10,868 research outputs found
Universal Compressed Sensing
In this paper, the problem of developing universal algorithms for compressed
sensing of stochastic processes is studied. First, R\'enyi's notion of
information dimension (ID) is generalized to analog stationary processes. This
provides a measure of complexity for such processes and is connected to the
number of measurements required for their accurate recovery. Then a minimum
entropy pursuit (MEP) optimization approach is proposed, and it is proven that
it can reliably recover any stationary process satisfying some mixing
constraints from sufficient number of randomized linear measurements, without
having any prior information about the distribution of the process. It is
proved that a Lagrangian-type approximation of the MEP optimization problem,
referred to as Lagrangian-MEP problem, is identical to a heuristic
implementable algorithm proposed by Baron et al. It is shown that for the right
choice of parameters the Lagrangian-MEP algorithm, in addition to having the
same asymptotic performance as MEP optimization, is also robust to the
measurement noise. For memoryless sources with a discrete-continuous mixture
distribution, the fundamental limits of the minimum number of required
measurements by a non-universal compressed sensing decoder is characterized by
Wu et al. For such sources, it is proved that there is no loss in universal
coding, and both the MEP and the Lagrangian-MEP asymptotically achieve the
optimal performance
Mixing Strategies in Data Compression
We propose geometric weighting as a novel method to combine multiple models
in data compression. Our results reveal the rationale behind PAQ-weighting and
generalize it to a non-binary alphabet. Based on a similar technique we present
a new, generic linear mixture technique. All novel mixture techniques rely on
given weight vectors. We consider the problem of finding optimal weights and
show that the weight optimization leads to a strictly convex (and thus,
good-natured) optimization problem. Finally, an experimental evaluation
compares the two presented mixture techniques for a binary alphabet. The
results indicate that geometric weighting is superior to linear weighting.Comment: Data Compression Conference (DCC) 201
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
Universal Codes from Switching Strategies
We discuss algorithms for combining sequential prediction strategies, a task
which can be viewed as a natural generalisation of the concept of universal
coding. We describe a graphical language based on Hidden Markov Models for
defining prediction strategies, and we provide both existing and new models as
examples. The models include efficient, parameterless models for switching
between the input strategies over time, including a model for the case where
switches tend to occur in clusters, and finally a new model for the scenario
where the prediction strategies have a known relationship, and where jumps are
typically between strongly related ones. This last model is relevant for coding
time series data where parameter drift is expected. As theoretical ontributions
we introduce an interpolation construction that is useful in the development
and analysis of new algorithms, and we establish a new sophisticated lemma for
analysing the individual sequence regret of parameterised models
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