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60a490594f8b2aab51f5806f657feea4f45a906496c1364c749c44704d0b32fb | Text | 5,998 | 77 | # CNN-brain-strains
Convolutional neural network for efficient estimation of regional brain strains [[link of the paper]](https://www.nature.com/articles/s41598-019-53551-1)
The demo for "Instantaneous Whole-brain Strain Estimation in Dynamic Head Impact" is provided here [[directory link]](https://github.com/Jilab-bi... |
a7a110c3ebee905314fa3788c5a9f52f0857a2ea877eab50e7ca52b520688761 | Text | 6,001 | 118 | #
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://github.com/MolecularNeurobiology/Breathe_Easy/blob/main/Logo_3.png"raw=true width="350">
<source media="(prefers-color-scheme: light)" srcset="https://github.com/MolecularNeurobiology/Breathe_Easy/blob/main/Logo_3.png"raw=true width="350">
... |
6c0d28196741657f42a04a787787d9497129b2fa0b4cea7c255057d960470732 | Text | 6,057 | 110 | # Mueller_et_al_2023_Nicotine_and_fear
This repository consists of fMRI-imaging data in form of beta/con images for different analyses of each subject, as well as .csv files of subjective ratings and SCR data for each subject. Subjects underwent a fear conditioning protocol with a fear acquisition (ACQ) on day 1 and 2... |
769d6fd8e18d6ce7d51d4192088368ea7c992770683a35d1559851883e72d36a | Text | 6,077 | 108 | # Nested-Cross-Validation
This repository implements a general nested cross-validation function. Ready to use with ANY estimator that implements the Scikit-Learn estimator interface.
## Installing the pacakge:
You can find the package on [pypi](https://pypi.org/project/nested-cv/)* and install it via pip by using the f... |
757f365195a77d551ed851bfc6bd126728dc827e95531d4539fd59e7d6288693 | Text | 6,085 | 168 | *******************************************
LISA: Landscape In-Silico deletion Analysis
*******************************************
.. image:: https://raw.githubusercontent.com/liulab-dfci/lisa2/master/docs/example_clustermap.png
:width: 200px
.. contents:: Table of Contents
About
-----
LISA is a statistical test... |
3d09c460b8586b5bc8218beef048b54dcbf92c73fa414bf0763c5c3763897f26 | Text | 6,118 | 112 | # SpatialKcorePercolation
SpatialKcorePercolation is a Python project for generating spatial networks and performing k-core percolation simulations to analyze percolation behavior. It includes functions for generating spatial networks with various parameters, performing k-core percolation simulations, and plot the simu... |
a48a8c68ffa22b1e849d6f8f43edb15646e464fbc8afa934db39be8cfa40b930 | Text | 6,167 | 114 | # ExVR - Open Virtual Psychology
## Summary
* [Description](#description)
* [Content](#content)
* [Papers](#papers)
* [Medias](#medias)
* [How to download](#how-to-download)
* [How to use](#how-to-use)
* [How to compile from code](#how-to-compile-from-code)
* [Authors](#authors)
## Description
ExVR is a solution fo... |
08d0751e00a79df1ff1c9603ca369f11eacfd157165369956fa0a127d8092a11 | Text | 6,227 | 154 | # FeatureCloud Ensemble GNN
## What is this APP about?
Feature Cloud Ensemble GNN is a federated learning APP that uses a graph neural network to train a model on distributed
data. The APP is based on the [EnsembleGNN](https://github.com/pievos101/Ensemble-GNN) Method 1.
The idea is to train multiple models locally w... |
e5399eb275ef26d6e16108dcb7c8b9caf51f792222ff50b67f302b858627be34 | Text | 6,316 | 143 | # Library for measuring performance of time series classification
## Motivation
F... |
da737d8cd4cebd68b13259ca17b1260f0fdae0d1c90b4733fc9555e815a5ec15 | Text | 6,320 | 88 | # mmo-analysis
[](https://www.biorxiv.org/content/10.1101/2023.05.22.541800v1) <br/>
**`mmo-analysis` is an open-source repository for a collection of MATLAB(R) scripts used for analysis in: Tong et al. (2023) Periodicity, mixed-mode oscillations, and multiple ... |
361322847cd1a2f2d984527e1ace0eb431f59e6ca11566473db2e02bf0dc09a4 | Text | 6,322 | 79 | [](https://hippunfold.readthedocs.io/en/main/?badge=main)
<img align="right" wi... |
d7233dd216df8f22b4725171d5a2fced5ca5db001b894379d3b8061eca80476d | Text | 6,337 | 35 | # glioma-Tcell-MDSC-treatment
<a href="https://github.com/stepien-lab/glioma-Tcell-MDSC-treatment/"><img src="https://img.shields.io/badge/GitHub-stepien--lab%2Fglioma--Tcell--MDSC--treatment-blue" /></a> <a href="https://doi.org/10.1016/j.jtbi.2024.111951"><img src="https://img.shields.io/badge/doi-10.1016%2Fj.jtbi.2... |
03c784184cb3eee92b48ee9a30a832ba09a544c13e85343b9e2356964a38b57e | Text | 6,387 | 111 | ---
