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d9990d33e7f8852af1d2e7c0ebe5e43a8e0f6aa5e9e8434120e92b16171a7dbf | Text | 7,262 | 105 | # TalkSumm
This repository contains a dataset and related code for the ACL 2019 paper *[TalkSumm: A Dataset and Scalable Annotation Method for Scientific Paper Summarization Based on Conference Talks](https://www.aclweb.org/anthology/P19-1204)*.
The dataset contains 1705 automatically-generated summaries of scientifi... |
71df2bcf74fe7eb50d0829f491b2476a240f91908357f56dd4d1bfcc614a7c8a | Text | 7,269 | 133 | # `bayesian_bootstrap`  [](https://badge.fury.io/py/bayesian_bootstrap)
`bayesian_bootstrap` is a package for Bayesian bootstrapping in Python. For an overview of the Bayesia... |
27029d5e2801a34cd72605843c9bcf3fa205be68368a6d3d9cb254e7a1fe835c | Text | 7,301 | 96 | # RootDetector
RootDetector helps researchers and students analyze minirhizotron root images. It can identify roots, calculate root and skeleton measurements, and compare images from different dates to visualize root growth and decay.
## What You Can Do
- Detect root... |
407c67fb02efc9f8812dbf7f22cd33d6e0f58d47c7abdedeb99d512f958d3b0f | Text | 7,332 | 132 | # local_interaction
This folder implements some pointwise approaches to decomposing multivariate entropy and mutual information into redundant, unique and synergistic terms.
These functions make use of the Python [discrete information theory (dit) toolbox](https://github.com/dit/dit).
To use these you will need Pyt... |
9b015ff780f13bd393bd4387b872c4c7484b8136717694ee64bc2a5348520bd5 | Text | 7,334 | 78 | ## Description
Lesion masks for the [PROSTATEx](https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges) prostate MRI dataset.
It comprises prostate MRI exams with PI-RADS score = 2+ lesions. These are classified as clinically significant or not. Only patients with PI-RADS score = 3+ le... |
620923d8614c1a7334a9686f0eee1e58f4e2014df7353456aad6035621b9a9f0 | Text | 7,338 | 99 | # GenomicSEM
R-package which allows the user to fit structural equation models
based on the summary statistics obtained from genome wide association studies (GWAS). Until explicitly stated otherwise the code on this github is an alpha version (now on version **0.0.5c**) and under active development. The code may thus... |
dcf19e062c0b10221eb2aefc977762529a221375527775eb2cc575792afee5a7 | Text | 7,413 | 146 | # Generative network modeling reveals a first quantitative definition of bilateral symmetry exhibited by a whole insect brain connectome
[](http://docs.neurodata.io/bilateral-connectome/) [](https://zenodo.org/badge/l... |
d94ce77ee67d00b08e584fd44fae37cac73559d336c5e6c4c3cea8bf956d018c | Text | 7,418 | 221 | # SparseGDLibrary : Sparse Gradient Descent Library in MATLAB
----------
Authors: [Hiroyuki Kasai](http://kasai.kasailab.com/)
Last page update: Oct. 15, 2018
Latest library version: 1.0.3 (see Release notes for more info)
Introduction
----------
The SparseGDLibrary is a **pure-Matlab** library of a collection of *... |
c01df741ffbd01ea0002160610ddaec261526aae4cad5e5b2c64655890a9063a | Text | 7,419 | 137 | # EnQA
A 3D-equivariant graph neural network for protein structure accuracy estimation. It can predict the quality of both tertiary and quaternary structures.
