6,713 research outputs found
A System for Induction of Oblique Decision Trees
This article describes a new system for induction of oblique decision trees.
This system, OC1, combines deterministic hill-climbing with two forms of
randomization to find a good oblique split (in the form of a hyperplane) at
each node of a decision tree. Oblique decision tree methods are tuned
especially for domains in which the attributes are numeric, although they can
be adapted to symbolic or mixed symbolic/numeric attributes. We present
extensive empirical studies, using both real and artificial data, that analyze
OC1's ability to construct oblique trees that are smaller and more accurate
than their axis-parallel counterparts. We also examine the benefits of
randomization for the construction of oblique decision trees.Comment: See http://www.jair.org/ for an online appendix and other files
accompanying this articl
Herding as a Learning System with Edge-of-Chaos Dynamics
Herding defines a deterministic dynamical system at the edge of chaos. It
generates a sequence of model states and parameters by alternating parameter
perturbations with state maximizations, where the sequence of states can be
interpreted as "samples" from an associated MRF model. Herding differs from
maximum likelihood estimation in that the sequence of parameters does not
converge to a fixed point and differs from an MCMC posterior sampling approach
in that the sequence of states is generated deterministically. Herding may be
interpreted as a"perturb and map" method where the parameter perturbations are
generated using a deterministic nonlinear dynamical system rather than randomly
from a Gumbel distribution. This chapter studies the distinct statistical
characteristics of the herding algorithm and shows that the fast convergence
rate of the controlled moments may be attributed to edge of chaos dynamics. The
herding algorithm can also be generalized to models with latent variables and
to a discriminative learning setting. The perceptron cycling theorem ensures
that the fast moment matching property is preserved in the more general
framework
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Mapping genetic interactions in cancer: a road to rational combination therapies.
The discovery of synthetic lethal interactions between poly (ADP-ribose) polymerase (PARP) inhibitors and BRCA genes, which are involved in homologous recombination, led to the approval of PARP inhibition as a monotherapy for patients with BRCA1/2-mutated breast or ovarian cancer. Studies following the initial observation of synthetic lethality demonstrated that the reach of PARP inhibitors is well beyond just BRCA1/2 mutants. Insights into the mechanisms of action of anticancer drugs are fundamental for the development of targeted monotherapies or rational combination treatments that will synergize to promote cancer cell death and overcome mechanisms of resistance. The development of targeted therapeutic agents is premised on mapping the physical and functional dependencies of mutated genes in cancer. An important part of this effort is the systematic screening of genetic interactions in a variety of cancer types. Until recently, genetic-interaction screens have relied either on the pairwise perturbations of two genes or on the perturbation of genes of interest combined with inhibition by commonly used anticancer drugs. Here, we summarize recent advances in mapping genetic interactions using targeted, genome-wide, and high-throughput genetic screens, and we discuss the therapeutic insights obtained through such screens. We further focus on factors that should be considered in order to develop a robust analysis pipeline. Finally, we discuss the integration of functional interaction data with orthogonal methods and suggest that such approaches will increase the reach of genetic-interaction screens for the development of rational combination therapies
Large Scale Variational Bayesian Inference for Structured Scale Mixture Models
Natural image statistics exhibit hierarchical dependencies across multiple
scales. Representing such prior knowledge in non-factorial latent tree models
can boost performance of image denoising, inpainting, deconvolution or
reconstruction substantially, beyond standard factorial "sparse" methodology.
We derive a large scale approximate Bayesian inference algorithm for linear
models with non-factorial (latent tree-structured) scale mixture priors.
Experimental results on a range of denoising and inpainting problems
demonstrate substantially improved performance compared to MAP estimation or to
inference with factorial priors.Comment: Appears in Proceedings of the 29th International Conference on
Machine Learning (ICML 2012
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
Noise Robustness of a Combined Phase Retrieval and Reconstruction Method for Phase-Contrast Tomography
Classical reconstruction methods for phase-contrast tomography consist of two
stages: phase retrieval and tomographic reconstruction. A novel algebraic
method combining the two was suggested by Kostenko et al. (Opt. Express, 21,
12185, 2013) and preliminary results demonstrating improved reconstruction
compared to a two-stage method given. Using simulated free-space propagation
experiments with a single sample-detector distance, we thoroughly compare the
novel method with the two-stage method to address limitations of the
preliminary results. We demonstrate that the novel method is substantially more
robust towards noise; our simulations point to a possible reduction in counting
times by an order of magnitude
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