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a550f1dbd1ca494f064ebd205a24eade7afc080b44b6a79a64d4f198f86e2424 | Text | 2,802 | 47 | # Code Repository for Flesch, Nagy et al: "Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals"
[](https://arxiv.org/abs/2203.11560) [](http://papers.nips.cc/paper/5654-deep-knowledge-tracing.pdf) model
which we used in [our paper](https://www.cs.colorado.edu/~mozer/Research/Selected%20Publications/reprints/KhajahLindseyMozer2016.pd... |
d563d34b54cebfafc9facadd1ac0b38dcd48179a4fc51c8f5260047725e4fdd0 | Text | 2,846 | 20 | # Identifying Patients with Acute Ischemic Stroke within a Six-Hour Window for the Treatment of Endovascular Thrombectomy Using Deep Learning and Perfusion Imaging
Hongyu Gao, [Yueyan Bian](https://github.com/bianyueyan), Gen Cheng, Huan Yu, Yuze Cao, Huixue Zhang, Jianjian Wang, Qian Li, Qi Yang and Lihua Wang
## Abs... |
01b9cb8db9ba58d2b17f3f4fcd29cfec88d6d227620dd2e8231e5480c3b413a7 | Text | 2,892 | 55 | ******************************************
This archive contains R code required to reproduce the results reported in Gousiadou et al. "Development of Neural Network Models to Predict the PAMPA Effective Permeability of New, Orally Administered Drugs Active Against the Coronavirus SARS-CoV-2".
R code was written by... |
ef2d533b1accc06549e833608620990246e50d72d5b8ec0025d39094e8a84e90 | Text | 2,896 | 46 | # Modesto_LIF_3D
[](https://github.com/ScreenNeuroPharm/3DNeuronalModel/blob/master/LICENSE)
> The repository contains the data and the functions needed to reproduce the analysis reported in the article "Modeling the three-dimensional connectivity of in vit... |
4a99bed4e935fc889cdb894985615956adf1fb5fca52973f903aba93498401d6 | Text | 2,909 | 59 | [](https://opensource.org/licenses/MIT) [](https://doi.org/10.5281/zenodo.6327572)
# CATHe
CATHe (short for CATH embeddings) is a deep learning tool designed to detect remote homologues... |
11a43921ea266cf4da599b81555d02b9a843de5ae2222dcff347b532254da26b | Text | 2,912 | 44 | Here's the corrected and improved version of the markdown:
# Epidemiology of COVID-19 Inpatients
> ✔ OPEN SCIENCE
This page contains code, details, and data (coming soon) of a multicentric research project on the epidemiology of COVID-19 inpatients.
Patient registry was retrieved from medical records and hospital i... |
e61c09a8db032db83f95f08a069564e234901d0dfd41ca8d51a253eac4f616a0 | Text | 2,913 | 52 | <p align="center"><img width="40%" src="logo/pytorch_logo_2018.svg" /></p>
--------------------------------------------------------------------------------
This repository provides tutorial code for deep learning researchers to learn [PyTorch](https://github.com/pytorch/pytorch). In the tutorial, most of the models w... |
b042d0510faad0803459ca000a2a3fb3b29ed82945552785195a9bcb0510a219 | Text | 2,944 | 63 | [](https://travis-ci.org/Zabolekar/readABF) [](https://cran.r-project.org/package=readABF)
## Installation
The package can be installed from CRAN in the usual manner:
`... |
4882d77e4b18cb6a25d14ee8f2c6b8e907c3e6afa38bee3c68f680a6aacd43b0 | Text | 2,983 | 62 | This is the LAMMPS software package.
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed unde... |
0d65feb8be5d8f31f65fff0be9a6abf0bbfd57f284a955cd292042d7a8a1d519 | Text | 2,997 | 90 | # README
## Background
This project is the project involved in the paper "A Low-power Hardware Architecture for Real-time CNN
Computing" experiment.
The following describes the directory structure of the project and a simple usage guide
The main directory structure of the project is as follow:
```
D:.
│ ... |
8687c777f2191a67da1531dd42c3e4a76e476eb252a4d443fdea38f0a88582ba | Text | 3,022 | 53 | # Confidence of probabilistic predictions modulates the cortical response to pain
Dounia Mulders, Ben Seymour, André, Mouraux, Flavia Mancini
Article in press in PNAS.
Associated [preprint](https://doi.org/10.1101/2022.08.11.503296)
](https://lbesson.mit-license.org/)
[]([https://doi.org/10.1101/862615](https://doi.org/10.1101/2022.04.23.489093))
This repository co... |
40413a91a088465caa9e8b8dde6a638ac99c40a3e224d43eb4556ee12b8fdafd | Text | 3,025 | 73 | 
<div align="center">
<p align="center">Scalable Neuroimaging Processing Engine for Minipig MRI</p>
</div>
## Introduction
PigSNIPE is a software package for analysis of Minipig brain Magnetic Resonance Images (MRI). It is developed by the [SINAPSE lab](https://medicine.uiowa.edu/psychiatry/... |
48f7630d06bfe707292c0ff27c01de4e903e5051b05c75c69b790ed5d27abae0 | Text | 3,031 | 34 | # bee_al_2021
This repo contains a model of the bee antennal lobe (AL) intended to investigate odour responses in the antennal lobe. The results of using this model are published in (UNDER REVIEW).
