Prediction of protein-protein interaction types using association rule based classification

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2009 Park et alBackground: Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches. Results: This work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification. We incorporated domain information from protein complexes in SCOP proteins and identified 354 domain-interaction sites. 14 interface properties were calculated from amino acid and secondary structure composition and then used to generate a set of association rules characterizing these domain-interaction sites employing the APRIORI algorithm. Our results regarding the classification of PPI types based on a set of discovered association rules shows that the discriminative ability of association rules can significantly impact on the prediction power of classification models. We also showed that the accuracy of the classification can be improved through the use of structural domain information and also the use of secondary structure content. Conclusion: The advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/SHP was supported by the Korea Research Foundation Grant funded by the Korean Government(KRF-2005-214-E00050). JAR has been supported by the Programme Alβan, the European Union Programme of High level Scholarships for Latin America, scholarship E04D034854CL. SK was supported by Soongsil University Research Fund

QCBA: Postoptimization of Quantitative Attributes in Classifiers based on Association Rules

The need to prediscretize numeric attributes before they can be used in association rule learning is a source of inefficiencies in the resulting classifier. This paper describes several new rule tuning steps aiming to recover information lost in the discretization of numeric (quantitative) attributes, and a new rule pruning strategy, which further reduces the size of the classification models. We demonstrate the effectiveness of the proposed methods on postoptimization of models generated by three state-of-the-art association rule classification algorithms: Classification based on Associations (Liu, 1998), Interpretable Decision Sets (Lakkaraju et al, 2016), and Scalable Bayesian Rule Lists (Yang, 2017). Benchmarks on 22 datasets from the UCI repository show that the postoptimized models are consistently smaller -- typically by about 50% -- and have better classification performance on most datasets

Efficient chain structure for high-utility sequential pattern mining

High-utility sequential pattern mining (HUSPM) is an emerging topic in data mining, which considers both utility and sequence factors to derive the set of high-utility sequential patterns (HUSPs) from the quantitative databases. Several works have been presented to reduce the computational cost by variants of pruning strategies. In this paper, we present an efficient sequence-utility (SU)-chain structure, which can be used to store more relevant information to improve mining performance. Based on the SU-Chain structure, the existing pruning strategies can also be utilized here to early prune the unpromising candidates and obtain the satisfied HUSPs. Experiments are then compared with the state-of-the-art HUSPM algorithms and the results showed that the SU-Chain-based model can efficiently improve the efficiency performance than the existing HUSPM algorithms in terms of runtime and number of the determined candidates

Evolving temporal association rules with genetic algorithms

A novel framework for mining temporal association rules by discovering itemsets with a genetic algorithm is introduced. Metaheuristics have been applied to association rule mining, we show the efficacy of extending this to another variant - temporal association rule mining. Our framework is an enhancement to existing temporal association rule mining methods as it employs a genetic algorithm to simultaneously search the rule space and temporal space. A methodology for validating the ability of the proposed framework isolates target temporal itemsets in synthetic datasets. The Iterative Rule Learning method successfully discovers these targets in datasets with varying levels of difficulty