Pareto optimal pairwise sequence alignment

A Foraging Strategy with Risk Response for Individual Robots in Adversarial Environments

As an essential problem in robotics, foraging means that robots collect objects from a given environment and return them to a specified location. On many occasions, robots are required to perform foraging tasks in adversarial environments, such as battlefield rescue, where potential adversaries may damage robots with a certain probability. The longer an individual robot moves through adversarial environments, the higher the probability of being damaged by adversaries. The robot system can gain utility only when the robot brings carried objects back to a predetermined home station. Such a risk of being damaged makes returning home at different locations potentially relevant to the expected utility produced by the robot. Thus, the individual robot faces a dilemma when it responds to the potential risks in adversarial environments: whether to return the carried resources home or continue foraging tasks. In this paper, two fundamental environment settings are discussed, homogeneous cases and heterogeneous cases. The former is analyzed as having both the optimal substructure property and the non-aftereffect property. Then, we present a dynamic programming algorithm that can find an optimal solution with polynomial time complexity. For the latter, it is proven that finding an optimal solution is \mathcal {NP} -hard. We then propose a heuristic algorithm: a division hierarchical path planning algorithm that is based on the idea of dividing the foraging routes generated initially into a certain number of subroutes to dilute risks. Finally, these algorithms are extensively evaluated in simulations, concluding that in adversarial environments, they can significantly improve the productivity of an individual robot before it is damaged.

Heuristics for multiobjective multiple sequence alignment

BACKGROUND

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment.

METHODS

We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments.

RESULTS AND CONCLUSIONS

The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show that our approaches can obtain better results than TCoffee and Clustal Omega in terms of the first ratio.

Multiple sequence alignment with affine gap by using multi-objective genetic algorithm

Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate and statistically significant multiple alignments is still a challenge. In this paper, we propose an efficient method by using multi-objective genetic algorithm (MSAGMOGA) to discover optimal alignments with affine gap in multiple sequence data. The main advantage of our approach is that a large number of tradeoff (i.e., non-dominated) alignments can be obtained by a single run with respect to conflicting objectives: affine gap penalty minimization and similarity and support maximization. To the best of our knowledge, this is the first effort with three objectives in this direction. The proposed method can be applied to any data set with a sequential character. Furthermore, it allows any choice of similarity measures for finding alignments. By analyzing the obtained optimal alignments, the decision maker can understand the tradeoff between the objectives. We compared our method with the three well-known multiple sequence alignment methods, MUSCLE, SAGA and MSA-GA. As the first of them is a progressive method, and the other two are based on evolutionary algorithms. Experiments on the BAliBASE 2.0 database were conducted and the results confirm that MSAGMOGA obtains the results with better accuracy statistical significance compared with the three well-known methods in aligning multiple sequence alignment with affine gap. The proposed method also finds solutions faster than the other evolutionary approaches mentioned above.

MOSAL: software tools for multiobjective sequence alignment

: Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of these alignments provide a potential explanation of the relationship between the sequences. We introduce MOSAL, a software tool that provides an open-source implementation and an on-line application for multiobjective pairwise sequence alignment.