Fractionally Predictive Spiking Neurons

Recent experimental work has suggested that the neural firing rate can be interpreted as a fractional derivative, at least when signal variation induces neural adaptation. Here, we show that the actual neural spike-train itself can be considered as the fractional derivative, provided that the neural signal is approximated by a sum of power-law kernels. A simple standard thresholding spiking neuron suffices to carry out such an approximation, given a suitable refractory response. Empirically, we find that the online approximation of signals with a sum of power-law kernels is beneficial for encoding signals with slowly varying components, like long-memory self-similar signals. For such signals, the online power-law kernel approximation typically required less than half the number of spikes for similar SNR as compared to sums of similar but exponentially decaying kernels. As power-law kernels can be accurately approximated using sums or cascades of weighted exponentials, we demonstrate that the corresponding decoding of spike-trains by a receiving neuron allows for natural and transparent temporal signal filtering by tuning the weights of the decoding kernel.Comment: 13 pages, 5 figures, in Advances in Neural Information Processing 201

Fast kinetic Monte Carlo simulation of strained heteroepitaxy in three dimensions

Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the associated lattice elasticity problems. The computational efficiency is further enhanced by using a superparticle surface coarsening approximation. Atomic hoppings simulating surface diffusion are sampled using a multi-step acceptance-rejection algorithm. It utilizes quick estimates of the atomic elastic energies from extensively tabulated values modulated by the local strain. A parameter controls the compromise between accuracy and efficiency of the acceptance-rejection algorithm.Comment: 10 pages, 4 figures, submitted to Proceedings of Barrett Lectures 2007, Journal of Scientific Computin

Inference Optimization using Relational Algebra

Exact inference procedures in Bayesian networks can be expressed using relational algebra; this provides a common ground for optimizations from the AI and database communities. Specifically, the ability to accomodate sparse representations of probability distributions opens up the way to optimize for their cardinality instead of the dimensionality; we apply this in a sensor data model.\u

Tuberculosis vaccine strain _Mycobacterium bovis_ BCG Russia is a natural _recA_ mutant

The current tuberculosis vaccine is a live vaccine derived from _Mycobacterium bovis_ and attenuated by serial _in vitro_ passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Guérin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains, we aimed to inactivate _recA_ by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was successful in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of _recA_ revealed that a single nucleotide insertion in the 5' part of _recA_ led to a translational frameshift with an early stop codon making BCG Russia a natural _recA_ mutant. At the protein level BCG Russia failed to express RecA. According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental _M. bovis_. Our data suggest that _recA_ inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to _M. bovis_ AF2122/97 wild type