## Requirements:
```
biopandas==0.3.0dev0
biopython==1.79
numpy==1.21.3
pandas==1.3.4
scipy==1.7.1
torch==1.10.0
```
Install [Transformer protein language mode... |
9f1d1a462d88e2a4c9e63a35421622761b29062cdb8e4a6901ad22ae02071395 | Text | 7,424 | 118 | 
---
### Disclaimer:
All modification of the [original selene code](https://github.com/FunctionLab/selene/) are provided under [Apache License, Version 2.0](https://opensource.org/licenses/Apache-2.0)
Selene is a Python library and command line interface for training d... |
15be58406a22d1988050a3f923ca445ccf1939ac1f66aceb926c637728f30a6b | Text | 7,595 | 148 | # PCWA
A highly parallel and fast event detector based on CWT transform. *PCWA* is a multiscale approach to finding events with any shape with a mother wavelet that matches with events shape (details provided in the *Nature Communications* paper). Unlike previous CWT-based peak finders, *PCWA* is able to fit with any u... |
a87ce60afccd07e63e9a06e024c864db313d766ee10d8da688131d291a9e9773 | Text | 7,701 | 111 | # STGAN (CVPR 2019)
**Tensorflow** implementation of [**STGAN: A Unified Selective Transfer Network for Arbitrary Image Attribute Editing**](https://arxiv.org/abs/1904.09709)
<p align="center"> <img src="./pic/arch.jpg" width="95%"><br><center>Overall architecture of our STGAN. Taking the image above as an example, i... |
b0435e673908bb75dc36e1ef8cc9143c42ba8907cff76180b5ff1c9ae2d348fb | Text | 7,730 | 61 | # EyeEvaluationSourceCode
MatLab codes and scripts related to image processing, pre-processing & Training versions of the AlexNet Convolutional Neural Network (NetTransfers I-V)
IMAGE PRE-PROCESSING
The project has been developed using the 'AlexNet' neural network. If you want to install the neural network in Mat... |
5b041c70f7ec0e48f9f28f82c887d721da86333d2f1db71140fb3b0b2e862513 | Text | 7,799 | 161 | # HarDNet-MSEG: A Simple Encoder-Decoder Polyp Segmentation Neural Network that Achieves over 0.9 Mean Dice and 86 FPS
> Arxiv Paper : [**HarDNet-MSEG: A Simple Encoder-Decoder Polyp Segmentation Neural Network that Achieves over 0.9 Mean Dice and 86 FPS**](https://arxiv.org/abs/2101.07172)
> ICCV 2019 Paper : [**Har... |
9353265240febc10c2762029dc4716940f57e8d4ce720daf9df07073ba916607 | Text | 7,819 | 140 | # Single CEll Variational Aneuploidy aNalysis
<div>
<img src="LogoSCEVAN.png" align="right" width="200">
<img src="SCEVAN_workflow.png" align="center" width="590" height="700">
</div>
Article: [A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data
](https://www.natu... |
7f653bdf64c328fce77ce977b1a7b020a5586c78094db16edfcb2675eb5f129d | Text | 7,821 | 102 | # Interactive maps of mutations to the SARS-CoV-2 RBD that reduce antibody binding
## This repository is obsolete, use the new escape calculatore
This repository and the calculator it creates **are now obsolete and have been replaced by a new and improved calculator.**
Please see:
- The new calculator at [https://jb... |
77e8a8522ff479784085753be4432920398dd21777e8e1a335a460998ee002db | Text | 7,859 | 98 | # GliaMorph Introduction
GliaMorph Toolkit to process and analyse Müller glia morphology (implemented as Fiji Macros to allow modular application).
**Publication:** Elisabeth Kugler, Isabel Bravo, Xhuljana Durmishi, Stefania Marcotti, Sara Beqiri, Alicia Carrington, Brian M. Stramer, Pierre Mattar, Ryan B. MacDonald;... |
71582b26d6a577d1786bfe5891c0ea2072b45429c46050b13d961f90c48b17a9 | Text | 7,880 | 97 | DrugEx
====================
This repository contains further developments by Gerard van Westen's Computational Drug Discovery group to **Drug Explorer (DrugEx)**, a _de novo_ drug design tool based on deep learning, originally developed by [Xuhan Liu](https://github.com/XuhanLiu/DrugEx/) & Gerard J.P. van Westen. [2,3,... |
50b8184db2678a69633af71284bdde96f5e79d080382b576c905745d6e72e898 | Text | 7,914 | 126 | These are scripts to fit models to _Paramecium_ recordings, and produce figures for the following paper:
An electrophysiological and kinematic model of Paramecium, the “swimming neuron”
Irene Elices, Anirudh Kulkarni, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Prevost, Romain Brette
Contact : romain.brette@inserm.... |
6f9d39a2c683c691a3f01fddb55b9a260a2c553f6bf1c396cb65ab60258c664b | Text | 7,951 | 72 | # 
## Welcome to the Model Zoo for MindSpore
The MindSpore models repository provides different task domains, classic SOTA model implementations and end-to-end solutions. The purpose is to make it easier for MindSpore users... |
6f82140c730356d133df5fb4e38b88e784b811125318d1db539d7ad553f4ec47 | Text | 7,999 | 85 | # Verbal N-back task created with jsPsych
<i>Created by the MEMO Team of Lyon Neuroscience Research Center (CRNL) (PI: Dezso Nemeth)</i>
<p>A verbal n-back task (<a href="https://psycnet.apa.org/doiLanding?doi=10.1037/h0043688">Kirchner, W. K., 1954</a>) created with the jsPsych library (<a href="https://link.spring... |
3264ffabf85008cac52fc1e01fb8796ce006fa980f55cbe2467e0130f4d8c390 | Text | 8,003 | 122 | Prediction IncluDinG INactivity (PIDGIN) Version 4.2
