SLIDER: Mining correlated motifs in protein-protein interaction networks

Abstract—Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the method SLIDER which uses local search with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks

Local Renyi entropic profiles of DNA sequences

<p>Abstract</p> <p>Background</p> <p>In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi entropy of probability density estimation (pdf) using the Parzen's window method and applied to Chaos Game Representation/Universal Sequence Maps (CGR/USM). Subsequent work proposed a fractal pdf kernel as a more exact solution for the iterated map representation. This report extends the concepts of continuous entropy by defining DNA sequence entropic profiles using the new pdf estimations to refine the density estimation of motifs.</p> <p>Results</p> <p>The new methodology enables two results. On the one hand it shows that the entropic profiles are directly related with the statistical significance of motifs, allowing the study of under and over-representation of segments. On the other hand, by spanning the parameters of the kernel function it is possible to extract important information about the scale of each conserved DNA region. The computational applications, developed in Matlab m-code, the corresponding binary executables and additional material and examples are made publicly available at <url>http://kdbio.inesc-id.pt/~svinga/ep/</url>.</p> <p>Conclusion</p> <p>The ability to detect local conservation from a scale-independent representation of symbolic sequences is particularly relevant for biological applications where conserved motifs occur in multiple, overlapping scales, with significant future applications in the recognition of foreign genomic material and inference of motif structures.</p

Stylistic atructures: a computational approach to text classification

The problem of authorship attribution has received attention both in the academic world (e.g. did Shakespeare or Marlowe write Edward III?) and outside (e.g. is this confession really the words of the accused or was it made up by someone else?). Previous studies by statisticians and literary scholars have sought "verbal habits" that characterize particular authors consistently. By and large, this has meant looking for distinctive rates of usage of specific marker words -- as in the classic study by Mosteller and Wallace of the Federalist Papers. The present study is based on the premiss that authorship attribution is just one type of text classification and that advances in this area can be made by applying and adapting techniques from the field of machine learning. Five different trainable text-classification systems are described, which differ from current stylometric practice in a number of ways, in particular by using a wider variety of marker patterns than customary and by seeking such markers automatically, without being told what to look for. A comparison of the strengths and weaknesses of these systems, when tested on a representative range of text-classification problems, confirms the importance of paying more attention than usual to alternative methods of representing distinctive differences between types of text. The thesis concludes with suggestions on how to make further progress towards the goal of a fully automatic, trainable text-classification system

Improved cross-language information retrieval via disambiguation and vocabulary discovery

Cross-lingual information retrieval (CLIR) allows people to find documents irrespective of the language used in the query or document. This thesis is concerned with the development of techniques to improve the effectiveness of Chinese-English CLIR. In Chinese-English CLIR, the accuracy of dictionary-based query translation is limited by two major factors: translation ambiguity and the presence of out-of-vocabulary (OOV) terms. We explore alternative methods for translation disambiguation, and demonstrate new techniques based on a Markov model and the use of web documents as a corpus to provide context for disambiguation. This simple disambiguation technique has proved to be extremely robust and successful. Queries that seek topical information typically contain OOV terms that may not be found in a translation dictionary, leading to inappropriate translations and consequent poor retrieval performance. Our novel OOV term translation method is based on the Chinese authorial practice of including unfamiliar English terms in both languages. It automatically extracts correct translations from the web and can be applied to both Chinese-English and English-Chinese CLIR. Our OOV translation technique does not rely on prior segmentation and is thus free from seg mentation error. It leads to a significant improvement in CLIR effectiveness and can also be used to improve Chinese segmentation accuracy. Good quality translation resources, especially bilingual dictionaries, are valuable resources for effective CLIR. We developed a system to facilitate construction of a large-scale translation lexicon of Chinese-English OOV terms using the web. Experimental results show that this method is reliable and of practical use in query translation. In addition, parallel corpora provide a rich source of translation information. We have also developed a system that uses multiple features to identify parallel texts via a k-nearest-neighbour classifier, to automatically collect high quality parallel Chinese-English corpora from the web. These two automatic web mining systems are highly reliable and easy to deploy. In this research, we provided new ways to acquire linguistic resources using multilingual content on the web. These linguistic resources not only improve the efficiency and effectiveness of Chinese-English cross-language web retrieval; but also have wider applications than CLIR