Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties, and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large (n=1340) microarray and Illumina GAII RNA-seq transcriptomics datasets. Availability and Implementation: Source code and binaries are freely available for download under GPL3 licence at http://minepy.sourceforge.net for minepy and through the CRAN repository http://cran.r-project.org for the R package minerva. All software is multiplatform (MS Windows, Linux and OSX).Comment: Bioinformatics 2012, in pres

TICAL - a web-tool for multivariate image clustering and data topology preserving visualization

In life science research bioimaging is often used to study two kinds of features in a sample simultaneously: morphology and co-location of molecular components. While bioimaging technology is rapidly proposing and improving new multidimensional imaging platforms, bioimage informatics has to keep pace in order to develop algorithmic approaches to support biology experts in the complex task of data analysis. One particular problem is the availability and applicability of sophisticated image analysis algorithms via the web so different users can apply the same algorithms to their data (sometimes even to the same data to get the same results) and independently from her/his whereabouts and from the technical features of her/his computer. In this paper we describe TICAL, a visual data mining approach to multivariate microscopy analysis which can be applied fully through the web.We describe the algorithmic approach, the software concept and present results obtained for different example images

GenomeVIP: A cloud platform for genomic variant discovery and interpretation

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets.</jats:p

Support Vector Machines in a real time tracking architecture

The standard approach to tracking an object of interest in a video stream is to use an object detector, a classifier and a tracker in sequential order. This work investigates the use of Support Vector Machines (SVM) as classifiers for real-time tracking systems, combining them with Kalman Filter predictors. Support Vector Machines have been proved successful in a variety of classification tasks such as recognizing faces, cars, handwriting and others. However their use has been hampered by the complexity and computational time involved in the training and classification stages. In recent years new methods and techniques for training and classification of Support Vector Machines have been discovered making possible their utilization in real-time applications. These methods have been explored and improved resulting in a framework for fast prototyping and development of real-time tracking systems. New optimal and sub-optimal methods for parallel SVM training based on biased and unbiased versions of the Sequential Minimal Optimization algorithm are presented. They provide a trade-off between time performance and accuracy. Time performance in the classification stage is significantly improved by reducing the number of support vectors with almost no loss in accuracy. New methods to allow the reduction with different kernels are presented. The effectiveness of the approach developed is demonstrated in a face tracking problem where the objective is to track the lips and eyes of a subject in a video stream in real-time

Concepção e realização de um framework para sistemas embarcados baseados em FPGA aplicado a um classificador Floresta de Caminhos Ótimos

