Efficient transfer entropy analysis of non-stationary neural time series

Information theory allows us to investigate information processing in neural systems in terms of information transfer, storage and modification. Especially the measure of information transfer, transfer entropy, has seen a dramatic surge of interest in neuroscience. Estimating transfer entropy from two processes requires the observation of multiple realizations of these processes to estimate associated probability density functions. To obtain these observations, available estimators assume stationarity of processes to allow pooling of observations over time. This assumption however, is a major obstacle to the application of these estimators in neuroscience as observed processes are often non-stationary. As a solution, Gomez-Herrero and colleagues theoretically showed that the stationarity assumption may be avoided by estimating transfer entropy from an ensemble of realizations. Such an ensemble is often readily available in neuroscience experiments in the form of experimental trials. Thus, in this work we combine the ensemble method with a recently proposed transfer entropy estimator to make transfer entropy estimation applicable to non-stationary time series. We present an efficient implementation of the approach that deals with the increased computational demand of the ensemble method's practical application. In particular, we use a massively parallel implementation for a graphics processing unit to handle the computationally most heavy aspects of the ensemble method. We test the performance and robustness of our implementation on data from simulated stochastic processes and demonstrate the method's applicability to magnetoencephalographic data. While we mainly evaluate the proposed method for neuroscientific data, we expect it to be applicable in a variety of fields that are concerned with the analysis of information transfer in complex biological, social, and artificial systems.Comment: 27 pages, 7 figures, submitted to PLOS ON

GPU-Based Simulation of Cellular Neural Networks for Image Processing

The inherent massive parallelism of cellular neural networks makes them an ideal computational platform for kernelbased algorithms and image processing. General-purpose GPUs provide similar massive parallelism, but it can be difficult to design algorithms to make optimal use of the hardware. The presented research includes a GPU abstraction based on cellular neural networks. The abstraction offers a simplified view of massively parallel computation which remains reasonably efficient. An image processing library with visualization software has been developed to showcase the flexibility and power of cellular computation on GPUs. Benchmarks of the library indicate that commodity GPUs can be used to significantly accelerate CNN research and offer a viable alternative to CPU-based image processing algorithms

The Swarm Computer, an Analog Cellular-Swarm Hybrid Architecture

The “killer apps” of cellular and swarm computing are image processing and optimization, respectively; however, applying these platforms to general-purpose computing remains impractical. Designing systems within the restrictive framework of cellular automata is extremely difficult, though often very efficient and scalable. On the other hand, swarm networks are very powerful but difficult to implement in hardware. Here we introduce a hybrid model, the Swarm Computer, which is both practical to program and efficient to implement. Applications in astrophysics and image processing are considered

A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Cognition-Based Networks: A New Perspective on Network Optimization Using Learning and Distributed Intelligence

IEEE Access Volume 3, 2015, Article number 7217798, Pages 1512-1530 Open Access Cognition-based networks: A new perspective on network optimization using learning and distributed intelligence (Article) Zorzi, M.a , Zanella, A.a, Testolin, A.b, De Filippo De Grazia, M.b, Zorzi, M.bc a Department of Information Engineering, University of Padua, Padua, Italy b Department of General Psychology, University of Padua, Padua, Italy c IRCCS San Camillo Foundation, Venice-Lido, Italy View additional affiliations View references (107) Abstract In response to the new challenges in the design and operation of communication networks, and taking inspiration from how living beings deal with complexity and scalability, in this paper we introduce an innovative system concept called COgnition-BAsed NETworkS (COBANETS). The proposed approach develops around the systematic application of advanced machine learning techniques and, in particular, unsupervised deep learning and probabilistic generative models for system-wide learning, modeling, optimization, and data representation. Moreover, in COBANETS, we propose to combine this learning architecture with the emerging network virtualization paradigms, which make it possible to actuate automatic optimization and reconfiguration strategies at the system level, thus fully unleashing the potential of the learning approach. Compared with the past and current research efforts in this area, the technical approach outlined in this paper is deeply interdisciplinary and more comprehensive, calling for the synergic combination of expertise of computer scientists, communications and networking engineers, and cognitive scientists, with the ultimate aim of breaking new ground through a profound rethinking of how the modern understanding of cognition can be used in the management and optimization of telecommunication network

Radial Basis Functions: Biomedical Applications and Parallelization

Radial basis function (RBF) is a real-valued function whose values depend only on the distances between an interpolation point and a set of user-specified points called centers. RBF interpolation is one of the primary methods to reconstruct functions from multi-dimensional scattered data. Its abilities to generalize arbitrary space dimensions and to provide spectral accuracy have made it particularly popular in different application areas, including but not limited to: finding numerical solutions of partial differential equations (PDEs), image processing, computer vision and graphics, deep learning and neural networks, etc. The present thesis discusses three applications of RBF interpolation in biomedical engineering areas: (1) Calcium dynamics modeling, in which we numerically solve a set of PDEs by using meshless numerical methods and RBF-based interpolation techniques; (2) Image restoration and transformation, where an image is restored from its triangular mesh representation or transformed under translation, rotation, and scaling, etc. from its original form; (3) Porous structure design, in which the RBF interpolation used to reconstruct a 3D volume containing porous structures from a set of regularly or randomly placed points inside a user-provided surface shape. All these three applications have been investigated and their effectiveness has been supported with numerous experimental results. In particular, we innovatively utilize anisotropic distance metrics to define the distance in RBF interpolation and apply them to the aforementioned second and third applications, which show significant improvement in preserving image features or capturing connected porous structures over the isotropic distance-based RBF method. Beside the algorithm designs and their applications in biomedical areas, we also explore several common parallelization techniques (including OpenMP and CUDA-based GPU programming) to accelerate the performance of the present algorithms. In particular, we analyze how parallel programming can help RBF interpolation to speed up the meshless PDE solver as well as image processing. While RBF has been widely used in various science and engineering fields, the current thesis is expected to trigger some more interest from computational scientists or students into this fast-growing area and specifically apply these techniques to biomedical problems such as the ones investigated in the present work

Graphics Processing Unit–Enhanced Genetic Algorithms for Solving the Temporal Dynamics of Gene Regulatory Networks

Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task. In this article, we study how to develop efficient parallel implementations of this method for the fine-grained parallel architecture of graphics processing units (GPUs) using the compute unified device architecture (CUDA) platform. An exhaustive and methodical study of various parallel genetic algorithm schemes—master-slave, island, cellular, and hybrid models, and various individual selection methods (roulette, elitist)—is carried out for this problem. Several procedures that optimize the use of the GPU’s resources are presented. We conclude that the implementation that produces better results (both from the performance and the genetic algorithm fitness perspectives) is simulating a few thousands of individuals grouped in a few islands using elitist selection. This model comprises 2 mighty factors for discovering the best solutions: finding good individuals in a short number of generations, and introducing genetic diversity via a relatively frequent and numerous migration. As a result, we have even found the optimal solution for the analyzed gene regulatory network (GRN). In addition, a comparative study of the performance obtained by the different parallel implementations on GPU versus a sequential application on CPU is carried out. In our tests, a multifold speedup was obtained for our optimized parallel implementation of the method on medium class GPU over an equivalent sequential single-core implementation running on a recent Intel i7 CPU. This work can provide useful guidance to researchers in biology, medicine, or bioinformatics in how to take advantage of the parallelization on massively parallel devices and GPUs to apply novel metaheuristic algorithms powered by nature for real-world applications (like the method to solve the temporal dynamics of GRNs)