Gene set based ensemble methods for cancer classification

Diagnosis of cancer very often depends on conclusions drawn after both clinical and microscopic examinations of tissues to study the manifestation of the disease in order to place tumors in known categories. One factor which determines the categorization of cancer is the tissue from which the tumor originates. Information gathered from clinical exams may be partial or not completely predictive of a specific category of cancer. Further complicating the problem of categorizing various tumors is that the histological classification of the cancer tissue and description of its course of development may be atypical. Gene expression data gleaned from micro-array analysis provides tremendous promise for more accurate cancer diagnosis. One hurdle in the classification of tumors based on gene expression data is that the data space is ultra-dimensional with relatively few points; that is, there are a small number of examples with a large number of genes. A second hurdle is expression bias caused by the correlation of genes. Analysis of subsets of genes, known as gene set analysis, provides a mechanism by which groups of differentially expressed genes can be identified. We propose an ensemble of classifiers whose base classifiers are ℓ1-regularized logistic regression models with restriction of the feature space to biologically relevant genes. Some researchers have already explored the use of ensemble classifiers to classify cancer but the effect of the underlying base classifiers in conjunction with biologically-derived gene sets on cancer classification has not been explored

How Important Is Data Quality? Best Classifiers vs Best Features

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] The task of choosing the appropriate classifier for a given scenario is not an easy-to-solve question. First, there is an increasingly high number of algorithms available belonging to different families. And also there is a lack of methodologies that can help on recommending in advance a given family of algorithms for a certain type of datasets. Besides, most of these classification algorithms exhibit a degradation in the performance when faced with datasets containing irrelevant and/or redundant features. In this work we analyze the impact of feature selection in classification over several synthetic and real datasets. The experimental results obtained show that the significance of selecting a classifier decreases after applying an appropriate preprocessing step and, not only this alleviates the choice, but it also improves the results in almost all the datasets tested.This work has been supported by the National Plan for Scientific and Technical Research and Innovation of the Spanish Government (Grant PID2019-109238 GB-C2), and by the Xunta de Galicia (Grant ED431C 2018/34) with the European Union ERDF funds. CITIC, as Research Center accredited by Galician University System, is funded by “Consellería de Cultura, Educación e Universidades from Xunta de Galicia”, supported in an 80% through ERDF Funds, ERDF Operational Programme Galicia 2014–2020, and the remaining 20% by “Secretaría Xeral de Universidades” (Grant ED431G 2019/01). Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431C 2018/34Xunta de Galicia; ED431G 2019/0

Feature selection algorithms for Malaysian dengue outbreak detection model

Dengue fever is considered as one of the most common mosquito borne diseases worldwide. Dengue outbreak detection can be very useful in terms of practical efforts to overcome the rapid spread of the disease by providing the knowledge to predict the next outbreak occurrence. Many studies have been conducted to model and predict dengue outbreak using different data mining techniques. This research aimed to identify the best features that lead to better predictive accuracy of dengue outbreaks using three different feature selection algorithms; particle swarm optimization (PSO), genetic algorithm (GA) and rank search (RS). Based on the selected features, three predictive modeling techniques (J48, DTNB and Naive Bayes) were applied for dengue outbreak detection. The dataset used in this research was obtained from the Public Health Department, Seremban, Negeri Sembilan, Malaysia. The experimental results showed that the predictive accuracy was improved by applying feature selection process before the predictive modeling process. The study also showed the set of features to represent dengue outbreak detection for Malaysian health agencies

Iterative Random Forests to detect predictive and stable high-order interactions

Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on Random Forests (RF), Random Intersection Trees (RITs), and through extensive, biologically inspired simulations, we developed the iterative Random Forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with same order of computational cost as RF. We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the early Drosophila embryo and alternative splicing of primary transcripts in human derived cell lines. In Drosophila, among the 20 pairwise transcription factor interactions iRF identifies as stable (returned in more than half of bootstrap replicates), 80% have been previously reported as physical interactions. Moreover, novel third-order interactions, e.g. between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated splicing regulation, and identified novel 5th and 6th order interactions, indicative of multi-valent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens new avenues of inquiry into the molecular mechanisms underlying genome biology