=======================================
UPDATE MAR 2022: The new no-orthologue models can be downloaded at https://doi.org/10.6084/m9.figshare.19108382.v1 - remove the old no_ortho directory, and download and unzip the folder in the PIDGINv4 root directory. See the ... |
14e376bc09890618871bf927ece817810bb8e4104c655c4b7cdfdd77504f2d12 | Text | 8,022 | 64 | # EyeEvaluationSourceCode
MatLab codes and scripts related to image processing, pre-processing & Training versions of the AlexNet Convolutional Neural Network (NetTransfers I-V)
IMAGE PRE-PROCESSING
The project has been developed using the 'AlexNet' neural network. If you want to install the neural network in MatLab,... |
2c694d4985a354030e317d76b312a80634be8a5a1b54e633efe17c6112544ac3 | Text | 8,027 | 162 | # ABT-MPNN: An atom-bond transformer-based message passing neural network for molecular property prediction
## Introduction
This repository provides codes and materials associated with the manuscript [ABT-MPNN: An atom-bond transformer-based message passing neural network for molecular property prediction](https://do... |
d4645ee354f863b4414a2582f4710842adbefe3ab35fa3eb9e65b1dd89ee3a55 | Text | 8,091 | 129 | # Spontaneous behaviour is structured by reinforcement without explicit reward
[](https://doi.org/10.5281/zenodo.7274803)
## Authors
Jeffrey E. Markowitz<sup>*1,7</sup>, Winthrop Gillis<sup>*1</sup>, Maya Jay<sup>*1</sup>, Jeffrey Wood<sup>1</sup>, Ryley ... |
cda059b3bbf32de509c93d8fe24d15d476d2ff84513ee2926988aa76abe4d58c | Text | 8,115 | 201 | # Project FIS PI19/00670
[](https://www.python.org/)
[](https://www.python.org/)
 已公布。
数据集下载地址：https://cail.oss-cn-qingdao.aliyuncs.com/CAIL2018_ALL_DATA.zip
使用该数据集请引用 [CAIL2018: A Large-Scale Legal Dataset for Judgment Prediction](https://... |
1d3700d9ddc2391b9d45f7ae77d3f23eea1d82d10ba65d57682750773775a1d8 | Text | 8,231 | 117 | # Tips for Publishing Research Code
<img src="https://upload.wikimedia.org/wikipedia/en/thumb/0/08/Logo_for_Conference_on_Neural_Information_Processing_Systems.svg/1200px-Logo_for_Conference_on_Neural_Information_Processing_Systems.svg.png" width=200>
**💡 Collated best practices from most popular ML research reposit... |
15502c38ead8d7247028d6dc8a9c67d5dfac6c189608edfdec170ffd20cc1a64 | Text | 8,261 | 102 | # 
[](https://travis-ci.com/nf-core/chipseq)
[](https://www.nextflow.io/)
[ revolutionized th... |
6cb7e14295ee45d5f189a49c8b984f3d978220a19de6ca073f9d74e52c1294bc | Text | 8,289 | 61 | # LSTM-Lex
This repo host the necessay files, data and codes/scripts that were utilized for the LSTM lexicon project.
## Summary of The Project
Words play a pivotal role in almost every aspect of language processing. The dual-stream model of spoken language processing (Hickok & Poeppel, 2007) suggests that processing ... |
129592c3a3492912f4c88d4959ebfe6ce37f414665bc00db5a820847630cd69e | Text | 8,330 | 192 | # TERMinator
This repo contains code for [Neural Network-Derived Potts Models for Structure-Based Protein Design using Backbone Atomic Coordinates and Tertiary Motifs](https://www.biorxiv.org/content/10.1101/2022.08.02.501736) by Alex J. Li, Mindren Lu, Israel Desta, Vikram Sundar, Gevorg Grigoryan, and Amy E. Keating.... |
166e567b7579f37b2711e37d5351158c2f738ca16ee11f97c29d2535e853175b | Text | 8,375 | 196 | <a href="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/README.md"><img src="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/data_config/icon/cxsystem_logo.png?sanitize=true" width="50%"></a>
# CxSystem2, A Flexible Cortical Simulation Framework
> Warning: CxSystem2 BUI is developed for ... |
d623d715da663733f5704eeae64bfa6857ca132c0d405dd0ebd1b9e4484794e4 | Text | 8,389 | 235 | NSP: Neural Simulation Pipeline
===============================
All the source code needed to run Neural Simulation Pipeline. The NSP is written in Bash and PowerShell (User Scripts). It currently supports GENESIS (the GEneral NEural SImulation System) and PGENESIS (Parallel GENESIS).
GENESIS is a general purpose ... |
c2d623bde8a7e55c61171d9f0cfff0fbb6375f45d4a65f900b7ac79530ff2df8 | Text | 8,433 | 205 | # tripseq-analysis
Analysis tools for TrIP-seq data. There are various individual tools inside to perform different tasks. Limited documentation below, contact stephen.floor@ucsf.edu with questions.
## transcriptome_properties.py
Calculate the properties of an input transcriptome (or regions thereof). Input form... |
d9d741de6d48047d5054a3e430d1ab4bb4ae4b414014ff1a97192402304b6e47 | Text | 8,497 | 151 | # B-KinD: Self-supervised keypoint Discovery in Behavioral Videos
[](https://colab.research.google.com/github/neuroethology/BKinD/blob/main/behavioral_keypoint_discovery_demo.ipynb)
We will run B-KinD on your videos by request! Please fill out ... |
9601dd9f248ae938f3575e4936fa31f4ad98510874d33d8d824c113c7a644b3c | Text | 8,519 | 185 | # Semantic Segmentation Editor
A web based labeling tool for creating AI training data sets (2D and 3D).
