Feature selection on wide multiclass problems using OVA-RFE

Feature selection is a pre–processing technique commonly used with high–dimensional datasets. It is aimed at reducing the dimensionality of the input space, discarding useless or redundant variables, in order to increase the performance and interpretability of models. For multiclass classification problems, recent works suggested that decomposing the multiclass problem in a set of binary ones, and doing the feature selection on the binary problems could be a sound strategy. In this work we combined the well–known Recursive Feature Elimination (RFE) algorithm with the simple One–Vs–All (OVA) technique for multiclass problems, to produce the new OVA–RFE selection method. We evaluated OVA–RFE using wide datasets from genomic and mass– spectrometry analysis, and several classifiers. In particular, we compared the new method with the traditional RFE (applied to a direct multiclass classifier) in terms of accuracy and stability. Our results show that OVA– RFE is no better than the traditional method, which is in opposition to previous results on similar methods. The opposite results are related to a different interpretation of the real number of variables in use by both methods.Fil: Granitto, Pablo Miguel. Erasmus Université Paul Cézanne Aix Marseille III; Francia. Universidad Nacional de Rosario; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Burgos, Andrés. Erasmus Université Paul Cézanne Aix Marseille III; Francia. Universidad Nacional de Rosario; Argentin

Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems

<p>Abstract</p> <p>Background</p> <p>The Signal-to-Noise-Ratio (SNR) is often used for identification of biomarkers for two-class problems and no formal and useful generalization of SNR is available for multiclass problems. We propose innovative generalizations of SNR for multiclass cancer discrimination through introduction of two indices, Gene Dominant Index and Gene Dormant Index (GDIs). These two indices lead to the concepts of dominant and dormant genes with biological significance. We use these indices to develop methodologies for discovery of dominant and dormant biomarkers with interesting biological significance. The dominancy and dormancy of the identified biomarkers and their excellent discriminating power are also demonstrated pictorially using the scatterplot of individual gene and 2-D Sammon's projection of the selected set of genes. Using information from the literature we have shown that the GDI based method can identify dominant and dormant genes that play significant roles in cancer biology. These biomarkers are also used to design diagnostic prediction systems.</p> <p>Results and discussion</p> <p>To evaluate the effectiveness of the GDIs, we have used four multiclass cancer data sets (Small Round Blue Cell Tumors, Leukemia, Central Nervous System Tumors, and Lung Cancer). For each data set we demonstrate that the new indices can find biologically meaningful genes that can act as biomarkers. We then use six machine learning tools, Nearest Neighbor Classifier (NNC), Nearest Mean Classifier (NMC), Support Vector Machine (SVM) classifier with linear kernel, and SVM classifier with Gaussian kernel, where both SVMs are used in conjunction with one-vs-all (OVA) and one-vs-one (OVO) strategies. We found GDIs to be very effective in identifying biomarkers with strong class specific signatures. With all six tools and for all data sets we could achieve better or comparable prediction accuracies usually with fewer marker genes than results reported in the literature using the same computational protocols. The dominant genes are usually easy to find while good dormant genes may not always be available as dormant genes require stronger constraints to be satisfied; but when they are available, they can be used for authentication of diagnosis.</p> <p>Conclusion</p> <p>Since GDI based schemes can find a small set of dominant/dormant biomarkers that is adequate to design diagnostic prediction systems, it opens up the possibility of using real-time qPCR assays or antibody based methods such as ELISA for an easy and low cost diagnosis of diseases. The dominant and dormant genes found by GDIs can be used in different ways to design more reliable diagnostic prediction systems.</p

Computational models and approaches for lung cancer diagnosis

The success of treatment of patients with cancer depends on establishing an accurate diagnosis. To this end, the aim of this study is to developed novel lung cancer diagnostic models. New algorithms are proposed to analyse the biological data and extract knowledge that assists in achieving accurate diagnosis results

Genetic algorithm-neural network: feature extraction for bioinformatics data.

