810 research outputs found
Fog Computing in Medical Internet-of-Things: Architecture, Implementation, and Applications
In the era when the market segment of Internet of Things (IoT) tops the chart
in various business reports, it is apparently envisioned that the field of
medicine expects to gain a large benefit from the explosion of wearables and
internet-connected sensors that surround us to acquire and communicate
unprecedented data on symptoms, medication, food intake, and daily-life
activities impacting one's health and wellness. However, IoT-driven healthcare
would have to overcome many barriers, such as: 1) There is an increasing demand
for data storage on cloud servers where the analysis of the medical big data
becomes increasingly complex, 2) The data, when communicated, are vulnerable to
security and privacy issues, 3) The communication of the continuously collected
data is not only costly but also energy hungry, 4) Operating and maintaining
the sensors directly from the cloud servers are non-trial tasks. This book
chapter defined Fog Computing in the context of medical IoT. Conceptually, Fog
Computing is a service-oriented intermediate layer in IoT, providing the
interfaces between the sensors and cloud servers for facilitating connectivity,
data transfer, and queryable local database. The centerpiece of Fog computing
is a low-power, intelligent, wireless, embedded computing node that carries out
signal conditioning and data analytics on raw data collected from wearables or
other medical sensors and offers efficient means to serve telehealth
interventions. We implemented and tested an fog computing system using the
Intel Edison and Raspberry Pi that allows acquisition, computing, storage and
communication of the various medical data such as pathological speech data of
individuals with speech disorders, Phonocardiogram (PCG) signal for heart rate
estimation, and Electrocardiogram (ECG)-based Q, R, S detection.Comment: 29 pages, 30 figures, 5 tables. Keywords: Big Data, Body Area
Network, Body Sensor Network, Edge Computing, Fog Computing, Medical
Cyberphysical Systems, Medical Internet-of-Things, Telecare, Tele-treatment,
Wearable Devices, Chapter in Handbook of Large-Scale Distributed Computing in
Smart Healthcare (2017), Springe
Inference, Orthology, and Inundation: Addressing Current Challenges in the Field of Metagenomics
The vast increase in the number of sequenced genomes has irreversibly changed the landscape of the biological sciences and has spawned the current post-genomic era of research. Genomic data have illuminated many adaptation and survival strategies between species and their habitats. Moreover, the analysis of prokaryotic genomic sequences is indispensible for understanding the mechanisms of bacterial pathogens and for subsequently developing effective diagnostics, drugs, and vaccines. Computational strategies for the annotation of genomic sequences are driven by the inference of function from reference genomes. However, the effectiveness of such methods is bounded by the fractional diversity of known genomes. Although metagenomes can reconcile this limitation by offering access to previously intangible organisms, harnessing metagenomic data comes with its own collection of challenges. Since the sequenced environmental fragments of metagenomes do not equate to discrete and fully intact genomes, this prevents the conventional establishment of orthologous relationships that are required for functional inference. Furthermore, the current surge in metagenomic data sets requires the development of compression strategies that can effectively accommodate large data sets that are comprised of multiple sequences and a greater proportion of auxiliary data, such as sequence headers. While modern hardware can provide vast amounts of inexpensive storage for biological databases, the compression of nucleotide sequence data is still of paramount importance in order to facilitate fast search and retrieval operations through a reduction in disk traffic. To address the issues of inference and orthology a novel protocol was developed for the prediction of functional interactions that supports data sources that lack information about orthologous relationships. To address the issue of database inundation, a compression protocol was designed that can differentiate between sequence data and auxiliary data, thereby offering reconciliation between sequence specific and general-purpose compression strategies. By resolving these and other challenges, it becomes possible to extend the potential utility of the emerging field of metagenomics
A genetic algorithm coupled with tree-based pruning for mining closed association rules
Due to the voluminous amount of itemsets that are generated, the association rules extracted from these itemsets contain redundancy, and designing an effective approach to address this issue is of paramount importance. Although multiple algorithms were proposed in recent years for mining closed association rules most of them underperform in terms of run time or memory. Another issue that remains challenging is the nature of the dataset. While some of the existing algorithms perform well on dense datasets others perform well on sparse datasets. This paper aims to handle these drawbacks by using a genetic algorithm for mining closed association rules. Recent studies have shown that genetic algorithms perform better than conventional algorithms due to their bitwise operations of crossover and mutation. Bitwise operations are predominantly faster than conventional approaches and bits consume lesser memory thereby improving the overall performance of the algorithm. To address the redundancy in the mined association rules a tree-based pruning algorithm has been designed here. This works on the principle of minimal antecedent and maximal consequent. Experiments have shown that the proposed approach works well on both dense and sparse datasets while surpassing existing techniques with regard to run time and memory
Turn-Key Stabilization and Digital Control of Scalable, N GTI Resonator Based Coherent Pulse Stacking Systems
Coherent Pulse Stacking Amplification (CPSA) is a new time-domain coherent addition
technique that overcomes the limitations on pulse energies achievable from optical amplifiers. It
uses reflecting resonators to transform a sequence of phase- and amplitude-modulated optical
pulses into a single output pulse enabling high pulse energy for fiber lasers.