The tool has been developed in the context of autonomous driving research.
It supports images (.jpg or .png) and point clouds (.pcd).
It is a [Meteor](http://www.meteor.com) app developed with [React](http://reactj... |
c4f41af6b42fd201ffbf357a24ba28393c0ae5ea187c9d147982185d8599dca1 | Text | 8,525 | 262 | # Latent Space 2D (LS2D)
<img src="docs/logos/logo-ls2d-v1.png" align="right" width="250">
<!-- ----------------------- -->
<!-- PROJECT SHIELDS -->
<!-- ----------------------- -->
<!--
[![Build][build-shield]][none-url]
[![Coverage][coverage-shield]][none-url]
[![Documentation][documentation-shield]][none-... |
97021c568559a4c14f9cbc137152c4ac2161ffe2b1fccb0208010456fd65fa42 | Text | 8,538 | 332 | ## **Modeling mechanisms and functions of hippocampal replay** ##
Simulation code for the computational study by Diekmann and Cheng (2023) published in eLife:\
A model of hippocampal replay driven by experience and environmental structure facilitates spatial learning\
https://doi.org/10.7554/eLife.82301
-------------... |
9c7dd97b077daff5cb73e277fd4e527a3d2e2edff05e2998849895a877264d27 | Text | 8,546 | 188 | # alphafold_finetune
Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions.
This repository is a collaborative effort: Justas Dauparas implemented the
AlphaFold changes necessary for fine-tuning and wrote a template of the
fine-tuning script. Amir Motmaen and Phil Bradley further develope... |
ba20ae50d13b90bb08df3d5c591eef5255d9a08de9bc58186f67920e0826c0bd | Text | 8,667 | 112 | # COVID 19 X-Ray Dataset
We are building a database of COVID-19 cases with chest X-ray or CT images. We are looking for COVID-19 cases as well as [MERS](https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome), [SARS](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome), and [ARDS](https://en.wikiped... |
0e09aca7bc1f7122facae8687d81c5948da4498fc79969fedff5a1249ff5c22d | Text | 8,692 | 94 | # <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/phys2bids_logo1280×640.png" height="150">
[](https://doi.org/10.5281/zenodo.3559868)
[](https://github.com/PaluchLabUCL/DeformingMesh3D/actions/workflows/build.yml)
# DM3D
##
**This is being moved. This is the original version that was published. I've moved it to
a version 1.0.x to signify feature c... |
e7c1bb0f7f77db0853e40fc456380954fef19847468dd7f4386b4cb243934ca5 | Text | 8,868 | 98 | [](https://mybinder.org/v2/gh/AllenInstitute/MicronsBinder/master?urlpath=lab) [](https://www.python.org/download/releases/3.7.0/)
# MicronsBinder
A collection of notebooks to provide examples of using data from [micron... |
cebc682a268fe0407453f4fed1f0f8c2af85517ef1ded2dfd8d32b30c2139151 | Text | 9,009 | 162 |
# 1. An introduction to MR-TOD-net
MR-TOD is a deep learning network designed to predict the voxel-wise track orientation distribution (TOD) from diffusion MRI signals. The network is based on a previously published network that predicts fiber orientation distributions (FODs) from diffusion MRI signals (Lin et al.... |
9d71bf713860db7bfb1b3adb2123fbb7f8762205b31520dc7265f0949f275768 | Text | 9,024 | 184 | [](https://doi.org/10.1093/bioinformatics/btaa461)
<p align="center">
<img src="https://raw.githubusercontent.com/wiki/BlueBrain/VessMorphoVis/images/logos/vmv-banner.jpeg" width="1200">
</p>
# Introduction
_VessMorphoVis_ is an integrated suite of toolbo... |
55ac3cf1f10caa3e2f0cc859a1484ad8c229829ec56245a9b2a1a50ef14d7613 | Text | 9,032 | 147 | <a name="readme"></a>
<!-- <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->
phys2cvr
========
[](https://pypi.org/project/phys2cvr/)
[![Release date](http... |
63a84b532bbbcd4ce10fda7093bf75cb086e4396b03ef68c08d57f79f63e1f34 | Text | 9,051 | 183 |
## StyleMapGAN - Official PyTorch Implementation
<p align="left"><img width="100%" src="assets/teaser.jpg" /></p>
> **StyleMapGAN: Exploiting Spatial Dimensions of Latent in GAN for Real-time Image Editing**<br>
> [Hyunsu Kim](https://github.com/blandocs), [Yunjey Choi](https://github.com/yunjey), [Junho Kim](... |