# A memory efficient implementation can be found [here](https://github.com/juglab/cryoCARE_pip).
---
# Cryo-CARE: Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data
Tim-Oliver Buchholz<sup>1</sup>, Mareike Jordan, Gaia Pigino, Florian Jug</br>
<sup>1... |
ed63a7d12d6e0a377c78df87607ee62368f1fd24e1e39da7053ecd06c66743f5 | Text | 6,500 | 113 | # Attention-Based CNN-BiLSTM for Sleep States Classification of Spatiotemporal Wide-Field Calcium Imaging Data
- Author:
- Xiaohui Zhang (University of Illinois at Urbana-Champaign, xiaohui8@illinois.edu)
- Eric C. Landsness (Washington University in St. Louis)
- Jin-Moo Lee (Washington University in St. Louis)
... |
f8a229086f27c3fa198b7191e23085e5d972761f58113eee9ac9cc4cfeb8e3c9 | Text | 6,505 | 150 | # OPFVTA Reexecution Study
[](https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2024.1376022/full)
[](https://articles.chymera.eu/fraaef-frontiers.pdf)
[](https://www.gnu.org/licenses/agpl-3.0)
[**ROS 2 version is available!!**](https://github.com/CIT-Autonomous-Robot-Lab/emcl2_ros2)
emcl is an alternative Monte Carlo localization (MCL) package to amcl (http://wiki.ros.org/am... |
d2a41d9a14f66beeb1015f9bc13b64390f5a61a7b5f225c3995d585fbe6d9541 | Text | 6,620 | 101 | # RadioVicuna
Script from the manuscript "Performance of an Open-Source Large Language Model in Extracting Information from Free-Text Radiology Reports" submitted to Radiology: Artificial Intelligence
## Installation
(Optional) - Download text-generation-webui https://github.com/oobabooga/text-generation-webui
1 - D... |
4426286166c6db7dfced20945e614983e2ed7e5e429c562385b60fa20e460106 | Text | 6,628 | 171 | # Penn Machine Learning Benchmarks
This repository contains the code and data for a large, curated set of benchmark datasets for evaluating and comparing supervised machine learning algorithms.
These data sets cover a broad range of applications, and include binary/multi-class classification problems and regression pr... |
302e7bbdc887e1307c3ca88b24edc2abbf4de5db3bc1e349913c001c93cafb88 | Text | 6,642 | 174 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Azimuth v0.5.0
<!-- badges: start -->
[](https://github.com/satijalab/azimuth)
<!-- badges: end -->
Azimuth is a Shiny app demonstrating a query-reference mapping algorithm... |
63183dfd2ff45c5f21f4248185b19dcdd5b3380a29198212e6c63eccec86419c | Text | 6,675 | 130 | RNAelem is a tool for learning sequence-structure motifs from a set of RNA sequences.
# Installation
```sh
git clone https://github.com/iyak/RNAelem.git
cd RNAelem
./waf configure --prefix=$HOME/local
./waf build test
./waf install
```
RNAelem is developed using Python3 and C++14, utilizing the `numpy` and `scipy` Py... |
623351f3c8b532957358286e2bfcda708ba93e24a559f81ca94945349e199a90 | Text | 6,727 | 149 | # AttentiveChrome
Reference Paper: [Attend and Predict: Using Deep Attention Model to Understand Gene Regulation by Selective Attention on Chromatin](https://arxiv.org/abs/1708.00339)
BibTex Citation:
```
@inproceedings{singh2017attend,
title={Attend and Predict: Understanding Gene Regulation by Selective Attention... |
4e0d7f618373c29448205ac35284b81bcf41820c119b8ced3d2966e6388e8b0b | Text | 6,783 | 103 | # HarmonyTM: Multi-center data harmonization applied to distributed learning for Parkinson’s disease classification
<div align="center">
</div>
<p align="center">
<img src="HarmonyTM.png?raw=true">
</p>
Implementation of a data harmonization method for distributed learning using the Travelling Model for unlearning ... |
44d123b4bc3adf16198dac97e43f21a4e0ccdf7caf459869e357040e8a3e642e | Text | 6,822 | 106 | # Deep brain stimulation of the _Tbr1_-deficient mouse model of autism spectrum disorder at the basolateral amygdala alters amygdalar connectivity, whole-brain synchronization and social behaviors
Tsan-Ting Hsu<sup>1</sup>, Tzyy-Nan Huang<sup>1</sup>, Chien-Yao Wang<sup>2</sup> and [Yi-Ping Hsueh](https://scholar.goo... |
75cca1f50dd6cdfb2779b316d359aff6cbc229999cb270fc5c919da697c1cf20 | Text | 6,940 | 112 | # BeliefStateRL
This is the code and experimental data to simulate and fit the Basic RL and Belief State RL models from version 2 of the [bioRxiv preprint Cole, et al., Prediction-error signals in anterior cingulate cortex drive task-switching, 2022](https://www.biorxiv.org/content/10.1101/2022.11.27.518096v2).
