58,749 research outputs found
Probabilistic Programming in Python using PyMC
Probabilistic programming (PP) allows flexible specification of Bayesian
statistical models in code. PyMC3 is a new, open-source PP framework with an
intutive and readable, yet powerful, syntax that is close to the natural syntax
statisticians use to describe models. It features next-generation Markov chain
Monte Carlo (MCMC) sampling algorithms such as the No-U-Turn Sampler (NUTS;
Hoffman, 2014), a self-tuning variant of Hamiltonian Monte Carlo (HMC; Duane,
1987). Probabilistic programming in Python confers a number of advantages
including multi-platform compatibility, an expressive yet clean and readable
syntax, easy integration with other scientific libraries, and extensibility via
C, C++, Fortran or Cython. These features make it relatively straightforward to
write and use custom statistical distributions, samplers and transformation
functions, as required by Bayesian analysis
The Emergence of Canalization and Evolvability in an Open-Ended, Interactive Evolutionary System
Natural evolution has produced a tremendous diversity of functional
organisms. Many believe an essential component of this process was the
evolution of evolvability, whereby evolution speeds up its ability to innovate
by generating a more adaptive pool of offspring. One hypothesized mechanism for
evolvability is developmental canalization, wherein certain dimensions of
variation become more likely to be traversed and others are prevented from
being explored (e.g. offspring tend to have similarly sized legs, and mutations
affect the length of both legs, not each leg individually). While ubiquitous in
nature, canalization almost never evolves in computational simulations of
evolution. Not only does that deprive us of in silico models in which to study
the evolution of evolvability, but it also raises the question of which
conditions give rise to this form of evolvability. Answering this question
would shed light on why such evolvability emerged naturally and could
accelerate engineering efforts to harness evolution to solve important
engineering challenges. In this paper we reveal a unique system in which
canalization did emerge in computational evolution. We document that genomes
entrench certain dimensions of variation that were frequently explored during
their evolutionary history. The genetic representation of these organisms also
evolved to be highly modular and hierarchical, and we show that these
organizational properties correlate with increased fitness. Interestingly, the
type of computational evolutionary experiment that produced this evolvability
was very different from traditional digital evolution in that there was no
objective, suggesting that open-ended, divergent evolutionary processes may be
necessary for the evolution of evolvability.Comment: SI can be found at: http://www.evolvingai.org/files/SI_0.zi
Tuning the average path length of complex networks and its influence to the emergent dynamics of the majority-rule model
We show how appropriate rewiring with the aid of Metropolis Monte Carlo
computational experiments can be exploited to create network topologies
possessing prescribed values of the average path length (APL) while keeping the
same connectivity degree and clustering coefficient distributions. Using the
proposed rewiring rules we illustrate how the emergent dynamics of the
celebrated majority-rule model are shaped by the distinct impact of the APL
attesting the need for developing efficient algorithms for tuning such network
characteristics.Comment: 10 figure
Particle Efficient Importance Sampling
The efficient importance sampling (EIS) method is a general principle for the
numerical evaluation of high-dimensional integrals that uses the sequential
structure of target integrands to build variance minimising importance
samplers. Despite a number of successful applications in high dimensions, it is
well known that importance sampling strategies are subject to an exponential
growth in variance as the dimension of the integration increases. We solve this
problem by recognising that the EIS framework has an offline sequential Monte
Carlo interpretation. The particle EIS method is based on non-standard
resampling weights that take into account the look-ahead construction of the
importance sampler. We apply the method for a range of univariate and bivariate
stochastic volatility specifications. We also develop a new application of the
EIS approach to state space models with Student's t state innovations. Our
results show that the particle EIS method strongly outperforms both the
standard EIS method and particle filters for likelihood evaluation in high
dimensions. Moreover, the ratio between the variances of the particle EIS and
particle filter methods remains stable as the time series dimension increases.
We illustrate the efficiency of the method for Bayesian inference using the
particle marginal Metropolis-Hastings and importance sampling squared
algorithms
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