The model uses PyGeNN, the Python interface for the GeNN simulator (https://github.com/genn-team/genn).
To use this softw... |
fb221473aa8d0df760a4e0bf2ede258778d20996ed02b2529c5676fdc1efc628 | Text | 3,044 | 81 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# GENOVA <img src="vignettes/logo_GENOVA.png" align="right" alt="" width="200" />
[]... |
f1c5fc4f7a0a7733b5155b75f46b14f8393fa5803501848f89fc0877cd21050c | Text | 3,055 | 35 | These files contain electrophysiological data as well as simultaneous video recordings and some analyses for the following paper:
An electrophysiological and behavioral model of Paramecium, the “swimming neuron”
Irene Elices, Anirudh Kulkarni, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Prevost, Romain Brette
Contac... |
e8700746efb6df51c117df7907dc3d785f80d925fc21e5e0b0e668e6fe2a9bba | Text | 3,060 | 82 | <h1>
<img src="https://github.com/2003100127/tmkit/blob/main/docs/source/img/tmkit_logo.png?raw=true" width="260" height="80">
<br>
</h1>
![](https://img.shields.io/badge/last_re... |
4fa2b979f78169db59a3cbed8cc0006e4891ecc5365ce893275b982801fb98f3 | Text | 3,062 | 56 |
# Cerebellar Damage Detection Tool
A software to detect cerebellar damage after tumor resection. Created by the Vision Lab at the Department of Dianostic Imaging, St. Jude Children's Resesarch Hospital.
<img src="./figs/SJ_Full_H_C.png" width="200"/>
## About
This software automatically detects and segments missin... |
63bb1d244e36a5a2bde8b57ee06e8910f89e321a93d9bb851a63fec73789b2ed | Text | 3,071 | 50 | # Spikebench: an open benchmark for spike train time-series classification
by
Ivan Lazarevich,
Ilya Prokin,
Boris Gutkin,
Victor Kazantsev
We propose _spikebench_ — a benchmark consisting of several individual neuron spike train classification tasks based on open-access data from a range of animals and brain regions.... |
d1cb8e8d7951f7e6358d7aff3a3eddf99e98f7da3ca1d155009a90716d0bedb3 | Text | 3,071 | 43 | # Detecting and Monitoring Plastic Waste Aggregations in Sentinel-2 Imagery
[Explore the Data](https://plastic.watch.earthrise.media/). [Read an overview of the project](https://gpw.earthrise.media/). [Read a paper detailing the work](https://example.com)
## Projec... |
42d0b75091a3e36e87ac86a02e0453ef345e63cfd2542e1b9be819b38995a4e6 | Text | 3,104 | 82 | # Requirements & Dependencies:
- Cmake >= 2.8
- Compiler supporting C++17
- Compiler support OpenMP >= 5
- Doxygen (optional)
No external libraries!
Include [```tclap```](https://github.com/eile/tclap) for the CLI.
# Installation & Build
```
mkdir build && cmake .. -DCMAKE_BUILD_TYPE=Release
```
The build proc... |
ab2905a94da85b14d767c3556ec82ea434ba0c28381ec5307d12fa2e988dc20f | Text | 3,114 | 70 | 
[](https://doi.org/10.5281/zenodo.5708490)
[
[](https://github.com/spinicist/QUIT/actions)
[](https://doi.org/10.21105/joss.00656)
[](https://zenodo.org/badge/l... |
3a8a467b830392dcc4f4f06dff7850f251f0417faf7935f392cd113ce0c475f5 | Text | 3,152 | 74 | # SMILES corrector
Collection of scripts to create and use SMILES corrector. The SMILES corrector is a transformer model that is trained to translate invalid SMILES sequences to valid SMILES sequences.
## Installation (with python v 3.9)
1. RDKit (version >= 2020.03)
$ conda install -c conda-forge rdkit
2. Numpy (v... |
e7564690fb9e96e7d91202ec2ebe32c925f10f1a3bf387e32bb7d8021e4bcd2e | Text | 3,153 | 48 | # NeuroPattToolbox
Neuropatt is a MATLAB toolbox to automatically detect, analyze and visualize spatiotemporal patterns in neural population activity. Data recorded by multi-electrode arrays, EEG, MEG, fMRI and other imaging methods such as VSD can optionally be filtered to extract the phase or amplitude of oscillation... |
2790cd307a79b250205c9d095ee48df6003ab07a85108da6ef16cc2ddb465f22 | Text | 3,155 | 69 | # PQN_py
**Piecewise Quadratic Neuron (PQN) model** is a spiking neuron model designed to faithfully reproduce a variety of neuronal activities with limited computational cost.