... |
14ff4004c5ef11e97d39bc1ab1386953f0edf20a1abc1616234e6e5a735794d1 | Text | 6,977 | 152 | # README
Model and analysis code corresponding to Ritvo, Nguyen, Turk-Browne & Norman (2023).
These models have been developed based on the [Emergent](https://github.com/emer/emergent) framework, developed primarily by the CCN lab at UCDavis. In our simulations, w... |
39cb8f1f0efa646f8551d028efdebe2e43445236c58269a413a60a7cc065eaef | Text | 7,025 | 69 | # UnitMatch
Ephys toolbox to match single units (electrophysiology) either within the same recording (oversplits) or across recordings, by using spatial position and waveform-based parameters - both standard and unstandard metrics to the field.
, a ground-up rewrite of Detectron in PyTorch.**
# Detectron
Detectron is Facebook AI Research's software system that implements state-of-the-art object detection algorithms, including [Mask R-CNN](https://arxiv.org/abs/... |
66cb631aab676cd0498d0dcb27a7d2207603d96303e6eab151bff121310c56cf | Text | 7,061 | 64 | ## About
This repository includes scripts to process and analyze images from all 1714 acute individuals with suspected stroke (with 1449 having stroke confirmed) in the [Stroke Outcome Optimization Project (SOOP)
](https://openneuro.org/datasets/ds004889), as well as the resulting images derived from the processing. T... |
7d0bfbb01ce2f39cc9eb4452375436092ec535f1267349536a7f8189a8252de6 | Text | 7,098 | 99 | ARE_matrices
|afterReaddepthAndGCNorm
{$tissue}.depth.GCnormTeng.HeightsMean.hg19.txt: ARE activity (by row) across different individuals (by column)
tiss2ARE.log10.quant.scaled.hg19.tsv.gz: average ARE activity for each tissue
|covariatesForQTL
{$tissue}.H3K27ac.top50.PEER_covariates.txt: top 50 peer factors ... |
61f62c09dfa1911d1a9446e75dfb44536123dd71417657830fe6ad2706fafb2b | Text | 7,212 | 162 | # Uni-p*K*<sub>a</sub>
The official implementation of the model Uni-p*K*<sub>a</sub> in the paper Bridging Machine Learning and Thermodynamics for Accurate p*K*<sub>a</sub> Prediction.
Interactive demo with available model weights at https://bohrium.dp.tech/notebooks/38543442597
Published paper at [[JACS Au](https://... |
80cfca0b689fa996ca3e45937cd0659ad50316c8c8e6bd1c7f056ea50ad19824 | Text | 7,238 | 156 | <!-- ---------------------------------------------------------------------- -->
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://cran.r-projec... |
965b41e799ded72f411bebccdc5b940c6d2840dbe747fb0b1f1d2a7e98077adb | Text | 7,304 | 94 | # DeepDeWedge
This repository contains an implementation of the DeepDeWedge method as described in our manuscript ["A Deep Learning Method for Simultaneous Denoising and Missing Wedge Reconstruction in Cryogenic Electron Tomography"](https://www.nature.com/articles/s41467-024-51438-y). Our implementation comes as a Py... |
cdc22487decb794384ca4c6034375596c781877657564282f40be8ba00840403 | Text | 7,422 | 162 | # splam-analysis-results
all the scripts to reproduce the results in the splam paper
## Generalization Tests
`benchmark/src_generalization_test/`
- all outputs from every step of the data processing will be saved in the corresponding folder of the step `{#}_output/`
- `{name}` refers to the name of the gene database... |
273de2d93ee624399b02e0bede0bfa29708261c50c01a8d62932e43228c205b4 | Text | 7,452 | 205 | This jupyter notebook connects to our GitHub repo and downloads the necessary data from there. Before running it please make sure to install the requirements into your environment and load the data as follows:
- `git clone https://github.com/meggl23/multi_agent_language --branch v5.0`
- `cd multi_agent_language`
- `unz... |
0e7b39cd9e6f4ebc291eb963c176defcfa39eec83a4da82427430805b0f233d0 | Text | 7,472 | 157 | # Single cell discovery of m6A RNA modifications in the hippocampus
This repository contains the code associated with the article titled "Single cell discovery of m6A modifications in the hippocampus." The code provided here was used for the analysis and generation of results presented in the article.
