7,686 research outputs found
Structural Agnostic Modeling: Adversarial Learning of Causal Graphs
A new causal discovery method, Structural Agnostic Modeling (SAM), is
presented in this paper. Leveraging both conditional independencies and
distributional asymmetries in the data, SAM aims at recovering full causal
models from continuous observational data along a multivariate non-parametric
setting. The approach is based on a game between players estimating each
variable distribution conditionally to the others as a neural net, and an
adversary aimed at discriminating the overall joint conditional distribution,
and that of the original data. An original learning criterion combining
distribution estimation, sparsity and acyclicity constraints is used to enforce
the end-to-end optimization of the graph structure and parameters through
stochastic gradient descent. Besides the theoretical analysis of the approach
in the large sample limit, SAM is extensively experimentally validated on
synthetic and real data
The Mathematics of Phylogenomics
The grand challenges in biology today are being shaped by powerful
high-throughput technologies that have revealed the genomes of many organisms,
global expression patterns of genes and detailed information about variation
within populations. We are therefore able to ask, for the first time,
fundamental questions about the evolution of genomes, the structure of genes
and their regulation, and the connections between genotypes and phenotypes of
individuals. The answers to these questions are all predicated on progress in a
variety of computational, statistical, and mathematical fields.
The rapid growth in the characterization of genomes has led to the
advancement of a new discipline called Phylogenomics. This discipline results
from the combination of two major fields in the life sciences: Genomics, i.e.,
the study of the function and structure of genes and genomes; and Molecular
Phylogenetics, i.e., the study of the hierarchical evolutionary relationships
among organisms and their genomes. The objective of this article is to offer
mathematicians a first introduction to this emerging field, and to discuss
specific mathematical problems and developments arising from phylogenomics.Comment: 41 pages, 4 figure
Learning loopy graphical models with latent variables: Efficient methods and guarantees
The problem of structure estimation in graphical models with latent variables
is considered. We characterize conditions for tractable graph estimation and
develop efficient methods with provable guarantees. We consider models where
the underlying Markov graph is locally tree-like, and the model is in the
regime of correlation decay. For the special case of the Ising model, the
number of samples required for structural consistency of our method scales
as , where p is the
number of variables, is the minimum edge potential, is
the depth (i.e., distance from a hidden node to the nearest observed nodes),
and is a parameter which depends on the bounds on node and edge
potentials in the Ising model. Necessary conditions for structural consistency
under any algorithm are derived and our method nearly matches the lower bound
on sample requirements. Further, the proposed method is practical to implement
and provides flexibility to control the number of latent variables and the
cycle lengths in the output graph.Comment: Published in at http://dx.doi.org/10.1214/12-AOS1070 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Denoising Autoencoders for fast Combinatorial Black Box Optimization
Estimation of Distribution Algorithms (EDAs) require flexible probability
models that can be efficiently learned and sampled. Autoencoders (AE) are
generative stochastic networks with these desired properties. We integrate a
special type of AE, the Denoising Autoencoder (DAE), into an EDA and evaluate
the performance of DAE-EDA on several combinatorial optimization problems with
a single objective. We asses the number of fitness evaluations as well as the
required CPU times. We compare the results to the performance to the Bayesian
Optimization Algorithm (BOA) and RBM-EDA, another EDA which is based on a
generative neural network which has proven competitive with BOA. For the
considered problem instances, DAE-EDA is considerably faster than BOA and
RBM-EDA, sometimes by orders of magnitude. The number of fitness evaluations is
higher than for BOA, but competitive with RBM-EDA. These results show that DAEs
can be useful tools for problems with low but non-negligible fitness evaluation
costs.Comment: corrected typos and small inconsistencie
Quantum-Assisted Learning of Hardware-Embedded Probabilistic Graphical Models
Mainstream machine-learning techniques such as deep learning and
probabilistic programming rely heavily on sampling from generally intractable
probability distributions. There is increasing interest in the potential
advantages of using quantum computing technologies as sampling engines to speed
up these tasks or to make them more effective. However, some pressing
challenges in state-of-the-art quantum annealers have to be overcome before we
can assess their actual performance. The sparse connectivity, resulting from
the local interaction between quantum bits in physical hardware
implementations, is considered the most severe limitation to the quality of
constructing powerful generative unsupervised machine-learning models. Here we
use embedding techniques to add redundancy to data sets, allowing us to
increase the modeling capacity of quantum annealers. We illustrate our findings
by training hardware-embedded graphical models on a binarized data set of
handwritten digits and two synthetic data sets in experiments with up to 940
quantum bits. Our model can be trained in quantum hardware without full
knowledge of the effective parameters specifying the corresponding quantum
Gibbs-like distribution; therefore, this approach avoids the need to infer the
effective temperature at each iteration, speeding up learning; it also
mitigates the effect of noise in the control parameters, making it robust to
deviations from the reference Gibbs distribution. Our approach demonstrates the
feasibility of using quantum annealers for implementing generative models, and
it provides a suitable framework for benchmarking these quantum technologies on
machine-learning-related tasks.Comment: 17 pages, 8 figures. Minor further revisions. As published in Phys.
Rev.
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