This thesis focuses on utilizing efficient algorithms for stabilization and optimization
aspects of CPSA and developing a robust, scalable, and distributed digital control system with
firmware and software integration for algorithms, to support the CPS (Coherent Pulse Stacking)
application. We have presented the theoretical foundation of the stochastic parallel gradient
descent (SPGD) for phase stabilization, discussed its performance criteria, its convergence, and its
stability. We have presented our software and hardware development for time-domain coherent
combing stabilization (specifically, an FPGA (Field Programmable Gate Array)-based Control
system with software/firmware development to support stabilization and optimization algorithms).
Analytical formulations of output stacked pulse profile as a function of input pulse train amplitudes
and phase and stacker cavity parameters have been derived so as to build up a foundation for a
GTI (Gires-Tournois-Interferometer) Cavity-based noise measurement technique. Time-domain
and frequency domain characterization techniques have been presented to analyze phase and
amplitude noise in the stacking system. Stacking sensitivity to errors in different control
parameters (stacker cavity phase, pulse amplitude, and phases) for different stacker configurations
have been analyzed. Noise measurement results using GTI cavities with different round-trip time
has have been presented and we have shown how effectively the stacking phase noise in the system
can be reduced by improving the noise performance of the mode-locked oscillator. Simulation and
Experimental results for stabilizing different stacker configurations have been presented. Finally
an algorithmic control system along with software/hardware development for optimizing
amplitudes and phases of the input burst has been implemented to increase stacking fidelity. A
complete detailed description, and simulation of the Genetic Algorithm as an alternative algorithm
for optimizing the stacked pulse fidelity has been presented. Comparison between SPGD and
Genetic Algorithm results has been done to evaluate their performance.
To summarize, this thesis provides theoretical, experimental, and implementation aspects
of controlling CPSA system by introducing efficient control algorithms and developing a turn-key
digital control system which is scalable to large number of stacker cavities.PHDElectrical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147664/1/msheikhs_1.pd
EFFICIENT IMAGE COMPRESSION AND DECOMPRESSION ALGORITHMS FOR OCR SYSTEMS
This paper presents an efficient new image compression and decompression methods for document images, intended for usage in the pre-processing stage of an OCR system designed for needs of the “Nikola Tesla Museum” in Belgrade. Proposed image compression methods exploit the Run-Length Encoding (RLE) algorithm and an algorithm based on document character contour extraction, while an iterative scanline fill algorithm is used for image decompression. Image compression and decompression methods are compared with JBIG2 and JPEG2000 image compression standards. Segmentation accuracy results for ground-truth documents are obtained in order to evaluate the proposed methods. Results show that the proposed methods outperform JBIG2 compression regarding the time complexity, providing up to 25 times lower processing time at the expense of worse compression ratio results, as well as JPEG2000 image compression standard, providing up to 4-fold improvement in compression ratio. Finally, time complexity results show that the presented methods are sufficiently fast for a real time character segmentation system
Efficient, Dependable Storage of Human Genome Sequencing Data
A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são críticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivíduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessíveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensíveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de 1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations
Proceedings of the 18th Irish Conference on Artificial Intelligence and Cognitive Science
These proceedings contain the papers that were accepted for publication at AICS-2007, the 18th Annual Conference on Artificial Intelligence and Cognitive Science, which was held in the Technological University Dublin; Dublin, Ireland; on the 29th to the 31st August 2007. AICS is the annual conference of the Artificial Intelligence Association of Ireland (AIAI)
Compressão eficiente de sequências biológicas usando uma rede neuronal
Background: The increasing production of genomic data has led to
an intensified need for models that can cope efficiently with the lossless
compression of biosequences. Important applications include long-term
storage and compression-based data analysis. In the literature, only a
few recent articles propose the use of neural networks for biosequence
compression. However, they fall short when compared with specific
DNA compression tools, such as GeCo2. This limitation is due to the
absence of models specifically designed for DNA sequences. In this
work, we combine the power of neural networks with specific DNA and
amino acids models. For this purpose, we created GeCo3 and AC2, two
new biosequence compressors. Both use a neural network for mixing
the opinions of multiple specific models.