## Introduction... |
9e05855e3279e5b8252847d8cb5a11285a27ceed3d43be1588ba7ffa4c7b6574 | Text | 7,486 | 130 | # AI-based differential diagnosis of dementia etiologies on multimodal data
This work is published in _Nature Medicine_ (https://doi.org/10.1038/s41591-024-03118-z).
## Introduction
This repository contains the implementation of a deep learning framework for the differential diagnosis of dementia etiologies using mu... |
320558a34b0de83ca608bcc164ba9ca807f05201441e4cafd817edcd3d0f2c8c | Text | 7,522 | 101 | # Natural image reconstruction from retinal ganglion cell spikes
All of the code used to fit the encoding models and generate reconstructions is provided in this repository. Because the
underlying datasets are large, and the full procedure for fitting encoding models and generating reconstructions is computationally ... |
921ced66b3eddc276de57bd00e6dd1bcba77e008493e0523d19cd73c2029b394 | Text | 7,599 | 136 | # Allo
A multi-mapped read rescue strategy for gene regulatory analyses.
**Genome Research paper now online:** [https://genome.cshlp.org/content/early/2024/07/10/gr.278638.123.abstract](https://genome.cshlp.org/content/early/2024/07/10/gr.278638.123.abstract)
### Releases
**v1.2.0**
The CNNs were retrained using T... |
da8d8d334993fa7a4449763d09cd5dfad517f7873a2c2c5e7856580e9e89359a | Text | 7,643 | 113 | FastANI
========================================================================
[](LICENSE)
[](https://anaconda.org/bioconda/fas... |
c9483d646aac0407093163a8a836b3527f49bf2f2db59a846191c81e0eeea691 | Text | 7,649 | 201 | DeepTreeAttention
==============================
[](https://github.com/Weecology/DeepTreeAttention/actions/)
Tree Species Prediction for the National Ecological Observatory Network (NEON)
Implementation of Hang et... |
185c8aa9e71f1292d8f703cf53477057906d59b90dabe1f73db7f0850dcfa1ed | Text | 7,656 | 137 | # README of ASTA-Seq (Allele-Specific Targeted Amplicon Sequencing) v 1.0
E. Blanco and M. Barrero (CRG, 2024)
`enrique.blanco at crg.eu`
`mercedes.barrero at crg.eu`
## Table of Contents
1. What is ASTA-Seq?
2. ASTA-Seq Command Line
3. How to Cite
## 1. What is ASTA-Seq
ASTA-Seq (Allele-Specific Targeted Amplico... |
ddd479dbb902dca13dbd393673fee7bc88e4abcdf8e9eecdb931b70ecd10c6b5 | Text | 7,751 | 156 |
Installation and implementation of PepNet
(version 1.0 2024/05/27)
1 Description
PepNet is an interpretable deep learning framework for predicting peptides with antimicrobial or anti-inflammatory activities by using a pretrained protein language model... |
a5c9b06f686a32ac213c5233ab4d070b03845dd0abfc9734674ac8ccdb81e3da | Text | 7,809 | 198 | # BrainSynth [](https://zenodo.org/doi/10.5281/zenodo.10014960)
Official implementation of "Realistic Morphology-preserving Generative Modelling of the Brain"
# Pretrained models
Experiments scripts have been provided in the experiments folder and are named based on the m... |
711d3f7199dbf382ade6e3da999aefea9ff6e4ca239e4f0b30892072674a3177 | Text | 7,812 | 108 | # CTNet for motor imagery EEG classification
### CTNet: A Convolutional Transformer Network for EEG-Based Motor Imagery Classification [[Paper](https://www.nature.com/articles/s41598-024-71118-7)]
core idea: CNN (an improved version of EEGNet) + Transformer encoder
Our research builds upon and improves the [EEG Confo... |
308bbb43ed9d1a366352e44432191202ae1f375403bbc7ef9c2925e5b19a236a | Text | 7,830 | 188 | Mozaik
------
Computational neurosceince is shifting towards more heterogeneous models of neuronal circuits, and application of complex experimental protocols. This escalation of complexity is not sufficiently met by existing tool chains. **Mozaik** is a workflow system for spiking neuronal network simulations written... |
19b13a1bda8da303fec66bfb6e80d45e602ef678dc364966b66effaa88870a32 | Text | 7,902 | 208 | <div align="center">
# 🧪 DECIMER Image Transformer 🖼️
### Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer
<p align="center">
<img src="https://github.com/Kohulan/DECIMER-Image_Transformer/blob/master/DECIMER_V2.png?raw=true" alt="DECIMER Logo" width="600">
</p>
[, 2024-07-20
[Code](https://github.com/arvidl/ibs-distress/tree/main/notebooks) and [data](./data/BGA_IBS_SSS_B_H_F_R_77x14.csv) accompanying the paper: <br>
A.J. Lundervold, J. Billing, B. Berentsen, G.A. Lie... |
25dbd498c8bef55a93209b0da9d2bb8b07d4c43be04d62eeabbec77e995e3721 | Text | 8,225 | 162 | 
# SAMRI
[](https://travis-ci.org/IBT-FMI/SAMRI)
