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

RMSE-ELM: Recursive Model based Selective Ensemble of Extreme Learning Machines for Robustness Improvement

Extreme learning machine (ELM) as an emerging branch of shallow networks has shown its excellent generalization and fast learning speed. However, for blended data, the robustness of ELM is weak because its weights and biases of hidden nodes are set randomly. Moreover, the noisy data exert a negative effect. To solve this problem, a new framework called RMSE-ELM is proposed in this paper. It is a two-layer recursive model. In the first layer, the framework trains lots of ELMs in different groups concurrently, then employs selective ensemble to pick out an optimal set of ELMs in each group, which can be merged into a large group of ELMs called candidate pool. In the second layer, selective ensemble is recursively used on candidate pool to acquire the final ensemble. In the experiments, we apply UCI blended datasets to confirm the robustness of our new approach in two key aspects (mean square error and standard deviation). The space complexity of our method is increased to some degree, but the results have shown that RMSE-ELM significantly improves robustness with slightly computational time compared with representative methods (ELM, OP-ELM, GASEN-ELM, GASEN-BP and E-GASEN). It becomes a potential framework to solve robustness issue of ELM for high-dimensional blended data in the future.Comment: Accepted for publication in Mathematical Problems in Engineering, 09/22/201

ADEPOS: Anomaly Detection based Power Saving for Predictive Maintenance using Edge Computing

In industry 4.0, predictive maintenance(PM) is one of the most important applications pertaining to the Internet of Things(IoT). Machine learning is used to predict the possible failure of a machine before the actual event occurs. However, the main challenges in PM are (a) lack of enough data from failing machines, and (b) paucity of power and bandwidth to transmit sensor data to cloud throughout the lifetime of the machine. Alternatively, edge computing approaches reduce data transmission and consume low energy. In this paper, we propose Anomaly Detection based Power Saving(ADEPOS) scheme using approximate computing through the lifetime of the machine. In the beginning of the machines life, low accuracy computations are used when the machine is healthy. However, on the detection of anomalies, as time progresses, the system is switched to higher accuracy modes. We show using the NASA bearing dataset that using ADEPOS, we need 8.8X less neurons on average and based on post-layout results, the resultant energy savings are 6.4 to 6.65XComment: Submitted to ASP-DAC 2019, Japa

Combining similarity in time and space for training set formation under concept drift

Concept drift is a challenge in supervised learning for sequential data. It describes a phenomenon when the data distributions change over time. In such a case accuracy of a classifier benefits from the selective sampling for training. We develop a method for training set selection, particularly relevant when the expected drift is gradual. Training set selection at each time step is based on the distance to the target instance. The distance function combines similarity in space and in time. The method determines an optimal training set size online at every time step using cross validation. It is a wrapper approach, it can be used plugging in different base classifiers. The proposed method shows the best accuracy in the peer group on the real and artificial drifting data. The method complexity is reasonable for the field applications

Evolving Ensemble Fuzzy Classifier

The concept of ensemble learning offers a promising avenue in learning from data streams under complex environments because it addresses the bias and variance dilemma better than its single model counterpart and features a reconfigurable structure, which is well suited to the given context. While various extensions of ensemble learning for mining non-stationary data streams can be found in the literature, most of them are crafted under a static base classifier and revisits preceding samples in the sliding window for a retraining step. This feature causes computationally prohibitive complexity and is not flexible enough to cope with rapidly changing environments. Their complexities are often demanding because it involves a large collection of offline classifiers due to the absence of structural complexities reduction mechanisms and lack of an online feature selection mechanism. A novel evolving ensemble classifier, namely Parsimonious Ensemble pENsemble, is proposed in this paper. pENsemble differs from existing architectures in the fact that it is built upon an evolving classifier from data streams, termed Parsimonious Classifier pClass. pENsemble is equipped by an ensemble pruning mechanism, which estimates a localized generalization error of a base classifier. A dynamic online feature selection scenario is integrated into the pENsemble. This method allows for dynamic selection and deselection of input features on the fly. pENsemble adopts a dynamic ensemble structure to output a final classification decision where it features a novel drift detection scenario to grow the ensemble structure. The efficacy of the pENsemble has been numerically demonstrated through rigorous numerical studies with dynamic and evolving data streams where it delivers the most encouraging performance in attaining a tradeoff between accuracy and complexity.Comment: this paper has been published by IEEE Transactions on Fuzzy System