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

Coupling different methods for overcoming the class imbalance problem

Many classification problems must deal with imbalanced datasets where one class \u2013 the majority class \u2013 outnumbers the other classes. Standard classification methods do not provide accurate predictions in this setting since classification is generally biased towards the majority class. The minority classes are oftentimes the ones of interest (e.g., when they are associated with pathological conditions in patients), so methods for handling imbalanced datasets are critical. Using several different datasets, this paper evaluates the performance of state-of-the-art classification methods for handling the imbalance problem in both binary and multi-class datasets. Different strategies are considered, including the one-class and dimension reduction approaches, as well as their fusions. Moreover, some ensembles of classifiers are tested, in addition to stand-alone classifiers, to assess the effectiveness of ensembles in the presence of imbalance. Finally, a novel ensemble of ensembles is designed specifically to tackle the problem of class imbalance: the proposed ensemble does not need to be tuned separately for each dataset and outperforms all the other tested approaches. To validate our classifiers we resort to the KEEL-dataset repository, whose data partitions (training/test) are publicly available and have already been used in the open literature: as a consequence, it is possible to report a fair comparison among different approaches in the literature. Our best approach (MATLAB code and datasets not easily accessible elsewhere) will be available at https://www.dei.unipd.it/node/2357

Parameter-Free Extreme Learning Machine for Imbalanced Classification

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A reduced labeled samples (RLS) framework for classification of imbalanced concept-drifting streaming data.

Stream processing frameworks are designed to process the streaming data that arrives in time. An example of such data is stream of emails that a user receives every day. Most of the real world data streams are also imbalanced as is in the stream of emails, which contains few spam emails compared to a lot of legitimate emails. The classification of the imbalanced data stream is challenging due to the several reasons: First of all, data streams are huge and they can not be stored in the memory for one time processing. Second, if the data is imbalanced, the accuracy of the majority class mostly dominates the results. Third, data streams are changing over time, and that causes degradation in the model performance. Hence the model should get updated when such changes are detected. Finally, the true labels of the all samples are not available immediately after classification, and only a fraction of the data is possible to get labeled in real world applications. That is because the labeling is expensive and time consuming. In this thesis, a framework for modeling the streaming data when the classes of the data samples are imbalanced is proposed. This framework is called Reduced Labeled Samples (RLS). RLS is a chunk based learning framework that builds a model using partially labeled data stream, when the characteristics of the data change. In RLS, a fraction of the samples are labeled and are used in modeling, and the performance is not significantly different from that of the 100% labeling. RLS maintains an ensemble of classifiers to boost the performance. RLS uses the information from labeled data in a supervised fashion, and also is extended to use the information from unlabeled data in a semi supervised fashion. RLS addresses both binary and multi class partially labeled data stream and the results show the basis of RLS is effective even in the context of multi class classification problems. Overall, the RLS is shown to be an effective framework for processing imbalanced and partially labeled data streams

Graph ensemble boosting for imbalanced noisy graph stream classification

© 2014 IEEE. Many applications involve stream data with structural dependency, graph representations, and continuously increasing volumes. For these applications, it is very common that their class distributions are imbalanced with minority (or positive) samples being only a small portion of the population, which imposes significant challenges for learning models to accurately identify minority samples. This problem is further complicated with the presence of noise, because they are similar to minority samples and any treatment for the class imbalance may falsely focus on the noise and result in deterioration of accuracy. In this paper, we propose a classification model to tackle imbalanced graph streams with noise. Our method, graph ensemble boosting, employs an ensemble-based framework to partition graph stream into chunks each containing a number of noisy graphs with imbalanced class distributions. For each individual chunk, we propose a boosting algorithm to combine discriminative subgraph pattern selection and model learning as a unified framework for graph classification. To tackle concept drifting in graph streams, an instance level weighting mechanism is used to dynamically adjust the instance weight, through which the boosting framework can emphasize on difficult graph samples. The classifiers built from different graph chunks form an ensemble for graph stream classification. Experiments on real-life imbalanced graph streams demonstrate clear benefits of our boosting design for handling imbalanced noisy graph stream

Cost-Sensitive Learning-based Methods for Imbalanced Classification Problems with Applications

Analysis and predictive modeling of massive datasets is an extremely significant problem that arises in many practical applications. The task of predictive modeling becomes even more challenging when data are imperfect or uncertain. The real data are frequently affected by outliers, uncertain labels, and uneven distribution of classes (imbalanced data). Such uncertainties create bias and make predictive modeling an even more difficult task. In the present work, we introduce a cost-sensitive learning method (CSL) to deal with the classification of imperfect data. Typically, most traditional approaches for classification demonstrate poor performance in an environment with imperfect data. We propose the use of CSL with Support Vector Machine, which is a well-known data mining algorithm. The results reveal that the proposed algorithm produces more accurate classifiers and is more robust with respect to imperfect data. Furthermore, we explore the best performance measures to tackle imperfect data along with addressing real problems in quality control and business analytics