[](https://repology.org/project/samri/versions)
... |
c2fa03d7eba5a3ee112833acef3fedf4396b1bd225035cb2ad9628937d5fc535 | Text | 8,328 | 150 | Official Repository for the Uni-Mol Series Methods
==================================================
<img src = "https://bohrium.oss-cn-zhangjiakou.aliyuncs.com/article/16664/d50607556c5c4076bf3df363a7f1aedf/4feaf601-09b6-4bcb-85a0-70890c36c444.png" width = 40%>
Welcome to the official repository for the Uni-Mol ser... |
f1bc9757cc7d838a0f2d69254e35e0e1dacf3d817d3b2e3d68ec5e047cd0c350 | Text | 8,404 | 155 | # Project Gene Connectivity
## 1. Introduction
This project aims to map gene connectivities using different deep-learning models such as MLP, Autoencoders, and GNNs with additional gene edges. Our primary contribu... |
1fe11e3bea2c48026ba18323f016d4c2d25fbf9962b47fe1d0bcc8f4a03de5ad | Text | 8,407 | 209 | <!-- PROJECT SHIELDS -->
<!--
*** I'm using markdown "reference style" links for readability.
*** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
*** See the bottom of this document for the declaration of the reference variables
*** for contributors-url, forks-url, etc. This is an optional, con... |
ebfd4228fb8ad5b91f321084e54ca77cde0e5543533bd19ed52b016613f63448 | Text | 8,557 | 203 | ## Long-Range Arena (LRA: pronounced ELRA).
Long-range arena is an effort toward systematic evaluation of efficient
transformer models. The project aims at establishing benchmark tasks/dtasets
using which we can evaluate transformer-based models in a systematic way, by
assessing their generalization power, computation... |
b925a22d8efd7a29608a0e10d3f2fb33d5d80df7de4ac6e34093853cd8e0274e | Text | 8,577 | 218 | ---
language: en
tags:
- exbert
license: apache-2.0
datasets:
- bookcorpus
- wikipedia
---
# DistilBERT base model (uncased)
This model is a distilled version of the [BERT base model](https://huggingface.co/bert-base-uncased). It was
introduced in [this paper](https://arxiv.org/abs/1910.01108). The code for the disti... |
dd65bef5251cc0714ab0a3908160919f9c23c60c19151e8ea8c7075e030a6e84 | Text | 8,591 | 164 | # Multiplying flow and pressure — data and interactive review tool
** | **[OpenReview](https://openreview.net/forum?id=mCOBKZmrzD)** | **[Poster](docs/equiformer_v2_poster.pdf)**
This repository contains the official PyTorch implementation of the w... |
83ce18948a0852e6b715e9b8c1743e23fbada236d02079ba5c8ced44ff7c74b0 | Text | 8,703 | 206 | ## Multi-person Human Pose Estimation with HRNet in PyTorch
This is an unofficial implementation of the paper
[*Deep High-Resolution Representation Learning for Human Pose Estimation*](https://arxiv.org/abs/1902.09212).
The code is a simplified version of the [official code](https://github.com/leoxiaobin/deep-high-... |
623f0ddc67afd56d249a2038d57ea9721e648644e2f8ebde986f33ba30e3c3e4 | Text | 8,712 | 91 | <center>
<h1>Small Angle Neutron Scattering (SANS) virtual experiments at KWS-1</h1>
<h4>Dr. José Ignacio Robledo</h4>
<h5>Jülich Centre for Neutron Science 2 - Forschungszentrum Jülich (JCNS2-FZJ)</h5>
<h5><em>j.robledo@fz-juelich.de</em></h5>
</center>
<h2> Introduction </h2>
This database is a result of the <b> <... |
881dc7aec26dfbd09cc4438bc6bd9d033663693af06f210f663cff50bdaaf9f9 | Text | 8,738 | 197 | <div align="center">
<br>
<a href="#"><img src="https://user-images.githubusercontent.com/24775272/210609554-e5918fe0-c845-493d-b362-4ff9cb473c57.png"/> </a>
<h4 align="center">A novel web server to discriminate lysine lactylation sites using automated machine learning.</h4>
</div>
<p align="center">
<a hre... |
9dd3f88f882533986f983c0fe65482b73abae819e3e038977675d2b57c97f79e | Text | 8,801 | 163 | # Telemanom (v2.0)
**v2.0** updates:
- Vectorized operations via numpy
- Object-oriented restructure, improved organization
- Merge branches into single branch for both processing modes (with/without labels)
- Update requirements.txt and Dockerfile
- Updated result output for both modes
- PEP8 cleanup
## Anomaly Det... |
2d73ad3f38ea119c3cbd951d939d700a60aa61bd9d910a66e8463ad60d300e4a | Text | 8,981 | 189 | # Chromoformer
[](https://zenodo.org/badge/latestdoi/432363545)
[](https://badge.fury.io/py/chromoformer)
This repository provides the official code implementations for... |
d10dbf7baa003fda2d91357e681caf3be9e92b2c76730628d9891a67d6138a5b | Text | 8,986 | 178 | # batchgenerators by MIC@DKFZ
Copyright German Cancer Research Center (DKFZ) and contributors.
