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

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

Autoencoders and Generative Adversarial Networks for Imbalanced Sequence Classification

Generative Adversarial Networks (GANs) have been used in many different applications to generate realistic synthetic data. We introduce a novel GAN with Autoencoder (GAN-AE) architecture to generate synthetic samples for variable length, multi-feature sequence datasets. In this model, we develop a GAN architecture with an additional autoencoder component, where recurrent neural networks (RNNs) are used for each component of the model in order to generate synthetic data to improve classification accuracy for a highly imbalanced medical device dataset. In addition to the medical device dataset, we also evaluate the GAN-AE performance on two additional datasets and demonstrate the application of GAN-AE to a sequence-to-sequence task where both synthetic sequence inputs and sequence outputs must be generated. To evaluate the quality of the synthetic data, we train encoder-decoder models both with and without the synthetic data and compare the classification model performance. We show that a model trained with GAN-AE generated synthetic data outperforms models trained with synthetic data generated both with standard oversampling techniques such as SMOTE and Autoencoders as well as with state of the art GAN-based models