Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data

Abstract Managing, processing and understanding big healthcare data is challenging, costly and demanding. Without a robust fundamental theory for representation, analysis and inference, a roadmap for uniform handling and analyzing of such complex data remains elusive. In this article, we outline various big data challenges, opportunities, modeling methods and software techniques for blending complex healthcare data, advanced analytic tools, and distributed scientific computing. Using imaging, genetic and healthcare data we provide examples of processing heterogeneous datasets using distributed cloud services, automated and semi-automated classification techniques, and open-science protocols. Despite substantial advances, new innovative technologies need to be developed that enhance, scale and optimize the management and processing of large, complex and heterogeneous data. Stakeholder investments in data acquisition, research and development, computational infrastructure and education will be critical to realize the huge potential of big data, to reap the expected information benefits and to build lasting knowledge assets. Multi-faceted proprietary, open-source, and community developments will be essential to enable broad, reliable, sustainable and efficient data-driven discovery and analytics. Big data will affect every sector of the economy and their hallmark will be ‘team science’.http://deepblue.lib.umich.edu/bitstream/2027.42/134522/1/13742_2016_Article_117.pd

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

Shared Nearest-Neighbor Quantum Game-Based Attribute Reduction with Hierarchical Coevolutionary Spark and Its Application in Consistent Segmentation of Neonatal Cerebral Cortical Surfaces

© 2012 IEEE. The unprecedented increase in data volume has become a severe challenge for conventional patterns of data mining and learning systems tasked with handling big data. The recently introduced Spark platform is a new processing method for big data analysis and related learning systems, which has attracted increasing attention from both the scientific community and industry. In this paper, we propose a shared nearest-neighbor quantum game-based attribute reduction (SNNQGAR) algorithm that incorporates the hierarchical coevolutionary Spark model. We first present a shared coevolutionary nearest-neighbor hierarchy with self-evolving compensation that considers the features of nearest-neighborhood attribute subsets and calculates the similarity between attribute subsets according to the shared neighbor information of attribute sample points. We then present a novel attribute weight tensor model to generate ranking vectors of attributes and apply them to balance the relative contributions of different neighborhood attribute subsets. To optimize the model, we propose an embedded quantum equilibrium game paradigm (QEGP) to ensure that noisy attributes do not degrade the big data reduction results. A combination of the hierarchical coevolutionary Spark model and an improved MapReduce framework is then constructed that it can better parallelize the SNNQGAR to efficiently determine the preferred reduction solutions of the distributed attribute subsets. The experimental comparisons demonstrate the superior performance of the SNNQGAR, which outperforms most of the state-of-the-art attribute reduction algorithms. Moreover, the results indicate that the SNNQGAR can be successfully applied to segment overlapping and interdependent fuzzy cerebral tissues, and it exhibits a stable and consistent segmentation performance for neonatal cerebral cortical surfaces

Big data analytics:Computational intelligence techniques and application areas

Big Data has significant impact in developing functional smart cities and supporting modern societies. In this paper, we investigate the importance of Big Data in modern life and economy, and discuss challenges arising from Big Data utilization. Different computational intelligence techniques have been considered as tools for Big Data analytics. We also explore the powerful combination of Big Data and Computational Intelligence (CI) and identify a number of areas, where novel applications in real world smart city problems can be developed by utilizing these powerful tools and techniques. We present a case study for intelligent transportation in the context of a smart city, and a novel data modelling methodology based on a biologically inspired universal generative modelling approach called Hierarchical Spatial-Temporal State Machine (HSTSM). We further discuss various implications of policy, protection, valuation and commercialization related to Big Data, its applications and deployment

Brain-inspired self-organization with cellular neuromorphic computing for multimodal unsupervised learning

