Experiments on local search for bi-objective unconstrained binary quadratic programming

International audienceThis article reports an experimental analysis on stochastic local search for approximating the Pareto set of bi-objective unconstrained binary quadratic programming problems. First, we investigate two scalarizing strategies that iteratively identify a high-quality solution for a sequence of sub-problems. Each sub-problem is based on a static or adaptive definition of weighted-sum aggregation coefficients, and is addressed by means of a state-of-the-art single-objective tabu search procedure. Next, we design a Pareto local search that iteratively improves a set of solutions based on a neighborhood structure and on the Pareto dominance relation. At last, we hybridize both classes of algorithms by combining a scalarizing and a Pareto local search in a sequential way. A comprehensive experimental analysis reveals the high performance of the proposed approaches, which substantially improve upon previous best-known solutions. Moreover, the obtained results show the superiority of the hybrid algorithm over non-hybrid ones in terms of solution quality, while requiring a competitive computational cost. In addition, a number of structural properties of the problem instances allow us to explain the main difficulties that the different classes of local search algorithms have to face

Efficient and accurate P-value computation for Position Weight Matrices

<p>Abstract</p> <p>Background</p> <p>Position Weight Matrices (PWMs) are probabilistic representations of signals in sequences. They are widely used to model approximate patterns in DNA or in protein sequences. The usage of PWMs needs as a prerequisite to knowing the statistical significance of a word according to its score. This is done by defining the P-value of a score, which is the probability that the background model can achieve a score larger than or equal to the observed value. This gives rise to the following problem: Given a P-value, find the corresponding score threshold. Existing methods rely on dynamic programming or probability generating functions. For many examples of PWMs, they fail to give accurate results in a reasonable amount of time.</p> <p>Results</p> <p>The contribution of this paper is two fold. First, we study the theoretical complexity of the problem, and we prove that it is NP-hard. Then, we describe a novel algorithm that solves the P-value problem efficiently. The main idea is to use a series of discretized score distributions that improves the final result step by step until some convergence criterion is met. Moreover, the algorithm is capable of calculating the exact P-value without any error, even for matrices with non-integer coefficient values. The same approach is also used to devise an accurate algorithm for the reverse problem: finding the P-value for a given score. Both methods are implemented in a software called TFM-PVALUE, that is freely available.</p> <p>Conclusion</p> <p>We have tested TFM-PVALUE on a large set of PWMs representing transcription factor binding sites. Experimental results show that it achieves better performance in terms of computational time and precision than existing tools.</p

No Evidence for Shared Representations of Task Sets in Joint Task Switching

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Knowledge of cervical tuberculosis lymphadenitis and its treatment in pastoral communities of the Afar region, Ethiopia

<p>Abstract</p> <p>Background</p> <p>Infection with <it>Mycobacterium bovis </it>(Mb) predominantly causes cervical TB lymphadenitis (TBL). Raw milk is considered the main source of Mb infection and raw milk is a major food source for Afar pastoralists. The aim of this study was to assess Afar pastoralists' knowledge concerning cervical TBL and its treatment.</p> <p>Methods</p> <p>A community-based cross-sectional survey involving 818 interviewees was conducted in two districts of the Afar Region, Ethiopia. In addition, two focus group discussions (FGDs) were conducted in each of the study areas, one with men and the other with women.</p> <p>Results</p> <p>Of the 818 interviewees [357 (43.6%) females and 461 (56.4%) males], 742 (90.7%) reported that they had knowledge of cervical TBL, mentioning that swelling(s) on the neck resulting in a lesion and scar are common symptoms. However, only 11 (1.5%) individuals mentioned that bacteria or germs are the causative agents of TBL. Three interviewees and a male discussant mentioned drinking raw milk as the cause of TBL. A considerable proportion (34.2%) of the interviewees and almost all the discussants suggested herbal medicine as an effective treatment. Male study participants were 1.82 times more likely to have overall knowledge of TBL than female study participants (adjusted OR, 1.82; 95% CI, 1.32 to 2.51, p < 0.001).</p> <p>Conclusion</p> <p>The pastoral community members in the study areas had little biomedical knowledge of the cause, the source of infection and the transmission route of cervical TBL. Furthermore, most community members believed that herbal medicines are the most effective treatment for TBL. Therefore, TB control programs in the Afar Region require the incorporation of public health education introducing current biomedical knowledge of the disease. In addition, further studies are important to elucidate which medicinal plants are used by Afar pastoralists to treat TBL.</p