5ce2cc299555d7142421a465e537fa768079d54393603b4f9fe97aecb9b0de37 | Text | 9,270 | 151 | # Trajectory Embedding for Behavior Analysis (TREBA)
<p align="center"><img src="images/Task_programming_methods_overall.png" width="80%" alt="" /></p>
Implementation from the paper:
> Jennifer J. Sun, Ann Kennedy, Eric Zhan, David J. Anderson, Yisong Yue, Pietro Perona. [Task Programming: Learning Data Efficient B... |
24e22d46a4844476750b8d9a361a508de41d7eae97934356c56698746871273e | Text | 9,281 | 142 | # squigulator
*squigulator* is a tool for simulating nanopore raw signal data. *squigulator* uses traditional pore models and gaussian noise for simulation. Due to simplicity, simulation would not be perfect, but takes miniscule effort to setup and run. Generating 100,000 reads (~1 Gbases) from human genome using *squ... |
e54bf75e7b9addd4b4b3ffb0c926029f325e75e0d5a4a12fcf6b27aca881a8e5 | Text | 9,319 | 102 | # Eagle-449
<b>AN ATLAS COMPILATION FOR VESTIBULAR RESEARCH</b><br><br>
This collection of atlases is provided by the Post-Concussion Vestibular Dysfunction (PCVD) research group at the Emory University School of Medicine, Atlanta, Georgia, United States. It consists of seven source atlases at 1mm isotropic resolution ... |
520f6b46abe252f0e507ba65f10999950309099d469264554f4a606361fa512d | Text | 9,595 | 289 | # Jibri
JItsi BRoadcasting Infrastructure
# What is Jibri
Jibri provides services for recording or streaming a Jitsi Meet conference.
It works by launching a Chrome instance rendered in a virtual framebuffer and
capturing and encoding the output with ffmpeg. It is intended to be run on a
separate machine (or a VM),... |
2771a357a1acdc6efa559cbf25b4c528db1e02b2f02f91c2f68b2923a435d22a | Text | 9,600 | 117 | # 
[](https://travis-ci.com/nf-core/atacseq)
[](https://www.nextflow.io/)
[ She adapts to her student: An expert pragmatic speaker tailoring her referring expressions to the layman listener. In: Frontiers 2023. (https://doi.org/10.3389/frai.2023.1017204)
Please, cite:
```
@ARTICLE{10.3389/frai.2023.10172... |
f12c009881dcd73d9c069899ce5aa867929346580b1631b688417acd0f43b882 | Text | 9,791 | 166 | # Thy1-haSyn-Gut-Brain
Code to accompany "Distinct patterns of gene expression changes in the colon and striatum of young mice overexpressing alpha-synuclein support Parkinson Disease as a multi-system process", Journal of Parkinson's Disease
- RNA-seq processing follows recommendations from Lexogen for QuantSeq
- ... |
0013810717fad097ec0482238c51bbe3dda294aaf59ce509d4f1ec1390ce4fef | Text | 9,941 | 217 |
mfcsc -- Mismatch between Functional Connectivity and Structural Connectivity
=============================================================================
JOURNAL ARTICLE
Civier O, Sourty M, Calamante F (2023) MFCSC: Novel method to calculate mismatch between functional and structu... |
e11dbc44708f2fa72f09b93a4e9a0ad48d41f40876e56781b731f78478080f7d | Text | 9,951 | 124 | Data processing for EuskalIBUR
==============================
This library is meant to run the data processing on the dataset *EuskalIBUR* (currently available on request).
It is meant to run in the container [*EuskalIBUR_Container*](https://git.bcbl.eu/smoia/euskalibur_container).
Warning
-------
At the moment, the ... |
7b84323cd58ae3b33cee6a2611dfac3ce540e128604a083cbaedbbb4ade62f98 | Text | 9,964 | 126 | # SWS_NVS_code
Welcome to the GitHub repository for
**Expectations boost the reconstruction of auditory features from electrophysiological responses to noisy speech**, a combined EEG-pupillometry study of degraded speech processing.
This repository contains the scripts and functions required to reproduce the analyse... |
553c72e0aa506355d5515cdcedc032513e3c82436da82d04bb7bdcb0a8015f26 | Text | 10,025 | 250 | # ISOWN ( Identification of SOmatic mutations Without Normal tissues)
Irina Kalatskaya & Quang Trinh
ikalats@gmail.com
### INTRODUCTION
ISOWN is a supervised machine learning algorithm for predicting somatic mutations from tumor only samples.
