New methodologies for performing pairwise tree-matching on carbohydrate sugar chain data were introduced in [3], in which well-known sequence alignment algorithms [12] were extended and an already known polynomial-time graph algorithm for finding the maximum common subtree (MCST) of two trees [7] was used to implement what is called the KEGG Carbohydrate Matcher, or KCaM. These new methodologie...

Recent experiments on atomic-scale metallic contacts have shown that the quantization of the conductance appears clearly only after the average of the experimental results. Motivated by these results we have analyzed a simplified model system in which a narrow neck is randomly coupled to wide ideal leads, both in absence and presence of time reversal invariance. Based on Random Matrix Theory we...

Sequence comparison is one of the most fundamental computational problems in bioinformatics. Pairwise sequence alignment methods align two sequences using a substitution matrix consisting of pairwise scores of aligning different residues with each other (like BLOSUM62), and give an alignment score for the given sequence-pair. This work 1 addresses the problem of accurately estimating statistica...

Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this...

Nodes in real-world networks are usually organized in local modules. These groups, called communities, are intuitively defined as subgraphs with a larger density of internal connections than of external links. In this work, we define a measure aimed at quantifying the statistical significance of single communities. Extreme and order statistics are used to predict the statistics associated with ...

Here x is a numeric vector of data values and y is an optional numeric vector of data values. If y is excluded, the function performs a one-sample t-test on the data contained in x, if it is included it performs a two-sample t-tests using both x and y. The option mu provides a number indicating the true value of the mean (or difference in means if you are performing a two sample test) under the...

The least-squares (or Lomb-Scargle) periodogram is a powerful tool which is used routinely in many branches of astronomy to search for periodicities in observational data. The problem of assessing statistical significance of candidate periodicities for different periodograms is considered. Based on results in extreme value theory, improved analytic estimations of false alarm probabilities are g...

Relative Entropy-based pruning has been shown to be efficient for pruning language models for more than a decade ago. Recently, this method has been applied to Phrase-based Machine Translation, and results suggest that this method is comparable the state-of-art pruning method based on significance tests. In this work, we show that these 2 methods are effective in pruning different types of phra...

Statistical significance of a local sequence alignment depends not only on the similarity score and on the sequence lengths, but also on a length of the alignment. Dependence of the alignment significance on the length of the sequences has been analyzed earlier, and is based on the idea that the longer sequences have more chances to share a local similarity with a bigger score. To the best of o...