The PQN_py provides a simple python implementation of the PQN model. You can choose from the following 8 mode. Each mode is fitted to reproduc... |
da680aa8836ef5195b6af110155dba94eb03fc83fc28c0073bf10d06ff226886 | Text | 3,186 | 72 | .. These are examples of badges you might want to add to your README:
please update the URLs accordingly
.. image:: https://api.cirrus-ci.com/github/<USER>/gratin.svg?branch=main
:alt: Built Status
:target: https://cirrus-ci.com/github/<USER>/gratin
.. image:: https://img.shields.io/cov... |
0950d6b70641f6efabe010fa75d44b9a8a90ecc5503830939a6d827a71bca8c6 | Text | 3,196 | 60 | [](http://travis-ci.org/phenoscape/owlery)
# Owlery
[Owlery](https://kb.phenoscape.org/owlery/docs/) is a set of REST web services, built on the [akka-http](https://akka.io) toolkit, which allow querying of an OWL reasoner containing a configured set ... |
935709b47aaadd021b72944c102e11da4b1a8bbee78edfd96b2ba1fac874b6d9 | Text | 3,227 | 32 | Track-It
=======
Track-It was created specifically to investigate mechanisms of sustained selective attention with young children.
Track-It presents the participant with a grid, with each of the grid locations optionally identified by a background image, and a target object moving on the grid along a random trajector... |
676f34e54abf6a58f729600cf2200e87eee10c3b6f9e04713c2d8d247ac7e295 | Text | 3,235 | 70 | # Nonlinear dynamics of coupled phase oscillators
`carpet` is a python package to study systems of coupled phase oscillators, such as
- [Kuramoto model](https://en.wikipedia.org/wiki/Kuramoto_model) with local coupling on a two-dimensional lattice
- cilia carpet model (see refere... |
c87af8d706793304340bf5e306b50d237fb2745489215ee6d23b99570165ea75 | Text | 3,239 | 73 | # Retina Vessel Segmentation from OCT Fundus Reconstruction with RF-UNet
This software is forked from lseventeen/FR-UNet and allows segmentation of blood vessels in **OCT reconstruction images** of the human eye retina. Details of the application of the software can be found in the paper:
> Marciniak, T.; Stankiewicz... |
8ea222f554db1dd165acc708455e9a177ac8645df6569692d908d44fabe42276 | Text | 3,248 | 26 | # GoPiGo C. elegans Connectome Code
The GoPiGoConnectomev(n).py Python program provided here can be used with a Raspberry Pi GoPiGo robotic kit created by Dexter Industries.
To run this code, from the Pi directory, type
```
sudo python connectome.py
```
The tiny worm Caenorhabditis elegans has only 302 neurons but ... |
9c35c459e3f2467d0438cfd9547ff8e34312cc0240079bb522d9b11ca0e7919b | Text | 3,289 | 78 | # Array Tomography Tool
## Running Array Tomography Tool
The easiest method to running the tool is to use Docker. First you will require
Docker installed on your computer - go to
https://www.docker.com/products/... |
61f6d5508ea4135b73fef4d5a7f89a491d7ada808374a3cdb98372496cfd314b | Text | 3,303 | 20 | # Deep learning-based risk prediction for interventional clinical trials based on protocol design: a retrospective study
Sohrab Ferdowsi, Julien Knafou, Nikolay Borissov, David Vicente Alvarez, Rahul Mishra, Poorya Amini, Douglas Teodoro
----------------
# Summary
### Background:
Clinical trials (CTs) constitute a m... |
e8ea1a9c0f6267819a808ffea30d079368926f37ab2097119a3d4fab5e8a41bf | Text | 3,334 | 51 | # Anatomical Region Labeling (ARL)
A deep-learning based anatomy region labeling for Cone-Beam Computed Tomography (CBCT) scans
This tool queries CBCT scans from an ARIA database (Varian Medical Systems, Palo Alto, CA) using a DICOM Query & Retrieval Tool (DQR) and classifies the scans into four distinct regions: head... |
c0c6cf9ae7a18ff172b4f14750b3c0d75a3eb4c3b21fae10730e5eda054db440 | Text | 3,341 | 61 | ## A Discourse-Aware Attention Model for Abstractive Summarization of Long Documents
This repository contains data and code for the NAACL 2018 paper ["A Discourse-Aware Attention Model for Abstractive Summarization of Long Documents"](https://arxiv.org/abs/1804.05685). Please note that the code is not actively maintai... |
1dfba37f6f3c0e118dbef5063c8936ede08c51520c4329e0b4bc4b8226ecb0e2 | Text | 3,349 | 53 | # Quantum Boolean networks
This directory contains Python and R scripts for perfoming the analyses presented in the article *"Quantum Boolean networks for molecular network analysis"* by Weidner et al.
All analysis were performed using R v4.1.0, python v3.9 and qiskit v0.36.2.
While some experiments such as those per... |
8f52b45e8203ac831b35a37f55c019b49e7649d29da9fb2f3c515aa834ad3e7c | Text | 3,368 | 64 | # Sader Calibration of Cantilever Stiffness
## Description
This is a python package written to calibrate cantilevers, for use in atomic force microscopy, using the method of Sader (Sader et al., 1998; Sader et al., 1999; Chon et al., 2000). This program uses the nidaqmx package to interface with an NI USB-6361 Data Aq... |
ba0ea1a329caa91cc5201835942a5e15fe70a3d11af52cb5b264d74a8f3cd651 | Text | 3,370 | 55 | # Confidence of probabilistic predictions modulates the cortical response to pain
Dounia Mulders, Ben Seymour, André, Mouraux, Flavia Mancini
Article published in [PNAS](https://www.pnas.org/doi/10.1073/pnas.2212252120).