### DEPENDENCIES
The following dependencies are needed to run ISOWN:
* ... |
dcb57758a9a439f90b8e3f239e7680e402a6c65dd79f63378942a9cec4a9be8e | Text | 10,221 | 187 | # MedMNIST-NAS-Bench
[](https://doi.org/10.5281/zenodo.20364514)
[](LICENSE)
[](https://creativecom... |
a4cefe14b4546b8c4bc40d45d011ff5ce55565383fa8cb6f35270b65772bbb77 | Text | 10,273 | 188 | # `pair_nequip` and `pair_allegro`: LAMMPS pair styles
> [!IMPORTANT]
> These pair styles now require the [10 September 2025](https://github.com/lammps/lammps/releases/tag/patch_10Sep2025) LAMMPS release, or newer versions. Furthermore, they require that the LAMMPS KOKKOS package is compiled in the default double-doub... |
8564126bff88e0efb247988232a7283caf7690622d88d56efdd4925ac614ecd5 | Text | 10,299 | 189 | # BOMA
Brain and Organoid Manifold Alignment
## Summary
3D organoids cultured from induced human pluripotent stem cells (hiPSCs) are useful models for understanding the longitude genomical dynamics during human brain development, however, the genomic differences between the brains and organoids are not well establishe... |
8c3cd3cbc506713023cea93a786f9ec68e8c69e869aba9d3cae73543e23c8989 | Text | 10,347 | 214 | CARLA Simulator
===============
[](https://carla-ue5.readthedocs.io)
[](http://carla.org)
[](https://github.com/carla-simulator/carla/releases)
[ is an automatic sleep stage classifer that takes an EEG or Polysomnography (PSG) recording as input and outputs a hypnogram. It is deep learning based, and therefore runs be... |
3d5d7790e4412cd0345cc8cfcf09ae6e421e4c1865b84b105d168e19a4a741f7 | Text | 10,416 | 190 | # FaderNetworks
PyTorch implementation of [Fader Networks](https://arxiv.org/pdf/1706.00409.pdf) (NIPS 2017).
<p align="center"><a href=https://github.com/facebookresearch/FaderNetworks/blob/master/images/interpolation.jpg?raw=true><img width="100%" src="./images/interpolation.jpg" /></a></p>
Fader Networks can gene... |
4fab1f277f23c9735e5d838142227354041863c506c55d97a77ee3a2cfe301a6 | Text | 10,468 | 247 | # Customized Upset Plots
[](https://zenodo.org/badge/latestdoi/240962726)
This repository contains scripts to produce customized upset plots, an alternative to Venn diagrams.
* Author: Chenxin Li, Ph.D., Assistant Professor at Department of Plant Biology, Michigan Stat... |
edf756f00fb7991de5032a986024d437809ae128256428eaef51df59997f9948 | Text | 10,577 | 165 | # Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease
This repository holds all code and data to reproduce results, figures and and supplementary data presented in "Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease".
The paper is ... |
b717ed2be00fc3c4658a484a170cf2de68ad1000d7235beb3fe33f42406c9fce | Text | 10,604 | 216 | <div align="center">
<img src="docs/_static/oxynet-mark.svg" alt="Oxynet" width="96" height="96">
<h1>pyoxynet</h1>
<p>The open-source models from the Oxynet research papers, for cardiopulmonary exercise test (CPET) data.</p>
<p>
<a href="https://pypi.org/project/pyoxynet/"><img src="https://img.shields.io/... |
76bc4bfc57917973323597e260110b28de631eed5d72c6c21a1928abf755564a | Text | 10,637 | 183 | # Scaling AutoLFADS
[](https://github.com/snel-repo/autolfads-tf2/tree/e6aae8aaa7deba2717d0c950c868b32349741258) [](https://hub.docker.com/u/ucsdtnel/autolfads) [](https://opensource.org/licenses/Apache-2.0)
---
<!--1) Add License file... |
3b3ed4f5ac51b7f8f6672a2fcd02922fee6e11ee7bfcc674f5a0b3a2cd624ceb | Text | 10,817 | 195 | # Siamese and triplet learning with online pair/triplet mining
PyTorch implementation of siamese and triplet networks for learning embeddings.
Siamese and triplet networks are useful to learn mappings from image to a compact Euclidean space where distances correspond to a measure of similarity [2]. Embeddings trained... |
bc9eca3515839b8ae4bf9c62d7e6b15cfa5ee11d3524803bf80220d0eaa5061d | Text | 10,817 | 133 | <a name="readme"></a>
<!-- <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->
phys2cvr
========
[](https://pypi.org/project/phys2cvr/)
[ by Isola et al.
[Article about this implemention](https://affinelayer.com/pix2pix/)
[Interactive Demo](https://affinelayer.com/pixsrv/)
Tensorflow implementation of pix2pix. Learns a mapping from input images to output images, like these ... |
0edb83b49bc33f4801be13a94f35e0bd840db5b04c4d69b32a3d7ac71585e591 | Text | 10,900 | 357 | # ActiveUnetSegmentations
For segmenting images using unet. Essentially a pixelwise classifier.
