Python for Information Theoretic Analysis of Neural Data

Information theory, the mathematical theory of communication in the presence of noise, is playing an increasingly important role in modern quantitative neuroscience. It makes it possible to treat neural systems as stochastic communication channels and gain valuable, quantitative insights into their sensory coding function. These techniques provide results on how neurons encode stimuli in a way which is independent of any specific assumptions on which part of the neuronal response is signal and which is noise, and they can be usefully applied even to highly non-linear systems where traditional techniques fail. In this article, we describe our work and experiences using Python for information theoretic analysis. We outline some of the algorithmic, statistical and numerical challenges in the computation of information theoretic quantities from neural data. In particular, we consider the problems arising from limited sampling bias and from calculation of maximum entropy distributions in the presence of constraints representing the effects of different orders of interaction in the system. We explain how and why using Python has allowed us to significantly improve the speed and domain of applicability of the information theoretic algorithms, allowing analysis of data sets characterized by larger numbers of variables. We also discuss how our use of Python is facilitating integration with collaborative databases and centralised computational resources

JIDT: An information-theoretic toolkit for studying the dynamics of complex systems

Complex systems are increasingly being viewed as distributed information processing systems, particularly in the domains of computational neuroscience, bioinformatics and Artificial Life. This trend has resulted in a strong uptake in the use of (Shannon) information-theoretic measures to analyse the dynamics of complex systems in these fields. We introduce the Java Information Dynamics Toolkit (JIDT): a Google code project which provides a standalone, (GNU GPL v3 licensed) open-source code implementation for empirical estimation of information-theoretic measures from time-series data. While the toolkit provides classic information-theoretic measures (e.g. entropy, mutual information, conditional mutual information), it ultimately focusses on implementing higher-level measures for information dynamics. That is, JIDT focusses on quantifying information storage, transfer and modification, and the dynamics of these operations in space and time. For this purpose, it includes implementations of the transfer entropy and active information storage, their multivariate extensions and local or pointwise variants. JIDT provides implementations for both discrete and continuous-valued data for each measure, including various types of estimator for continuous data (e.g. Gaussian, box-kernel and Kraskov-Stoegbauer-Grassberger) which can be swapped at run-time due to Java's object-oriented polymorphism. Furthermore, while written in Java, the toolkit can be used directly in MATLAB, GNU Octave, Python and other environments. We present the principles behind the code design, and provide several examples to guide users.Comment: 37 pages, 4 figure

CoCalc as a Learning Tool for Neural Network Simulation in the Special Course "Foundations of Mathematic Informatics"

The role of neural network modeling in the learning content of the special course "Foundations of Mathematical Informatics" was discussed. The course was developed for the students of technical universities - future IT-specialists and directed to breaking the gap between theoretic computer science and it's applied applications: software, system and computing engineering. CoCalc was justified as a learning tool of mathematical informatics in general and neural network modeling in particular. The elements of technique of using CoCalc at studying topic "Neural network and pattern recognition" of the special course "Foundations of Mathematic Informatics" are shown. The program code was presented in a CoffeeScript language, which implements the basic components of artificial neural network: neurons, synaptic connections, functions of activations (tangential, sigmoid, stepped) and their derivatives, methods of calculating the network's weights, etc. The features of the Kolmogorov-Arnold representation theorem application were discussed for determination the architecture of multilayer neural networks. The implementation of the disjunctive logical element and approximation of an arbitrary function using a three-layer neural network were given as an examples. According to the simulation results, a conclusion was made as for the limits of the use of constructed networks, in which they retain their adequacy. The framework topics of individual research of the artificial neural networks is proposed.Comment: 16 pages, 3 figures, Proceedings of the 13th International Conference on ICT in Education, Research and Industrial Applications. Integration, Harmonization and Knowledge Transfer (ICTERI, 2018

Decentralized learning with budgeted network load using Gaussian copulas and classifier ensembles

We examine a network of learners which address the same classification task but must learn from different data sets. The learners cannot share data but instead share their models. Models are shared only one time so as to preserve the network load. We introduce DELCO (standing for Decentralized Ensemble Learning with COpulas), a new approach allowing to aggregate the predictions of the classifiers trained by each learner. The proposed method aggregates the base classifiers using a probabilistic model relying on Gaussian copulas. Experiments on logistic regressor ensembles demonstrate competing accuracy and increased robustness in case of dependent classifiers. A companion python implementation can be downloaded at https://github.com/john-klein/DELC

Communication-Computation Efficient Gradient Coding

This paper develops coding techniques to reduce the running time of distributed learning tasks. It characterizes the fundamental tradeoff to compute gradients (and more generally vector summations) in terms of three parameters: computation load, straggler tolerance and communication cost. It further gives an explicit coding scheme that achieves the optimal tradeoff based on recursive polynomial constructions, coding both across data subsets and vector components. As a result, the proposed scheme allows to minimize the running time for gradient computations. Implementations are made on Amazon EC2 clusters using Python with mpi4py package. Results show that the proposed scheme maintains the same generalization error while reducing the running time by $32\%$ compared to uncoded schemes and $23\%$ compared to prior coded schemes focusing only on stragglers (Tandon et al., ICML 2017)