5,311 research outputs found
Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches
In the past two decades, functional Magnetic Resonance Imaging has been used
to relate neuronal network activity to cognitive processing and behaviour.
Recently this approach has been augmented by algorithms that allow us to infer
causal links between component populations of neuronal networks. Multiple
inference procedures have been proposed to approach this research question but
so far, each method has limitations when it comes to establishing whole-brain
connectivity patterns. In this work, we discuss eight ways to infer causality
in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality,
Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and
Transfer Entropy. We finish with formulating some recommendations for the
future directions in this area
Channel-Recurrent Autoencoding for Image Modeling
Despite recent successes in synthesizing faces and bedrooms, existing
generative models struggle to capture more complex image types, potentially due
to the oversimplification of their latent space constructions. To tackle this
issue, building on Variational Autoencoders (VAEs), we integrate recurrent
connections across channels to both inference and generation steps, allowing
the high-level features to be captured in global-to-local, coarse-to-fine
manners. Combined with adversarial loss, our channel-recurrent VAE-GAN
(crVAE-GAN) outperforms VAE-GAN in generating a diverse spectrum of high
resolution images while maintaining the same level of computational efficacy.
Our model produces interpretable and expressive latent representations to
benefit downstream tasks such as image completion. Moreover, we propose two
novel regularizations, namely the KL objective weighting scheme over time steps
and mutual information maximization between transformed latent variables and
the outputs, to enhance the training.Comment: Code: https://github.com/WendyShang/crVAE. Supplementary Materials:
http://www-personal.umich.edu/~shangw/wacv18_supplementary_material.pd
Multi-Entity Dependence Learning with Rich Context via Conditional Variational Auto-encoder
Multi-Entity Dependence Learning (MEDL) explores conditional correlations
among multiple entities. The availability of rich contextual information
requires a nimble learning scheme that tightly integrates with deep neural
networks and has the ability to capture correlation structures among
exponentially many outcomes. We propose MEDL_CVAE, which encodes a conditional
multivariate distribution as a generating process. As a result, the variational
lower bound of the joint likelihood can be optimized via a conditional
variational auto-encoder and trained end-to-end on GPUs. Our MEDL_CVAE was
motivated by two real-world applications in computational sustainability: one
studies the spatial correlation among multiple bird species using the eBird
data and the other models multi-dimensional landscape composition and human
footprint in the Amazon rainforest with satellite images. We show that
MEDL_CVAE captures rich dependency structures, scales better than previous
methods, and further improves on the joint likelihood taking advantage of very
large datasets that are beyond the capacity of previous methods.Comment: The first two authors contribute equall
Probabilistic reasoning and inference for systems biology
One of the important challenges in Systems Biology is reasoning and performing hypotheses testing in uncertain conditions, when available knowledge may be incomplete and the experimental data may contain substantial noise.
In this thesis we develop methods of probabilistic reasoning and inference
that operate consistently within an environment of uncertain knowledge and data. Mechanistic mathematical models are used to describe hypotheses about biological systems.
We consider both deductive model based reasoning and model inference from data. The main contributions are a novel modelling approach using continuous time Markov chains that enables deductive derivation of model behaviours and their properties, and the application of Bayesian inferential methods to solve the inverse problem of model inference and comparison, given uncertain knowledge and noisy data.
In the first part of the thesis, we consider both individual and population
based techniques for modelling biochemical pathways using continuous time Markov chains, and demonstrate why the latter is the most appropriate. We illustrate a new approach, based on symbolic intervals of concentrations, with an example portion of the ERK signalling pathway. We demonstrate that the resulting model approximates the same dynamic system as traditionally defined using ordinary differential equations. The advantage of the new approach is quantitative logical analysis; we formulate a number of biologically significant queries in the temporal logic CSL and use probabilistic symbolic model checking to investigate their veracity.
In the second part of the thesis, we consider the inverse problem of model
inference and testing of alternative hypotheses, when models are defined by non-linear ordinary differential equations and the experimental data is noisy and sparse. We compare and evaluate a number of statistical techniques, and implement an effective Bayesian inferential framework for systems biology based on Markov chain Monte Carlo methods and estimation of marginal likelihoods by annealing-melting integration. We illustrate the framework with two case studies, one of which involves an open problem concerning the mediation of ERK phosphorylation in the ERK pathway
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