Findings: We benchmark GeCo3 as a reference-free DNA compressor
in five datasets, including a balanced and comprehensive dataset
of DNA sequences, the Y-chromosome and human mitogenome, two
compilations of archaeal and virus genomes, four whole genomes, and
two collections of FASTQ data of a human virome and ancient DNA.
GeCo3 achieves a solid improvement in compression over the previous
version (GeCo2) of 2:4%, 7:1%, 6:1%, 5:8%, and 6:0%, respectively.
As a reference-based DNA compressor, we benchmark GeCo3 in four
datasets constituted by the pairwise compression of the chromosomes
of the genomes of several primates. GeCo3 improves the compression in
12:4%, 11:7%, 10:8% and 10:1% over the state-of-the-art. The cost of
this compression improvement is some additional computational time
(1:7_ to 3:0_ slower than GeCo2). The RAM is constant, and the tool
scales efficiently, independently from the sequence size. Overall, these
values outperform the state-of-the-art. For AC2 the improvements and
costs over AC are similar, which allows the tool to also outperform the
state-of-the-art.
Conclusions: The GeCo3 and AC2 are biosequence compressors with
a neural network mixing approach, that provides additional gains over
top specific biocompressors. The proposed mixing method is portable,
requiring only the probabilities of the models as inputs, providing easy
adaptation to other data compressors or compression-based data analysis
tools. GeCo3 and AC2 are released under GPLv3 and are available
for free download at https://github.com/cobilab/geco3 and
https://github.com/cobilab/ac2.Contexto: O aumento da produção de dados genómicos levou a uma
maior necessidade de modelos que possam lidar de forma eficiente com
a compressão sem perdas de biosequências. Aplicações importantes
incluem armazenamento de longo prazo e análise de dados baseada em
compressão. Na literatura, apenas alguns artigos recentes propõem o
uso de uma rede neuronal para compressão de biosequências. No entanto,
os resultados ficam aquém quando comparados com ferramentas
de compressão de ADN específicas, como o GeCo2. Essa limitação
deve-se à ausência de modelos específicos para sequências de ADN.
Neste trabalho, combinamos o poder de uma rede neuronal com modelos
específicos de ADN e aminoácidos. Para isso, criámos o GeCo3 e
o AC2, dois novos compressores de biosequências. Ambos usam uma
rede neuronal para combinar as opiniões de vários modelos específicos.
Resultados: Comparamos o GeCo3 como um compressor de ADN
sem referência em cinco conjuntos de dados, incluindo um conjunto
de dados balanceado de sequências de ADN, o cromossoma Y e o mitogenoma
humano, duas compilações de genomas de arqueas e vírus,
quatro genomas inteiros e duas coleções de dados FASTQ de um viroma
humano e ADN antigo. O GeCo3 atinge uma melhoria sólida
na compressão em relação à versão anterior (GeCo2) de 2,4%, 7,1%,
6,1%, 5,8% e 6,0%, respectivamente. Como um compressor de ADN
baseado em referência, comparamos o GeCo3 em quatro conjuntos
de dados constituídos pela compressão aos pares dos cromossomas
dos genomas de vários primatas. O GeCo3 melhora a compressão em
12,4%, 11,7%, 10,8% e 10,1% em relação ao estado da arte. O custo
desta melhoria de compressão é algum tempo computacional adicional
(1,7 _ a 3,0 _ mais lento do que GeCo2). A RAM é constante e a
ferramenta escala de forma eficiente, independentemente do tamanho
da sequência. De forma geral, os rácios de compressão superam o estado
da arte. Para o AC2, as melhorias e custos em relação ao AC são
semelhantes, o que permite que a ferramenta também supere o estado
da arte.
Conclusões: O GeCo3 e o AC2 são compressores de sequências biológicas
com uma abordagem de mistura baseada numa rede neuronal,
que fornece ganhos adicionais em relação aos biocompressores específicos
de topo. O método de mistura proposto é portátil, exigindo apenas
as probabilidades dos modelos como entradas, proporcionando uma fácil
adaptação a outros compressores de dados ou ferramentas de análise
baseadas em compressão. O GeCo3 e o AC2 são distribuídos sob GPLv3
e estão disponíveis para download gratuito em https://github.com/
cobilab/geco3 e https://github.com/cobilab/ac2.Mestrado em Engenharia de Computadores e Telemátic
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