Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Multilayer probability extreme learning machine for device-free localization

Device-free localization (DFL) is becoming one of the new techniques in wireless localization field, due to its advantage that the target to be localized does not need to attach any electronic device. One of the key issues of DFL is how to characterize the influence of the target on the wireless links, such that the target’s location can be accurately estimated by analyzing the changes of the signals of the links. Most of the existing related research works usually extract the useful information from the links through manual approaches, which are labor-intensive and time-consuming. Deep learning approaches have attempted to automatically extract the useful information from the links, but the training of the conventional deep learning approaches are time-consuming, because a large number of parameters need to be fine-tuned multiple times. Motivated by the fast learning speed and excellent generalization performance of extreme learning machine (ELM), which is an emerging training approach for generalized single hidden layer feedforward neural networks (SLFNs), this paper proposes a novel hierarchical ELM based on deep learning theory, named multilayer probability ELM (MP-ELM), for automatically extracting the useful information from the links, and implementing fast and accurate DFL. The proposed MP-ELM is stacked by ELM autoencoders, so it also keeps the very fast learning speed of ELM. In addition, considering the uncertainty and redundant links existing in DFL, MP-ELM outputs the probabilistic estimation of the target’s location instead of the deterministic output. The validity of the proposed MP-ELM-based DFL is evaluated both in the indoor and the outdoor environments, respectively. Experimental results demonstrate that the proposed MP-ELM can obtain better performance compared with classic ELM, multilayer ELM (ML-ELM), hierarchical ELM (H-ELM), deep belief network (DBN), and deep Boltzmann machine (DBM)

Towards a more efficient and cost-sensitive extreme learning machine: A state-of-the-art review of recent trend

In spite of the prominence of extreme learning machine model, as well as its excellent features such as insignificant intervention for learning and model tuning, the simplicity of implementation, and high learning speed, which makes it a fascinating alternative method for Artificial Intelligence, including Big Data Analytics, it is still limited in certain aspects. These aspects must be treated to achieve an effective and cost-sensitive model. This review discussed the major drawbacks of ELM, which include difficulty in determination of hidden layer structure, prediction instability and Imbalanced data distributions, the poor capability of sample structure preserving (SSP), and difficulty in accommodating lateral inhibition by direct random feature mapping. Other drawbacks include multi-graph complexity, global memory size, one-by-one or chuck-by-chuck (a block of data), global memory size limitation, and challenges with big data. The recent trend proposed by experts for each drawback is discussed in detail towards achieving an effective and cost-sensitive mode

A Novel SMOTE-Based Classification Approach to Online Data Imbalance Problem

In many practical engineering applications, data are usually collected in online pattern. However, if the classes of these data are severely imbalanced, the classification performance will be restricted. In this paper, a novel classification approach is proposed to solve the online data imbalance problem by integrating a fast and efficient learning algorithm, that is, Extreme Learning Machine (ELM), and a typical sampling strategy, that is, the synthetic minority oversampling technique (SMOTE). To reduce the severe imbalance, the granulation division for major-class samples is made according to the samples’ distribution characteristic, and the original samples are replaced by the obtained granule core to prepare a balanced sample set. In online stage, we firstly make granulation division for minor-class and then conduct oversampling using SMOTE in the region around granule core and granule border. Therefore, the training sample set is gradually balanced and the online ELM model is dynamically updated. We also theoretically introduce fuzzy information entropy to prove that the proposed approach has the lower bound of model reliability after undersampling. Numerical experiments are conducted on two different kinds of datasets, and the results demonstrate that the proposed approach outperforms some state-of-the-art methods in terms of the generalization performance and numerical stability

An insight into imbalanced Big Data classification: outcomes and challenges

Big Data applications are emerging during the last years, and researchers from many disciplines are aware of the high advantages related to the knowledge extraction from this type of problem. However, traditional learning approaches cannot be directly applied due to scalability issues. To overcome this issue, the MapReduce framework has arisen as a “de facto” solution. Basically, it carries out a “divide-and-conquer” distributed procedure in a fault-tolerant way to adapt for commodity hardware. Being still a recent discipline, few research has been conducted on imbalanced classification for Big Data. The reasons behind this are mainly the difficulties in adapting standard techniques to the MapReduce programming style. Additionally, inner problems of imbalanced data, namely lack of data and small disjuncts, are accentuated during the data partitioning to fit the MapReduce programming style. This paper is designed under three main pillars. First, to present the first outcomes for imbalanced classification in Big Data problems, introducing the current research state of this area. Second, to analyze the behavior of standard pre-processing techniques in this particular framework. Finally, taking into account the experimental results obtained throughout this work, we will carry out a discussion on the challenges and future directions for the topic.This work has been partially supported by the Spanish Ministry of Science and Technology under Projects TIN2014-57251-P and TIN2015-68454-R, the Andalusian Research Plan P11-TIC-7765, the Foundation BBVA Project 75/2016 BigDaPTOOLS, and the National Science Foundation (NSF) Grant IIS-1447795

Data classification methodology for electronic noses using uniform manifold approximation and projection and extreme learning machine

The classification and use of robust methodologies in sensor array applications of electronic noses (ENs) remain an open problem. Among the several steps used in the developed methodologies, data preprocessing improves the classification accuracy of this type of sensor. Data preprocessing methods, such as data transformation and data reduction, enable the treatment of data with anomalies, such as outliers and features, that do not provide quality information; in addition, they reduce the dimensionality of the data, thereby facilitating the tasks of a machine learning classifier. To help solve this problem, in this study, a machine learning methodology is introduced to improve signal processing and develop methodologies for classification when an EN is used. The proposed methodology involves a normalization stage to scale the data from the sensors, using both the well-known min-max approach and the more recent mean-centered unitary group scaling (MCUGS). Next, a manifold learning algorithm for data reduction is applied using uniform manifold approximation and projection (UMAP). The dimensionality of the data at the input of the classification machine is reduced, and an extreme learning machine (ELM) is used as a machine learning classifier algorithm. To validate the EN classification methodology, three datasets of ENs were used. The first dataset was composed of 3600 measurements of 6 volatile organic compounds performed by employing 16 metal-oxide gas sensors. The second dataset was composed of 235 measurements of 3 different qualities of wine, namely, high, average, and low, as evaluated by using an EN sensor array composed of 6 different sensors. The third dataset was composed of 309 measurements of 3 different gases obtained by using an EN sensor array of 2 sensors. A 5-fold cross-validation approach was used to evaluate the proposed methodology. A test set consisting of 25% of the data was used to validate the methodology with unseen data. The results showed a fully correct average classification accuracy of 1 when the MCUGS, UMAP, and ELM methods were used. Finally, the effect of changing the number of target dimensions on the reduction of the number of data was determined based on the highest average classification accuracy.This work was funded in part with resources from the Fondo de Ciencia, Tecnología e Innovación (FCTeI) del Sistema General de Regalías (SGR) from Colombia. The authors express their gratitude to the Administrative Department of Science, Technology, and Innovation–Colciencias with the grant 779–“Convocatoria para la Formación de Capital Humano de Alto Nivel para el Departamento de Boyacá 2017” for sponsoring the research presented herein. This study has been partially funded by the Spanish Agencia Estatal de Investigación (AEI)-Ministerio de Economía, Industria y Competitividad (MINECO), and the Fondo Europeo de Desarrollo Regional (FEDER) through research projects DPI2017-82930-C2-1-R and PGC2018-097257-B-C33; and by the Generalitat de Catalunya through research projects 2017-SGR-388 and 2017-SGR-1278.Peer ReviewedPostprint (published version