We title it active because currently we use it in conjunction with
[active contours](https://franciscrickinstitute.github.io/dm3d-pages/)
for both creating training data and segmenting the resulting network
predictions.... |
b9da50098f37aa763b12d4b5f4f837b7dc7827a08bd93d36f5f714d543b33935 | Text | 11,191 | 170 | <a href="https://apps.apple.com/app/id1452689527" target="_blank">
<img src="https://user-images.githubusercontent.com/26833433/98699617-a1595a00-2377-11eb-8145-fc674eb9b1a7.jpg" width="1000"></a>
 
<a href="https://github.com/ultralytics/yolov5/actions"><img src="https://github.com/ultralytics/yolov5/workflows/CI... |
715c411751963d3f2183f7b43bd21d92146b74358650635ab9123caa5901c40b | Text | 11,217 | 227 | # HR-pQCT-Segmentation
## Citing
Neeteson, N.J., Besler, B.A., Whittier, D.E. et al. Automatic segmentation of trabecular and cortical compartments in HR-pQCT images using an embedding-predicting U-Net and morphological post-processing. Sci Rep 13, 252 (2023). https://doi.org/10.1038/s41598-022-27350-0
## Model weig... |
58b1bba0d5acce8cc90e6762ed8c8ab7514c8808c2c21af367553dd4d07f06ee | Text | 11,352 | 187 | # QTI+ & QTI±: Matlab Implementation
This repository contains the Matab implementation of the routines used in the papers [Q-space trajectory imaging with positivity constraints (QTI+)](https://www.sciencedirect.com/science/article/pii/S1053811921004754) by Herberthson et. al., and [Diffusivity-limited q-space traject... |
1e52447fd26359d7ac00b9372d41a89e71233c2de52daf2448c11dfffa981d63 | Text | 11,380 | 197 | # Scaling AutoLFADS
[](https://github.com/snel-repo/autolfads-tf2/tree/e6aae8aaa7deba2717d0c950c868b32349741258) [](https://hub.docker.com/r/ucsdtnel/autolfads) [ that evaluates 16 commonly-used explainable AI algorithms on a novel problem of multi-modal medical image analysis tasks.
We generate explanati... |
91eaf7bb6f5c40356301dbf99abec14c31ea4197139efef2f392844171ebd4d1 | Text | 11,702 | 233 | # Neural Microcircuit Simulation and Analysis Toolkit (NMSAT)
NMSAT is a python package that provides a set of tools to build, simulate and analyse neuronal
microcircuit models with any degree of complexity, as well as to probe the circuits with arbitrarily
complex input stimuli / signals and to analyse the relevant ... |
819acd8d9a40692da5964dc48170979ec2e05b23ffae979575af17369640cfa7 | Text | 11,995 | 238 | 
NMSAT is a python package that provides a set of tools to build, simulate and analyse neuronal
microcircuit models with any degree of complexity, as well as to probe the circuits with arbitrarily
complex input stimuli / signals and to analyse the relevant functional aspects of s... |
4a4614ce7a8416d393fc2b7a616142818d8ffa921c982b743faaa5f22a910191 | Text | 12,025 | 232 | <div class="container" >
<p align="center">
<a href="LICENSE"><img src="https://img.shields.io/github/license/carlwharris/DeepAction?color=blue"></a>
<a href="#"><img alt="GitHub release (latest by date)" src="https://img.shields.io/github/v/release/carlwharris/DeepAction?color=brightgreen"></a>
<a href="#"><img ... |
7a9ce41582e0859c4c294b91ba0f8099a80497c03ba19d4aca221397d5903a41 | Text | 12,186 | 247 | # SimSwap: An Efficient Framework For High Fidelity Face Swapping
## Proceedings of the 28th ACM International Conference on Multimedia
**The official repository with Pytorch**
**Our method can realize **arbitrary face swapping** on images and videos with **one single trained model**.**
***We are recruiting full-time... |
2b362185fcb7db52a01e118ef9dd95d28111f36de447fcbbf7b1a040a1da5b3f | Text | 12,221 | 104 | # Restoring statistical validity in group analyses of motion-corrupted MRI data – an extension to relaxometry data (QUIQI II) - Analysis code
Authors: Rita Oliveira, Quentin Raynaud, Nadège Corbin, Giulia Di Domenicantonio, Martina F. Callaghan, Antoine Lutti
Laboratory for Neuroimaging Research
Lausanne Universit... |
cb77135a5432e47f81f0c51d753be6898273f918c13522cb446f1ab5cd6ad6d9 | Text | 12,339 | 227 | # Torch-NILM: An effective deep learning toolkit for Non Intrusive Load Monitoring in Pytorch
## Description
**[Torch-NILM](https://doi.org/10.3390/en15072647)** is the first NILM-specific deep learning toolkit build on **[Pytorch](https://pytorch.org)** and
**[Python](https://www.python.org)**. The purpose of the to... |
2886bc0949dfbe5227bd66af67ce8a24038747204ca77b5bba85019f9e0491c0 | Text | 12,599 | 161 | # DrugEx
<img src='figures/logo.png' width=20% align=right>
<p align=left width=70%>
DrugEx is an open-source software library for <i>de novo</i> design of small molecules with deep learning generative models in a multi-objective reinforcement learning framework. The package contains multiple generator architectures ... |
d450beb66f547d2b574209fde4f142f2f8cf667ed2a0abf0645d2a348d530b21 | Text | 12,726 | 147 | # EfficientMed-XNet: per-seed results, efficiency measurements, and reproduction notebook
Companion record of the paper
> *EfficientMed-XNet: A Compact, Resolution-Preserving Convolutional Network for Low-Resolution Medical Image Classification*
> Salah El Bikri, Nasreddine Hafidi, Mourad Nachaoui. LM2I, Faculty... |
da86ed5b3a970033f2474d74eee37069dcb5a6158d64a3f8d671b5bbf677e35f | Text | 12,733 | 253 | # super-HTS
**Super High-Throughput Screening of Enzyme Mutants**
Train a neural network to learn to predict the binding energy of **combinatorial libraries** of enzyme variants with a target ligand. The training data can come from more established (but slower) computational methods based on... |
3834eaac96b05006fa8732c9948c7915c8304850590b278baeb43327398cb9f9 | Text | 12,926 | 224 | # mismatch: A Python Package for Modeling Biomarker Discordance
`mismatch` is a Python package and analysis pipeline for modeling discordance between biological markers, with a focus on neuroimaging and biomarker data in Alzheimer’s disease.
