ZOOpt: Toolbox for Derivative-Free Optimization

Recent advances of derivative-free optimization allow efficient approximating the global optimal solutions of sophisticated functions, such as functions with many local optima, non-differentiable and non-continuous functions. This article describes the ZOOpt (https://github.com/eyounx/ZOOpt) toolbox that provides efficient derivative-free solvers and are designed easy to use. ZOOpt provides a Python package for single-thread optimization, and a light-weighted distributed version with the help of the Julia language for Python described functions. ZOOpt toolbox particularly focuses on optimization problems in machine learning, addressing high-dimensional, noisy, and large-scale problems. The toolbox is being maintained toward ready-to-use tool in real-world machine learning tasks

Pycobra: A Python Toolbox for Ensemble Learning and Visualisation

We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface to compare and blend any existing machine learning algorithm available in Python libraries (as long as a \texttt{predict} method is given), and visualisation tools such as Voronoi tessellations. \texttt{pycobra} is fully \texttt{scikit-learn} compatible and is released under the MIT open-source license. \texttt{pycobra} can be downloaded from the Python Package Index (PyPi) and Machine Learning Open Source Software (MLOSS). The current version (along with Jupyter notebooks, extensive documentation, and continuous integration tests) is available at \href{https://github.com/bhargavvader/pycobra}{https://github.com/bhargavvader/pycobra} and official documentation website is \href{https://modal.lille.inria.fr/pycobra}{https://modal.lille.inria.fr/pycobra}

Wyrm: A Brain-Computer Interface Toolbox in Python

In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm (https://github.com/bbci/wyrm), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm’s software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python.BMBF, 01GQ0850, Bernstein Fokus Neurotechnologie - Nichtinvasive Neurotechnologie für Mensch-Maschine InteraktionBMBF, 16SV5839, Maschinelles Lernen zur Optimierung der Kommunikation schwerstgelähmter Patienten per BC

FISSA: A neuropil decontamination toolbox for calcium imaging signals

In vivo calcium imaging has become a method of choice to image neuronal population activity throughout the nervous system. These experiments generate large sequences of images. Their analysis is computationally intensive and typically involves motion correction, image segmentation into regions of interest (ROIs), and extraction of fluorescence traces of each ROI. Out of focus fluorescence from surrounding neuropil and other cells can strongly contaminate the signal assigned to a given ROI. In this study, we introduce the FISSA toolbox (Fast Image Signal Separation Analysis) for neuropil decontamination. Given pre-defined ROIs, the FISSA toolbox automatically extracts the surrounding local neuropil and performs blind-source separation with non-negative matrix factorization. Using both simulated and in vivo data, we show that this toolbox performs similarly or better than existing published methods. FISSA requires only little RAM, allowing for fast processing of large datasets even on a standard laptop. The FISSA toolbox is available in Python, with an option for MATLAB format outputs, and can easily be integrated into existing workflows. It is available from Github and the standard Python repositories

MatSWMM - An open-source toolbox for designing real-time control of urban drainage systems

This manuscript describes the MatSWMM toolbox, an open-source Matlab, Python, and LabVIEW-based software package for the analysis and design of real-time control (RTC) strategies in urban drainage systems (UDS). MatSWMM includes control-oriented models of UDS, and the storm water management model (SWMM) of the US Environmental Protection Agency (EPA), as well as systematic-system edition functionalities. Furthermore, MatSWMM is also provided with a population-dynamics-based controller for UDS with three of the fundamental dynamics, i.e., the Smith, projection, and replicator dynamics. The simulation algorithm, and a detailed description of the features of MatSWMM are presented in this manuscript in order to illustrate the capabilities that the tool has for educational and research purposes.Peer ReviewedPostprint (author's final draft

Somoclu: An Efficient Parallel Library for Self-Organizing Maps

Somoclu is a massively parallel tool for training self-organizing maps on large data sets written in C++. It builds on OpenMP for multicore execution, and on MPI for distributing the workload across the nodes in a cluster. It is also able to boost training by using CUDA if graphics processing units are available. A sparse kernel is included, which is useful for high-dimensional but sparse data, such as the vector spaces common in text mining workflows. Python, R and MATLAB interfaces facilitate interactive use. Apart from fast execution, memory use is highly optimized, enabling training large emergent maps even on a single computer.Comment: 26 pages, 9 figures. The code is available at https://peterwittek.github.io/somoclu