Branch and bound computation of exact p-values

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Branch and bound computation of exact p-values

UNLABELLED P-value computation is often used in bioinformatics to quantify the surprise, or significance, associated with a given observation. An implementation is provided that computes the exact p-value associated with any observed sample, against a null multinomial distribution, using the likelihood-ratio statistic. The efficient branch and bound code, far exceeding the full enumeration impl...

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Efficient and Exact MAP-MRF Inference using Branch and Bound

We propose two novel Branch-and-Bound (BB) methods to efficiently solve exact MAPMRF inference on problems with a large number of states (per variable) H. By organizing the data in a suitable structure, the time complexity of our best method for evaluating the bound at each branch is reduced from O(H) to O(H). This permits searching for the MAP solution in O(BH +Q) instead of O(BH) (without usi...

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We present a novel exact algorithm for the minimum graph bisection problem, whose goal is to partition a graph into two equallysized cells while minimizing the number of edges between them. Our algorithm is based on the branch-and-bound framework and, unlike most previous approaches, it is fully combinatorial. We present stronger lower bounds, improved branching rules, and a new decomposition t...

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Computing exact P-values for DNA motifs

MOTIVATION Many heuristic algorithms have been designed to approximate P-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown. RESULTS...

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Sequential Computation of p-values based on (Re-)Sampling with a Guaranteed Error Bound

When explicit forms of p-values are not available or cannot be evaluated efficiently, e.g. in the case of a bootstrap test, one usually resorts to simulation. Especially when a simulation step is computationally expensive it is of interest to draw a small number of samples. This article introduces a sequential procedure to evaluate the p-value using simulation. It guarantees that, up to a small...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2006

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btl357