Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression

Background: Hinge-bending movements in proteins comprising two or more domains form a large class of functional movements. Hinge-bending regions demarcate protein domains and collectively control the domain movement. Consequently, the ability to recognise sequence features of hinge-bending regions and to be able to predict them from sequence alone would benefit various areas of protein research. For example, an understanding of how the sequence features of these regions relate to dynamic properties in multi-domain proteins would aid in the rational design of linkers in therapeutic fusion proteins. Results: The DynDom database of protein domain movements comprises sequences annotated to indicate whether the amino acid residue is located within a hinge-bending region or within an intradomain region. Using statistical methods and Kernel Logistic Regression (KLR) models, this data was used to determine sequence features that favour or disfavour hinge-bending regions. This is a difficult classification problem as the number of negative cases (intradomain residues) is much larger than the number of positive cases (hinge residues). The statistical methods and the KLR models both show that cysteine has the lowest propensity for hinge-bending regions and proline has the highest, even though it is the most rigid amino acid. As hinge-bending regions have been previously shown to occur frequently at the terminal regions of the secondary structures, the propensity for proline at these regions is likely due to its tendency to break secondary structures. The KLR models also indicate that isoleucine may act as a domain-capping residue. We have found that a quadratic KLR model outperforms a linear KLR model and that improvement in performance occurs up to very long window lengths (eighty residues) indicating long-range correlations. Conclusion: In contrast to the only other approach that focused solely on interdomain hinge-bending regions, the method provides a modest and statistically significant improvement over a random classifier. An explanation of the KLR results is that in the prediction of hinge-bending regions a long-range correlation is at play between a small number amino acids that either favour or disfavour hinge-bending regions. The resulting sequence-based prediction tool, HingeSeek, is available to run through a webserver at hingeseek.cmp.uea.ac.uk

Extracting Implicit Social Relation for Social Recommendation Techniques in User Rating Prediction

Recommendation plays an increasingly important role in our daily lives. Recommender systems automatically suggest items to users that might be interesting for them. Recent studies illustrate that incorporating social trust in Matrix Factorization methods demonstrably improves accuracy of rating prediction. Such approaches mainly use the trust scores explicitly expressed by users. However, it is often challenging to have users provide explicit trust scores of each other. There exist quite a few works, which propose Trust Metrics to compute and predict trust scores between users based on their interactions. In this paper, first we present how social relation can be extracted from users' ratings to items by describing Hellinger distance between users in recommender systems. Then, we propose to incorporate the predicted trust scores into social matrix factorization models. By analyzing social relation extraction from three well-known real-world datasets, which both: trust and recommendation data available, we conclude that using the implicit social relation in social recommendation techniques has almost the same performance compared to the actual trust scores explicitly expressed by users. Hence, we build our method, called Hell-TrustSVD, on top of the state-of-the-art social recommendation technique to incorporate both the extracted implicit social relations and ratings given by users on the prediction of items for an active user. To the best of our knowledge, this is the first work to extend TrustSVD with extracted social trust information. The experimental results support the idea of employing implicit trust into matrix factorization whenever explicit trust is not available, can perform much better than the state-of-the-art approaches in user rating prediction

An ontology enhanced parallel SVM for scalable spam filter training

This is the post-print version of the final paper published in Neurocomputing. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2013 Elsevier B.V.Spam, under a variety of shapes and forms, continues to inflict increased damage. Varying approaches including Support Vector Machine (SVM) techniques have been proposed for spam filter training and classification. However, SVM training is a computationally intensive process. This paper presents a MapReduce based parallel SVM algorithm for scalable spam filter training. By distributing, processing and optimizing the subsets of the training data across multiple participating computer nodes, the parallel SVM reduces the training time significantly. Ontology semantics are employed to minimize the impact of accuracy degradation when distributing the training data among a number of SVM classifiers. Experimental results show that ontology based augmentation improves the accuracy level of the parallel SVM beyond the original sequential counterpart

Knowledge Base Population using Semantic Label Propagation

A crucial aspect of a knowledge base population system that extracts new facts from text corpora, is the generation of training data for its relation extractors. In this paper, we present a method that maximizes the effectiveness of newly trained relation extractors at a minimal annotation cost. Manual labeling can be significantly reduced by Distant Supervision, which is a method to construct training data automatically by aligning a large text corpus with an existing knowledge base of known facts. For example, all sentences mentioning both 'Barack Obama' and 'US' may serve as positive training instances for the relation born_in(subject,object). However, distant supervision typically results in a highly noisy training set: many training sentences do not really express the intended relation. We propose to combine distant supervision with minimal manual supervision in a technique called feature labeling, to eliminate noise from the large and noisy initial training set, resulting in a significant increase of precision. We further improve on this approach by introducing the Semantic Label Propagation method, which uses the similarity between low-dimensional representations of candidate training instances, to extend the training set in order to increase recall while maintaining high precision. Our proposed strategy for generating training data is studied and evaluated on an established test collection designed for knowledge base population tasks. The experimental results show that the Semantic Label Propagation strategy leads to substantial performance gains when compared to existing approaches, while requiring an almost negligible manual annotation effort.Comment: Submitted to Knowledge Based Systems, special issue on Knowledge Bases for Natural Language Processin