Associated [preprint](https://doi.org/10.1101/2022.08.11.503296)
## Installation:
To install this tool, run the following steps in your shell:
```
git cl... |
8e43fd6f19cbfb51dc4d6f29016d65a80184fc9597835b44e65bebd87cfc0a6b | Text | 3,378 | 63 | # Image-To-Image Generative Adversarial Networks for Synthesizing Perfusion Parameter Maps from DSC-MR Images In Cerebrovascular Disease
## Aim
The aim of the project was to synthesize perfusion parameter maps from dynamic susceptibility contrast magnetic resonance imaging. For this, we implemented a pix2pix GAN as w... |
b3dcfdbe526704a7ed96e29f80df7339a8ec01ec9a96402c3f6099cbd79befae | Text | 3,393 | 103 | # TriNet
## 1.Making predictions for sequences
### 1.1 Description
TriNet is a tri-fusion netural network for anticancer and antimicrobial peptides recognition. By inputting the peptide sequences and PSSM profiles, this software can use the pre-trained model to identify anticancer and antimicrobial peptides.
### 1.2... |
c249cf16302bf353181906e2b318ed478bf397393eab923b0b414c5b124103f8 | Text | 3,408 | 8 | # T-Ridership (http://t-ridership.com/)
T-Ridership is a novel web-based application, based on a hybrid optimized dynamic programming inspired by neural networks algorithm to optimize public transit for safety concerning COVID-19. Two main steps are taken in the analysis: the first is detecting high-density stations by... |
7dce3c3b3699b6ad84453a6e79ecf743d7b0f76832405eebb306520d24d37b21 | Text | 3,434 | 101 | [](https://github.com/google-research/nisaba/blob/main/LICENSE)
[](https://elifesciences.org/articles/80942)
# ProteInfer
ProteInfer is an approach for predicting the functional properties... |
2df7dac22ff8bbed3227184f7c149e0fb6bf2a98fddb646fcc27b2b9e18e60bd | Text | 3,446 | 65 | # DeepCT
_DeepCT_ can learn complex interconnections of epigenetic features
and infer unmeasured data from any available input. Furthermore,
it can learn cell type-specific properties,
build biologically meaningful vector representations of cell types,
and utilize these representations to generate cell type-specif... |
6bedf84a53b257abf7a2fa910c2f3309114eb01e9ee862150fb6993dbd267405 | Text | 3,470 | 78 | # ClassNSeg
Implementation of the paper: <a href="https://arxiv.org/abs/1906.06876">Multi-task Learning for Detecting and Segmenting Manipulated Facial Images and Videos</a> (BTAS 2019).
You can clone this repository into your favorite directory:
$ git clone https://github.com/nii-yamagishilab/ClassNSeg
## Req... |
bbf6afd6a205e7ba5889433c03574fd4cfdd7ae18b49fe2415d2ef35c73bd907 | Text | 3,471 | 125 | This README.txt file was generated on 2021-10-13 by Tim Gernat.
GENERAL INFORMATION
1. Title of dataset
Trophallaxis interactions of three honey bee colonies
2. Author information
A. Principal investigator contact information
Name: Gene E. Robinson
Institution: University of Il... |
d3701a9d106ec8074a4c62f103b88fdf2df959109e12a96a863db6d0dd12bb88 | Text | 3,493 | 63 | # EEG Source Template Matching
A toolbox for fitting ERP data to group average topographic templates created from functional areas mapped by fMRI and the topographies calculated using individually defined BEM forward models.
This toolbox can be used to determine the contribution of functional brain
sources to the E... |
4285654cd774a7e9148875df7585dcb417fda4907974de1847f0de0957ea88d8 | Text | 3,496 | 31 | # CASM-dataset
## CASM: A long-term Consistent Artificial-intelligence based Soil Moisture dataset based on machine learning and remote sensing
by Olya Skulovich, Pierre Gentine, Columbia University
Scripts used to create CASM dataset
The dataset is available at https://doi.org/10.5281/zenodo.7072511
The Consisten... |
bd941cf85b057b02c5f137d8342ee5ad36e570c9f37e29748c8c4dc2d72e0626 | Text | 3,499 | 107 | # TriNet
## 1.Making predictions for sequences
### 1.1 Description
TriNet is a tri-fusion netural network for anticancer and antimicrobial peptides recognition. By inputting the peptide sequences and PSSM profiles, this software can use the pre-trained model to identify anticancer and antimicrobial peptides.
### 1.2... |
940a7ed91f87355db5c6cecb46d76a2494d58cd26aff2b50f6420ad962f146e8 | Text | 3,522 | 8 | # T-Ridership (http://t-ridership.com/)
T-Ridership is a novel web-based application, based on a hybrid optimized dynamic programming inspired by neural networks algorithm to optimize public transit for safety concerning COVID-19. Two main steps are taken in the analysis: the first is detecting high-density stations by... |
4f1ab089397677654822ef7c14e64a732e5aa1ae997f7130335b768301391892 | Text | 3,526 | 61 | README
Pandas DataFrame
to load:
import pickle
pickle_filename = 'YOUR_DATA_PATH/df_name.pkl' # change accordingly
with open(pickle_filename, 'rb') as pickle_in:
df_name = pickle.load(pickle_in)
Motorneuron data:
Fish 3 Trial 1 and Fish 5 Trial 2 for Figure 3.
