3,088 research outputs found
Multi-Source Neural Variational Inference
Learning from multiple sources of information is an important problem in
machine-learning research. The key challenges are learning representations and
formulating inference methods that take into account the complementarity and
redundancy of various information sources. In this paper we formulate a
variational autoencoder based multi-source learning framework in which each
encoder is conditioned on a different information source. This allows us to
relate the sources via the shared latent variables by computing divergence
measures between individual source's posterior approximations. We explore a
variety of options to learn these encoders and to integrate the beliefs they
compute into a consistent posterior approximation. We visualise learned beliefs
on a toy dataset and evaluate our methods for learning shared representations
and structured output prediction, showing trade-offs of learning separate
encoders for each information source. Furthermore, we demonstrate how conflict
detection and redundancy can increase robustness of inference in a multi-source
setting.Comment: AAAI 2019, Association for the Advancement of Artificial Intelligence
(AAAI) 201
Multi-Channel Stochastic Variational Inference for the Joint Analysis of Heterogeneous Biomedical Data in Alzheimer's Disease
The joint analysis of biomedical data in Alzheimer's Disease (AD) is
important for better clinical diagnosis and to understand the relationship
between biomarkers. However, jointly accounting for heterogeneous measures
poses important challenges related to the modeling of the variability and the
interpretability of the results. These issues are here addressed by proposing a
novel multi-channel stochastic generative model. We assume that a latent
variable generates the data observed through different channels (e.g., clinical
scores, imaging, ...) and describe an efficient way to estimate jointly the
distribution of both latent variable and data generative process. Experiments
on synthetic data show that the multi-channel formulation allows superior data
reconstruction as opposed to the single channel one. Moreover, the derived
lower bound of the model evidence represents a promising model selection
criterion. Experiments on AD data show that the model parameters can be used
for unsupervised patient stratification and for the joint interpretation of the
heterogeneous observations. Because of its general and flexible formulation, we
believe that the proposed method can find important applications as a general
data fusion technique.Comment: accepted for presentation at MLCN 2018 workshop, in Conjunction with
MICCAI 2018, September 20, Granada, Spai
Sharing deep generative representation for perceived image reconstruction from human brain activity
Decoding human brain activities via functional magnetic resonance imaging
(fMRI) has gained increasing attention in recent years. While encouraging
results have been reported in brain states classification tasks, reconstructing
the details of human visual experience still remains difficult. Two main
challenges that hinder the development of effective models are the perplexing
fMRI measurement noise and the high dimensionality of limited data instances.
Existing methods generally suffer from one or both of these issues and yield
dissatisfactory results. In this paper, we tackle this problem by casting the
reconstruction of visual stimulus as the Bayesian inference of missing view in
a multiview latent variable model. Sharing a common latent representation, our
joint generative model of external stimulus and brain response is not only
"deep" in extracting nonlinear features from visual images, but also powerful
in capturing correlations among voxel activities of fMRI recordings. The
nonlinearity and deep structure endow our model with strong representation
ability, while the correlations of voxel activities are critical for
suppressing noise and improving prediction. We devise an efficient variational
Bayesian method to infer the latent variables and the model parameters. To
further improve the reconstruction accuracy, the latent representations of
testing instances are enforced to be close to that of their neighbours from the
training set via posterior regularization. Experiments on three fMRI recording
datasets demonstrate that our approach can more accurately reconstruct visual
stimuli
Deep generative modeling for single-cell transcriptomics.
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task
Multi-view Learning as a Nonparametric Nonlinear Inter-Battery Factor Analysis
Factor analysis aims to determine latent factors, or traits, which summarize
a given data set. Inter-battery factor analysis extends this notion to multiple
views of the data. In this paper we show how a nonlinear, nonparametric version
of these models can be recovered through the Gaussian process latent variable
model. This gives us a flexible formalism for multi-view learning where the
latent variables can be used both for exploratory purposes and for learning
representations that enable efficient inference for ambiguous estimation tasks.
Learning is performed in a Bayesian manner through the formulation of a
variational compression scheme which gives a rigorous lower bound on the log
likelihood. Our Bayesian framework provides strong regularization during
training, allowing the structure of the latent space to be determined
efficiently and automatically. We demonstrate this by producing the first (to
our knowledge) published results of learning from dozens of views, even when
data is scarce. We further show experimental results on several different types
of multi-view data sets and for different kinds of tasks, including exploratory
data analysis, generation, ambiguity modelling through latent priors and
classification.Comment: 49 pages including appendi
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