SAFS: A Deep Feature Selection Approach for Precision Medicine

In this paper, we propose a new deep feature selection method based on deep architecture. Our method uses stacked auto-encoders for feature representation in higher-level abstraction. We developed and applied a novel feature learning approach to a specific precision medicine problem, which focuses on assessing and prioritizing risk factors for hypertension (HTN) in a vulnerable demographic subgroup (African-American). Our approach is to use deep learning to identify significant risk factors affecting left ventricular mass indexed to body surface area (LVMI) as an indicator of heart damage risk. The results show that our feature learning and representation approach leads to better results in comparison with others

An Incremental Construction of Deep Neuro Fuzzy System for Continual Learning of Non-stationary Data Streams

Existing FNNs are mostly developed under a shallow network configuration having lower generalization power than those of deep structures. This paper proposes a novel self-organizing deep FNN, namely DEVFNN. Fuzzy rules can be automatically extracted from data streams or removed if they play limited role during their lifespan. The structure of the network can be deepened on demand by stacking additional layers using a drift detection method which not only detects the covariate drift, variations of input space, but also accurately identifies the real drift, dynamic changes of both feature space and target space. DEVFNN is developed under the stacked generalization principle via the feature augmentation concept where a recently developed algorithm, namely gClass, drives the hidden layer. It is equipped by an automatic feature selection method which controls activation and deactivation of input attributes to induce varying subsets of input features. A deep network simplification procedure is put forward using the concept of hidden layer merging to prevent uncontrollable growth of dimensionality of input space due to the nature of feature augmentation approach in building a deep network structure. DEVFNN works in the sample-wise fashion and is compatible for data stream applications. The efficacy of DEVFNN has been thoroughly evaluated using seven datasets with non-stationary properties under the prequential test-then-train protocol. It has been compared with four popular continual learning algorithms and its shallow counterpart where DEVFNN demonstrates improvement of classification accuracy. Moreover, it is also shown that the concept drift detection method is an effective tool to control the depth of network structure while the hidden layer merging scenario is capable of simplifying the network complexity of a deep network with negligible compromise of generalization performance.Comment: This paper has been published in IEEE Transactions on Fuzzy System

Intelligent search for distributed information sources using heterogeneous neural networks

As the number and diversity of distributed information sources on the Internet exponentially increase, various search services are developed to help the users to locate relevant information. But they still exist some drawbacks such as the difficulty of mathematically modeling retrieval process, the lack of adaptivity and the indiscrimination of search. This paper shows how heteroge-neous neural networks can be used in the design of an intelligent distributed in-formation retrieval (DIR) system. In particular, three typical neural network models - Kohoren's SOFM Network, Hopfield Network, and Feed Forward Network with Back Propagation algorithm are introduced to overcome the above drawbacks in current research of DIR by using their unique properties. This preliminary investigation suggests that Neural Networks are useful tools for intelligent search for distributed information sources

SCANN: Synthesis of Compact and Accurate Neural Networks

Deep neural networks (DNNs) have become the driving force behind recent artificial intelligence (AI) research. An important problem with implementing a neural network is the design of its architecture. Typically, such an architecture is obtained manually by exploring its hyperparameter space and kept fixed during training. This approach is time-consuming and inefficient. Another issue is that modern neural networks often contain millions of parameters, whereas many applications and devices require small inference models. However, efforts to migrate DNNs to such devices typically entail a significant loss of classification accuracy. To address these challenges, we propose a two-step neural network synthesis methodology, called DR+SCANN, that combines two complementary approaches to design compact and accurate DNNs. At the core of our framework is the SCANN methodology that uses three basic architecture-changing operations, namely connection growth, neuron growth, and connection pruning, to synthesize feed-forward architectures with arbitrary structure. SCANN encapsulates three synthesis methodologies that apply a repeated grow-and-prune paradigm to three architectural starting points. DR+SCANN combines the SCANN methodology with dataset dimensionality reduction to alleviate the curse of dimensionality. We demonstrate the efficacy of SCANN and DR+SCANN on various image and non-image datasets. We evaluate SCANN on MNIST and ImageNet benchmarks. In addition, we also evaluate the efficacy of using dimensionality reduction alongside SCANN (DR+SCANN) on nine small to medium-size datasets. We also show that our synthesis methodology yields neural networks that are much better at navigating the accuracy vs. energy efficiency space. This would enable neural network-based inference even on Internet-of-Things sensors.Comment: 13 pages, 8 figure

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

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