Hierarchical information clustering by means of topologically embedded graphs

We introduce a graph-theoretic approach to extract clusters and hierarchies in complex data-sets in an unsupervised and deterministic manner, without the use of any prior information. This is achieved by building topologically embedded networks containing the subset of most significant links and analyzing the network structure. For a planar embedding, this method provides both the intra-cluster hierarchy, which describes the way clusters are composed, and the inter-cluster hierarchy which describes how clusters gather together. We discuss performance, robustness and reliability of this method by first investigating several artificial data-sets, finding that it can outperform significantly other established approaches. Then we show that our method can successfully differentiate meaningful clusters and hierarchies in a variety of real data-sets. In particular, we find that the application to gene expression patterns of lymphoma samples uncovers biologically significant groups of genes which play key-roles in diagnosis, prognosis and treatment of some of the most relevant human lymphoid malignancies.Comment: 33 Pages, 18 Figures, 5 Table

The importance of data classification using machine learning methods in microarray data

The detection of genetic mutations has attracted global attention. several methods have proposed to detect diseases such as cancers and tumours. One of them is microarrays, which is a type of representation for gene expression that is helpful in diagnosis. To unleash the full potential of microarrays, machine-learning algorithms and gene selection methods can be implemented to facilitate processing on microarrays and to overcome other potential challenges. One of these challenges involves high dimensional data that are redundant, irrelevant, and noisy. To alleviate this problem, this representation should be simplified. For example, the feature selection process can be implemented by reducing the number of features adopted in clustering and classification. A subset of genes can be selected from a pool of gene expression data recorded on DNA micro-arrays. This paper reviews existing classification techniques and gene selection methods. The effectiveness of emerging techniques, such as the swarm intelligence technique in feature selection and classification in microarrays, are reported as well. These emerging techniques can be used in detecting cancer. The swarm intelligence technique can be combined with other statistical methods for attaining better results

Hybrid feature selection based on principal component analysis and grey wolf optimizer algorithm for Arabic news article classification

The rapid growth of electronic documents has resulted from the expansion and development of internet technologies. Text-documents classification is a key task in natural language processing that converts unstructured data into structured form and then extract knowledge from it. This conversion generates a high dimensional data that needs further analusis using data mining techniques like feature extraction, feature selection, and classification to derive meaningful insights from the data. Feature selection is a technique used for reducing dimensionality in order to prune the feature space and, as a result, lowering the computational cost and enhancing classification accuracy. This work presents a hybrid filter-wrapper method based on Principal Component Analysis (PCA) as a filter approach to select an appropriate and informative subset of features and Grey Wolf Optimizer (GWO) as wrapper approach (PCA-GWO) to select further informative features. Logistic Regression (LR) is used as an elevator to test the classification accuracy of candidate feature subsets produced by GWO. Three Arabic datasets, namely Alkhaleej, Akhbarona, and Arabiya, are used to assess the efficiency of the proposed method. The experimental results confirm that the proposed method based on PCA-GWO outperforms the baseline classifiers with/without feature selection and other feature selection approaches in terms of classification accuracy

Tooth Color Detection Using PCA and KNN Classifier Algorithm Based on Color Moment

Matching the suitable color for tooth reconstruction is an important step that can make difficulties for the dentists due to the subjective factors  of color selection. Accurate color matching system is mainly result based on images analyzing and processing techniques of recognition system.  This system consist of three parts, which are data collection from digital teeth color images, data preparation for taking color analysis technique and extracting the features, and data classification involve feature selection for reducing the features number of this system. The teeth images which is used in this research are 16 types of teeth that are taken from RSGM UNAIR SURABAYA. Feature extraction is taken by the characteristics of the RGB, HSV and LAB based on the color moment calculation such as mean, standard deviation, skewness, and kurtosis parameter. Due to many formed features from each color space, it is required addition method for reducing the number of features by choosing the essential information like Principal Component Analysis (PCA) method. Combining the PCA feature selection technique to the clasification process using K Nearest Neighbour (KNN) classifier  algorithm can be improved the accuracy performance of this system. On the experiment result, it showed that only using  KNN classifier achieve accuracy percentage up to 97.5 % in learning process and 92.5 % in testing process while combining PCA with KNN classifier can reduce the 36 features to the 26 features which can improve the accuracy percentage up to 98.54 % in learning process and  93.12% in testing process. Adding PCA as the feature selection method can be improved the accuracy performance of this color matching system with little number of features.Â

An automatic adaptive method to combine summary statistics in approximate Bayesian computation