Using Artificial Intelligence for COVID-19 Detection in Blood Exams: A Comparative Analysis

COVID-19 is an infectious disease that was declared a pandemic by the World Health Organization (WHO) in early March 2020. Since its early development, it has challenged health systems around the world. Although more than 12 billion vaccines have been administered, at the time of writing, it has more than 623 million confirmed cases and more than 6 million deaths reported to the WHO. These numbers continue to grow, soliciting further research efforts to reduce the impacts of such a pandemic. In particular, artificial intelligence techniques have shown great potential in supporting the early diagnosis, detection, and monitoring of COVID-19 infections from disparate data sources. In this work, we aim to make a contribution to this field by analyzing a high-dimensional dataset containing blood sample data from over forty thousand individuals recognized as infected or not with COVID-19. Encompassing a wide range of methods, including traditional machine learning algorithms, dimensionality reduction techniques, and deep learning strategies, our analysis investigates the performance of different classification models, showing that accurate detection of blood infections can be obtained. In particular, an F-score of 84% was achieved by the artificial neural network model we designed for this task, with a rate of 87% correct predictions on the positive class. Furthermore, our study shows that the dimensionality of the original data, i.e. the number of features involved, can be significantly reduced to gain efficiency without compromising the final prediction performance. These results pave the way for further research in this field, confirming that artificial intelligence techniques may play an important role in supporting medical decision-making

Improving Statistical Learning within Functional Genomic Experiments by means of Feature Selection

A Statistical learning approach concerns with understanding and modelling complex datasets. Based on a given training data, its main aim is to build a model that maps the relationship between a set of input features and a considered response in a predictive way. Classification is the foremost task of such a learning process. It has applications encompassing many important fields in modern biology, including microarray data as well as other functional genomic experiments. Microarray technology allow measuring tens of thousands of genes (features) simultaneously. However, the expressions of these genes are usually observed in a small number, tens to few hundreds, of tissue samples (observations). This common characteristic of high dimensionality has a great impact on the learning processes, since most of genes are noisy, redundant or non-relevant to the considered learning task. Both the prediction accuracy and interpretability of a constructed model are believed to be enhanced by performing the learning process based only on selected informative features. Motivated by this notion, a novel statistical method, named Proportional Overlapping Scores (POS), is proposed for selecting features based on overlapping analysis of gene expression data across different classes of a considered classification task. This method results in a measure, called POS score, of a feature’s relevance to the learning task. POS is further extended to minimize the redundancy among the selected features. The proposed approaches are validated on several publicly available gene expression datasets using widely used classifiers to observe effects on their prediction accuracy. Selection stability is also examined to address the captured biological knowledge in the obtained results. The experimental results of classification error rates computed using the Random Forest, k NearestNeighbor and Support VectorMachine classifiers show that the proposals achieve a better performance than widely used gene selection methods

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

Systematic Review on Missing Data Imputation Techniques with Machine Learning Algorithms for Healthcare

Missing data is one of the most common issues encountered in data cleaning process especially when dealing with medical dataset. A real collected dataset is prone to be incomplete, inconsistent, noisy and redundant due to potential reasons such as human errors, instrumental failures, and adverse death. Therefore, to accurately deal with incomplete data, a sophisticated algorithm is proposed to impute those missing values. Many machine learning algorithms have been applied to impute missing data with plausible values. However, among all machine learning imputation algorithms, KNN algorithm has been widely adopted as an imputation for missing data due to its robustness and simplicity and it is also a promising method to outperform other machine learning methods. This paper provides a comprehensive review of different imputation techniques used to replace the missing data. The goal of the review paper is to bring specific attention to potential improvements to existing methods and provide readers with a better grasps of imputation technique trends