An Open Source Pattern Recognition Toolbox for MATLAB

Pattern recognition and machine learning are becoming integral parts of algorithms in a wide range of applications. Different algorithms and approaches for machine learning include different tradeoffs between performance and computation, so during algorithm development it is often necessary to explore a variety of different approaches to a given task. A toolbox with a unified framework across multiple pattern recognition techniques enables algorithm developers the ability to rapidly evaluate different choices prior to deployment. MATLAB is a widely used environment for algorithm development and prototyping, and although several MATLAB toolboxes for pattern recognition are currently available these are either incomplete, expensive, or restrictively licensed. In this work we describe a MATLAB toolbox for pattern recognition and machine learning known as the PRT (Pattern Recognition Toolbox), licensed under the permissive MIT license. The PRT includes many popular techniques for data preprocessing, supervised learning, clustering, regression and feature selection, as well as a methodology for combining these components using a simple, uniform syntax. The resulting algorithms can be evaluated using cross-validation and a variety of scoring metrics to ensure robust performance when the algorithm is deployed. This paper presents an overview of the PRT as well as an example of usage on Fisher's Iris dataset

Keeping track of worm trackers

C. elegans is used extensively as a model system in the neurosciences due to its well defined nervous system. However, the seeming simplicity of this nervous system in anatomical structure and neuronal connectivity, at least compared to higher animals, underlies a rich diversity of behaviors. The usefulness of the worm in genome-wide mutagenesis or RNAi screens, where thousands of strains are assessed for phenotype, emphasizes the need for computational methods for automated parameterization of generated behaviors. In addition, behaviors can be modulated upon external cues like temperature, O2 and CO2 concentrations, mechanosensory and chemosensory inputs. Different machine vision tools have been developed to aid researchers in their efforts to inventory and characterize defined behavioral “outputs”. Here we aim at providing an overview of different worm-tracking packages or video analysis tools designed to quantify different aspects of locomotion such as the occurrence of directional changes (turns, omega bends), curvature of the sinusoidal shape (amplitude, body bend angles) and velocity (speed, backward or forward movement)

Information Theoretical Estimators Toolbox

We present ITE (information theoretical estimators) a free and open source, multi-platform, Matlab/Octave toolbox that is capable of estimating many different variants of entropy, mutual information, divergence, association measures, cross quantities, and kernels on distributions. Thanks to its highly modular design, ITE supports additionally (i) the combinations of the estimation techniques, (ii) the easy construction and embedding of novel information theoretical estimators, and (iii) their immediate application in information theoretical optimization problems. ITE also includes a prototype application in a central problem class of signal processing, independent subspace analysis and its extensions.Comment: 5 pages; ITE toolbox: https://bitbucket.org/szzoli/ite

Review of analytical instruments for EEG analysis

Since it was first used in 1926, EEG has been one of the most useful instruments of neuroscience. In order to start using EEG data we need not only EEG apparatus, but also some analytical tools and skills to understand what our data mean. This article describes several classical analytical tools and also new one which appeared only several years ago. We hope it will be useful for those researchers who have only started working in the field of cognitive EEG