Fuzzy Logic for Elimination of Redundant Information of Microarray Data

Gene subset selection is essential for classification and analysis of microarray data. However, gene selection is known to be a very difficult task since gene expression data not only have high dimensionalities, but also contain redundant information and noises. To cope with these difficulties, this paper introduces a fuzzy logic based pre-processing approach composed of two main steps. First, we use fuzzy inference rules to transform the gene expression levels of a given dataset into fuzzy values. Then we apply a similarity relation to these fuzzy values to define fuzzy equivalence groups, each group containing strongly similar genes. Dimension reduction is achieved by considering for each group of similar genes a single representative based on mutual information. To assess the usefulness of this approach, extensive experimentations were carried out on three well-known public datasets with a combined classification model using three statistic filters and three classifiers

Feature Selection Algorithm for High Dimensional Data using Fuzzy Logic

Feature subset selection is an effective way for reducing dimensionality removing irrelevant data increasing learning accuracy and improving results comprehensibility This process improved by cluster based FAST Algorithm and Fuzzy Logic FAST Algorithm can be used to Identify and removing the irrelevant data set This algorithm process implements using two different steps that is graph theoretic clustering methods and representative feature cluster is selected Feature subset selection research has focused on searching for relevant features The proposed fuzzy logic has focused on minimized redundant data set and improves the feature subset accurac

A systematic review of data quality issues in knowledge discovery tasks

Hay un gran crecimiento en el volumen de datos porque las organizaciones capturan permanentemente la cantidad colectiva de datos para lograr un mejor proceso de toma de decisiones. El desafío mas fundamental es la exploración de los grandes volúmenes de datos y la extracción de conocimiento útil para futuras acciones por medio de tareas para el descubrimiento del conocimiento; sin embargo, muchos datos presentan mala calidad. Presentamos una revisión sistemática de los asuntos de calidad de datos en las áreas del descubrimiento de conocimiento y un estudio de caso aplicado a la enfermedad agrícola conocida como la roya del café.Large volume of data is growing because the organizations are continuously capturing the collective amount of data for better decision-making process. The most fundamental challenge is to explore the large volumes of data and extract useful knowledge for future actions through knowledge discovery tasks, nevertheless many data has poor quality. We presented a systematic review of the data quality issues in knowledge discovery tasks and a case study applied to agricultural disease named coffee rust

Effect of Feature Selection on Gene Expression Datasets Classification Accurac

Feature selection attracts researchers who deal with machine learning and data mining. It consists of selecting the variables that have the greatest impact on the dataset classification, and discarding the rest. This dimentionality reduction allows classifiers to be fast and more accurate. This paper traits the effect of feature selection on the accuracy of widely used classifiers in literature. These classifiers are compared with three real datasets which are pre-processed with feature selection methods. More than 9% amelioration in classification accuracy is observed, and k-means appears to be the most sensitive classifier to feature selection

Knowledge Generation with Rule Induction in Cancer Omics

The explosion of omics data availability in cancer research has boosted the knowledge of the molecular basis of cancer, although the strategies for its definitive resolution are still not well established. The complexity of cancer biology, given by the high heterogeneity of cancer cells, leads to the development of pharmacoresistance for many patients, hampering the efficacy of therapeutic approaches. Machine learning techniques have been implemented to extract knowledge from cancer omics data in order to address fundamental issues in cancer research, as well as the classification of clinically relevant sub-groups of patients and for the identification of biomarkers for disease risk and prognosis. Rule induction algorithms are a group of pattern discovery approaches that represents discovered relationships in the form of human readable associative rules. The application of such techniques to the modern plethora of collected cancer omics data can effectively boost our understanding of cancer-related mechanisms. In fact, the capability of these methods to extract a huge amount of human readable knowledge will eventually help to uncover unknown relationships between molecular attributes and the malignant phenotype. In this review, we describe applications and strategies for the usage of rule induction approaches in cancer omics data analysis. In particular, we explore the canonical applications and the future challenges and opportunities posed by multi-omics integration problems.Peer reviewe

Granular Support Vector Machines Based on Granular Computing, Soft Computing and Statistical Learning

With emergence of biomedical informatics, Web intelligence, and E-business, new challenges are coming for knowledge discovery and data mining modeling problems. In this dissertation work, a framework named Granular Support Vector Machines (GSVM) is proposed to systematically and formally combine statistical learning theory, granular computing theory and soft computing theory to address challenging predictive data modeling problems effectively and/or efficiently, with specific focus on binary classification problems. In general, GSVM works in 3 steps. Step 1 is granulation to build a sequence of information granules from the original dataset or from the original feature space. Step 2 is modeling Support Vector Machines (SVM) in some of these information granules when necessary. Finally, step 3 is aggregation to consolidate information in these granules at suitable abstract level. A good granulation method to find suitable granules is crucial for modeling a good GSVM. Under this framework, many different granulation algorithms including the GSVM-CMW (cumulative margin width) algorithm, the GSVM-AR (association rule mining) algorithm, a family of GSVM-RFE (recursive feature elimination) algorithms, the GSVM-DC (data cleaning) algorithm and the GSVM-RU (repetitive undersampling) algorithm are designed for binary classification problems with different characteristics. The empirical studies in biomedical domain and many other application domains demonstrate that the framework is promising. As a preliminary step, this dissertation work will be extended in the future to build a Granular Computing based Predictive Data Modeling framework (GrC-PDM) with which we can create hybrid adaptive intelligent data mining systems for high quality prediction

Interval based fuzzy systems for identification of important genes from microarray gene expression data: Application to carcinogenic development

AbstractIn the present article, we develop two interval based fuzzy systems for identification of some possible genes mediating the carcinogenic development in various tissues. The methodology involves dimensionality reduction, classifying the genes through incorporation of the notion of linguistic fuzzy sets low, medium and high, and finally selection of some possible genes mediating a particular disease, obtained by a rule generation/grouping technique. The effectiveness of the proposed methodology, is demonstrated using five microarray gene expression datasets dealing with human lung, colon, sarcoma, breast cancer and leukemia. Moreover, the superior capability of the methodology in selecting important genes, over five other existing gene selection methods, viz., Significance Analysis of Microarrays (SAM), Signal-to-Noise Ratio (SNR), Neighborhood analysis (NA), Bayesian Regularization (BR) and Data-adaptive (DA) is demonstrated, in terms of the enrichment of each GO category of the important genes based on P-values. The results are appropriately validated by earlier investigations, gene expression profiles and t-test. The proposed methodology has been able to select genes that are more biologically significant in mediating the development of a disease than those obtained by the others

A fuzzified BRAIN algorithm for learning DNF from incomplete data

Aim of this paper is to address the problem of learning Boolean functions from training data with missing values. We present an extension of the BRAIN algorithm, called U-BRAIN (Uncertainty-managing Batch Relevance-based Artificial INtelligence), conceived for learning DNF Boolean formulas from partial truth tables, possibly with uncertain values or missing bits. Such an algorithm is obtained from BRAIN by introducing fuzzy sets in order to manage uncertainty. In the case where no missing bits are present, the algorithm reduces to the original BRAIN