Python Computational-neuroscience Resources

Computational Xmas Tree This repo contains the code for the computational illumination of a Christmas Tree! It is based on the work by Matt Parker fro

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

ICLR Computational Geometry & Topology Challenge 2022 Welcome to the ICLR 2022 Computational Geometry & Topology challenge 2022 --- by the ICLR 2022 W

NATURAL-LANGUAGE-PROCESSING-AND-COMPUTATIONAL-LAB-II DLO8012: NLP & CSL804: CL-II [SEMESTER VIII] Syllabus NLP - Reference Books THE WALL MEGA SATISH

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology Self-Supervised Vision Transformers Learn Visual Concepts in Histopatholog

autolfads-tf2 A TensorFlow 2.0 implementation of LFADS and AutoLFADS. Installati

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

Table of Contents The general idea How these scripts work? Loading data Needed modules and global variables Parsing the arrays in dataset Extracting a

NeuroGen: activation optimized image synthesis for discovery neuroscience NeuroGen is a framework for synthesizing images that control brain activatio

WikiPron WikiPron is a command-line tool and Python API for mining multilingual pronunciation data from Wiktionary, as well as a database of pronuncia

POTHER: Patch-Voted Deep Learning-based Chest X-ray Bias Analysis for COVID-19 Detection Source code related to the article submitted to the Internati

coldcuts coldcuts is an R package that allows you to draw and plot automatically segmentations from 3D voxel arrays. The name is inspired by one of It

CSPML (crystal structure prediction with machine learning-based element substitution) CSPML is a unique methodology for the crystal structure predicti

HistoKT: Cross Knowledge Transfer in Computational Pathology Exciting News! HistoKT has been accepted to ICASSP 2022. HistoKT: Cross Knowledge Transfe

A310 Computational Neuroscience - Okinawa Institute of Science and Technology, 2022 This repository contains modeling practice materials and homework

TensorDebugger (TDB) is a visual debugger for deep learning. It extends TensorFlow (Google's Deep Learning framework) with breakpoints + real-time visualization of the data flowing through the computational graph.

Computational Optimal Transport for Machine Learning Reading Group Over the last few years, optimal transport (OT) has quickly become a central topic

Python implementation of 3D facial mesh exaggeration using the techniques described in the paper: Computational Caricaturization of Surfaces.

A computational optimization project towards the goal of gerrymandering the results of a hypothetical election in the UK.

TIA Toolbox Computational Pathology Toolbox developed at the TIA Centre Getting Started All Users This package is for those interested in digital path

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

MothPruning Scientific Overview Originally inspired by biological nervous systems, deep neural networks (DNNs) are powerful computational tools for mo

=================================================== Nitime: timeseries analysis for neuroscience data ===============================================

Continual learning paper repository This repository contains an incomplete (but dynamically updated) list of papers exploring continual learning in ma

MNE-Python MNE-Python software is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data such as MEG, E

PyCharge PyCharge is an open-source computational electrodynamics Python simulator that can calculate the electromagnetic fields and potentials genera

pyiron pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform: Atomi

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

Allen Institute Visual Behavior Analysis package This repository contains code for analyzing behavioral data from the Allen Brain Observatory: Visual

The neural architecture of language: Integrative modeling converges on predictive processing Code accompanying the paper The neural architecture of la

OctaDist Octahedral distortion calculator: A tool for calculating distortion parameters in coordination complexes. https://octadist.github.io/ Registe

Autopilot Docs Paper Forum Hardware Autopilot is a Python framework for performing complex, hardware-intensive behavioral experiments with swarms of n

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

Computational Methods for Physics & Astronomy Book version at: https://restrepo.github.io/ComputationalMethods by: Sebastian Bustamante 2014/2015 Dieg

Cross-Camera Convolutional Color Constancy, ICCV 2021 (Oral) Mahmoud Afifi1,2, Jonathan T. Barron2, Chloe LeGendre2, Yun-Ta Tsai2, and Francois Bleibe

Illumination_Decomposition Code for TIP 2017 paper --- Illumination Decomposition for Photograph with Multiple Light Sources. This code implements the

Computational modelling of ray propagation through optical elements using the principles of geometric optics (Ray Tracer) Introduction By applying the

Flow Flow is a computational framework for deep RL and control experiments for traffic microsimulation. See our website for more information on the ap

How to apply? Create your config.ini file following the example provided in config.ini Choose one of the options below to run: Run with Python3 pip in

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

Machine Learning for Argument-Based Computational Persuasion This repo contains the source code and a benchmark for predicting user's utilities with M

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

H2G-Net This repository contains the code relevant for the proposed design H2G-Net, which was introduced in the manuscript "Hybrid guiding: A multi-re

Imaging Transcriptomics Imaging transcriptomics is a methodology that allows to identify patterns of correlation between gene expression and some prop

PyTCI A toolbox that estimates the integration window of a sensory response using the "Temporal Context Invariance" paradigm (TCI). The TCI method Int