Fish 5 Trial 2 for figure 4.
C... |
b06beeb3c0b6665b2c7405db57d073bb455adf58bda4e2ce77c984f5663a97ee | Text | 3,555 | 96 | # SciTLDR
This repository contains the dataset, model weights, and generation code for our paper "[TLDR: Extreme Summarization of Scientific Documents](https://arxiv.org/abs/2004.15011)".
## Dataset
SciTLDR is split in to a 60/20/20 train/dev/test split. For each file, each line is a json, formatted as follows
```
... |
2397e282a51594e4f7e042036037fc8aab764cffebe635e7a90f88a04251d007 | Text | 3,562 | 40 | # The Affective Slider (AS)
The Affective Slider (AS) is a new digital scale for the self-assessment of emotion
composed of two slider controls that measure pleasure (sad - happy) and arousal (sleepy - wideawake). It can
be easily included in electronic surveys and questionnaires.
The AS is released under a [Creative... |
09407bab383f9d4d96e32b46742b1ef5f3755bd52484e49ba5c1f98096c544fd | Text | 3,600 | 56 | # ACT2 (LREC2022)
This repository contains the ACT2 multi-disciplinary citation classification dataset ([paper](http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.363.pdf)).
The released data comprises
- the main dataset `ACT2_dataset.tsv`.
- the 229 pdfs containing the 4000 citations from the datset (`pdf... |
dd5c58150108134be847f19db0262102c20fb4043fab50e5b1ae5741659085ba | Text | 3,605 | 111 | ## About Brain Network code repository:
This repository contains all the code and data used within the following manuscript:
[**Interconnected sub-networks of the macaque monkey gustatory connectome**](TODO: XX)
Renee Hartig, Ali Karimi, Henry C. Evrard
## How to get the code repository:
You can download the co... |
4f8f71e410f87f2f490eaa9eaf5a90a969397610662f35a5ff1610426baedd47 | Text | 3,617 | 56 | # propriostim
## Requirements
- MATLAB R2020b or higher
- Download and extract `data.zip` from [Zenodo](https://doi.org/10.5281/zenodo.5159752) in `data` folder in this directory.
- For neuron-demo: NEURON 7.7 or higher
## Main usage
The `main` script allows to visualize joint kinematics, muscle elongations, ... |
cbf9326929144b0e5cb9b7f49363eef2d6bb7d3dc43bf41b54898a52b2384599 | Text | 3,627 | 82 | Spectral imaging enables contrast agent-free real-time ischemia monitoring in laparoscopic surgery
==============================
Ischemia monitoring in real time via out-of-distribution detection with invertible neural networks
Project Organization
------------
├── README.md <- The top-level README for... |
c8e6d9112509b71dab931243e97cf70c61f9c229894e8e9a34124596e3bbf1e8 | Text | 3,651 | 76 | This code repository contains the files required to reproduce the analysis and figures in the paper "Capacity Limits Lead to Information Bottlenecks for Ongoing Rapid Motor Behaviour."
Unless otherwise noted, all code is original to the analysis for these works.
1. DATA ANALYSIS
- The script automateRunningData.m goe... |
d5ed64968c71397313918a0dcf790b360e79aed32f09da7f31bb4c9862a2ff58 | Text | 3,670 | 39 | MatlabAUC
=========
Matlab functions for estimating receiver operating curves (ROC) and the area under the ROC curve (AUC), and various methods for estimating parametric and non-parametric confidence intervals for the AUC estimates. Also included is code for a simple bootstrap test for the estimated area under the ROC... |
bfeb4e57c32e594a1c37b6803c7b0dd3f05f5bd723dd5ccf9e269f52bd6107d6 | Text | 3,694 | 31 | # OMPmodel
Python code implementing the OMP model described in Pajevic et al, "Oligodendrocyte-mediated Myelin Plasticity", eLife, 2023 [1]. The code in ompsimulator.py, omputils.py, generate_runs.py was originally used to simulate the data and obtain the results reported in the manuscript. These files are provided ma... |
9c3d7176e715814c065ae644d5dfa9ee924b01b637a153b6321fb776ac4d1943 | Text | 3,698 | 73 | .. These are examples of badges you might want to add to your README:
please update the URLs accordingly
.. image:: https://api.cirrus-ci.com/github/<USER>/palm-tools.svg?branch=main
:alt: Built Status
:target: https://cirrus-ci.com/github/<USER>/palm-tools
.. image:: https://readthedocs.org... |
253557edcb0a5693315c991802f029978b597ddb4aa75dc5638f126e5ef67e70 | Text | 3,703 | 66 | [](https://osprspoxappcharite.z13.web.core.windows.net/)
[](https://osprspoxappstanford.z13.web.core.windows.net/)
# Po... |
fd1bf2f1993cc9ca8087e70d8458ce0b6144a5161ab2adf24fc2911dd4ad8af7 | Text | 3,714 | 55 | # panx2-simulation
Details of molecular dynamics simulations in article "Cryo-EM structure of human heptameric pannexin 2 channel" written by Dr. Hang Zhang.