Orientadores: Eurípedes Guilherme de Oliveira Nóbrega, Isabelle Fantoni-Coichot, Vincent FrémontTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica, Université de Technologie de CompiègneResumo: Muitas aplicações modernas dependem de métodos de Inteligência Artificial, tais como classificação automática. Entretanto, o alto custo computacional associado a essas técnicas limita seu uso em plataformas embarcadas com recursos restritos. Grandes quantidades de dados podem superar o poder computacional disponível em tais ambientes, o que torna o processo de projetá-los uma tarefa desafiadora. As condutas de processamento mais comuns usam muitas funções de custo computacional elevadas, o que traz a necessidade de combinar alta capacidade computacional com eficiência energética. Uma possível estratégia para superar essas limitações e prover poder computacional suficiente aliado ao baixo consumo de energia é o uso de hardware especializado como, por exemplo, FPGA. Esta classe de dispositivos é amplamente conhecida por sua boa relação desempenho/consumo, sendo uma alternativa interessante para a construção de sistemas embarcados eficazes e eficientes. Esta tese propõe um framework baseado em FPGA para a aceleração de desempenho de um algoritmo de classificação a ser implementado em um sistema embarcado. A aceleração do desempenho foi atingida usando o esquema de paralelização SIMD, aproveitando as características de paralelismo de grão fino dos FPGA. O sistema proposto foi implementado e testado em hardware FPGA real. Para a validação da arquitetura, um classificador baseado em Teoria dos Grafos, o OPF, foi avaliado em uma proposta de aplicação e posteriormente implementado na arquitetura proposta. O estudo do OPF levou à proposição de um novo algoritmo de aprendizagem para o mesmo, usando conceitos de Computação Evolutiva, visando a redução do tempo de processamento de classificação, que, combinada à implementação em hardware, oferece uma aceleração de desempenho suficiente para ser aplicada em uma variedade de sistemas embarcadosAbstract: Many modern applications rely on Artificial Intelligence methods such as automatic classification. However, the computational cost associated with these techniques limit their use in resource constrained embedded platforms. A high amount of data may overcome the computational power available in such embedded environments while turning the process of designing them a challenging task. Common processing pipelines use many high computational cost functions, which brings the necessity of combining high computational capacity with energy efficiency. One of the strategies to overcome this limitation and provide sufficient computational power allied with low energy consumption is the use of specialized hardware such as FPGA. This class of devices is widely known for their performance to consumption ratio, being an interesting alternative to building capable embedded systems. This thesis proposes an FPGA-based framework for performance acceleration of a classification algorithm to be implemented in an embedded system. Acceleration is achieved using SIMD-based parallelization scheme, taking advantage of FPGA characteristics of fine-grain parallelism. The proposed system is implemented and tested in actual FPGA hardware. For the architecture validation, a graph-based classifier, the OPF, is evaluated in an application proposition and afterward applied to the proposed architecture. The OPF study led to a proposition of a new learning algorithm using evolutionary computation concepts, aiming at classification processing time reduction, which combined to the hardware implementation offers sufficient performance acceleration to be applied in a variety of embedded systemsDoutoradoMecanica dos Sólidos e Projeto MecanicoDoutor em Engenharia Mecânica3077/2013-09CAPE

Big Data Analytics for Earth Sciences: the EarthServer approach

Big Data Analytics is an emerging field since massive storage and computing capabilities have been made available by advanced e-infrastructures. Earth and Environmental sciences are likely to benefit from Big Data Analytics techniques supporting the processing of the large number of Earth Observation datasets currently acquired and generated through observations and simulations. However, Earth Science data and applications present specificities in terms of relevance of the geospatial information, wide heterogeneity of data models and formats, and complexity of processing. Therefore, Big Earth Data Analytics requires specifically tailored techniques and tools. The EarthServer Big Earth Data Analytics engine offers a solution for coverage-type datasets, built around a high performance array database technology, and the adoption and enhancement of standards for service interaction (OGC WCS and WCPS). The EarthServer solution, led by the collection of requirements from scientific communities and international initiatives, provides a holistic approach that ranges from query languages and scalability up to mobile access and visualization. The result is demonstrated and validated through the development of lighthouse applications in the Marine, Geology, Atmospheric, Planetary and Cryospheric science domains

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

Computational Modeling of Biological Neural Networks on GPUs: Strategies and Performance

Simulating biological neural networks is an important task for computational neuroscientists attempting to model and analyze brain activity and function. As these networks become larger and more complex, the computational power required grows significantly, often requiring the use of supercomputers or compute clusters. An emerging low-cost, highly accessible alternative to many of these resources is the Graphics Processing Unit (GPU) - specialized massively-parallel graphics hardware that has seen increasing use as a general purpose computational accelerator thanks largely due to NVIDIA\u27s CUDA programming interface. We evaluated the relative benefits and limitations of GPU-based tools for large-scale neural network simulation and analysis, first by developing an agent-inspired spiking neural network simulator then by adapting a neural signal decoding algorithm. Under certain network configurations, the simulator was able to outperform an equivalent MPI-based parallel implementation run on a dedicated compute cluster, while the decoding algorithm implementation consistently outperformed its serial counterpart. Additionally, the GPU-based simulator was able to readily visualize network spiking activity in real-time due to the close integration with standard computer graphics APIs. The GPU was shown to provide significant performance benefits under certain circumstances while lagging behind in others. Given the complex nature of these research tasks, a hybrid strategy that combines GPU- and CPU-based approaches provides greater performance than either separately