MOTIVATION: With rapidly expanding protein structure databases, efficiently retrieving structures similar to a given protein is an important problem. It involves two major issues: (i) effective protein structure representation that captures inherent relationship between fragments and facilitates efficient comparison between the structures and (ii) effective framework to address different retrieval requirements. Recently, researchers proposed vector space model of proteins using bag of fragments representation (FragBag), which corresponds to the basic information retrieval model. RESULTS: In this article, we propose an improved representation of protein structures using latent dirichlet allocation topic model. Another important requirement is to retrieve proteins, whether they are either close or remote homologs. In order to meet diverse objectives, we propose multi-viewpoint based framework that combines multiple representations and retrieval techniques. We compare the proposed representation and retrieval framework on the benchmark dataset developed by Kolodny and co-workers. The results indicate that the proposed techniques outperform state-of-the-art methods. AVAILABILITY: http://www.cse.iitm.ac.in/~ashishvt/research/protein-lda/. CONTACT: [email protected].

Multi grain sentiment analysis is the task of simultaneously classifying sentiment expressed at different levels of granularity, as opposed to single level at a time. Models built for multi grain sentiment analysis assume fully labeled corpus at fine grained level or coarse grained level or both. Huge amount of online reviews are not fully labeled at any of the levels, but are partially labeled at both the levels. We propose a multi grain collective classification framework to not only exploit the information available at all the levels but also use intra dependencies at each level and inter dependencies between the levels. We demonstrate empirically that the proposed framework enables better performance at both the levels compared to baseline approaches.