## Dependencies
* **Schrodinger 2018**: https://www.schrodinger.com/
* **Gromacs 2021**：https://www.gromacs.org/
* **charmm-gui version 3.8**：https://www.charm... |
4e1fee8ac90e1e642e29ff43b3274f962495ab7e4a0e40af814e43a7b1c5b7e6 | Text | 3,727 | 102 | 
ModelTest-NG is a tool for selecting the best-fit model of evolution
for DNA and protein alignments.
ModelTest-NG supersedes jModelTest and ProtTest in one single tool,
with graphical and command console interfaces.
##... |
6204f375dd726a730771fa05992961d59296375998993adaa44b950fddf4e2be | Text | 3,746 | 107 |
This README describes the Bayesian Network (BN) structure learning solver and
its utilities collectively called BNOmics. The software enables a purely data
driven BN structure learning and is best used in combination with a python
shell, such as Ipython, for on-the-fly experimentation and research. It could,
however, ... |
b28d7f6b0c78caa49c3b3404ffd26df7599ba3dc95c2d8a95acc806089dc2fc4 | Text | 3,768 | 91 | [](https://travis-ci.com/kaldi-asr/kaldi)
[](https://gitpod.io/#https://github.com/kaldi-asr/kaldi)
Kaldi Speech Recognition Toolkit
=====================... |
65b8f1726c1a6481ed1448ae1d1d944a1c621469a6989cbaec66d3c29f18aa79 | Text | 3,786 | 87 | # Downsampling Routines for an Open-Access Neonatal EEG Dataset
Python and Matlab code to downsample neonatal EEG files stored at the Zenodo repository [DOI:
10.5281/zenodo.7477575](https://doi.org/10.5281/zenodo.7477575).
The EEG is recorded from newborn infants in the neonatal intensive care unit using 2
different ... |
784b49f0443a7e2c6240a5ca341ae8e166aceb2619c35d4217f42df111642d65 | Text | 3,794 | 51 | # SynapseCLR
SynapseCLR is a contrastive learning framework for navigating 3D electron microscopy data. A graphical overview of SynapseCLR pipeline and downstream applications is shown below:
# Navigating this Reposit... |
799a9cd9a3b1c1dfa875378b231485e8e2d4870444953645e7be8dd2c0565e3d | Text | 3,810 | 62 | # AgentBind-brain #
AgentBind is a deep-learning framework that analyzes gene-regulatory regions in the human genome and identifies genomic positions with strong effects on regulatory activities. This Github repository contains code for an experiment in which we apply AgentBind to analyzing H3K27ac signals in brain cel... |
058f1eaf6a5596d995f9b10d2a641ae3671aee13b590703662d1efad8ee8f25c | Text | 3,814 | 72 | Meta-Learning Biologically Plausible Plasticity Rules with Random Feedback Pathways
======================================
This repository contains a PyTorch implementation of the meta-learning approach for developing interpretable, biologically plausible plasticity rules that improve online learning performance with ... |
6f5fdcf25a7bd639dbfcdf999ddd2c2f9fdb0c8cfc8e810cb0e27bb003b1e8b6 | Text | 3,862 | 63 | # food4thought
This repo includes the visual food localizer, the code and the links to data required to replicate the results of the paper: ["Selectivity for food in human ventral visual cortex"](https://www.nature.com/articles/s42003-023-04546-2).
## Localizer
The visual food localizer is built on the fLoc localiz... |
43227cc4eb98334c4604e8f87f45b4b161a458be9f658bf01e8d577a4ad9fb60 | Text | 3,865 | 44 | # ASRT_PDP_jsPsych
<i>Created by the MEMO Team of Lyon Neuroscience Research Center (CRNL) (PI: Dezso Nemeth)</i>
<img src="static/logo_memo.png" height="100">
A Process Dissociation Procedures Task for the <a href="https://github.com/vekteo/ASRT_JSPsych">ASRT paradigm</a> created with the jsPSych library (<a href="... |
ee8a648d6c567340350606689aaedb471b4fe24434ed5fee5fbbcbe3f77ef7db | Text | 3,913 | 49 | # resVAE ensemble
resVAE ensemble is the successor of [resVAE](https://github.com/lab-conrad/resvae) that utilizes rank aggregation with ensemble, among other improvements.
Give it a try if you:
1. Have feature-barcode matrix data (scRNA-seq counts, scATAC-seq peaks, output from CellRanger etc)
2. Have some sort of ... |
4caf444405b843e03aadb2b32085bc239a21e4b61f7b29e57abf29032c795dfd | Text | 3,931 | 105 | # StyleT2I: Toward Compositional and High-Fidelity Text-to-Image Synthesis [CVPR 2022]
**TL;DR**: We introduce a new framework, StyleT2I, to achieve compositional and high-fidelity text-to-image synthesis results.
**Figure 1.** When the text input contains underrepresented compositions of ... |
d1c9ef38e239ac2535ca2fba80e0956520727aa4bf192d29789764354d472c3b | Text | 3,932 | 60 | # Cryo-ZSSR
This is the repository for Cryo-ZSSR: Multiple Image Super Resolution Using Deep Internal Learning: [Link to paper](https://arxiv.org/pdf/2011.11020.pdf)
## Environment
To run the code, please first create a conda environment `environment.yml` which should include all the necessary packages/add-ons.
