4,794 research outputs found
HyperVAE: A Minimum Description Length Variational Hyper-Encoding Network
We propose a framework called HyperVAE for encoding distributions of
distributions. When a target distribution is modeled by a VAE, its neural
network parameters \theta is drawn from a distribution p(\theta) which is
modeled by a hyper-level VAE. We propose a variational inference using Gaussian
mixture models to implicitly encode the parameters \theta into a low
dimensional Gaussian distribution. Given a target distribution, we predict the
posterior distribution of the latent code, then use a matrix-network decoder to
generate a posterior distribution q(\theta). HyperVAE can encode the parameters
\theta in full in contrast to common hyper-networks practices, which generate
only the scale and bias vectors as target-network parameters. Thus HyperVAE
preserves much more information about the model for each task in the latent
space. We discuss HyperVAE using the minimum description length (MDL) principle
and show that it helps HyperVAE to generalize. We evaluate HyperVAE in density
estimation tasks, outlier detection and discovery of novel design classes,
demonstrating its efficacy
Probabilistic Methodology and Techniques for Artefact Conception and Development
The purpose of this paper is to make a state of the art on probabilistic methodology and techniques for artefact conception and development. It is the 8th deliverable of the BIBA (Bayesian Inspired Brain and Artefacts) project. We first present the incompletness problem as the central difficulty that both living creatures and artefacts have to face: how can they perceive, infer, decide and act efficiently with incomplete and uncertain knowledge?. We then introduce a generic probabilistic formalism called Bayesian Programming. This formalism is then used to review the main probabilistic methodology
and techniques. This review is organized in 3 parts: first the probabilistic models from Bayesian networks to Kalman filters and from sensor fusion to CAD systems, second the inference techniques and finally the learning and model acquisition and comparison methodologies. We conclude with the perspectives of the BIBA project as they rise from this state of the art
Model predictive control techniques for hybrid systems
This paper describes the main issues encountered when applying model predictive control to hybrid processes. Hybrid model predictive control (HMPC) is a research field non-fully developed with many open challenges. The paper describes some of the techniques proposed by the research community to overcome the main problems encountered. Issues related to the stability and the solution of the optimization problem are also discussed. The paper ends by describing the results of a benchmark exercise in which several HMPC schemes were applied to a solar air conditioning plant.Ministerio de EduaciĂłn y Ciencia DPI2007-66718-C04-01Ministerio de EduaciĂłn y Ciencia DPI2008-0581
Inference algorithms for gene networks: a statistical mechanics analysis
The inference of gene regulatory networks from high throughput gene
expression data is one of the major challenges in systems biology. This paper
aims at analysing and comparing two different algorithmic approaches. The first
approach uses pairwise correlations between regulated and regulating genes; the
second one uses message-passing techniques for inferring activating and
inhibiting regulatory interactions. The performance of these two algorithms can
be analysed theoretically on well-defined test sets, using tools from the
statistical physics of disordered systems like the replica method. We find that
the second algorithm outperforms the first one since it takes into account
collective effects of multiple regulators
Mechanism Deduction from Noisy Chemical Reaction Networks
We introduce KiNetX, a fully automated meta-algorithm for the kinetic
analysis of complex chemical reaction networks derived from semi-accurate but
efficient electronic structure calculations. It is designed to (i) accelerate
the automated exploration of such networks, and (ii) cope with model-inherent
errors in electronic structure calculations on elementary reaction steps. We
developed and implemented KiNetX to possess three features. First, KiNetX
evaluates the kinetic relevance of every species in a (yet incomplete) reaction
network to confine the search for new elementary reaction steps only to those
species that are considered possibly relevant. Second, KiNetX identifies and
eliminates all kinetically irrelevant species and elementary reactions to
reduce a complex network graph to a comprehensible mechanism. Third, KiNetX
estimates the sensitivity of species concentrations toward changes in
individual rate constants (derived from relative free energies), which allows
us to systematically select the most efficient electronic structure model for
each elementary reaction given a predefined accuracy. The novelty of KiNetX
consists in the rigorous propagation of correlated free-energy uncertainty
through all steps of our kinetic analyis. To examine the performance of KiNetX,
we developed AutoNetGen. It semirandomly generates chemistry-mimicking reaction
networks by encoding chemical logic into their underlying graph structure.
AutoNetGen allows us to consider a vast number of distinct chemistry-like
scenarios and, hence, to discuss assess the importance of rigorous uncertainty
propagation in a statistical context. Our results reveal that KiNetX reliably
supports the deduction of product ratios, dominant reaction pathways, and
possibly other network properties from semi-accurate electronic structure data.Comment: 36 pages, 4 figures, 2 table
BioDiVinE: A Framework for Parallel Analysis of Biological Models
In this paper a novel tool BioDiVinEfor parallel analysis of biological
models is presented. The tool allows analysis of biological models specified in
terms of a set of chemical reactions. Chemical reactions are transformed into a
system of multi-affine differential equations. BioDiVinE employs techniques for
finite discrete abstraction of the continuous state space. At that level,
parallel analysis algorithms based on model checking are provided. In the
paper, the key tool features are described and their application is
demonstrated by means of a case study
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