sha256 stringlengths 64 64 | language stringclasses 27
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4567c6274b5b2828ac55fbf6898a81455256032425c3bbedd01eae8a7df2edb3 | Text | 983 | 27 | =================================================================
SFMT ver. 1.5
SIMD oriented Fast Mersenne Twister(SFMT)
Mutsuo Saito (Hiroshima University) and
Makoto Matsumoto (The University of Tokyo)
Copyright (C) 2006, 2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima
University.
Copyright (c) 2012 Muts... |
ab44efc87db3838b9d80baf018aea390ec4a4635d2bc4e66bef90991d3e162b3 | Text | 1,046 | 19 | # artemis_code
A summary of the available resources is available in /docs/index.html - please view this first.
Detailed READMEs specific to subfolders are available within them.
There are 4 folders of interest in this workflowr.
(1) analysis - contains code needed to generate each figure, table and supplementary fi... |
b9d99e3fe4ae78564b4ffafb1165b418e2084ffcd439a7f2a3ee2178dfa8515d | Text | 1,049 | 24 | GENERAL:
vgm has been developped by Johannes Reichold (JR) and Franca Schmid (FS). Please cite the following papers when using it:
[1] Schmid, F., Tsai, P. S., Kleinfeld, D., Jenny, P., & Weber, B. (2017). Depth-dependent flow and pressure characteristics in cortical microvascular networks. PLoS computational biology, ... |
0aa7fd4ddf6098700154d63523d54266805e39abf6d84690aa858528bb8a1a62 | Text | 1,058 | 26 | # UTCS3_RGM_Source
This is the source code for the UTCS (Unified Task Control System) RGM (Reach-Grasp-Manipulate) task.
It can difficult to compile without duplicating the folder structure in the orignal dev machine.
It can only be compiled in Visual Studio 2022 (on 64-bit windows 10 or 11).
The code depends on th... |
9726339f48d32b1c768ec61e514aad6e7f75691883e4fd9732ba915d44d9f624 | Text | 1,067 | 18 | # compositional-predictive-map
This repository contains all the code implemented for the study:
Piray, P. and Daw, N.D., "Reconciling flexibility and efficiency: medial entorhinal cortex represents a compositional cognitive map", *Nature Communications*, 2025.
[https://www.nature.com/articles/s41467-025-62733-7](h... |
1f9f0173569851432ebb79db6efe97677ebfcd67d8d32f3ca2c1dc0a01f6836c | Text | 1,091 | 24 | # tcr_docking_angle
# Brian Pierce 10/18/17
# updated in 2020
Be sure to install the GNU Scientific Library (GSL) prior to compilation.
To compile, type "make". You may need to first recompile the required FAST library in the
"fast" subdirectory.
This program takes in the structure of a TCR-peptide-MHC complex, con... |
f3cf7e853e119911cb5ce66fad6c583a96103ba6682fb4babe521321d6f0e4e4 | Text | 1,095 | 24 | raw_XXXX is the raw data of different group
raw_COVID: COVID-19 (Rows:900 and columns:159);
raw_Suspected: Suspected (Rows:900 and columns:156);
raw_Healthy: Healthy Individuals (Rows:900 and columns:150);
raw_Tube: Raman spectra of Cryopreservation Tubes with normal saline (... |
3cdf14937d72aaac7fab08f2d64ff9f66e9825c5616acdad873eed565fa1e9be | Text | 1,136 | 11 | # Dream Machine
The Dream Machine, formerly known as *Traumschreiber*, is a lightweight, low-cost, mobile EEG device developed at the Neuroinforamtics group at Osnabrück University. This repository contains all affiliated projects and theses.
### This includes:
- BoardDesign: The Printed Circuit Board (PCB) design of ... |
21b55ddee5f0dc26275de57c65d05cd441661af5561d02a2fb60fd7b3fde7161 | Text | 1,147 | 53 | # mmMOI
# Introduction
A Multi-omics Integration Framework using Multi-label Guided Learning and Multi-scale Fusion
# Download
Download datases and trained model: https://pan.baidu.com/s/13xJdqeqx7jr_uyM7iP8HIg?pwd=sgrc#list/path=%2F&parentPath=%2F
* Our project structure is like:
```
mmMOI
- MoDF
- SoRL
- datase... |
45919e768710b7a580d82da77420ea2eb55a9deec86a37f409ae4bb2c45021a2 | Text | 1,201 | 26 | # behavior-analysis
Behavioral analysis methods related to "Sub-second characterization of mouse spontaneous locomotion behavior in Parkinsonism"
The folder contains following data:
-Modeling Notebook (in modeling.ipynb Jupyter file)
Notebook with python scripts used to model the data using MoSeq,
depends on the MoSeq... |
f2aafafc64350568795079a88e0358083bb08f190b840e64ca10b3727563874a | Text | 1,206 | 7 | <h1>Pyramidal tract neurons and Parkinson’s disease in simulated mouse primary motor cortex</h1>
<p>Pyramidal tract neurons are the most direct output to muscles from the primary motor cortex (M1). <a href="https://www.jneurosci.org/content/41/25/5553">Liqiang Chu et al (2021)</a> have shown that layer 5 pyramidal trac... |
d8e1d05c27edddf50a3ad9e1448199302d6a7fc8525254bf81453ad23e0c34b7 | Text | 1,207 | 35 | Readme for DREAM: A Dream EEG and Mentation database
Rubén Herzog
SYSTEM REQUIREMENTS
Windows, Linux or Mac with Python 3.12.3.