Please make sure that your usage of this code is in compliance with its
[`license`](https://github.com/MIC-DKFZ/batchgenerators/blob/master/LICENSE).
batchgenerators is a python package for data augmentation. It is develope... |
fc868c40698d11b036e3f11b1170d7c7bec0b12c77803e67ff64f8a066ba2571 | Text | 9,059 | 250 | <h1 align="center">
<img src="https://raw.githubusercontent.com/WoLpH/numpy-stl/develop/docs/images/logo.png" alt="numpy-stl" width="280">
</h1>
[](https://github.com/w... |
a16e5092d97da93fe124bb9dddc5299f627375e58f94923cb87644220644d8c7 | Text | 9,186 | 104 | # bioNLP System for BioNER and BioNEN
... |
6a2bf83b95ae25e0a1db1c404ff804dc70e22f709a6c0cb37cd4d597a2c09fe3 | Text | 9,240 | 176 | # Multiplying flow and pressure — data and interactive review tool
[](https://doi.org/10.5281/zenodo.21786466)
](https://pypi.org/project/ecg-augmentations/)
[](https://github.com/klean2050/ecg-augmentations/actions/workflows/ci.yml)
[![License: MIT](https://img.sh... |
a4eb4258d2be3b09fd88cc879266ab1c29792ce11791a2660c30711208d3a1c7 | Text | 9,286 | 151 | OVERVIEW OF THE SCRIPTS COLLECTED IN THIS FOLDER
This repository contains the analysis scripts that were used to analyze the data related to the paper "Freezing of gait in Parkinson’s disease is related to imbalanced stopping-related cortical activity" (Cockx et al.).
It is subdivided in the following folders:
1. PREPR... |
139ea4560bc0f80c559c84ad80c17301108b98b397e6155dac0139828da2c550 | Text | 9,353 | 126 | # Reconstructing and Analyzing the Invariances of LDCT Denoising Networks
[](https://doi.org/10.1002/mp.17413)
This repository contains code for the paper:
> Elias Eulig, Fabian Jäger, Joscha Maier, Björn Ommer, and Marc Kachelrieß. Reconstructing ... |
c1316df807c00582d52ec7ff6949e198c8168c1bed18d334f011d10a94e247a1 | Text | 9,572 | 290 | .. image:: https://github.com/skorch-dev/skorch/blob/master/assets/skorch_bordered.svg
:width: 30%
------------
|build| |coverage| |docs| |huggingface| |powered|
A scikit-learn compatible neural network library that wraps PyTorch.
.. |build| image:: https://github.com/skorch-dev/skorch/workflows/tests/badge.svg
... |
7299bbe3d7e1cd381f9517a1dfced42e146402da248a135ba9b4db4a110a900a | Text | 9,710 | 178 | <div align="center">
[](https://github.com/PhoenixDL/rising/actions/workflows/unittests.yml)
[](https://travis-ci.org/tshmak/lassosum)
=======================
*New!! A standalone version of `lassosum` is now available. Please see [here](https://github.com/tshmak/lassosum/blob/master/lassosum_standalone.md#lassosum-standalone-versi... |
476e987619d15ff18666f10f60dee168a0ea9f1940793892328ddcb385cb390c | Text | 10,204 | 186 | # Hybrid Spatiotemporal Neural Network (HSTNN)
## Introduction
Hybrid Spatiotemporal Neural Network (HSTNN) enables fine-grained hybridization of RNNs/LSTMs and SNNs. The three-stage training approach offers the flexible trade-off among accuracy, robustness, and computational cost.