To infer the parameters of mechanistic models with intractable likelihoods, techniques such as approximate Bayesian computation (ABC) are increasingly being adopted. One of the main disadvantages of ABC in practical situations, however, is that parameter inference must generally rely on summary statistics of the data. This is particularly the case for problems involving high-dimensional data, such as biological imaging experiments. However, some summary statistics contain more information about parameters of interest than others, and it is not always clear how to weight their contributions within the ABC framework. We address this problem by developing an automatic, adaptive algorithm that chooses weights for each summary statistic. Our algorithm aims to maximize the distance between the prior and the approximate posterior by automatically adapting the weights within the ABC distance function. Computationally, we use a nearest neighbour estimator of the distance between distributions. We justify the algorithm theoretically based on properties of the nearest neighbour distance estimator. To demonstrate the effectiveness of our algorithm, we apply it to a variety of test problems, including several stochastic models of biochemical reaction networks, and a spatial model of diffusion, and compare our results with existing algorithms

A Hybrid Metaheuristics based technique for Mutation Based Disease Classification

Due to recent advancements in computational biology, DNA microarray technology has evolved as a useful tool in the detection of mutation among various complex diseases like cancer. The availability of thousands of microarray datasets makes this field an active area of research. Early cancer detection can reduce the mortality rate and the treatment cost. Cancer classification is a process to provide a detailed overview of the disease microenvironment for better diagnosis. However, the gene microarray datasets suffer from a curse of dimensionality problems also the classification models are prone to be overfitted due to small sample size and large feature space. To address these issues, the authors have proposed an Improved Binary Competitive Swarm Optimization Whale Optimization Algorithm (IBCSOWOA) for cancer classification, in which IBCSO has been employed to reduce the informative gene subset originated from using minimum redundancy maximum relevance (mRMR) as filter method. The IBCSOWOA technique has been tested on an artificial neural network (ANN) model and the whale optimization algorithm (WOA) is used for parameter tuning of the model. The performance of the proposed IBCSOWOA is tested on six different mutation-based microarray datasets and compared with existing disease prediction methods. The experimental results indicate the superiority of the proposed technique over the existing nature-inspired methods in terms of optimal feature subset, classification accuracy, and convergence rate. The proposed technique has illustrated above 98% accuracy in all six datasets with the highest accuracy of 99.45% in the Lung cancer dataset

Empirical Assessment of Machine Learning Techniques for Software Requirements Risk Prediction

[EN] Software risk prediction is the most sensitive and crucial activity of Software Development Life Cycle (SDLC). It may lead to success or failure of a project. The risk should be predicted earlier to make a software project successful. A Model is proposed for the prediction of software requirement risks using requirement risk dataset and machine learning techniques. Also, a comparison is done between multiple classifiers that are K-Nearest Neighbour (KNN), Average One Dependency Estimator (A1DE), Naïve Bayes (NB), Composite Hypercube on Iterated Random Projection (CHIRP), Decision Table (DT), Decision Table/ Naïve Bayes Hybrid Classifier (DTNB), Credal Decision Trees (CDT), Cost-Sensitive Decision Forest (CS-Forest), J48 Decision Tree (J48), and Random Forest (RF) to achieve best suited technique for the model according to the nature of dataset. These techniques are evaluated using various evaluation metrics including CCI (correctly Classified Instances), Mean Absolute Error (MAE), Root Mean Square Error (RMSE), Relative Absolute Error (RAE), Root Relative Squared Error (RRSE), precision, recall, F-measure, Matthew¿s Correlation Coefficient (MCC), Receiver Operating Characteristic Area (ROC area), Precision-Recall Curves area (PRC area), and accuracy. The inclusive outcome of this study shows that in terms of reducing error rates, CDT outperforms other techniques achieving 0.013 for MAE, 0.089 for RMSE, 4.498% for RAE, and 23.741% for RRSE. However, in terms of increasing accuracy, DT, DTNB and CDT achieve better results.This work was supported by by Generalitat Valenciana, Conselleria de Innovacion, Universidades, Ciencia y Sociedad Digital, (project AICO/019/224)Naseem, R.; Shaukat, Z.; Irfan, M.; Shah, MA.; Ahmad, A.; Muhammad, F.; Glowacz, A.... (2021). Empirical Assessment of Machine Learning Techniques for Software Requirements Risk Prediction. Electronics. 10(2):1-19. https://doi.org/10.3390/electronics1002016811910

Development of data processing methods for high resolution mass spectrometry-based metabolomics with an application to human liver transplantation

Direct Infusion (DI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) is becoming a popular measurement platform in metabolomics. This thesis aims to advance the data processing and analysis pipeline of the DI FT-ICR based metabolomics, and broaden its applicability to a clinical research. To meet the first objective, the issue of missing data that occur in a final data matrix containing metabolite relative abundances measured for each sample analysed, is addressed. The nature of these data and their effect on the subsequent data analyses are investigated. Eight common and/or easily accessible missing data estimation algorithms are examined and a three stage approach is proposed to aid the identification of the optimal one. Finally, a novel survival analysis approach is introduced and assessed as an alternative way of missing data treatment prior univariate analysis. To address the second objective, DI FT-ICR MS based metabolomics is assessed in terms of its applicability to research investigating metabolomic changes occurring in liver grafts throughout the human orthotopic liver transplantation (OLT). The feasibility of this approach to a clinical setting is validated and its potential to provide a wealth of novel metabolic information associated with OLT is demonstrated