The `mismatch` approach was originally developed to study the discordanc... |
d2d313282c6946cfab31a3aa593b01cfd8e5f68398c7f982747c719842aa4ff6 | Text | 12,934 | 206 | FAST-iCLIP
==========
Fully Automated and Standardized iCLIP (FAST-iCLIP) is a fully automated tool to process iCLIP data. Please cite the following paper:
`Zarnegar B, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. Ultraefficient irCLIP pipeline for characterization for protein-RNA interactions. Nature Methods (2016... |
ee4584ab81886503323b4342b7639b83659e66da6a5be1810b68630eca051e52 | Text | 13,189 | 190 | # <p align=center>`TediGAN`</p>
[](https://arxiv.org/abs/2012.03308)
[](https://opensource.org/licenses/MIT)
[ priors
using GWAS summary statistics and an external LD reference panel.
- Details of the development and evaluation of PRS-CS are described in: \
T Ge, CY Chen, Y Ni, YCA Feng, JW Smoller.... |
00ec1c609f7a40f60885283f756c9c05ae4c51520541899357f5761013a5b204 | Text | 13,446 | 135 | <h1>
<picture>
<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-chipseq_logo_dark.png">
<img alt="nf-core/chipseq" src="docs/images/nf-core-chipseq_logo_light.png">
</picture>
</h1>
[](htt... |
030efd9876bd05cc3231776a6cb54dc3288db93795a4b8d1fb3f57437886c045 | Text | 13,539 | 347 | Decoupled Neural Interfaces for PyTorch
=======================================
This tiny library is an implementation of
`Decoupled Neural Interfaces using Synthetic Gradients <https://arxiv.org/abs/1608.05343>`_
for `PyTorch <http://pytorch.org/>`_.
It's very simple to use as it was designed to enable researchers to... |
3394971f4fe863c23bb942553f3e2ab67f3729fc9f91ac79d1c17d27fbc3cae9 | Text | 13,836 | 200 | <br><br>
<p align="center">
<img src="https://github.com/vniems/BD-Lithium/blob/main/IMAGES/HEADER/BD_Lithium_project.png" width="770">
</p>
<br>
<h1 align="center">Bipolar Disorder and Lithium Response: Pharmacogenomic Study
<p>
*Learning protein constitutive motifs from sequence data*
*Learning neural assemblies of larval zebrafish from whole-brain neural recordings. Credit: Thijs L. van der Plas*
This repository consists of a high-le... |
19f7c36bcce4b06c25d85ebc7e93ae34c4a251ef85aaeeb5e13f7785d358c5df | Text | 13,943 | 384 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Generalized Additive Latent and Mixed Models <a href="https://docs.ropensci.org/galamm/"><img src="man/figures/logo.png" align="right" height="139" alt="galamm website" /></a>
<!-- badges: start -->
[![CRAN
status](https://www.r-pkg.org/badges... |
0973ffd124432fb5734f0fa8b5d1bc2269ce8506c4898b3e86e79ba92b4be39e | Text | 14,198 | 154 | # lhcMR
:grey\_exclamation: The `lhcMR` R package is a work in progress :grey\_exclamation:
## Overview
`lhcMR` is an R package that performs bi-directional causal estimation between a pair of traits, while accounting for the presence of a potential heritable confounder acting on the pair. The method termed `LHC-MR... |
8a2349e8539126463ff316db1676c7d38e5405673aead95eb3179c1595407c5c | Text | 14,219 | 226 | # ForceID-Study-1
Repository for the article, 'Deep Metric Learning for Scalable Gait Based Person Re-identification Using Force Platform Data'.
Shield: [![CC BY-NC 4.0][cc-by-nc-shield]][cc-by-nc]
This work is licensed under a
[Creative Commons Attribution-NonCommercial 4.0 International License][cc-by-nc].
[![CC ... |
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