Removing Inter-Experimental Variability from Functional Data in Systems Neuroscience This repository is the official implementation of [https://www.bi

Few-shot Deep HDR Deghosting This repository contains code and pretrained models for our paper: Self-Gated Memory Recurrent Network for Efficient Scal

"Dataflow variables are spectacularly expressive in concurrent programming" Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum Quick overview Ne

pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of

Introduction The brain is the perfect place to look for inspiration to develop more efficient neural networks. One of the main differences with modern

giotto-tda is a high-performance topological machine learning toolbox in Python built on top of scikit-learn and is distributed under the G

Factorisation-based Image Labelling Overview This is a scheme for training and applying the factorisation-based image labelling (FIL) framework. Some

Introduction The field of connectomics aims to reconstruct the wiring diagram of the brain by mapping the neural connections at the level of individua

BookNLP BookNLP is a natural language processing pipeline that scales to books and other long documents (in English), including: Part-of-speech taggin

Clinica Software platform for clinical neuroimaging studies Homepage | Documentation | Paper | Forum | See also: AD-ML, AD-DL ClinicaDL About The Proj

pyRiemann pyRiemann is a python package for covariance matrices manipulation and classification through Riemannian geometry. The primary target is cla

Exposure: A White-Box Photo Post-Processing Framework ACM Transactions on Graphics (presented at SIGGRAPH 2018) Yuanming Hu1,2, Hao He1,2, Chenxi Xu1,

NoCodeSeg: Deep segmentation made easy! This is the official repository for the manuscript "Code-free development and deployment of deep segmentation

StackNet This repository contains StackNet Meta modelling methodology (and software) which is part of my work as a PhD Student in the computer science

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

Rotapy Purpose Generate Gaussian 09 input files for the rotamers of an input compound. Distance to the axis of rotation remains constant throughout th

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

POS-Tagger This repository details the creation of a Part-of-Speech tagger using Trigram Hidden Markov Models to predict word tags in a word sequence.

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Documentation redrawing Python package provinding tools for artistic interactive applications using AI Created by ReDrawing Campinas team for the Open

Generalized Shape Metrics on Neural Representations In neuroscience and in deep learning, quantifying the (dis)similarity of neural representations ac

DQC: Differentiable Quantum Chemistry Differentiable quantum chemistry package. Currently only support differentiable density functional theory (DFT)

feature-set-comp Compares various time-series feature sets on computational performance, within-set structure, and between-set relationships. Reposito

PsychoPy is an open-source package for creating experiments in behavioral science. It aims to provide a single package that is: precise enoug

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

pulse2percept: A Python-based simulation framework for bionic vision Retinal degenerative diseases such as retinitis pigmentosa and macular degenerati

pyHype: Computational Fluid Dynamics in Python pyHype is a Python framework for developing parallelized Computational Fluid Dynamics software to solve

MaD GUI Machine Learning and Data Analytics Graphical User Interface MaD GUI is a basis for graphical annotation and computational analysis of time se

MUSCO - Multimodal Descriptions of Social Concepts Automatic Modeling of (Highly Abstract) Social Concepts evoked by Art Images This project aims to i

CS 506 - Computational Tools for Data Science Code, slides, and notes for Boston University CS506 Fall 2021 The Final Project Repository can be found

PyoMyo Python module for the Thalmic Labs Myo armband. Cross platform and multithreaded and works without the Myo SDK. pip install pyomyo Documentati

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

nlcc Install pip install nlcc Must have Open-AI Codex key: export OPENAI_API_KEY=your key here then nlcc key bindings ctrl-w copy to clipboard (Note

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

Contrastive Learning of Object Representations Supervisor: Prof. Dr. Gemma Roig Institutions: Goethe University CVAI - Computational Vision & Artifici

Hello 🤟 #Team-Greider The team of 20 people for HackBio'2021 Virtual Bioinformatics Internship 💝 🖨️ 👨‍💻 HackBio: https://thehackbio.com 💬 Ask us

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

JittorVis - Visual understanding of deep learning model.

House-GAN++ Code and instructions for our paper: House-GAN++: Generative Adversarial Layout Refinement Network towards Intelligent Computational Agent

PICCL: Philosophical Integrator of Computational and Corpus Libraries PICCL offers a workflow for corpus building and builds on a variety of tools. Th

AntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series. It can be used for example to e

ReproZip ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used comm

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

NuPIC Numenta Platform for Intelligent Computing The Numenta Platform for Intelligent Computing (NuPIC) is a machine intelligence platform that implem

Colibri Core by Maarten van Gompel, [email protected], Radboud University Nijmegen Licensed under GPLv3 (See http://www.gnu.org/licenses/gpl-3.0.html

Ucto for Python This is a Python binding to the tokeniser Ucto. Tokenisation is one of the first step in almost any Natural Language Processing task,

NuPIC Numenta Platform for Intelligent Computing The Numenta Platform for Intelligent Computing (NuPIC) is a machine intelligence platform that implem