10,059 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
Generative models versus underlying symmetries to explain biological pattern
Mathematical models play an increasingly important role in the interpretation
of biological experiments. Studies often present a model that generates the
observations, connecting hypothesized process to an observed pattern. Such
generative models confirm the plausibility of an explanation and make testable
hypotheses for further experiments. However, studies rarely consider the broad
family of alternative models that match the same observed pattern. The
symmetries that define the broad class of matching models are in fact the only
aspects of information truly revealed by observed pattern. Commonly observed
patterns derive from simple underlying symmetries. This article illustrates the
problem by showing the symmetry associated with the observed rate of increase
in fitness in a constant environment. That underlying symmetry reveals how each
particular generative model defines a single example within the broad class of
matching models. Further progress on the relation between pattern and process
requires deeper consideration of the underlying symmetries
On the Equivalence Between Deep NADE and Generative Stochastic Networks
Neural Autoregressive Distribution Estimators (NADEs) have recently been
shown as successful alternatives for modeling high dimensional multimodal
distributions. One issue associated with NADEs is that they rely on a
particular order of factorization for . This issue has been
recently addressed by a variant of NADE called Orderless NADEs and its deeper
version, Deep Orderless NADE. Orderless NADEs are trained based on a criterion
that stochastically maximizes with all possible orders of
factorizations. Unfortunately, ancestral sampling from deep NADE is very
expensive, corresponding to running through a neural net separately predicting
each of the visible variables given some others. This work makes a connection
between this criterion and the training criterion for Generative Stochastic
Networks (GSNs). It shows that training NADEs in this way also trains a GSN,
which defines a Markov chain associated with the NADE model. Based on this
connection, we show an alternative way to sample from a trained Orderless NADE
that allows to trade-off computing time and quality of the samples: a 3 to
10-fold speedup (taking into account the waste due to correlations between
consecutive samples of the chain) can be obtained without noticeably reducing
the quality of the samples. This is achieved using a novel sampling procedure
for GSNs called annealed GSN sampling, similar to tempering methods that
combines fast mixing (obtained thanks to steps at high noise levels) with
accurate samples (obtained thanks to steps at low noise levels).Comment: ECML/PKDD 201
Biologically Inspired Dynamic Textures for Probing Motion Perception
Perception is often described as a predictive process based on an optimal
inference with respect to a generative model. We study here the principled
construction of a generative model specifically crafted to probe motion
perception. In that context, we first provide an axiomatic, biologically-driven
derivation of the model. This model synthesizes random dynamic textures which
are defined by stationary Gaussian distributions obtained by the random
aggregation of warped patterns. Importantly, we show that this model can
equivalently be described as a stochastic partial differential equation. Using
this characterization of motion in images, it allows us to recast motion-energy
models into a principled Bayesian inference framework. Finally, we apply these
textures in order to psychophysically probe speed perception in humans. In this
framework, while the likelihood is derived from the generative model, the prior
is estimated from the observed results and accounts for the perceptual bias in
a principled fashion.Comment: Twenty-ninth Annual Conference on Neural Information Processing
Systems (NIPS), Dec 2015, Montreal, Canad
Models for transcript quantification from RNA-Seq
RNA-Seq is rapidly becoming the standard technology for transcriptome
analysis. Fundamental to many of the applications of RNA-Seq is the
quantification problem, which is the accurate measurement of relative
transcript abundances from the sequenced reads. We focus on this problem, and
review many recently published models that are used to estimate the relative
abundances. In addition to describing the models and the different approaches
to inference, we also explain how methods are related to each other. A key
result is that we show how inference with many of the models results in
identical estimates of relative abundances, even though model formulations can
be very different. In fact, we are able to show how a single general model
captures many of the elements of previously published methods. We also review
the applications of RNA-Seq models to differential analysis, and explain why
accurate relative transcript abundance estimates are crucial for downstream
analyses
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