With the advance of gene expression data in the bioinformatics field, the questions which frequently arise, for both computer and medical scientists, are which genes are significantly involved in discriminating cancer classes and which genes are significant with respect to a specific cancer pathology. Numerous computational analysis models have been developed to identify informative genes from the microarray data, however, the integrity of the reported genes is still uncertain. This is mainly due to the misconception of the objectives of microarray study. Furthermore, the application of various preprocessing techniques in the microarray data has jeopardised the quality of the microarray data. As a result, the integrity of the findings has been compromised by the improper use of techniques and the ill-conceived objectives of the study. This research proposes an innovative hybridised model based on genetic algorithms (GAs) and artificial neural networks (ANNs), to extract the highly differentially expressed genes for a specific cancer pathology. The proposed method can efficiently extract the informative genes from the original data set and this has reduced the gene variability errors incurred by the preprocessing techniques. The novelty of the research comes from two perspectives. Firstly, the research emphasises on extracting informative features from a high dimensional and highly complex data set, rather than to improve classification results. Secondly, the use of ANN to compute the fitness function of GA which is rare in the context of feature extraction. Two benchmark microarray data have been taken to research the prominent genes expressed in the tumour development and the results show that the genes respond to different stages of tumourigenesis (i.e. different fitness precision levels) which may be useful for early malignancy detection. The extraction ability of the proposed model is validated based on the expected results in the synthetic data sets. In addition, two bioassay data have been used to examine the efficiency of the proposed model to extract significant features from the large, imbalanced and multiple data representation bioassay data

RENT—Repeated Elastic Net Technique for Feature Selection

publishedVersio

Blood Pressure Estimation from Speech Recordings: Exploring the Role of Voice-over Artists

Hypertension, a prevalent global health concern, is associated with cardiovascular diseases and significant morbidity and mortality. Accurate and prompt Blood Pressure monitoring is crucial for early detection and successful management. Traditional cuff-based methods can be inconvenient, leading to the exploration of non-invasive and continuous estimation methods. This research aims to bridge the gap between speech processing and health monitoring by investigating the relationship between speech recordings and Blood Pressure estimation. Speech recordings offer promise for non-invasive Blood Pressure estimation due to the potential link between vocal characteristics and physiological responses. In this study, we focus on the role of Voice-over Artists, known for their ability to convey emotions through voice. By exploring the expertise of Voice-over Artists in controlling speech and expressing emotions, we seek valuable insights into the potential correlation between speech characteristics and Blood Pressure. This research sheds light on presenting an innovative and convenient approach to health assessment. By unraveling the specific role of Voice-over Artists in this process, the study lays the foundation for future advancements in healthcare and human-robot interactions. Through the exploration of speech characteristics and emotional expression, this investigation offers valuable insights into the correlation between vocal features and Blood Pressure levels. By leveraging the expertise of Voice-over Artists in conveying emotions through voice, this study enriches our understanding of the intricate relationship between speech recordings and physiological responses, opening new avenues for the integration of voice-related factors in healthcare technologies

Genetic algorithm-neural network : feature extraction for bioinformatics data

With the advance of gene expression data in the bioinformatics field, the questions which frequently arise, for both computer and medical scientists, are which genes are significantly involved in discriminating cancer classes and which genes are significant with respect to a specific cancer pathology. Numerous computational analysis models have been developed to identify informative genes from the microarray data, however, the integrity of the reported genes is still uncertain. This is mainly due to the misconception of the objectives of microarray study. Furthermore, the application of various preprocessing techniques in the microarray data has jeopardised the quality of the microarray data. As a result, the integrity of the findings has been compromised by the improper use of techniques and the ill-conceived objectives of the study. This research proposes an innovative hybridised model based on genetic algorithms (GAs) and artificial neural networks (ANNs), to extract the highly differentially expressed genes for a specific cancer pathology. The proposed method can efficiently extract the informative genes from the original data set and this has reduced the gene variability errors incurred by the preprocessing techniques. The novelty of the research comes from two perspectives. Firstly, the research emphasises on extracting informative features from a high dimensional and highly complex data set, rather than to improve classification results. Secondly, the use of ANN to compute the fitness function of GA which is rare in the context of feature extraction. Two benchmark microarray data have been taken to research the prominent genes expressed in the tumour development and the results show that the genes respond to different stages of tumourigenesis (i.e. different fitness precision levels) which may be useful for early malignancy detection. The extraction ability of the proposed model is validated based on the expected results in the synthetic data sets. In addition, two bioassay data have been used to examine the efficiency of the proposed model to extract significant features from the large, imbalanced and multiple data representation bioassay data.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Challenges in biomedical data science: data-driven solutions to clinical questions

Data are influencing every aspect of our lives, from our work activities, to our spare time and even to our health. In this regard, medical diagnosis and treatments are often supported by quantitative measures and observations, such as laboratory tests, medical imaging or genetic analysis. In medicine, as well as in several other scientific domains, the amount of data involved in each decision-making process has become overwhelming. The complexity of the phenomena under investigation and the scale of modern data collections has long superseded human analysis and insights potential

Signal processing methods for mental fatigue measurement and monitoring using EEG

Ph.DDOCTOR OF PHILOSOPH