546 research outputs found
Tree-guided group lasso for multi-response regression with structured sparsity, with an application to eQTL mapping
We consider the problem of estimating a sparse multi-response regression
function, with an application to expression quantitative trait locus (eQTL)
mapping, where the goal is to discover genetic variations that influence
gene-expression levels. In particular, we investigate a shrinkage technique
capable of capturing a given hierarchical structure over the responses, such as
a hierarchical clustering tree with leaf nodes for responses and internal nodes
for clusters of related responses at multiple granularity, and we seek to
leverage this structure to recover covariates relevant to each
hierarchically-defined cluster of responses. We propose a tree-guided group
lasso, or tree lasso, for estimating such structured sparsity under
multi-response regression by employing a novel penalty function constructed
from the tree. We describe a systematic weighting scheme for the overlapping
groups in the tree-penalty such that each regression coefficient is penalized
in a balanced manner despite the inhomogeneous multiplicity of group
memberships of the regression coefficients due to overlaps among groups. For
efficient optimization, we employ a smoothing proximal gradient method that was
originally developed for a general class of structured-sparsity-inducing
penalties. Using simulated and yeast data sets, we demonstrate that our method
shows a superior performance in terms of both prediction errors and recovery of
true sparsity patterns, compared to other methods for learning a
multivariate-response regression.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS549 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Splitting Methods for Convex Clustering
Clustering is a fundamental problem in many scientific applications. Standard
methods such as -means, Gaussian mixture models, and hierarchical
clustering, however, are beset by local minima, which are sometimes drastically
suboptimal. Recently introduced convex relaxations of -means and
hierarchical clustering shrink cluster centroids toward one another and ensure
a unique global minimizer. In this work we present two splitting methods for
solving the convex clustering problem. The first is an instance of the
alternating direction method of multipliers (ADMM); the second is an instance
of the alternating minimization algorithm (AMA). In contrast to previously
considered algorithms, our ADMM and AMA formulations provide simple and unified
frameworks for solving the convex clustering problem under the previously
studied norms and open the door to potentially novel norms. We demonstrate the
performance of our algorithm on both simulated and real data examples. While
the differences between the two algorithms appear to be minor on the surface,
complexity analysis and numerical experiments show AMA to be significantly more
efficient.Comment: 37 pages, 6 figure
Multi-scale Mining of fMRI data with Hierarchical Structured Sparsity
International audienceInverse inference, or "brain reading", is a recent paradigm for analyzing functional magnetic resonance imaging (fMRI) data, based on pattern recognition and statistical learning. By predicting some cognitive variables related to brain activation maps, this approach aims at decoding brain activity. Inverse inference takes into account the multivariate information between voxels and is currently the only way to assess how precisely some cognitive information is encoded by the activity of neural populations within the whole brain. However, it relies on a prediction function that is plagued by the curse of dimensionality, since there are far more features than samples, i.e., more voxels than fMRI volumes. To address this problem, different methods have been proposed, such as, among others, univariate feature selection, feature agglomeration and regularization techniques. In this paper, we consider a sparse hierarchical structured regularization. Specifically, the penalization we use is constructed from a tree that is obtained by spatially-constrained agglomerative clustering. This approach encodes the spatial structure of the data at different scales into the regularization, which makes the overall prediction procedure more robust to inter-subject variability. The regularization used induces the selection of spatially coherent predictive brain regions simultaneously at different scales. We test our algorithm on real data acquired to study the mental representation of objects, and we show that the proposed algorithm not only delineates meaningful brain regions but yields as well better prediction accuracy than reference methods
Mapping constrained optimization problems to quantum annealing with application to fault diagnosis
Current quantum annealing (QA) hardware suffers from practical limitations
such as finite temperature, sparse connectivity, small qubit numbers, and
control error. We propose new algorithms for mapping boolean constraint
satisfaction problems (CSPs) onto QA hardware mitigating these limitations. In
particular we develop a new embedding algorithm for mapping a CSP onto a
hardware Ising model with a fixed sparse set of interactions, and propose two
new decomposition algorithms for solving problems too large to map directly
into hardware.
The mapping technique is locally-structured, as hardware compatible Ising
models are generated for each problem constraint, and variables appearing in
different constraints are chained together using ferromagnetic couplings. In
contrast, global embedding techniques generate a hardware independent Ising
model for all the constraints, and then use a minor-embedding algorithm to
generate a hardware compatible Ising model. We give an example of a class of
CSPs for which the scaling performance of D-Wave's QA hardware using the local
mapping technique is significantly better than global embedding.
We validate the approach by applying D-Wave's hardware to circuit-based
fault-diagnosis. For circuits that embed directly, we find that the hardware is
typically able to find all solutions from a min-fault diagnosis set of size N
using 1000N samples, using an annealing rate that is 25 times faster than a
leading SAT-based sampling method. Further, we apply decomposition algorithms
to find min-cardinality faults for circuits that are up to 5 times larger than
can be solved directly on current hardware.Comment: 22 pages, 4 figure
Planar Ultrametric Rounding for Image Segmentation
We study the problem of hierarchical clustering on planar graphs. We
formulate this in terms of an LP relaxation of ultrametric rounding. To solve
this LP efficiently we introduce a dual cutting plane scheme that uses minimum
cost perfect matching as a subroutine in order to efficiently explore the space
of planar partitions. We apply our algorithm to the problem of hierarchical
image segmentation
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