## Project Structure
Currently, thi... |
5abc2462374b19d88f1eed94663bbf69c83bfafe1eecc8d7198bb977cbfe842e | Text | 10,253 | 288 | <div align="center">
# GCDM-SBDD
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://pytorchlightning.ai/"><img alt="Lightning" src="https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlightni... |
a00c53a5d5cfe4338e1d0608b5564719b65a1740aaf9c8e1d1051a18aa9fd950 | Text | 10,357 | 215 | # ML4H
`ML4H` is a toolkit for machine learning on clinical data of all kinds including genetics, labs, imaging, clinical notes, and more. The diverse data modalities of biomedicine offer different perspectives on the underlying challenge of understanding human health. For this reason, `ML4H` is built on a foundation o... |
1bc04cc59c2cfa0903f957da938da91c04aba53fa387979c12d67324cd9063b8 | Text | 10,418 | 244 | # IBM Analog Hardware Acceleration Kit
[](https://aihwkit.readthedocs.io/en/latest/?badge=latest)
[](https://travis-c... |
aa283080969e59b1f2d2b76be15cc269b11fe33c8936e06491561da02e03302d | Text | 10,441 | 141 | # Neurobiology and Centiles in Psychosis
This repository contains code and data created in support of the project García-San-Martín, N.; Bethlehem, R. AI; Mihalik, A. et al. *"Molecular and micro-architectural mapping of gray matter alterations in psychosis"* Mol. Psychiatry (2024). All code was written in Matlab and ... |
35b6d8b3837aa17194f74ec6c049d0c572b814f3648ae1b33636a831aaec75bb | Text | 10,683 | 282 | # fmri.pipeline
`fmri.pipeline` is an R package for setting up, submitting, and tracking hierarchical fMRI GLM analyses on high-performance computing systems. It is designed for studies where the scientifically interesting model is larger than a single FEAT or SPM job: many subjects, many runs, multiple model variants... |
0cbaa800c096b18587143a805a6567747ca61ef64ff0c24b4c575dd17539821b | Text | 10,753 | 123 | # Deep learning-enhanced widefield neuron finder (DeepWonder)
<img src="img/deepwonder_logo.png" width="800" align="center">
Implementation for deep widefield neuron finder (DeepWonder)
 ](https://doi.org/10.5281/zenodo.12697233)
<p align="center">
<img src="data/misc/cover_wide.png" alt="alt text" width="800px" align="middle"/>
</p>
*Image: Y... |
7189176c5c8e65745930c74378b85bed80afd54804c106d8c3a886b20309be1b | Text | 11,051 | 158 | # Eventer
Copyright © 2019
Email: eventer.neuroscience@gmail.com
Website: https://eventerneuro.netlify.app/
GitHub repository: https://github.com/acp29/eventer/
Eventer is distributed under the GNU General Public Licence v3.0
*Eventer is software for the detection of spontaneous synaptic events measured by... |
0de910fbc97a2733551e3887bfb91e4a6e835dd33d6ce33d7d7593dfe4c36edd | Text | 11,128 | 100 | # Oxford Covid-19 Government Response Tracker (OxCGRT)
This repository contains the final version of the Oxford Covid-19 Government Response Tracker (OxCGRT).
The Oxford Covid-19 Government Response Tracker (OxCGRT) collected information on which pandemic response measures were enacted by governments, and when. Durin... |
b84acfe1333481d28b18d354114c61a3bf9fa08be26c5566044a578dfaf4c7be | Text | 11,169 | 283 | # Long read circRNA
This is a tool designed to be run on a linux system since it uses many standard GNU tools.
It might also work on Mac OS X system.
Provides a workflow for detection of circRNA in nanopore data.
## Installation
For conveince clone the repository to the home directory:
```
cd ~
git clone https://g... |
81fd536886c700bd1d349a5db592c2b799fea80c8840471c379e5097d890c642 | Text | 11,269 | 208 | > [!WARNING]
> This repository has been archived and is no longer maintained.
> The code is provided for historical reference and may contain unpatched or unknown vulnerabilities.
> It should not be used in production systems.
# Malaria Screener
Official repository for Malaria Screener.
This software was develope... |
2bd9bc01b30d21b0e3dd723eb9edccb2c5159d76d9487cac39136c30fb9574d2 | Text | 11,353 | 218 | # DeepCAD-RT: Real-time denoising of fluorescence time-lapse imaging using deep self-supervised learning
<center><img src="https://github.com/cabooster/DeepCAD-RT/blob/page/images/logo.PNG?raw=true" width="700" align="middle" /></center>
### [Project page](https://cabooster.github.io/DeepCAD-RT/) | [Paper](https:... |
cf53c808e971e51553f644858f80579caa5980234d742567e2ef4b1184bac271 | Text | 11,807 | 326 | Microprocessor controlled multi machine vision camera acquisition (Kinect, Basler, Flir)
==============================
Python library for parallel video acquisition. It abstracts Basler (pypylon) and flir (pyspin) libraries to allow simultaneous recording from both.
