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

Continuous Iterative Guided Spectral Class Rejection Classification Algorithm: Part 1

This paper outlines the changes necessary to convert the iterative guided spectral class rejection (IGSCR) classification algorithm to a soft classification algorithm. IGSCR uses a hypothesis test to select clusters to use in classification and iteratively refines clusters not yet selected for classification. Both steps assume that cluster and class memberships are crisp (either zero or one). In order to make soft cluster and class assignments (between zero and one), a new hypothesis test and iterative refinement technique are introduced that are suitable for soft clusters. The new hypothesis test, called the (class) association significance test, is based on the normal distribution, and a proof is supplied to show that the assumption of normality is reasonable. Soft clusters are iteratively refined by creating new clusters using information contained in a targeted soft cluster. Soft cluster evaluation and refinement can then be combined to form a soft classification algorithm, continuous iterative guided spectral class rejection (CIGSCR)

Mining Association Rules Based on Certainty

Abstract: The paper proposed a new kind of classification algorithm based on support and certainty, which scanned the same datasets several times to discover certain frequent item sets whose length complied with the fixed increment. The algorithm produced the Boolean association rules by means of the width preference-traversing mode. The experiment shows this algorithm of association rules based on certainty and support architecture could generate a accurate association rules compared with other classification algorithm and improve the accuracy and perceptiveness of association rules effectively

Using fuzzy association rule mining in cancer classification

The classification of the cancer tumors based on gene expression profiles has been extensively studied in numbers of studies. A wide variety of cancer datasets have been implemented by the various methods of gene selection and classification to identify the behavior of the genes in tumors and find the relationships between them and outcome of diseases. Interpretability of the model, which is developed by fuzzy rules and linguistic variables in this study, has been rarely considered. In addition, creating a fuzzy classifier with high performance in classification that uses a subset of significant genes which have been selected by different types of gene selection methods is another goal of this study. A new algorithm has been developed to identify the fuzzy rules and significant genes based on fuzzy association rule mining. At first, different subset of genes which have been selected by different methods, were used to generate primary fuzzy classifiers separately and then proposed algorithm was implemented to mix the genes which have been associated in the primary classifiers and generate a new classifier. The results show that fuzzy classifier can classify the tumors with high performance while presenting the relationships between the genes by linguistic variables

MapReduce network enabled algorithms for classification based on association rules

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.There is growing evidence that integrating classification and association rule mining can produce more efficient and accurate classifiers than traditional techniques. This thesis introduces a new MapReduce based association rule miner for extracting strong rules from large datasets. This miner is used later to develop a new large scale classifier. Also new MapReduce simulator was developed to evaluate the scalability of proposed algorithms on MapReduce clusters. The developed associative rule miner inherits the MapReduce scalability to huge datasets and to thousands of processing nodes. For finding frequent itemsets, it uses hybrid approach between miners that uses counting methods on horizontal datasets, and miners that use set intersections on datasets of vertical formats. The new miner generates same rules that usually generated using apriori-like algorithms because it uses the same confidence and support thresholds definitions. In the last few years, a number of associative classification algorithms have been proposed, i.e. CPAR, CMAR, MCAR, MMAC and others. This thesis also introduces a new MapReduce classifier that based MapReduce associative rule mining. This algorithm employs different approaches in rule discovery, rule ranking, rule pruning, rule prediction and rule evaluation methods. The new classifier works on multi-class datasets and is able to produce multi-label predications with probabilities for each predicted label. To evaluate the classifier 20 different datasets from the UCI data collection were used. Results show that the proposed approach is an accurate and effective classification technique, highly competitive and scalable if compared with other traditional and associative classification approaches. Also a MapReduce simulator was developed to measure the scalability of MapReduce based applications easily and quickly, and to captures the behaviour of algorithms on cluster environments. This also allows optimizing the configurations of MapReduce clusters to get better execution times and hardware utilization

Diagnosis and Prognosis of Breast Cancer Using Multi Classification Algorithm

Data mining is the process of analysing data from different views points and condensing it into useful information. There are several types of algorithms in data mining such as Classification algorithms, Regression,Segmentation algorithms, Association algorithms, Sequence analysis algorithms, etc.,. The classification algorithm can be usedto bifurcate the data set from the given data set and foretell one or more discrete variables, based on the other attributes in the dataset. The ID3 (Iterative Dichotomiser 3) algorithm is an original data set S as the root node. An unutilised attribute of the data set S calculates the entropy H(S) (or Information gain IG (A)) of the attribute. Upon its selection, the attribute should have the smallest entropy (or largest information gain) value. A genetic algorithm (GA) is aheuristic quest that imitates the process of natural selection. Genetic algorithm can easily select cancer data set, from the given data set using GA operators, such as mutation, selection, and crossover. A method existed earlier (KNN+GA) was not successful for breast cancer and primary tumor. Our method of creating new algorithm GA+ID3 easily identifies breast cancer data set from the given data set. The multi classification algorithm diagnosis and prognosis of breast cancer data set is identified by this paper