```... |
3514a323503f38f3df3d90e2889ab35cb3c09c51e3e71c97fef03b5e0ab4ab91 | Text | 3,940 | 88 | # Emotional Chatting Machine: Emotional Conversation Generation with Internal and External Memory
Perception and expression of emotion are key factors to the success of dialogue systems or conversational agents. However, this problem has not been studied in large-scale conversation generation so far. In this [paper]... |
00e4eaab4b0628ee7365045a438793e6b86aeac4555d25d2dcb1f3ce71813772 | Text | 3,976 | 77 | dndscv
=====
Description
---
The **dNdScv** R package is a group of maximum-likelihood dN/dS methods designed to
quantify selection in cancer and somatic evolution (Martincorena *et al.*, 2017). The
package contains functions to quantify dN/dS ratios for missense, nonsense and
essential splice mutations, at the l... |
425649a73b3da73fc2b767f99f60bfce6c772827f57ed0e29af63f11e881e6d6 | Text | 3,980 | 103 | # Analyzing lidar-as-a-camera sensor 'images'
Analysis of object detectors and image segmentation models on images from lidar sensors
## Introduction
This work explores the potential of general-purpose DL perception algorithms, specifically detection and segmentation neural networks, for processing image-like output... |
ca7ee41fb312c3ee4e9d914866758b03deeefb1fb3c3417f492e97e2e2e31a9f | Text | 3,981 | 56 | # statistics
statistical analysis code
## Description
This repository is for STATA code written by Larisa Tereshchenko for statistical analysis of the data. I provide this code in the spirit of openness, to enable replication of my analyses. The details of used data, and full descriptions of statistical methods are pr... |
e78585a8f0a864e63d80001a2ba88a88a39b0f11f5a367ed8113b43893332971 | Text | 3,989 | 133 | # DeepCT inference helper
A Snakemake-based pipeline to obtain DeepCT predictions
for a VCF file.
## How to run
0. Download and unpack large files (previously stored via git-lfs):
```
wget https://nxt.2a2i.org/index.php/s/CAQYtAkPnyRJ42F/download -O DeepCT-inference-helper-large-files.zip
unzip DeepCT-inference-help... |
7d53c75400919daf60cdd9316911d5e7ad96c022f540479952e22e3dd9a6421f | Text | 3,999 | 71 | # BATMAN
## Overview
Welcome to the BATMAN repository for the code used in BATMAN: a Brain-like Approach for Tracking Maritime Activity and Nuance.
## Getting Started
Clone the repository and navigate into root directory of the project:
```
cd batman
```
We recommended the use of a virtual environment to utiliz... |
c767d64cacb4195851f7bddfa726fb8d29742046501f98dfe7963d5cd2285a8b | Text | 4,007 | 47 | ## [**Investigating associations between blood metabolites, later life brain imaging measures, and genetic risk for Alzheimer’s disease**](https://doi.org/10.1186/s13195-023-01184-y)
_Rebecca E. Green, Jodie Lord, Marzia A. Scelsi, Jin Xu, Andrew Wong, Sarah Naomi-James, Alex Handy, Lachlan Gilchrist, Dylan M. William... |
f295d05d44942229456eaf73969e0d4861b0691d0048ed54c6ae1d785e6b1086 | Text | 4,007 | 113 | # Data-Efficient architectures and training for Image classification
This repository contains PyTorch evaluation code, training code and pretrained models for the following papers:
<details>
<summary>
<a href="README_deit.md">DeiT</a> Data-Efficient Image Transformers, ICML 2021 [<b>bib</b>]
</summary>
```
@InProce... |
30423b9cface4963772638457cf703ccbb2eb932fd54bb72e3d5a54bef6808b9 | Text | 4,030 | 74 | # DetNAS
This project provides the implementation for [DetNAS: Backbone Search for Object Detection](https://arxiv.org/abs/1903.10979).
As we originally conducted the experiments in the paper using the internal framework Brain++, this project is a reimplemented version on PyTorch.
In addition, this project is based on ... |
acd4678a947bf8752da9e8e5abcf2117282deebd6d35ac062e9bab3eca44e463 | Text | 4,063 | 66 | # Empirical Proxy Measures Paper Code and Results
This repository included code and aggregated results from the forthcoming paper:
Populationmodeling with machine learning can enhancemeasures of mental health. (2021). Kamalaker Dadi, Gaël Varoquaux, Josselin Houenou, Danilo Bzdok,
Bertrand Thirion, Denis Engemann.
... |
eebbf33c7bb84ec2bba02e3c096dc08d7c1c53bc6aa70c4957ebe7a0348af7ab | Text | 4,067 | 77 | # Bifurcation-analysis-of-spinal-motoneuron-firing-behaviour
### Authors:
Muhammad Mustafa 1* , Mohamed H. Mousa 2* , Mohamed S. Saad 3 , Tamer Basha 1 , and Sherif M.Elbasiouny 2,4
### Affiliation:
1. Department of Systems and Biomedical Engineering, Faculty of Engineering, Cairo University, Giza, Postal code: 12... |
581e4f69341ae2871967381b58d101552c0e1bc722a27b9a19286c83278bd0ec | Text | 4,072 | 93 |
MatchAnnot is a python script which accepts a SAM file of IsoSeq
transcripts aligned to a genomic reference and matches them to an
annotation database in GTF format.
