Variation methods in Bayesian image restoration

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Bayesian ocean colour modelling

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On the hierarchical classification of G protein-coupled receptors

MOTIVATION: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. RESULTS: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases.

A weakly-supervised Bayesian model for violence detection from social media

Social streams have proven to be the mostup-to-date and inclusive information on cur-rent events. In this paper we propose a novelprobabilistic modelling framework, called violence detection model (VDM), which enables the identification of text containing violent content and extraction of violence-related topics over social media data. The proposed VDM model does not require any labeled corpora for training, instead, it only needs the in-corporation of word prior knowledge which captures whether a word indicates violence or not. We propose a novel approach of deriving word prior knowledge using the relative entropy measurement of words based on the in-tuition that low entropy words are indicative of semantically coherent topics and therefore more informative, while high entropy words indicates words whose usage is more topical diverse and therefore less informative. Our proposed VDM model has been evaluated on the TREC Microblog 2011 dataset to identify topics related to violence. Experimental results show that deriving word priors using our proposed relative entropy method is more effective than the widely-used information gain method. Moreover, VDM gives higher violence classification results and produces more coherent violence-related topics compared toa few competitive baselines.

A simple Bayesian modelling approach to event extraction from Twitter

With the proliferation of social media sites, social streams have proven to contain the most up-to-date information on current events. Therefore, it is crucial to extract events from the social streams such as tweets. However, it is not straightforward to adapt the existing event extraction systems since texts in social media are fragmented and noisy. In this paper we propose a simple and yet effective Bayesian model, called Latent Event Model (LEM), to extract structured representation of events from social media. LEM is fully unsupervised and does not require annotated data for training. We evaluate LEM on a Twitter corpus. Experimental results show that the proposed model achieves 83% in F-measure, and outperforms the state-of-the-art baseline by over 7%.© 2014 Association for Computational Linguistics.

TATPred:a Bayesian method for the identification of twin arginine translocation pathway signal sequences

The twin arginine translocation (TAT) system ferries folded proteins across the bacterial membrane. Proteins are directed into this system by the TAT signal peptide present at the amino terminus of the precursor protein, which contains the twin arginine residues that give the system its name. There are currently only two computational methods for the prediction of TAT translocated proteins from sequence. Both methods have limitations that make the creation of a new algorithm for TAT-translocated protein prediction desirable. We have developed TATPred, a new sequence-model method, based on a Nave-Bayesian network, for the prediction of TAT signal peptides. In this approach, a comprehensive range of models was tested to identify the most reliable and robust predictor. The best model comprised 12 residues: three residues prior to the twin arginines and the seven residues that follow them. We found a prediction sensitivity of 0.979 and a specificity of 0.942.

The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods

Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties into several smaller, more meaningful groups. Two commonly used clustering techniques are introduced in the following section: principal component analysis (PCA) and hierarchical clustering. PCA calculates the variance between variables and groups them into a few uncorrelated groups or principal components (PCs) that are orthogonal to each other. Hierarchical clustering is carried out by separating data into many clusters and merging similar clusters together. Here, we use an example of human leukocyte antigen (HLA) supertype classification to demonstrate the usage of the two methods. Two programs, Generating Optimal Linear Partial Least Square Estimations (GOLPE) and Sybyl, are used for PCA and hierarchical clustering, respectively. However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R.

Alpha helical trans-membrane proteins:enhanced prediction using a Bayesian approach

Membrane proteins, which constitute approximately 20% of most genomes, are poorly tractable targets for experimental structure determination, thus analysis by prediction and modelling makes an important contribution to their on-going study. Membrane proteins form two main classes: alpha helical and beta barrel trans-membrane proteins. By using a method based on Bayesian Networks, which provides a flexible and powerful framework for statistical inference, we addressed alpha-helical topology prediction. This method has accuracies of 77.4% for prokaryotic proteins and 61.4% for eukaryotic proteins. The method described here represents an important advance in the computational determination of membrane protein topology and offers a useful, and complementary, tool for the analysis of membrane proteins for a range of applications.