Cortical plasticity is one of the main features that enable our ability to learn and adapt in our environment. Indeed, the cerebral cortex self-organizes itself through structural and synaptic plasticity mechanisms that are very likely at the basis of an extremely interesting characteristic of the human brain development: the multimodal association. In spite of the diversity of the sensory modalities, like sight, sound and touch, the brain arrives at the same concepts (convergence). Moreover, biological observations show that one modality can activate the internal representation of another modality when both are correlated (divergence). In this work, we propose the Reentrant Self-Organizing Map (ReSOM), a brain-inspired neural system based on the reentry theory using Self-Organizing Maps and Hebbian-like learning. We propose and compare different computational methods for unsupervised learning and inference, then quantify the gain of the ReSOM in a multimodal classification task. The divergence mechanism is used to label one modality based on the other, while the convergence mechanism is used to improve the overall accuracy of the system. We perform our experiments on a constructed written/spoken digits database and a DVS/EMG hand gestures database. The proposed model is implemented on a cellular neuromorphic architecture that enables distributed computing with local connectivity. We show the gain of the so-called hardware plasticity induced by the ReSOM, where the system's topology is not fixed by the user but learned along the system's experience through self-organization.Comment: Preprin

Self-building Artificial Intelligence and machine learning to empower big data analytics in smart cities

YesThe emerging information revolution makes it necessary to manage vast amounts of unstructured data rapidly. As the world is increasingly populated by IoT devices and sensors that can sense their surroundings and communicate with each other, a digital environment has been created with vast volumes of volatile and diverse data. Traditional AI and machine learning techniques designed for deterministic situations are not suitable for such environments. With a large number of parameters required by each device in this digital environment, it is desirable that the AI is able to be adaptive and self-build (i.e. self-structure, self-configure, self-learn), rather than be structurally and parameter-wise pre-defined. This study explores the benefits of self-building AI and machine learning with unsupervised learning for empowering big data analytics for smart city environments. By using the growing self-organizing map, a new suite of self-building AI is proposed. The self-building AI overcomes the limitations of traditional AI and enables data processing in dynamic smart city environments. With cloud computing platforms, the selfbuilding AI can integrate the data analytics applications that currently work in silos. The new paradigm of the self-building AI and its value are demonstrated using the IoT, video surveillance, and action recognition applications.Supported by the Data to Decisions Cooperative Research Centre (D2D CRC) as part of their analytics and decision support program and a La Trobe University Postgraduate Research Scholarship

Efficient Implementation of Stochastic Inference on Heterogeneous Clusters and Spiking Neural Networks

Neuromorphic computing refers to brain inspired algorithms and architectures. This paradigm of computing can solve complex problems which were not possible with traditional computing methods. This is because such implementations learn to identify the required features and classify them based on its training, akin to how brains function. This task involves performing computation on large quantities of data. With this inspiration, a comprehensive multi-pronged approach is employed to study and efficiently implement neuromorphic inference model using heterogeneous clusters to address the problem using traditional Von Neumann architectures and by developing spiking neural networks (SNN) for native and ultra-low power implementation. In this regard, an extendable high-performance computing (HPC) framework and optimizations are proposed for heterogeneous clusters to modularize complex neuromorphic applications in a distributed manner. To achieve best possible throughput and load balancing for such modularized architectures a set of algorithms are proposed to suggest the optimal mapping of different modules as an asynchronous pipeline to the available cluster resources while considering the complex data dependencies between stages. On the other hand, SNNs are more biologically plausible and can achieve ultra-low power implementation due to its sparse spike based communication, which is possible with emerging non-Von Neumann computing platforms. As a significant progress in this direction, spiking neuron models capable of distributed online learning are proposed. A high performance SNN simulator (SpNSim) is developed for simulation of large scale mixed neuron model networks. An accompanying digital hardware neuron RTL is also proposed for efficient real time implementation of SNNs capable of online learning. Finally, a methodology for mapping probabilistic graphical model to off-the-shelf neurosynaptic processor (IBM TrueNorth) as a stochastic SNN is presented with ultra-low power consumption