At least 16 Gb of RAM Memory
INSTALLATION GUIDE
The following python packages should be installed
pip install mne
pip install numpy
pip install pandas
pip install pycatch22
pip install jobli... |
4e4e5df58f12d8105a5c7338fb0610ffc1d7f4facb52d64732f7589d844be349 | Text | 1,208 | 32 | # Transl.-Psychiatry2025
This repository contains the analysis code used in our study investigating how brain network dynamics, derived from resting-state fMRI, change before and after interventions in patients with depression and healthy controls.
We employed a Hidden Markov Model (HMM) approach to extract brain dy... |
ec7659c6495882cdf5a022c4713b00185a41a523b6ed46690ade71565832d642 | Text | 1,209 | 28 | # Implications of shared motor and perceptual activations on the sensorimotor cortex for neuroprosthetic decoding
Code to recreate the figures from Silva*, Liu*, ..., and Chang. "Implications of shared motor and perceptual activations on the sensorimotor cortex for neuroprosthetic decoding", _Journal of Neural Enginee... |
6f48fe92fb6c4c9b717ec61c5eb2fc636c55814640806d1ccdadf8e356a3950e | Text | 1,268 | 9 | This folder contains the neuromorphic vision dataset named as 'CIFAR10-DVS' obtained by displaying the moving images of the CIFAR-10 dataset(http://www.cs.toronto.edu/~kriz/cifar.html) on a LCD monitor. The dataset is used for event-driven scene classification and pattern recognition. These recordings can be displayed ... |
caca7890cd588af532b9f7c1fdc86d6f82b53685e4f25af7d6884801dc147719 | Text | 1,320 | 42 | # ORdeconvolution
Cleaning up Olfactory Receptor expression from Olfactory Sensory Neurons single cell data
## Getting Started
You will need the umi.distributions.txt file resulting from the [quantification from ESAT](https://github.com/garber-lab/inDrop_Processing)
### Prerequisites
R;
bedtools 2.27.1 or higher;
R... |
2558058dd0597be5023408f523f5df3bd496e616a3f3935835fe1b529a6c8dd4 | Text | 1,336 | 29 | # brain-xgboost-dividedattn-wangetal
This respiratory contains the R, MATLAB, and Python code for analysing the behavioural (GLMM, correlation) and fMRI data (GLM, XGBoost) and generating the figures for Wang et al. (under review). Behavioural data and beta estimates from the first-level fMRI model are available, but ... |
acaf427c18a3496a3d5efcbe0eae396433350528b731e50c319ee13644e526d2 | Text | 1,363 | 25 | # Multi-fidelity Graph Neural Networks for Predicting Toluene/Water Partition Coefficients
## Data
- `data/ext_sampl9.csv`: Contains external SAMPL9 dataset used for validation.
- `data/ext_zamora.csv`: Contains external Zamora dataset used for validation.
- `data/hf_exp.csv`: High-fidelity experimental data fo... |
3c5be19976c289feda6f9f944dd99563beb8b2291a30582df861df12ba20f0f6 | Text | 1,375 | 53 | # "Is Your Classifier Better than Mine? Pitfalls in Statistical Tests for Model Comparison by Cross-Validation"
The manuscript explains how p-values can be influenced by various factors, including the number of cross-validations (CV), repetitions, and sample sizes.
The code to reproduce the results is here.
---
## T... |
3ca53417df93a3b8e32d4eb426b9fcf321be00c5d59d35816686acf0f3717b5d | Text | 1,401 | 22 | ## Description
This package contains a set of Fiji macros developed to quantify axonal fibers within the mouse brain in fluorescence miscroscopy images.
## Contents
- **fiber_quantification_IF_FP.ijm** macro to quantify fluo-immunolabeled/fluorescent protein expressing fibers at high magnification.
