114,604 research outputs found
Simulation of Rapidly-Exploring Random Trees in Membrane Computing with P-Lingua and Automatic Programming
Methods based on Rapidly-exploring Random Trees (RRTs) have been
widely used in robotics to solve motion planning problems. On the other hand, in the
membrane computing framework, models based on Enzymatic Numerical P systems
(ENPS) have been applied to robot controllers, but today there is a lack of planning
algorithms based on membrane computing for robotics. With this motivation, we
provide a variant of ENPS called Random Enzymatic Numerical P systems with
Proteins and Shared Memory (RENPSM) addressed to implement RRT algorithms
and we illustrate it by simulating the bidirectional RRT algorithm. This paper is an
extension of [21]a. The software presented in [21] was an ad-hoc simulator, i.e, a tool
for simulating computations of one and only one model that has been hard-coded.
The main contribution of this paper with respect to [21] is the introduction of a novel
solution for membrane computing simulators based on automatic programming. First,
we have extended the P-Lingua syntax –a language to define membrane computing
models– to write RENPSM models. Second, we have implemented a new parser based
on Flex and Bison to read RENPSM models and produce source code in C language
for multicore processors with OpenMP. Finally, additional experiments are presented.Ministerio de Economía, Industria y Competitividad TIN2017-89842-
Computational convergence of the path integral for real dendritic morphologies
Neurons are characterised by a morphological structure unique amongst biological cells, the core of which is the dendritic tree. The vast number of dendritic geometries, combined with heterogeneous properties of the cell membrane, continue to challenge scientists in predicting neuronal input-output relationships, even in the case of sub-threshold dendritic currents. The Green’s function obtained for a given dendritic geometry provides this functional relationship for passive or quasi-active dendrites and can be constructed by a sum-over-trips approach based on a path integral formalism. In this paper, we introduce a number of efficient algorithms for realisation of the sum-over-trips framework and investigate the convergence of these algorithms on different dendritic geometries. We demonstrate that the convergence of the trip sampling methods strongly depends on dendritic morphology as well as the biophysical properties of the cell membrane. For real morphologies, the number of trips to guarantee a small convergence error might become very large and strongly affect computational efficiency. As an alternative, we introduce a highly-efficient matrix method which can be applied to arbitrary branching structures
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Recent advances in electron microscopy have enabled the imaging of single
cells in 3D at nanometer length scale resolutions. An uncharted frontier for in
silico biology is the ability to simulate cellular processes using these
observed geometries. Enabling such simulations requires watertight meshing of
electron micrograph images into 3D volume meshes, which can then form the basis
of computer simulations of such processes using numerical techniques such as
the Finite Element Method. In this paper, we describe the use of our recently
rewritten mesh processing software, GAMer 2, to bridge the gap between poorly
conditioned meshes generated from segmented micrographs and boundary marked
tetrahedral meshes which are compatible with simulation. We demonstrate the
application of a workflow using GAMer 2 to a series of electron micrographs of
neuronal dendrite morphology explored at three different length scales and show
that the resulting meshes are suitable for finite element simulations. This
work is an important step towards making physical simulations of biological
processes in realistic geometries routine. Innovations in algorithms to
reconstruct and simulate cellular length scale phenomena based on emerging
structural data will enable realistic physical models and advance discovery at
the interface of geometry and cellular processes. We posit that a new frontier
at the intersection of computational technologies and single cell biology is
now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies
available upon reques
An Efficient Threshold-Driven Aggregate-Label Learning Algorithm for Multimodal Information Processing
The aggregate-label learning paradigm tackles the long-standing temporary credit assignment (TCA) problem in neuroscience and machine learning, enabling spiking neural networks to learn multimodal sensory clues with delayed feedback signals. However, the existing aggregate-label learning algorithms only work for single spiking neurons, and with low learning efficiency, which limit their real-world applicability. To address these limitations, we first propose an efficient threshold-driven plasticity algorithm for spiking neurons, namely ETDP. It enables spiking neurons to generate the desired number of spikes that match the magnitude of delayed feedback signals and to learn useful multimodal sensory clues embedded within spontaneous spiking activities. Furthermore, we extend the ETDP algorithm to support multi-layer spiking neural networks (SNNs), which significantly improves the applicability of aggregate-label learning algorithms. We also validate the multi-layer ETDP learning algorithm in a multimodal computation framework for audio-visual pattern recognition. Experimental results on both synthetic and realistic datasets show significant improvements in the learning efficiency and model capacity over the existing aggregate-label learning algorithms. It, therefore, provides many opportunities for solving real-world multimodal pattern recognition tasks with spiking neural networks
A Kernel-Based Membrane Clustering Algorithm
The existing membrane clustering algorithms may fail to
handle the data sets with non-spherical cluster boundaries. To overcome
the shortcoming, this paper introduces kernel methods into membrane
clustering algorithms and proposes a kernel-based membrane clustering
algorithm, KMCA. By using non-linear kernel function, samples in
original data space are mapped to data points in a high-dimension feature
space, and the data points are clustered by membrane clustering
algorithms. Therefore, a data clustering problem is formalized as a kernel
clustering problem. In KMCA algorithm, a tissue-like P system is
designed to determine the optimal cluster centers for the kernel clustering
problem. Due to the use of non-linear kernel function, the proposed
KMCA algorithm can well deal with the data sets with non-spherical
cluster boundaries. The proposed KMCA algorithm is evaluated on nine
benchmark data sets and is compared with four existing clustering algorithms
Improved Algorithms for Simulating Crystalline Membranes
The physics of crystalline membranes, i.e. fixed-connectivity surfaces
embedded in three dimensions and with an extrinsic curvature term, is very rich
and of great theoretical interest. To understand their behavior, numerical
simulations are commonly used. Unfortunately, traditional Monte Carlo
algorithms suffer from very long auto-correlations and critical slowing down in
the more interesting phases of the model. In this paper we study the
performance of improved Monte Carlo algorithms for simulating crystalline
membrane, such as hybrid overrelaxation and unigrid methods, and compare their
performance to the more traditional Metropolis algorithm. We find that although
the overrelaxation algorithm does not reduce the critical slowing down, it
gives an overall gain of a factor 15 over the Metropolis algorithm. The unigrid
algorithm does, on the other hand, reduce the critical slowing down exponent to
z apprx. 1.7.Comment: 14 pages, 1 eps-figur
An empirical comparison of supervised machine learning techniques in bioinformatics
Research in bioinformatics is driven by the experimental data.
Current biological databases are populated by vast amounts of
experimental data. Machine learning has been widely applied to
bioinformatics and has gained a lot of success in this research
area. At present, with various learning algorithms available in the
literature, researchers are facing difficulties in choosing the best
method that can apply to their data. We performed an empirical
study on 7 individual learning systems and 9 different combined
methods on 4 different biological data sets, and provide some
suggested issues to be considered when answering the following
questions: (i) How does one choose which algorithm is best
suitable for their data set? (ii) Are combined methods better than
a single approach? (iii) How does one compare the effectiveness
of a particular algorithm to the others
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