87,026 research outputs found
A flexible framework for sparse simultaneous component based data integration
<p>Abstract</p> <p>1 Background</p> <p>High throughput data are complex and methods that reveal structure underlying the data are most useful. Principal component analysis, frequently implemented as a singular value decomposition, is a popular technique in this respect. Nowadays often the challenge is to reveal structure in several sources of information (e.g., transcriptomics, proteomics) that are available for the same biological entities under study. Simultaneous component methods are most promising in this respect. However, the interpretation of the principal and simultaneous components is often daunting because contributions of each of the biomolecules (transcripts, proteins) have to be taken into account.</p> <p>2 Results</p> <p>We propose a sparse simultaneous component method that makes many of the parameters redundant by shrinking them to zero. It includes principal component analysis, sparse principal component analysis, and ordinary simultaneous component analysis as special cases. Several penalties can be tuned that account in different ways for the block structure present in the integrated data. This yields known sparse approaches as the lasso, the ridge penalty, the elastic net, the group lasso, sparse group lasso, and elitist lasso. In addition, the algorithmic results can be easily transposed to the context of regression. Metabolomics data obtained with two measurement platforms for the same set of <it>Escherichia coli </it>samples are used to illustrate the proposed methodology and the properties of different penalties with respect to sparseness across and within data blocks.</p> <p>3 Conclusion</p> <p>Sparse simultaneous component analysis is a useful method for data integration: First, simultaneous analyses of multiple blocks offer advantages over sequential and separate analyses and second, interpretation of the results is highly facilitated by their sparseness. The approach offered is flexible and allows to take the block structure in different ways into account. As such, structures can be found that are exclusively tied to one data platform (group lasso approach) as well as structures that involve all data platforms (Elitist lasso approach).</p> <p>4 Availability</p> <p>The additional file contains a MATLAB implementation of the sparse simultaneous component method.</p
Info-Greedy sequential adaptive compressed sensing
We present an information-theoretic framework for sequential adaptive
compressed sensing, Info-Greedy Sensing, where measurements are chosen to
maximize the extracted information conditioned on the previous measurements. We
show that the widely used bisection approach is Info-Greedy for a family of
-sparse signals by connecting compressed sensing and blackbox complexity of
sequential query algorithms, and present Info-Greedy algorithms for Gaussian
and Gaussian Mixture Model (GMM) signals, as well as ways to design sparse
Info-Greedy measurements. Numerical examples demonstrate the good performance
of the proposed algorithms using simulated and real data: Info-Greedy Sensing
shows significant improvement over random projection for signals with sparse
and low-rank covariance matrices, and adaptivity brings robustness when there
is a mismatch between the assumed and the true distributions.Comment: Preliminary results presented at Allerton Conference 2014. To appear
in IEEE Journal Selected Topics on Signal Processin
Parallel Algorithms for Summing Floating-Point Numbers
The problem of exactly summing n floating-point numbers is a fundamental
problem that has many applications in large-scale simulations and computational
geometry. Unfortunately, due to the round-off error in standard floating-point
operations, this problem becomes very challenging. Moreover, all existing
solutions rely on sequential algorithms which cannot scale to the huge datasets
that need to be processed.
In this paper, we provide several efficient parallel algorithms for summing n
floating point numbers, so as to produce a faithfully rounded floating-point
representation of the sum. We present algorithms in PRAM, external-memory, and
MapReduce models, and we also provide an experimental analysis of our MapReduce
algorithms, due to their simplicity and practical efficiency.Comment: Conference version appears in SPAA 201
Sequential Gaussian Processes for Online Learning of Nonstationary Functions
Many machine learning problems can be framed in the context of estimating
functions, and often these are time-dependent functions that are estimated in
real-time as observations arrive. Gaussian processes (GPs) are an attractive
choice for modeling real-valued nonlinear functions due to their flexibility
and uncertainty quantification. However, the typical GP regression model
suffers from several drawbacks: i) Conventional GP inference scales
with respect to the number of observations; ii) updating a GP model
sequentially is not trivial; and iii) covariance kernels often enforce
stationarity constraints on the function, while GPs with non-stationary
covariance kernels are often intractable to use in practice. To overcome these
issues, we propose an online sequential Monte Carlo algorithm to fit mixtures
of GPs that capture non-stationary behavior while allowing for fast,
distributed inference. By formulating hyperparameter optimization as a
multi-armed bandit problem, we accelerate mixing for real time inference. Our
approach empirically improves performance over state-of-the-art methods for
online GP estimation in the context of prediction for simulated non-stationary
data and hospital time series data
Block Coordinate Descent for Sparse NMF
Nonnegative matrix factorization (NMF) has become a ubiquitous tool for data
analysis. An important variant is the sparse NMF problem which arises when we
explicitly require the learnt features to be sparse. A natural measure of
sparsity is the L norm, however its optimization is NP-hard. Mixed norms,
such as L/L measure, have been shown to model sparsity robustly, based
on intuitive attributes that such measures need to satisfy. This is in contrast
to computationally cheaper alternatives such as the plain L norm. However,
present algorithms designed for optimizing the mixed norm L/L are slow
and other formulations for sparse NMF have been proposed such as those based on
L and L norms. Our proposed algorithm allows us to solve the mixed norm
sparsity constraints while not sacrificing computation time. We present
experimental evidence on real-world datasets that shows our new algorithm
performs an order of magnitude faster compared to the current state-of-the-art
solvers optimizing the mixed norm and is suitable for large-scale datasets
- …