Tarek F. Gharib

Personalized Web Search Ranking Based on Different Information Resources

The goal of personalized search is to provide user with results that accurately satisfy their specific goal of the search. In this paper, a hybrid personalized search re-ranking approach is proposed to provide users with results reordered according to their interests. User preferences are automatically learned into a concept-based user profile. This profile is then employed in the re-ranking process with other information resources to personalize results. Our experiments have shown interesting results in enhancing the quality of web search.

An efficient framework based on usage and semantic data for next page prediction

The World Wide Web is becoming the most important source to search for information or products. But the size and the unstructured nature of the available information makes the location of the right information a challenging task. Recommender systems and web usage mining techniques are two of the main methods used to overcome information overload. In this paper, we present a framework for the next page prediction that exploits users’ access history combined with his semantic interests to generate personalized and accurate recommendations. We are suggesting two different approaches for decision fusion between usage and semantic data. The two proposed techniques offered a 47.3% and 54.3% improvement in prediction accuracy over conventional methods for next page prediction. The suggested framework also employs user clustering to focus the search which reduced the prediction time by an average of 68.7% and 63.4%.

A modified cutoff scanning matrix protein representation for enhancing protein function prediction

Protein function prediction is an active research area in bioinformatics. Protein functions are highly related to their structures. Therefore, effective structure based protein representations are required. Pires et al. [BMC Genomics, 12, S12 (2011)] proposed a cutoff scanning matrix (CSM) method for protein representation that utilizes distance patterns between protein residues and a maximum cutoff. This paper proposes a modified cutoff scanning matrix (MCSM) representation for enhancing protein function prediction. The proposed representation considers the whole protein instead of using cutoff. A comparative analysis was done to evaluate the proposed MCSM method and the original CSM method. Two different classification algorithms, Random Forest and K-nearest neighbor (KNN), were used in the analysis. The aspect of protein function considered is based on enzyme activity. The results show that the proposed MCSM representation outperforms the CSM representation with a prediction accuracy of 90.12% and 80.27% for superfamily and family level, respectively, with accuracy improvement of about 5 % on average.

A new protein structure representation for efficient protein function prediction.

One of the challenging problems in bioinformatics is the prediction of protein function. Protein function is the main key that can be used to classify different proteins. Protein function can be inferred experimentally with very small throughput or computationally with very high throughput. Computational methods are sequence based or structure based. Structure-based methods produce more accurate protein function prediction. In this article, we propose a new protein structure representation for efficient protein function prediction. The representation is based on three-dimensional patterns of protein residues. In the analysis, we used protein function based on enzyme activity through six mechanistically diverse enzyme superfamilies: amidohydrolase, crotonase, haloacid dehalogenase, isoprenoid synthase type I, and vicinal oxygen chelate. We applied three different classification methods, naïve Bayes, k-nearest neighbors, and random forest, to predict the enzyme superfamily of a given protein. The prediction accuracy using the proposed representation outperforms a recently introduced representation method that is based only on the distance patterns. The results show that the proposed representation achieved prediction accuracy up to 98%, with improvement of about 10% on average.

IMIDB: An Algorithm for Indexed Mining of Incremental Databases

Abstract Association rules provide important knowledge that can be extracted from transactional databases. Owing to the massive exchange of information nowadays, databases become dynamic and change rapidly and periodically: new transactions are added to the database and/or old transactions are updated or removed from the database. Incremental mining was introduced to overcome the problem of maintaining previously generated association rules in dynamic databases. In this paper, we propose an efficient algorithm (IMIDB) for incremental itemset mining in large databases. The algorithm utilizes the trie data structure for indexing dynamic database transactions. Performance comparison of the proposed algorithm to recently cited algorithms shows that a significant improvement of about two orders of magnitude is achieved by our algorithm. Also, the proposed algorithm exhibits linear scalability with respect to database size.

A Framework to Accelerate Protein Structure Comparison Tools

At the center of computational structural biology, protein structure comparison is a key problem. The steady increase in the number of protein structures encourages the development of massively parallel tools. While the focus of research is to propose data-analytical methods to tackle this problem, there are limited research proposing generic tools to run these methods in parallel environments. Herein, we propose a scalable framework to handle this steady increase. The proposed framework runs the sequential tools on parallel environments. It is a GUI-based and requiring no scripting or installation procedures. The framework includes optimally distributing protein structure database over the existing computing resources, tracking the remote processes course of execution, and merging the results to form the final output. The first stage realizes the biological database distribution as an optimization problem in order to maximize the cluster resources utilization and minimize the execution time. The experimental results show linear and nearly optimal speedups with no loss in accuracy. The framework is available at http://biocloud.hnu.edu.cn/ppsc/.