7,531 research outputs found
Group invariance principles for causal generative models
The postulate of independence of cause and mechanism (ICM) has recently led
to several new causal discovery algorithms. The interpretation of independence
and the way it is utilized, however, varies across these methods. Our aim in
this paper is to propose a group theoretic framework for ICM to unify and
generalize these approaches. In our setting, the cause-mechanism relationship
is assessed by comparing it against a null hypothesis through the application
of random generic group transformations. We show that the group theoretic view
provides a very general tool to study the structure of data generating
mechanisms with direct applications to machine learning.Comment: 16 pages, 6 figure
Network Inference from Co-Occurrences
The recovery of network structure from experimental data is a basic and
fundamental problem. Unfortunately, experimental data often do not directly
reveal structure due to inherent limitations such as imprecision in timing or
other observation mechanisms. We consider the problem of inferring network
structure in the form of a directed graph from co-occurrence observations. Each
observation arises from a transmission made over the network and indicates
which vertices carry the transmission without explicitly conveying their order
in the path. Without order information, there are an exponential number of
feasible graphs which agree with the observed data equally well. Yet, the basic
physical principles underlying most networks strongly suggest that all feasible
graphs are not equally likely. In particular, vertices that co-occur in many
observations are probably closely connected. Previous approaches to this
problem are based on ad hoc heuristics. We model the experimental observations
as independent realizations of a random walk on the underlying graph, subjected
to a random permutation which accounts for the lack of order information.
Treating the permutations as missing data, we derive an exact
expectation-maximization (EM) algorithm for estimating the random walk
parameters. For long transmission paths the exact E-step may be computationally
intractable, so we also describe an efficient Monte Carlo EM (MCEM) algorithm
and derive conditions which ensure convergence of the MCEM algorithm with high
probability. Simulations and experiments with Internet measurements demonstrate
the promise of this approach.Comment: Submitted to IEEE Transactions on Information Theory. An extended
version is available as University of Wisconsin Technical Report ECE-06-
Symbolic Partial-Order Execution for Testing Multi-Threaded Programs
We describe a technique for systematic testing of multi-threaded programs. We
combine Quasi-Optimal Partial-Order Reduction, a state-of-the-art technique
that tackles path explosion due to interleaving non-determinism, with symbolic
execution to handle data non-determinism. Our technique iteratively and
exhaustively finds all executions of the program. It represents program
executions using partial orders and finds the next execution using an
underlying unfolding semantics. We avoid the exploration of redundant program
traces using cutoff events. We implemented our technique as an extension of
KLEE and evaluated it on a set of large multi-threaded C programs. Our
experiments found several previously undiscovered bugs and undefined behaviors
in memcached and GNU sort, showing that the new method is capable of finding
bugs in industrial-size benchmarks.Comment: Extended version of a paper presented at CAV'2
netgwas: An R Package for Network-Based Genome-Wide Association Studies
Graphical models are powerful tools for modeling and making statistical
inferences regarding complex associations among variables in multivariate data.
In this paper we introduce the R package netgwas, which is designed based on
undirected graphical models to accomplish three important and interrelated
goals in genetics: constructing linkage map, reconstructing linkage
disequilibrium (LD) networks from multi-loci genotype data, and detecting
high-dimensional genotype-phenotype networks. The netgwas package deals with
species with any chromosome copy number in a unified way, unlike other
software. It implements recent improvements in both linkage map construction
(Behrouzi and Wit, 2018), and reconstructing conditional independence network
for non-Gaussian continuous data, discrete data, and mixed
discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely
occur in genetics and genomics such as genotype data, and genotype-phenotype
data. We demonstrate the value of our package functionality by applying it to
various multivariate example datasets taken from the literature. We show, in
particular, that our package allows a more realistic analysis of data, as it
adjusts for the effect of all other variables while performing pairwise
associations. This feature controls for spurious associations between variables
that can arise from classical multiple testing approach. This paper includes a
brief overview of the statistical methods which have been implemented in the
package. The main body of the paper explains how to use the package. The
package uses a parallelization strategy on multi-core processors to speed-up
computations for large datasets. In addition, it contains several functions for
simulation and visualization. The netgwas package is freely available at
https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot
be longer than 1,920 characters", the abstract appearing here is slightly
shorter than that in the PDF fil
Nonparametric Estimation of Multi-View Latent Variable Models
Spectral methods have greatly advanced the estimation of latent variable
models, generating a sequence of novel and efficient algorithms with strong
theoretical guarantees. However, current spectral algorithms are largely
restricted to mixtures of discrete or Gaussian distributions. In this paper, we
propose a kernel method for learning multi-view latent variable models,
allowing each mixture component to be nonparametric. The key idea of the method
is to embed the joint distribution of a multi-view latent variable into a
reproducing kernel Hilbert space, and then the latent parameters are recovered
using a robust tensor power method. We establish that the sample complexity for
the proposed method is quadratic in the number of latent components and is a
low order polynomial in the other relevant parameters. Thus, our non-parametric
tensor approach to learning latent variable models enjoys good sample and
computational efficiencies. Moreover, the non-parametric tensor power method
compares favorably to EM algorithm and other existing spectral algorithms in
our experiments
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