Acquisition is done in parallel using a microcont... |
19f561735d36247103da48aae781f0b824d248bc163c90a6358afef1ce4806ee | Text | 11,817 | 200 | # Mustache <img src="images/mustache.png" width="100"> [](https://pypi.org/project/mustache-hic/) [](https://opensource.org/licenses/MIT) [, audio, and video recordings from 42 participants. Each participant engaged in a cue-based conversation sc... |
9fa9e333431f1d63a757985350ba500f7d14582c20c096e9603f39da84e8c23a | Text | 12,002 | 199 | # SERGIO (Single-cell ExpRession of Genes In silicO)
[](https://zenodo.org/badge/latestdoi/197455649)
SERGIO v1.0.0
Saurabh Sinha’s Lab, University of Illinois at Urbana-Champaign [Sinha Lab](https://www.sinhalab.net/sinha-s-home)
Developed by Payam Dibaeinia
## Descri... |
7692942f4b072299743072a010ac0df8557a56bdf69550bf2b560819b2bf2f8b | Text | 12,266 | 163 | Versions:
Packages.txt - Lists Python, MATLAB, and R versions and relevant packages with corresponding versions.
----------
Files:
atlasMvec2.csv - Upper triangular matrix vectorization indices.
colenetlabels.txt - Network labels retrieved from: https://github.com/ColeLab/ColeAnticevicNetPartition
arrow3.m - Scrip... |
a9f27287f594e161a50a44afe8af7dadec757cb7d0fbe5a46bef79c0a7965d2f | Text | 12,512 | 262 | # Structured State Spaces for Sequence Modeling
This repository provides the official implementations and experiments for models related to [S4](https://arxiv.org/abs/2111.00396),
including [HiPPO](https://arxiv.org/abs/2008.07669), [LSSL](https://arxiv.org/abs/2110.13985), [SaShiMi](https://arxiv.org/abs/2202.09729),... |
05f4ab0852e591ca06def9971c1552e933ad0f7e988d2e76d662f82423945792 | Text | 12,527 | 125 | > [!IMPORTANT]
> ### 🚀 Dmipy is revived — and has a new home
>
> This original **AthenaEPI/dmipy** (2019) toolbox has been **revived, subsumed, and substantially expanded** under the new **[`dmrai-lab/dmipy`](https://github.com/dmrai-lab/dmipy)** umbrella. The project is now two engines that share one acquisition-and-... |
90dd3913a73825f38fd01c66b75521bd05c3728759defee19df6412ba1814e44 | Text | 12,615 | 308 | # mindr: an R package that converts markdown (.md) or rmarkdown (.Rmd) files to mind maps, and vice versa
## Introduction
With 'mindr' you can draw a mind map in markdown syntax, or start a markdown document from a mind map!
mindr is an R packag... |
d4de127f4b8745860ea50dadb62e138cdf6b1ec072f62131d37f25e77448ddbb | Text | 12,747 | 271 | <img height=40 src='http://my5C.umassmed.edu/images/3DG.png' title='3D-Genome' />
<img height=30 src='http://my5C.umassmed.edu/images/dekkerlabbioinformatics.gif' />
<img height=30 src='http://my5C.umassmed.edu/images/umasslogo.gif' />
# cworld::dekker
a collection of perl/python/R scripts f... |
0a209a1d3b8ce2576cb3def838554d859ac2d931ce26eef6a2908ea594943a7a | Text | 12,816 | 105 | > [!IMPORTANT]
> **NiiVue is moving to [niivue/mono](https://github.com/niivue/mono).** The new monorepo contains a rewritten `@niivue/niivue` package with WebGPU and WebGL2 support, smaller bundle sizes, and a more extensible architecture. The monorepo package will be our **v1.0.0** release candidate. All releases in ... |
d424a9bae351e9139a27512f1eaeca443d4da60fa621b6e0ac1aa83b5e9424d5 | Text | 12,884 | 107 | # SquareRR_AOPS
Animated Abstract (loading ... please wait):
## Describtion
The provided repository serves as a demonstration of the application of deep learning techniques in the prediction of the spec... |
1d72233e4d0684058e2ac4f2581ae18512042c611c29c431012930b5ee638b60 | Text | 12,886 | 233 | # e-CARE: a New Dataset for Exploring Explainable Causal Reasoning
## 1. Brief Introduction
Understanding causality has vital importance for various Natural Language Processing (NLP) applications. Beyond the labeled instances, conceptual explanations of the causality can provide a deep understanding of the causal fact... |
bae75c44186577bf2d20edd63215bd2f12a4d9e932238a5fde973eb6ddce646f | Text | 12,899 | 193 | # CNNC
# Title: Deep learning for inferring gene relationships from single-cell expression data
Originally, CNNC is short for Convolutional neural network co-expression analysis. Co-expression is just one of the tasks CNNC can do, but the name (CNNC) derived from it looks very nice.
## see `https://www.pnas.org... |
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