The aligner used must be splice-aware. MatchAnnot has been developed
using the STAR aligner (http://code.google.com/p/rna-star). The
reference su... |
67c54354f841f8fbffce6ff3ea60e6b2927427ef6cbad9054f3f5b8e8571a71e | Text | 4,110 | 88 | # Rally Estonia End-to-End Driving
This repository contains a framework to train End-to-End driving models using the Rally Estonia dataset. It includes
scripts to train models as well dataset of over 750 km of driving in all seasons.
## Articles and Theses
Following work has been produced using the framework:
- [L... |
9ec80388e261b22e832ac68ab47ed6c640a53145f066b3b3be82d2c2a9e78e12 | Text | 4,123 | 81 | # AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting
**[Paer](https://academic.oup.com/bioinformatics/article/39/1/btac760/6849514)|[User maunual](https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/PAP/10.1093_bioinform... |
afb1a6c5c255e0d284ae116399c88a5563a2d710d304293e053de3c131146a20 | Text | 4,138 | 140 | # DARELA: DA RELease Analysis
DARELA is a Python library that provides computational models written using differential equations to analyze and quantify the kinetics of dopamine (DA) release, reuptake, and diffusion. The models can be used to fit data from in vivo fast-scan cyclic voltammetry (FSCV) experiments.
For ... |
648c662916d10e63a333bcf52b9ca36e439bf065e8a45238c0986075a681bf5a | Text | 4,143 | 110 | Debarcer
========
A package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes. For information on getting started, including installing and running ```Debarcer```, see the [wiki](https://github.com/oicr-gsi/debarcer/wiki/)
Note : The repository for the original release of Debarce... |
09466e37d3c3a1b45922dba989c4d06d2b5844075ca2b3b557a2d905dd958934 | Text | 4,146 | 88 | maggot_models
==============================
Modeling the Drosophila larva connectome
Installation and setup
--------
If you are new to Python development, my recommended practives are [here](https://github.com/bdpedigo/giskard/blob/master/python_start.md)
Currently, the recommended setup is to use conda or minico... |
1d48233c9d814c5ee33f2101c6db415a0f28c0b5857d53a99d07cd355d91dc0c | Text | 4,175 | 79 | # Application-Specific Super-resolution using DenseEncoder-Decoder (DenseED) blocks
This repository includes the code used for the geenration of super-resolution of microscopy images training using the small data (a small training dataset and really useful for biomedical applications like X-ray, MRI and in vivo imaging... |
6371f5db4e72d21a9475c68c6ccea1857b1b692cb826f73404f21704fd70155c | Text | 4,178 | 71 | # MedMNIST Experiments
Training and evaluation scripts to reproduce both 2D and 3D experiments in our [MedMNIST](https://github.com/MedMNIST/MedMNIST/) paper, including PyTorch, auto-sklearn, AutoKeras and Google AutoML Vision together with their weights ;)
# Code Structure
* [`MedMNIST2D/`](./MedMNIST2D/): trainin... |
a6228b8fd8f092686965411f108008cc38a6dbc91ecac11f72d03f4291868318 | Text | 4,187 | 56 | # 2m2c
This repository contains the simulation code and analysis for our model of basal ganglia learning that includes both the DMS and DLS. The publication that describes this model can be found here: [Distinct cortico-striatal compartments drive competition between adaptive and automatized behavior - PubMed (nih.gov... |
7edb5563c8d73f6c986150556dd0f5e00f178433f91e35c2702f825f1a03e837 | Text | 4,194 | 91 | # Graph Neural Network-Based Anomaly Detection (GNNAD)
`gnnad` is a package for anomaly detection on multivariate time series data.
This model builds on the recently-proposed Graph Deviation Network (GDN)[^2], a graph neural network model that uses embeddings to capture inter-sensor relationships as a learned graph, ... |
c51928215dc38f298b59f819a076b188781016d4a93c16d50c1745692e685174 | Text | 4,194 | 58 | ## [MiniSeg: An Extremely Minimum Network for Efficient COVID-19 Segmentation](https://yun-liu.github.io/papers/(AAAI'2021)MiniSeg%20-%20An%20Extremely%20Minimum%20Network%20for%20Efficient%20COVID-19%20Segmentation.pdf)
The rapid spread of the new pandemic, i.e., COVID-19, has severely threatened global health. Deep-... |
bce2d889ea4f3a5894ef11f97bf9bc1addf6eb01a7ddd26d6bfdbf72cfe31dec | Text | 4,226 | 67 | # Catactor: a pipeline for consensus scATAC-seq analysis using meta-analytic marker genes
<img src="https://dl.dropboxusercontent.com/s/mgv0mmx0p0rctvm/logo_catactor.png?dl=0" width="300">
* Risa Karakida Kawaguchi, Ziqi Tang, Stephan Fischer, Rohit Tripathy, Peter K. Koo, Jesse Gillis. [Exploiting marker genes for ... |
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