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

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types. Results. We introduce TRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools, TRaIT supports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena. TRaIT improves accuracy, robustness to data-specific errors and computational complexity compared to competing methods. Conclusions. We show that the application of TRaIT to single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses

Joint QoS multicast routing and channel assignment in multiradio multichannel wireless mesh networks using intelligent computational methods

Copyright @ 2010 Elsevier B.V. All rights reserved.In this paper, the quality of service multicast routing and channel assignment (QoS-MRCA) problem is investigated. It is proved to be a NP-hard problem. Previous work separates the multicast tree construction from the channel assignment. Therefore they bear severe drawback, that is, channel assignment cannot work well with the determined multicast tree. In this paper, we integrate them together and solve it by intelligent computational methods. First, we develop a unified framework which consists of the problem formulation, the solution representation, the fitness function, and the channel assignment algorithm. Then, we propose three separate algorithms based on three representative intelligent computational methods (i.e., genetic algorithm, simulated annealing, and tabu search). These three algorithms aim to search minimum-interference multicast trees which also satisfy the end-to-end delay constraint and optimize the usage of the scarce radio network resource in wireless mesh networks. To achieve this goal, the optimization techniques based on state of the art genetic algorithm and the techniques to control the annealing process and the tabu search procedure are well developed separately. Simulation results show that the proposed three intelligent computational methods based multicast algorithms all achieve better performance in terms of both the total channel conflict and the tree cost than those comparative references.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1

Spin network quantum simulator

We propose a general setting for a universal representation of the quantum structure on which quantum information stands, whose dynamical evolution (information manipulation) is based on angular momentum recoupling theory. Such scheme complies with the notion of 'quantum simulator' in the sense of Feynmann, and is shown to be related with the topological quantum field theory approach to quantum computation.Comment: revtex, 6 pages + 5 figure

An Efficient Index for Visual Search in Appearance-based SLAM

Vector-quantization can be a computationally expensive step in visual bag-of-words (BoW) search when the vocabulary is large. A BoW-based appearance SLAM needs to tackle this problem for an efficient real-time operation. We propose an effective method to speed up the vector-quantization process in BoW-based visual SLAM. We employ a graph-based nearest neighbor search (GNNS) algorithm to this aim, and experimentally show that it can outperform the state-of-the-art. The graph-based search structure used in GNNS can efficiently be integrated into the BoW model and the SLAM framework. The graph-based index, which is a k-NN graph, is built over the vocabulary words and can be extracted from the BoW's vocabulary construction procedure, by adding one iteration to the k-means clustering, which adds small extra cost. Moreover, exploiting the fact that images acquired for appearance-based SLAM are sequential, GNNS search can be initiated judiciously which helps increase the speedup of the quantization process considerably

Probabilistic Graphical Model Representation in Phylogenetics

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution