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1178105faaf4304e4c8d28946f2edc9f03a341272d6b5c5c2fbb77d4ef90a46b | Text | 3,679 | 52 | # The neural representation of visually evoked emotion is high-dimensional, categorical, and distributed across transmodal brain regions
This repository contains the data and code for reproducing results in our paper: [Horikawa, Cowen, Keltner, and Kamitani (2020) The neural representation of visually evoked emotion i... |
e5288733783308a8d1e1eb31c3d874cca79faea79ba63856abcb70f512760f4c | Text | 3,679 | 53 | # MLHessian-TSopt
This repository contains wrapper scripts for running and analyzing transition state calculations using NewtonNet deep learning model and Sella optimizer.
## Script overview
- `Scripts/split.ipynb`: Wrapper notebook for model training data splitting from Transition-1x dataset with augmentation from ... |
98fad5a13673c0644e3720373945eef48dd83ce69ded2f5c97220edf62be7031 | Text | 3,693 | 80 | # DeepH-E3
This code is the implementation of the DeepH-E3 method described in the paper *General framework for E(3)-equivariant neural network representation of density functional theory Hamiltonian* ([arXiv:2210.13955](https://arxiv.org/abs/2210.13955)).
You can find demo input files and instructions in these ... |
0f18b06dae4dcbe52543a8714fa5ab0e687ca69d62e4846d037b084e2f8bbce3 | Text | 3,697 | 92 | # <p align="center"> Deep Learning Resilience Inference for Complex Networked Systems </p>
##### <p align="center"> Chang Liu<sup>1</sup>, [Fengli Xu<sup>1</sup>](https://fenglixu.github.io/), [Chen Gao<sup>1</sup>](https://fi.ee.tsinghua.edu.cn/~gaochen/), [Zhaocheng Wang<sup>1</sup>](http://oa.ee.tsinghua.edu.cn/~bc... |
e9baa34befe6d77ede9e11288dc894814b6b1230aec963eab5d9b39939ae5338 | Text | 3,702 | 51 | # KinaseDocker² - Paper reproduction code
*Code to reproduce the work described in the paper*
https://doi.org/10.26434/chemrxiv-2024-46rxl
# Docking
A selection of activities were docked in multiple structures per kinase. Docking was done using both AutoDock VinaGPU and DiffDock.
## VinaGPU
Docking with VinaGPU requ... |
bf751c636474a1b7af55fd97875be23a71f338f44aca03bf9d9c5e74af61a1af | Text | 3,705 | 77 | # From Text to Concrete: Developing Sustainable Concretes with In-Context Learning
This repository contains the code and dataset for the study "From Text to Concrete: Developing Sustainable Concretes with In-Context Learning". The project aims to improve the development of sustainable concrete formulations using in-co... |
633cca08fe1b76e0be7eb8334afc82aaed69e6465dd487e1ce577ee7407cdeb5 | Text | 3,717 | 59 | # peaky_pitchshift code
This repository is the code for the article "Fundamental frequency predominantly drives talker differences in auditory brainstem responses to continuous speech" by Polonenko & Maddox (2024).
Jasa-EL: Melissa J. Polonenko, Ross K. Maddox; Fundamental frequency predominantly drives talker differe... |
927c406cd838953f05a897d5230db9e4ec0c8943d3337e7b90751ff42b0c4064 | Text | 3,718 | 40 | # VENcelltypes
This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula described in [Hodge, Miller, et al 2020](https://www.nature.com/articles/s41467-020-14952-3).
While this is set up as an R library for convenience, it is really just a wrapper for the analysis functions... |
1b30e9abe187a6605e5952b70729a56146f4716d7092198fe5c838a9d804b2b2 | Text | 3,720 | 132 | # Mouse_behavioral_annotation
The "Mouse behavioral annotation" repository is dedicated to developing and implementing a pipeline that can help annotate mouse behaviors.
## Step 1: Boris annotation
BORIS can be downloaded using the following link
https://www.boris.unito.it/
A detailed guide regarding the usage of bor... |
fd50393c688a2ac024b743b2df88728b75180cdcb1c7e670e217acc10940a2d8 | Text | 3,737 | 83 | [](https://zenodo.org/doi/10.5281/zenodo.11165561)
# Contrastive-Signal-Dependent-Plasticity (CSDP)
This is the supporting code for the Science Advances paper:
<a href="https://www.science.org/doi/10.1126/sciadv.adn6076">"Contrastive-Signal-Dependent-Plasticity: Self-Supe... |
7af95a8f165e2a7ca14a4a8e44fef9ec99cdae0cc7e118b9cfb5953bc90ba2df | Text | 3,739 | 111 | # **HotPP: High order tensor Passing Potential**
[](https://hotpp.readthedocs.io/en/latest/?badge=latest)
# Introduction
`HotPP` is an open-source package designed for constructing message passing network interatomic potentials. It fa... |
e0dbe36f00f6664f53a4e9c7366f5c4ff34c78796635dafce35875b19f3f99e4 | Text | 3,756 | 86 | ### How to get BioShell on your machine? ###
**Note**, that because `bioshell` is written in C++11, you will need CMake (https://cmake.org) and relatively modern C++ compiler such as gcc 5.0 or clang 10.0.
1. **Install `zlib` library in developer version**
On Ubuntu linux it can be installed by the command:
... |
5a8c42642e3d6646a0ab763fd3cc55c9ac980efe641f731ea30d98911e339308 | Text | 3,767 | 110 | # **HotPP: High order tensor Passing Potential**
[](https://hotpp.readthedocs.io/en/latest/?badge=latest)
# Introduction
`HotPP` is an open-source package designed for constructing message passing network interatomic potentials. It fa... |
be376cf513649d23feafc10167c3b1b5eb95574787a6e8b167ad4cd7a9a36ea9 | Text | 3,771 | 86 | # Brain-behaviour Predictions
This repository holds the scripts for prediction of behavioural and simualted behavioural data for the Burden of Reliability project (doi:...). Below is the necessary information to calculate predictions. While some pipelines have been tested to work out of the box, please note that this ... |
67f4b94646b363cad8fd1ec9897dbb1718e2f0fd6a92b139ec8ec3a360501177 | Text | 3,785 | 86 | # Brain-behaviour Predictions
This repository holds the scripts for prediction of behavioural and simualted behavioural data for the Burden of Reliability project (doi:...). Below is the necessary information to calculate predictions. While some pipelines have been tested to work out of the box, please note that this ... |
68410b26d0a4b18565870882ddf20feba687ca75e1ddca5cebe62ccd9ba5949e | Text | 3,798 | 68 | [](https://zenodo.org/badge/latestdoi/533072698)
# cropDiffusionR: Exploring the Diffusion of Agricultural Crops
`cropDiffusionR` is an *R* package implementing functions to perform
analysis on the relationship between maize agriculture and temperature changes in prehisto... |
e317c5b52b9d1d0089e9010dfbfcd485aefbae5eb3a097c6b0847aa92d620a42 | Text | 3,814 | 57 | # Developmental Mouse Brain Common Coordinate Framework (DevCCF) Code Release
This Repository contains a partial set of in house code used in creating the Developmental Mouse Brain Common Coordinate Framework (DevCCF) in Kronman et al. (doi: 10.1101/2023.09.14.557789). This incluses the following projects, each with... |
27c3771d6ae3e3d4eb7b20cf1249e0fdb7a4ac4f4dc9c749a319656db1ce9fc2 | Text | 3,821 | 86 | # Latent Diffusion Model for PET Resolution Recovery (LDM-RR)
[Enhancing Amyloid PET Quantification: MRI-guided Super-Resolution using Latent Diffusion Models](https://www.mdpi.com/2075-1729/14/12/1580)\
*Life 2024*, Special Issue: Alzheimer’s Disease: Recent Developments in Pathogenesis, Diagnosis, and Therapy
## Ove... |
cc338dc0ed77db8578d28cf787072368e989783928dcbf3734194f063e88a5f1 | Text | 3,827 | 122 | # deepSRAMP
[SRAMP](http://www.cuilab.cn/sramp) is a popular mammalian m6A site predictor we previously developed ([Nucleic Acids Res 2016](https://pubmed.ncbi.nlm.nih.gov/26896799/)). SRAMP has been totally cited by more than 570 papers (Google Scholar, 4-16, 2024) and represents the mostly used algorithm in this fie... |
5e909c25bfaa7240921f52bf0f40d00d1dbb87137f15c2e7098ff96464a45dc1 | Text | 3,828 | 114 |
.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20build/badge.svg
:target: https://github.com/sappelhoff/pyprep/actions?query=workflow%3A%22Python+build%22
:alt: Python build
.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20tests/badge.svg
:target: https://github.com/sapp... |
3cb10e0b3c7e17abc80d22273f8dcefcb1ff8fed097061d53a974294c628d75c | Text | 3,838 | 82 | # NeCA: 3D Coronary Artery Tree Reconstruction from Two 2D Projections via Neural Implicit Representation
# 1. Overview
This is the official code repository for the [NeCA](https://www.mdpi.com/2306-5354/11/12/1227) paper by Yiying Wang, Abhirup Banerjee and Vicente Grau, published at Bioengineering (Invited: free of ... |
6f91249d411594c0e2d03ccf091d06cd6105c73965106a02ffe293c789fa4a28 | Text | 3,844 | 57 | # HiDDEN: A machine learning label refinement method for detection of disease-relevant populations in case-control single-cell transcriptomics
[](https://doi.org/10.5281/zenodo.13823942)
This repo contains:
* 🐍📦 a python **library** *hiddensc*
* 📍📚 a... |
d32bd7b1230544d99095d5a7095168a5dd322f9ec1ce181773f1a44b91d5833a | Text | 3,847 | 91 | # Nucleus
Pipeline to detect individual nuclei in crowded immunofluorescence images. Effective in 2D embryo sections and single-z plane images. Additionally, a range of tools are available for estimating 3D nuclei in whole-embryo, organoid, or embryo model confocal microscopy stacks.
<p align="center">
<img width=51... |
613f195ec6a0282d1032cb182b1dea73df4e7eca8ef5d7901496b31cb4a9d6c0 | Text | 3,850 | 47 | # Cardiac-Digital-Twin
This repository contains the code developed for the study:
_Harnessing 12-lead ECG and MRI data to personalise repolarisation profiles in cardiac digital twin models for enhanced virtual drug testing_
https://doi.org/10.1016/j.media.2024.103361
## Example data
The meshes, ECGs, electrodes, ce... |
e0e37e0d39e95e450e697ffa9f8bdb28e40461ab6a0880d00439d6d1afe1d1e0 | Text | 3,851 | 76 | # Exclusively Dark (ExDark) Image Dataset (Official Site)
[ArXiv](http://cs-chan.com/doc/cviu.pdf)
Updated on Sept 30, 2026 (Updated the README.md. Added DATASET_TERMS.md, RIGHTS_NOTICE.md & THIRD_PARTY_NOTICES.md)
Updated on Sept 02, 2022 (Updated the dataset link)
Updated on June 02, 2019 (Code for low-light image... |
2a24772ac40fd3f838f8564c22215a1cba2e74bed21303bdf4b224236345be77 | Text | 3,860 | 69 | # **DENOISING: Dynamic Enhancement and Noise Overcoming in Multimodal Neural Observations via High-density CMOS-based Biosensors**
<p align="center">
<img width="1090" height="614" src="https://github.com/HayderAminLab/DENOISING/assets/158823360/1c5ad1e1-5746-44b4-8a2c-92ceecde429b">
</p>
A computational framework... |
590d4b84c7328f812fbceea992db10a8b369011e4e553613ef0b6bd374dc317a | Text | 3,861 | 88 | # Dopamine and DBS accelerate the neural dynamics of volitional action in Parkinson’s disease
This repository contains the code used for analyses in the paper _Dopamine and
DBS accelerate the neural dynamics of volitional action in Parkinson’s disease_,
which has been released as a preprint at bioRxiv:
https://www.bi... |
5712ebecfd1da1d6705336d8d54cb292ef7695770a636202fe95a8ffbfc4f51b | Text | 3,872 | 106 | # ADNI-FI-clustering
Study using code published in [GeroScience](https://doi.org/10.1007/s11357-022-00669-2). See citation below if using code.
<br>
<br>
Code and files to compute, refine and run analyses for frailty indices
<br>
based on data from the Alzheimer's Disease Neuroimaging Iniative (ADNI):
<br>
http://adni... |
781e55747df616568573ce3640d23abc21b680296db16eda8ce9c740b23d6348 | Text | 3,875 | 48 | # Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
__Implementation description__
We collected 45 paired data... |
f6c07cc59c00d3d36ab7b3fa843f258c35ac4de50087e6f93c4eb4cbd89d2044 | Text | 3,884 | 66 | # Sensory-Thalamic-Localizer
[](https://www.gnu.org/licenses/gpl-3.0) <br>
Analysis code for the Auditory and Visual Sensory Thalamic Localizer Task<br>
Released under the GNU Public License version 3.
To use this code, see the script: main_TL_anal... |
92bd4ed54226bfdea3d50c44763ecaa2765dc18dbf05e65e9dc1ab66e8d82633 | Text | 3,896 | 50 | # PEPerMINT
PEPerMINT (PEPtide Mass spectrometry Imputation NeTwork) is a graph-based deep neural network for the imputation of peptide abundance values in mass-spectrometry-based proteomics datasets.
## Installation
The implementation and evaluation of PEPerMINT are mostly based on our [PyProteoNet Python framework](... |
835037e217f5e12ff63ba38d3c6f1e81d63012a25695d1b8d7b0e8d4d8d19df2 | Text | 3,906 | 50 | # Indoor Localization Competition
We organized an online fingerprint-based indoor localization competition in 2021. It attracted 1000+ teams worldwide. The teams were provided with a 60 GB dataset including WiFi, BLE, IMU, and geomagnetic field strength data collected from 200+ buildings to build their localization al... |
fcc0d6bbc3921aa8e5d5e4ef239b399e3515991677fbdd6102c5fc7f0d29148b | Text | 3,920 | 71 | # Colab tutorials for Coral
These Jupyter notebooks provide interactive Python tutorials for
development with Coral. You can download these files and run them on a
local Jupyter notebook, but they're designed for execution with Google
Colab, using the links below.
Train and build a model for the Edge TPU:
+ [Retrain... |
78dd97e24ab000008ae09e8f2eac0d900888bc089ebf2802125714fb55330b66 | Text | 3,921 | 87 | # Flytracking
## Disclaimer
This package was initially developed by [Jiun Bae](https://github.com/jiunbae). You can find the original repo at https://github.com/jiunbae/tracking-fly.
The author agreed to release this package without any condition, so the CC0-1.0 license was assigned here.
Please cite the following... |
888c3b0a28ec533f40259a8e6c9a26b4decfef910ad71b87c9e776567ceeebcc | Text | 3,922 | 79 | # Introduction
This lightweight tool can be used to generate a PolyVoxel Score across a set of MNI registered T2-Weighted scans capturing the iron deposition seen in the architypal "Hemochromatosis Brain". This pattern of brain iron desposition may relevant for Parkinson's Disease risk. Two papers discussing details ca... |
54a97ebba214a3860e3b6f8d2ecb49c5cd2e66a4c4f2c3962991c738a7940525 | Text | 3,936 | 110 | # Continuous and Data-Driven Descriptors (CDDD)
Implementation of the Paper "Learning Continuous and Data-Driven Molecular
Descriptors by Translating Equivalent Chemical Representations" by Robin Winter, Floriane Montanari, Frank Noe and Djork-Arne Clevert.<sup>1</sup>
<img src="example/model.png" width="75%" he... |
71e3d8942d89a9572852f8455c0622211d856ca129332cd679016a6289f2a333 | Text | 3,952 | 123 |
.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20build/badge.svg
:target: https://github.com/sappelhoff/pyprep/actions?query=workflow%3A%22Python+build%22
:alt: Python build
.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20tests/badge.svg
:target: https://github.com/sapp... |
45693215c8e091891414513032e33c8be66101eb0a5b6915e9e84ed71d66a27b | Text | 3,954 | 79 | # Introduction
This lightweight tool can be used to generate a PolyVoxel Score across a set of MNI registered T2-Weighted or T2* scans capturing the iron deposition seen in the architypal "Hemochromatosis Brain". This pattern of brain iron desposition may relevant for Parkinson's Disease risk. Two papers discussing det... |
b9322567c1c14cd3ab0873b81751c25fb553733d1af90c4b3845293fff0755ba | Text | 3,971 | 42 | # Semantic_Segmentation_Picker
## Semantic segmentation-based detection algorithm for challenging cryo-electron microscopy RNP samples
**Semantic_Segmentation_Picker** is a MATLAB code based on semantic segmentation designed for the automatic detection of challenging influenza A virus ribonucleoproteins (RNPs) and th... |
2486520148c7c42c5162b269ee3df9d437eb789b3ea73dfc0d76e588a3746e98 | Text | 3,991 | 82 | # Automated Cell Type Identification using Neural Networks
## Overview
ACTINN (Automated Cell Type Identification using Neural Networks) is a bioinformatic tool to quickly and accurately identify cell types in scRNA-Seq. For details, please read the paper:
https://academic.oup.com/bioinformatics/advance-article/doi/10... |
574f1064a1cddf3b3f14e09cd73bb4f31e599c0804aa932cc3a2ec7f9fc4ff91 | Text | 4,013 | 99 | `neuroquery_image_search` is a Python package and command-line tool to search
the [NeuroQuery dataset](https://neuroquery.org) with a brain image.
While NeuroQuery accepts text as an input and produces a predicted brain image
and list of related studies, NeuroQuery Image Search takes an *image* as input
and produces a... |
8aafbcf1fde823285de34f817d46ed2e8769ae2d2e96c6f20dc6cdb4d4978517 | Text | 4,013 | 102 | # scConfluence
[](https://github.com/cantinilab/scconfluence/actions/workflows/main.yml)
[](https://codecov.io/github/cantinilab/scconflu... |
bc235ac138c5dfe989197e4d63e0234267ee914336cd0b55f8e226242af13141 | Text | 4,017 | 48 | # CGRclust: Chaos Game Representation for Twin Contrastive Clustering of Unlabelled DNA Sequences
## Overview
[CGRclust](https://arxiv.org/abs/2407.02538) is a novel unsupervised clustering framework that utilizes Chaos Game Representation (CGR) of DNA sequences combined with twin contrastive learning and convolution... |
d9b6a4ef9c6ef25d99118ed1cbd2d71b53caa996f6c679ca285ccfe2c889f37e | Text | 4,033 | 84 | # fMRI BOLD signal deconvolution
This repository provides [Python](https://github.com/IHB-IBR-department/BOLD_deconvolution/blob/main/python_code/bold_deconvolution.py) and [MATLAB](https://github.com/IHB-IBR-department/BOLD_deconvolution/blob/main/matlab_code/bold_deconvolution.m) functions to perform hemodynamic d... |
d47c0d39a3b9aa5601989bee0bd7bcf1c1f5e71f0835454d99432f5a72400388 | Text | 4,036 | 113 | # iGWOS
**i**ntegrated **G**enome-**W**ide **O**ff-target cleavage **S**earch platform
## Introduction
iGWOS is designed for the optimal genome-wide off-target sites (OTS) prediction by integrating the available OTS prediction tools in a complementary way. iGWOS integrates OTS prediction tools with an Adaboost framewo... |
da37314bf2afed8116740bbf4c9a700fda49c96ade05bb8208bb525558487d01 | Text | 4,053 | 15 | # Spooletal2024
This repository contains data from the article "Auditory pallial regulation of the social behavior network". Further information, questions, and requests should be directed to, and will be fulfilled by, the corresponding author, Luke Remage-Healey (healey@cns.umass.edu).
## Description of the data and... |
ecae4a3fadfaeb3b1d89c9e37b4318c8fac20d78110dfd8a51777a6844e5de12 | Text | 4,075 | 65 | # Cancer-Net Open Source Initiative - Cancer-Net SCa
<p align="center">
<img src="assets/cancernet_logo.png" alt="CancerNet Logo" width="25%" height="25%">
<br>
</p>
**Update 2024-02-11:** We added the pretrained Cancer-Net SCa-DC-AC model (Double-Condensing Attention Condenser) in the `models` folder.
**Note: The... |
7bd3c2d5afa556ec55638618a4de31499f60cc5eddfd9c68dca39c409a5dccf4 | Text | 4,113 | 71 | # PRETTIER MRI
### Perceptual super-resolution in multiple sclerosis MRI
Our paper has been [published in Frontiers in Neuroscience](https://doi.org/10.3389/fnins.2024.1473132), you can also check out the [pre-print](https://www.medrxiv.org/content/10.1101/2024.08.02.24311394v1) version.
This repository contains the... |
b93c79d641a3f103e45480e75f345a2636151d98ef5b385c03193661d3ab7eb3 | Text | 4,113 | 95 | # AnDePeD
Accompanying repository for our paper on real-time anomaly detection on periodic
server farm telemetry data. We introduce our new algorithms; AnDePeD and AnDePeD Pro.
## Code
This folder contains the following real-time, unidimensional anomaly detection
algorithm implementations.
#### Our novel methods
-... |
eabe2211f8669c7cd3fb9f941f6bbe626f4bc062e7b69247a03055c5426e0a1a | Text | 4,128 | 86 | # Dataspace v. 1.3
**Dataspace (short: dspace) is a set of data structures, analysis functions and
a graphical user interface intended to facilitate data analysis in various
fields of science.**
![Dataspace for Zebra Finch Song Development](https://raw.githubusercontent.com/skollmor/dspace/master/App/Docs/+ds... |
daafd0d2d91ce9936925de25feca6cd1835955b93a21015379b1f1dab1b9731e | Text | 4,143 | 82 | # Stitcher
Reconstruction of 3D Surfaces
# Introduction
Based on [Fuchs, Henry, Zvi M. Kedem, and Samuel P. Uselton. "Optimal surface reconstruction from planar contours." Communications of the ACM 20.10 (1977): 693-702.](https://dl.acm.org/doi/abs/10.1145/359842.359846?casa_token=QG0Dw4j_pZMAAAAA:5hFtaJwiRkrrcLh3P... |
ab41dc92ee25697ee7889661deaa3bc6b1d6e1756613c9db19af6025878056b7 | Text | 4,144 | 90 | # ALL_INT_SNN: *An All Integer-based Spiking Neural Network with Dynamic Threshold Adaptation*
***
**This code can be used as the supplemental material for the paper: "*An All Integer-based Spiking Neural Network with Dynamic Threshold Adaptation*". (Submitted to *Frontiers in Neuroscience*, June, 2024)** .
***
## C... |
c55ae62ead8d54ffbfe00316af8944f8acfd3382b0e79a31d28c2a3059d56829 | Text | 4,165 | 135 | # Interferobot: aligning an optical interferometer by a reinforcement learning agent
This repository is the official implementation of [Interferobot: aligning an optical interferometer by a reinforcement learning agent ](http://arxiv.org/abs/2006.02252).
<p float="center">
<img src="gif/0.gif" width="400"/>
<img... |
d6ab3912e4d500464a555fdfa47f5c22c971a16ab9c660dbecbea2d0020bed50 | Text | 4,193 | 79 | # pyseg_system (v 2.0.0)
De novo analysis for cryo-electron tomography.
This GitHub repository have two branches (git checkout <feature_branch>):
* **master**: (default) stable Python 3 version.
* **python2**: old Python 2.7 (deprecated).
* **python3**: branch with the latest modifications and improved.
## What's new... |
d35bd8a07fa47a9bf56fd1e222a64d139b227fd76bec957fccc76b4b2c09831a | Text | 4,198 | 32 | # Biologically-informed deep neural networks provide quantitative assessment of intratumoral heterogeneity in post-treatment glioblastoma
**BioNet**: A biologically-informed neural network model, to predict regional di... |
61ca8c8fcf9be3eb50b906277c859abcc7a4575c2c718cf008fdabce5c65c73b | Text | 4,202 | 61 | <img src="xpresso_logo.png" width="300">
# Xpresso: Predicting gene expression levels from genomic sequence
This repository is intended to accompany our publication, primarily to enhance the reproducibility of our results. For more information please refer to:
Agarwal V, Shendure J. [Predicting mRNA abundance direct... |
d30474b19d489c22b1438b5973bac8f92a85eeed0f60af8fe8c654f640a0d284 | Text | 4,210 | 110 | # maldi-nn
Deep learning tools and models for MALDI-TOF mass spectra analysis.
Package features:
- Reading and preprocessing functions for MALDI-TOF MS spectra.
- Model definitions to process SMILES strings with state-of-the-art techniques (for feature-based AMR prediction).
- Model definitions to pre-train state-of-t... |
6930dcc704484fa76e7ed9cb22375d85b56e93f0f0accfb162049c43e5ac5cfc | Text | 4,224 | 83 | # single-cell-simulator
This repository contains the code necessary to reproduce supporting simulations and related figures in:
> All-optical reporting of inhibitory receptor driving force in the nervous system, by
> Selfe, Steyn, Shorer, Burman, Düsterwald, Abdelfattah, Schreiter, Newey, Akerman and Raimondo
## :scr... |
998f6a6985f249b7e51ffd2bf6fdea6801e2cb41be5ef06ce394363913c1f9ac | Text | 4,227 | 63 | # Neuro-Cognitive Multivel Causal Modeling (NC-MCM)
This repository provides the [Julia](https://julialang.org/) code for learning and the Python code for visualizing neuro-cognitive multilevel causal models (NC-MCMs), as described in [M. Grosse-Wentrup, A. Kumar, A. Meunier, and M. Zimmer, Neuro-Cognitive Multilevel ... |
2ca439faf5345219615a2d91c28ec9646641924e06e8c58f57a70356df1b2364 | Text | 4,233 | 90 | # 3D_SOSP_fMRI
This repository houses the sequence and analysis scripts for the paper **Combining the benefits of 3D acquisitions and spiral readouts for VASO fMRI at UHF** [https://doi.org/10.1162/imag_a_00308]
# Sequence (pulseq):
## Intial configuration steps:
1) Clone this repository
```shell
git clone https... |
56d8d1bb52430a25d9ce146a9e71404bb395127ebd113b746186659f8138b45c | Text | 4,242 | 51 | # replay_detection_cross_validation
Matlab analysis code for validating hippocampal replay detection methods. For more information about the replay analysis framework, please read: https://www.biorxiv.org/content/10.1101/2022.12.12.520040v3
## Prerequisites and installation
- MATLAB 2019a or newer (working on MATLAB 2... |
29abafd8af4a71aab9e63a4370017390702526509800d4ad22a92f919dd039e8 | Text | 4,244 | 101 | # Gut Analysis Toolbox
[](https://doi.org/10.1242/jcs.261950)
**To get started with using GAT, please go to the** [**Documentation**](https://gut-analysis-toolbox.gitbook.io/docs/).
***********
<p align="center">
<i... |
e087eb5462fb68b8e4a44440a35787a35fdb2ddf4ad490269dd0adda9434d66c | Text | 4,268 | 86 |
# 2023_CL062_Tao_Bhandawat
2023_CL062_Tao_Bhandawat contains the code that accompanies the paper:
Tao L, Ayembem D, Barranca VJ, Bhandawat V (2024) **Neurons underlying aggression-like actions that are shared by both males and females in *Drosophila*.** The Journal of Neuroscience; doi: https://doi.org/10.1523/JN... |
ac1eae6a5df85e9c5da8d0ad635bf52c36879c96a602ff625cdd8ad28b9f5c5d | Text | 4,270 | 24 | # VascularImagingAnalysis
This repository contains the code used to extract the in vivo vascular responses recorded using two-photon microscopy or optical imaging spectroscopy for the following papers:
1. Bonnar, O., Shaw, K., Anderle, S., Grijseels, D. M., Clarke, D., Bell, L., King, S. L., & Hall, C. N. (2023). APOE4... |
3b8e8f13f4288e84421934c6cec00664d8ab44331f1cb32dcbf892834c95b31f | Text | 4,301 | 56 | 
# PyntBCI
The Python Noise-Tagging Brain-Computer Interfacing (PyntBCI) library is a specialized Python toolbox developed for the noise-tagging brain-computer interfacing (BCI) project at the Donders Institute for Brain, Cognition, and Behaviour at Radboud University in Nijmegen, the Nethe... |
45b8289d9e052bbb57106d5a62598441aa7a4ee325745d92565927b3c4351e1c | Text | 4,307 | 112 | # PNETwa-MLP
# Table of Contents
- [Introduction](#introduction)
- [Install model](#install-model)
- [Step 1](#step-1)
- [Step 2](#step-2)
- [ Training model](#training-model)
- [Step 1](#step-1-1)
- [Step 2](#step-2-1)
- [Step 3](#step-3)
- [Step 4](#step-4)
- [Step 5](#step-5)
- [Step 6](#step-6)
- ... |
95df38cc6f2f06a254840595ac061bb8e6446be723fbd84de0a1333e7150af10 | Text | 4,313 | 122 | # PiNN: Pair-wise interaction Neural Network
PiNN<sup>[1](#fn1),[2](#fn2)</sup> is a pair-wise interaction neural network Python library built on top... |
fb5f9a3e9aa0472083656b604e79041f4e1cf818ff0365c14e4420ba62dad29f | Text | 4,317 | 108 | # ElasticAI.creator
Design, train and compile neural networks optimized specifically for FPGAs.
Obtaining a final model is typically a three stage process.
* design and train it using the layers provided in the `elasticai.creator.nn` package.
* translate the model to a target representation, e.g. VHDL
* compile the in... |
ba8e689f6649139e2f34fa0c83715db7fc277bc1d5180f564cafe0ba6b8efb10 | Text | 4,327 | 78 | # full spectrum sources
Source codes for the full-spectrum neuronal morphometry analysis project. This project is led by Prof. Hanchuan Peng at SEU, and it is a collaborative work across several groups worldwide, with major contributions from Yufeng Liu, Shengdian Jiang, Yingxin Li, Sujun Zhao, and source code refactor... |
b2cfe6776597b1b0f3770a3c779c7c1ba31b46a5dd9c93acf1ed366c799e2e8c | Text | 4,339 | 48 | # [ReconNet: Non-Iterative Reconstruction of Images From Compressively Sensed Measurements](http://www.cv-foundation.org/openaccess/content_cvpr_2016/papers/Kulkarni_ReconNet_Non-Iterative_Reconstruction_CVPR_2016_paper.pdf)
[Kuldeep Kulkarni](https://kuldeepkulkarni.github.io/), [Suhas Lohit](https://www.linkedin.com/... |
2682930ba39f1e6aa9689cf2e6fefdff326ccf9901f325cf20e00fb568e44fc0 | Text | 4,346 | 108 | # Publication
This repository was developed for the analysis of the data generated during the making of the following paper (please cite when using any tools derived from this repository):
- [ J. Xu, M. Girardi-Schappo, J.-C. Béïque, A. Longtin, L. Maler (2024): _Shortcutting from self-motion signals: quantifying tra... |
46d0fd94c0287f3a8c4dce93f05729a08a589f56d8d89acd921acd3688d547a3 | Text | 4,347 | 71 | # Multimodal vs. Unimodal ML for Mental-Health Marker Detection
**Published research** — this repository contains the code behind:
> Drougkas, G., Bakker, E.M. & Spruit, M. **Multimodal machine learning for language and speech markers identification in mental health.** *BMC Medical Informatics and Decision Making* **... |
ad90cc74ba39af5f7ae368df3b71486b87beda162a91dfc2e6c353fae15636e6 | Text | 4,357 | 64 | # Nexus-Console for Advanced Low-Field MRI
[](https://www.gnu.org/licenses/gpl-3.0.de.html)
[]... |
48d39d11ad39dcc5114ffe7c0e41c6b5726cfe14d16e8a799aae4fe509d98d07 | Text | 4,403 | 74 | # VBA toolbox
Official website: [https://mbb-team.github.io/VBA-toolbox/](https://mbb-team.github.io/VBA-toolbox)
## What is the VBA toolbox?
Most models of neurobiological and behavioral data can be broken down into processes that evolve over time and static observation mappings. Given these evolution and observati... |
112b6cb9d62ea78e26485bbafd145f57700388d75e402ab5328960e38f4ac0b0 | Text | 4,424 | 71 | ## Introduction
Non-Contact Atomic Force Microscopy with CO-functionalized metal tips (referred to as HR-AFM) provides access to the internal structure of individual molecules adsorbed on a surface with totally unprecedented resolution. Previous works have shown that deep learning (DL) models can retrieve the chemical ... |
1a509bf75ab41a03ee7fb38a23505bde57d3fff11b3ad1969311cf13d62de926 | Text | 4,425 | 82 | # SpikerNet_StarProtocols
This repository is a supplement to Coventry and Bartlett's tutorial on using Deep Reinforcement Learning for Closed-loop Neural Control, an algorithm we call SpikerNet.
# Initializati... |
2932760fcec06a3aa74468766ba5929af47426ed5dc596fa8c9f33c9e8533b86 | Text | 4,425 | 30 | # ExSeqProcessing
This is the software library for processing Expansion Sequencing, ExSeq, experiments as seen in [Alon et al 2021](https://doi.org/10.1126/science.aax2656). This pipeline takes multi-round in situ sequencing data (including morphological information for spatial context) and convert it into RNA reads i... |
3458275c12354644df2a782ad5f7372166a05df196375974c59a7f9330169c0f | Text | 4,429 | 118 | # hybridLFPy
Python module implementing a hybrid scheme for predictions of
extracellular potentials (local field potentials, LFPs) of spiking
neuron network simulations.
## Project Status
[](https://zenodo.org/badge/latestdoi/36443206)
[![Documentation Status](https://rea... |
78bf2cec5b971c5e9a43b98cc59623d3902ed8ff0c26a2a8de4459d4abc2af86 | Text | 4,431 | 137 | ---
title: "Syntactic Motion Parser"
format: html
execute:
keep-md: TRUE
eval: FALSE
editor: visual
---
**Koki Mimura***, Jumpei Matsumoto, Daichi Mochihashi, Tomoaki Nakamura, Hisao Nishijo, Makoto Higuchi, Toshiyuki Hirabayashi, Takafumi Minamimoto: Unsupervised decomposition of natural monkey behavior into ... |
3bb23d17385d737befb8c7a9075158e194cdd1545aa27c3a0137a18f96288b88 | Text | 4,457 | 48 | Julia version of 3D Watershed
=========================================
[](https://travis-ci.org/seung-lab/Watershed.jl)
This is a translation of [Zlateski's C++ Watershed code](https://github.com/seung-lab/watershed).
Hierarchical watersh... |
250f41325c2d44272495acd38b803a72601d3392a7d8cd845d7868ee388c4ff7 | Text | 4,471 | 131 | # trajectory_distance
=====================
**trajectory_distance** is a Python module for computing distances between 2D-trajectory objects.
It is implemented in Cython.
## Description
9 distances between trajectories are available in the **trajectory_distance** package.
1. SSPD (Symmetric Segment-Path Distance) ... |
7a8443f6a0167e3f7608c9986b914d896d62b0de49aa300c9c07dee9301f13e0 | Text | 4,481 | 89 | # Hybrid-Spectral-Net for Hyperspectral Image Classification.
[](https://opensource.org/licenses/MIT)
[![PWC](https://img.shields.io/endpoint.svg?url=https://paperswithcode.com/badge/hybridsn-exploring-3d-2d-cnn-feature/hyperspectral-image-classificati... |
3edd8748d2074c3486a646600f927792afb14f7fdce503c958d7c03af850e510 | Text | 4,516 | 126 | # Annotatability
Annotatability, a method to identify meaningful patterns in single-cell genomics data through annotation-trainability analysis, which estimates annotation congruence using a rich but often overlooked signal, namely the training dynamics of a deep neural network.
![workflow](https://github.com/nitzanl... |
e701b17327b8007ea15288679436622fb298416ff5689816039e56247fc4a7cd | Text | 4,523 | 112 | # nBP
Implementation of backprop on Intel's neuromorphic research chip Loihi using gated synfire chains.
This is the code used in the following publication:
Renner, A., Sheldon, F., Zlotnik, A., Tao, L., & Sornborger, A.
The backpropagation algorithm implemented on spiking neuromorphic hardware.
Nature Communications... |
03695d1ea9d9d6b5a216c8d9fbafd569742c014a98661d0c22b6b63853b235ab | Text | 4,541 | 86 |
# Install
```bash
mkdir -p $HOME/Github && cd $HOME/Github
git clone -b 3D-MERFISH https://github.com/rx3fang/MERlin.git
conda env create -f MERlin/merlin_env.yml
conda activate merlin_env
pip install -e ./MERlin
merlin -h
MERlin - the MERFISH decoding pipeline
usage: merlin [-h] [--profile] [--generate-only] [--conf... |
ba334f52ffe78e9b75591284400d7c56bcf1493f042bdee90936cadbbad51486 | Text | 4,542 | 105 | # PGPS
The code and dataset of IJCAI 2023 paper "[*A Multi-Modal Neural Geometric Solver with Textual Clauses Parsed from Diagram*](https://arxiv.org/abs/2302.11097)". We propose a new neural solver **PGPSNet**, fusing multi-modal information through structural and semantic
pre-training, data augmentation, and self-lim... |
9dd1b03e71512612dfefee26ad353ce4c41bef34261454bf4f21662276a781d5 | Text | 4,549 | 100 | # HiCDiffusion
Table of Contents
=================
* [What is HiCDiffusion?](#what-is-consensusv)
* [Citation](#citation)
* [Data](#data)
* [Requirements](#requirements)
* [Training and testing (advanced)](#training-and-testing-(advanced))
* [Predicting](#predicting)
* [Parameters](#parameters)
## What is HiCDiffusi... |
b489d5881190a1f7eba8490862d3640ec4f82e6196b44c7cc4ec4b4292f0873e | Text | 4,549 | 67 | [](https://reporter.nih.gov/project-details/10525501)
[](https://doi.org/10.17605/OSF.IO/NQGEH)
[![Stage 2 RegReport DOI](https://img.shields.io/badge/D... |
b6661660ddaf8b064c4942d1f6210721d61397479b18780b3c67e212213f3944 | Text | 4,549 | 121 | # Intraoperative-HFO-analysis
Cascaded Residual-based Dictionary Learning to Distinguish HFOs from Pseudo-HFOs
# Demo Code for the Paper:
**"Using High-Frequency Oscillations from Brief Intraoperative Neural Recordings to Predict the Seizure Onset Zone"**
## Overview
This repository contains the demo code that impl... |
16a2c3d7d9a1ad53040a4c3965a582799fdd06610d23aa0e5cd329061d3d7ccb | Text | 4,561 | 100 | # marmoset-trajectory_and_network_encoding_model
# Overview
Contains code for analysis and visualization of data for a manuscript in final stages of preparation. Some of the code
is complete, but some requires cleanup prior to publishing.
# Software Requirements
This code has been tested on Linux and Windows 10 i... |
2d0ab75a7eb93f82ca915c439be228781775a9dc078cfa5142537942cc5159bb | Text | 4,574 | 68 | # rodent-tracking
system to track rodent activity in their home cages
---
### hardware:
#### Camera
This system is based on a [ELP USB camera](<http://www.webcamerausb.com/elp-20mp-1080p-cmos-ov2710-cmos-sensor-infrared-usb-camera-module-with-ir-led-for-day-night-video-surveillance-p-188.html>), they are quite neat... |
0c75e6eb558461953446227db136994565cd72d3c7fcbd7dfa77e67dd49aa05e | Text | 4,584 | 75 | # Repo Archived
**This project has been replaced by [ft](https://github.com/fiberseq/fibertools-rs) which is a binary that replaces this pipeline in a single command**!
# `fiberseq-smk`: A Snakemake workflow for making **fiberseq** data
[](http... |
efbe7d9523aa9746cc37b3b720800c9ea48bdc607fc2b5b423eacaaea41be658 | Text | 4,596 | 72 | # Documentation for users of Nvidia GPU machines with CUDA
All the code of BrainQCNet-CNN for compatible GPUs is available in this repo.
## Pre-requisites:
Nvidia drivers and CUDA installed.
## Step 1: Install Docker
https://docs.docker.com/get-docker/
## Step 2: Install Nvidia Container toolkit
Linux system: ht... |
657c39a28853d6ba932590f166be14050c961cc411f63cd63612c6089f40c3c4 | Text | 4,613 | 70 | # Bismark
[](https://github.com/FelixKrueger/Bismark/actions/workflows/rust_ci.yml)
[](https://crates.io/crates/bismark)
[
Xron (ˈkairɑn) is a methylation basecaller that could identify m6A methylation modification from ONT direct RNA sequencing.
Using a deep learning CNN+RNN+CTC structure to establish end-to-end basecalling for the nanopore sequencer... |
467370a63b5603d50af60d74ec24d5697d62d8c4995c971f79e4ca1a9c557971 | Text | 4,655 | 74 | # CBCL_Aff_Validation
Code for the manuscript on validation of CBCL-Aff on three datasets (ABCD, HBN, BHRC)
# Authors
[Marie Zelenina](https://github.com/mariezelenina)
Daniel S. Pine
[Argyris Stringaris](https://github.com/Argyris36)
[Dylan M. Nielson](https://github.com/Shotgunosine)
# Important links
## Prer... |
c2a7200a7236316003e2d0af5bc25e65bb3626dc7a8a8c38bd14314bcb82a8f3 | Text | 4,658 | 101 | [](https://zenodo.org/doi/10.5281/zenodo.13840245)
# marmoset-trajectory_and_network_encoding_model
# Overview
Contains code for analysis and visualization of data for a manuscript in final stages of preparation. Some of the code
is complete, but some requires cleanup pr... |
dd8f65af484afb9a710656e6cc6a7d337e3559d4fc11c2ef4a218cb49bcf2bf6 | Text | 4,663 | 81 | # README
Paper: [MultiSports: A Multi-Person Video Dataset of Spatio-Temporally Localized Sports Actions](https://arxiv.org/pdf/2105.07404.pdf)
Homepage: [DeeperAction/MultiSports](https://deeperaction.github.io/datasets/multisports.html)
## Download Data and Annotations
Our data and annotations can now be download... |
fdd236814abb3d6f11ab1d6859c838abaad4996924850b00ede0e258a542d26e | Text | 4,665 | 113 | # pycudadecon
This package provides a python wrapper and convenience functions for
[cudaDecon](https://github.com/scopetools/cudaDecon), which is a CUDA/C++
implementation of an accelerated Richardson Lucy Deconvolution
algorithm<sup>1</sup>.
* CUDA accelerated deconvolution with a handful of artifact-reducing featur... |
490c534f239c7d260192fc71dbb6c003d0237f666d22c780725d46f4f23b6f64 | Text | 4,687 | 98 | # GearBind
For the latest version of GearBind code and the link to the datasets, please refer to https://github.com/DeepGraphLearning/GearBind.
## Overview
GearBind is a pretrainable geometric graph neural network for protein-protein binding affinity change (ddG_bind) prediction.
It is pretrained on CATH using contr... |
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