studies. Our new heuristic for inversion medians, ASM, which dominates all others in our framework, puts that issue to rest by providing near-optimal solutions within seconds to minutes on even the largest genomes

Average-Case Complexity

We survey the average-case complexity of problems in NP. We discuss various notions of good-on-average algorithms, and present completeness results due to Impagliazzo and Levin. Such completeness results establish the fact that if a certain specific (but somewhat artificial) NP problem is easy-on-average with respect to the uniform distribution, then all problems in NP are easy-on-average with respect to all samplable distributions. Applying the theory to natural distributional problems remain an outstanding open question. We review some natural distributional problems whose average-case complexity is of particular interest and that do not yet fit into this theory. A major open question whether the existence of hard-on-average problems in NP can be based on the P$\neq$NP assumption or on related worst-case assumptions. We review negative results showing that certain proof techniques cannot prove such a result. While the relation between worst-case and average-case complexity for general NP problems remains open, there has been progress in understanding the relation between different ``degrees'' of average-case complexity. We discuss some of these ``hardness amplification'' results

The automatic design of hyper-heuristic framework with gene expression programming for combinatorial optimization problems

Hyper-heuristic approaches aim to automate heuristic design in order to solve multiple problems instead of designing tailor-made methodologies for individual problems. Hyper-heuristics accomplish this through a high level heuristic (heuristic selection mechanism and an acceptance criterion). This automates heuristic selection, deciding whether to accept or reject the returned solution. The fact that different problems or even instances, have different landscape structures and complexity, the design of efficient high level heuristics can have a dramatic impact on hyper-heuristic performance. In this work, instead of using human knowledge to design the high level heuristic, we propose a gene expression programming algorithm to automatically generate, during the instance solving process, the high level heuristic of the hyper-heuristic framework. The generated heuristic takes information (such as the quality of the generated solution and the improvement made) from the current problem state as input and decides which low level heuristic should be selected and the acceptance or rejection of the resultant solution. The benefit of this framework is the ability to generate, for each instance, different high level heuristics during the problem solving process. Furthermore, in order to maintain solution diversity, we utilize a memory mechanism which contains a population of both high quality and diverse solutions that is updated during the problem solving process. The generality of the proposed hyper-heuristic is validated against six well known combinatorial optimization problem, with very different landscapes, provided by the HyFlex software. Empirical results comparing the proposed hyper-heuristic with state of the art hyper-heuristics, conclude that the proposed hyper-heuristic generalizes well across all domains and achieves competitive, if not superior, results for several instances on all domains