Neuromorphic Learning Systems for Supervised and Unsupervised Applications

The advancements in high performance computing (HPC) have enabled the large-scale implementation of neuromorphic learning models and pushed the research on computational intelligence into a new era. Those bio-inspired models are constructed on top of unified building blocks, i.e. neurons, and have revealed potentials for learning of complex information. Two major challenges remain in neuromorphic computing. Firstly, sophisticated structuring methods are needed to determine the connectivity of the neurons in order to model various problems accurately. Secondly, the models need to adapt to non-traditional architectures for improved computation speed and energy efficiency. In this thesis, we address these two problems and apply our techniques to different cognitive applications. This thesis first presents the self-structured confabulation network for anomaly detection. Among the machine learning applications, unsupervised detection of the anomalous streams is especially challenging because it requires both detection accuracy and real-time performance. Designing a computing framework that harnesses the growing computing power of the multicore systems while maintaining high sensitivity and specificity to the anomalies is an urgent research need. We present AnRAD (Anomaly Recognition And Detection), a bio-inspired detection framework that performs probabilistic inferences. We leverage the mutual information between the features and develop a self-structuring procedure that learns a succinct confabulation network from the unlabeled data. This network is capable of fast incremental learning, which continuously refines the knowledge base from the data streams. Compared to several existing anomaly detection methods, the proposed approach provides competitive detection accuracy as well as the insight to reason the decision making. Furthermore, we exploit the massive parallel structure of the AnRAD framework. Our implementation of the recall algorithms on the graphic processing unit (GPU) and the Xeon Phi co-processor both obtain substantial speedups over the sequential implementation on general-purpose microprocessor (GPP). The implementation enables real-time service to concurrent data streams with diversified contexts, and can be applied to large problems with multiple local patterns. Experimental results demonstrate high computing performance and memory efficiency. For vehicle abnormal behavior detection, the framework is able to monitor up to 16000 vehicles and their interactions in real-time with a single commodity co-processor, and uses less than 0.2ms for each testing subject. While adapting our streaming anomaly detection model to mobile devices or unmanned systems, the key challenge is to deliver required performance under the stringent power constraint. To address the paradox between performance and power consumption, brain-inspired hardware, such as the IBM Neurosynaptic System, has been developed to enable low power implementation of neural models. As a follow-up to the AnRAD framework, we proposed to port the detection network to the TrueNorth architecture. Implementing inference based anomaly detection on a neurosynaptic processor is not straightforward due to hardware limitations. A design flow and the supporting component library are developed to flexibly map the learned detection networks to the neurosynaptic cores. Instead of the popular rate code, burst code is adopted in the design, which represents numerical value using the phase of a burst of spike trains. This does not only reduce the hardware complexity, but also increases the result\u27s accuracy. A Corelet library, NeoInfer-TN, is implemented for basic operations in burst code and two-phase pipelines are constructed based on the library components. The design can be configured for different tradeoffs between detection accuracy, hardware resource consumptions, throughput and energy. We evaluate the system using network intrusion detection data streams. The results show higher detection rate than some conventional approaches and real-time performance, with only 50mW power consumption. Overall, it achieves 10^8 operations per Joule. In addition to the modeling and implementation of unsupervised anomaly detection, we also investigate a supervised learning model based on neural networks and deep fragment embedding and apply it to text-image retrieval. The study aims at bridging the gap between image and natural language. It continues to improve the bidirectional retrieval performance across the modalities. Unlike existing works that target at single sentence densely describing the image objects, we elevate the topic to associating deep image representations with noisy texts that are only loosely correlated. Based on text-image fragment embedding, our model employs a sequential configuration, connects two embedding stages together. The first stage learns the relevancy of the text fragments, and the second stage uses the filtered output from the first one to improve the matching results. The model also integrates multiple convolutional neural networks (CNN) to construct the image fragments, in which rich context information such as human faces can be extracted to increase the alignment accuracy. The proposed method is evaluated with both synthetic dataset and real-world dataset collected from picture news website. The results show up to 50% ranking performance improvement over the comparison models