- **fiber_quan... |
2b5485b094041ee89a6ec06a3d8244ab3acd41af5567178803db627dd01eea56 | Text | 1,416 | 3 | # Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience
Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, yet its epigenetic underpinnings remain elusive. Here, we generate and integrate single-cell epigenomic and t... |
9a591c1bc12653d51ed21ea5d461aa747a5caeb88a008649c51ee442f224b5d0 | Text | 1,416 | 29 | # Time-cell-sequences-during-delay-intervals-are-not-dependent-on-brain-states
SYSTEM REQUIREMENTS
- Software dependencies:
MATLAB (MathWorks) version r2020a
Open-source Matlab codes:
Neuralynx MATLAB Import/Export MEX Files V.6.0.0: https://neuralynx.fh-co.com/research-software/#matlab-netcom-utilities
Toolbox for c... |
89494bb32d99b691c9b197cf77b9a2ab03c4db67dcc36d769ee8c65d7bb28259 | Text | 1,443 | 44 | # AdiposityGSEM
Title: Modeling the genomic architecture of adiposity and anthropometrics across the lifespan
Priprint on medRxiv:
https://doi.org/10.1101/2024.08.14.24312003
`GenomicSEM_efa_cfa_multivariateGWAS.sh`
A vignette-style script including code used to:
1. wrangle the input GWAS summary statistics
2. pe... |
243e1026afb116f9afc335f9ff95f9ed12a49ae8a5fe8e2d801fe7d7e19e2321 | Text | 1,469 | 43 | # Myopic-Net
By Zengshuo Wang, Haohan Zou, Yin Guo, Minghe Sun, Xin Zhao, Yan Wang, Mingzhu Sun.
This repository contains an official implementation of Myopic-Net for the paper "Myopic-Net: Deep Learning-Based Direct Identification of Myopia Onset and Progression", which has been accepted by Translational Vision Scie... |
6646c701da3175b45b2738750210aab64efd321c5fb8b6cbadecb6ca1e2aaddd | Text | 1,542 | 25 | # Ear Landmark Detection with CNN
There are 55 landmarks on human ear which help identifying the person. This model has 500 training images, 105 test images and corresponding landmarks focused on right ear. I also modified the images and landmarks to represent other forms such as left ear, rotated etc. You can get 300... |
005b943f57174cde86fb533d9f09efd55781962b502f44adac73aa989655caaa | Text | 1,548 | 37 | # trvaep [](https://badge.fury.io/py/trvaep)
## Introduction
A pytorch implementation of trVAE (transfer Variational Autoencoder). trVAE is a deep generative model which learns mapping between multiple different styles (conditions). trVAE can be used for style transf... |
753343b3cae754c5992a811dab9a9cd541471ce9dbf5699317e094d6c2f42b6a | Text | 1,665 | 54 | # Connectoflow pipeline
=======================
[](https://github.com/scilus/connectoflow/releases)
Run our state-of-the-art connectivity pipeline
If you use this pipeline, please cite:
```
Kurtzer GM, Sochat V, Bauer MW ... |
ed369aa87c2ecacdf0e5466f2fffb0e2d82709871002f6342f6ff35b503287be | Text | 1,699 | 37 | # MD_DL_BA
Code for the paper published on [Bioinformatics](https://academic.oup.com/bioinformatics/article/41/8/btaf429/8238154): "Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction" by Pierre-Yves Libouban, Camille Parisel, Maxime Song, Samia Aci-Sèche, Jose C... |
10486ed0d780dd2485ec3c3743f711a03a1b280a25e386848fd0dd697580de7c | Text | 1,743 | 38 | # Virtual sequence: all in one medical image-to-image translation
In this work, we propose the "EVery domain All at once" image-to-image (EVA-I2I) translation model, which uses contrastive language-image pre-training (CLIP) to learn and represent various domains and further designs prompts to drive I2I translation.
The... |
36b6cc54bffa1b7eec2db0fac8202e47d5b934b2e5b598f371ae285d9c3716bd | Text | 1,754 | 23 | # Neuromelanin
R scripts for the quantification of intracellular and extracellular Neuromelanin (iNM/eNM)
# Overview
The following repository contains scripts used for the quantification of iNM and eNM
1) NM brightfield images were initially analyzed using the 'TrueAI' feature of [VS200 software](https://www.olympus-l... |
b0c83b70379eb9ee71b5ebb3713b4e28d62f0cec7dd9405653e48297799ce47d | Text | 1,791 | 36 | # ConvLSTM_pytorch
**[This](https://github.com/ndrplz/ConvLSTM_pytorch/blob/master/convlstm.py)** file **contains the implementation of Convolutional LSTM in PyTorch** made by [me](https://github.com/ndrplz) and [DavideA](https://github.com/DavideA).
We started from [this](https://github.com/rogertrullo/pytorch_convls... |
5e73e217a367a0b1ede1b730e30603a353feb845af770566e6903d7f9466069a | Text | 1,794 | 39 | # aweSOM
[](https://github.com/molinfo-vienna/aweSOM/actions/workflows/check.yml)
[![Tests status](https://img.shields.io/github/actions/workflow/status/molinfo-vienna/aweSOM/test.yml?label=t... |
72dc2a1d43bb090555aeae8053ec00eb8091a413f451971dd5589eccc789879b | Text | 1,794 | 35 | # Exploring the Latent Structure of Behavior Using the Human Connectome Project’s Data
This is the repository to store the analysis code for the paper "Exploring the Latent Structure of Behavior Using the Human Connectome Project’s Data".
## System Requirements
To install the required packages and run the code, you ... |
a7396eae2cda0a1e577df727adffe1c7be7500dd1470f2b0993b60d26f280808 | Text | 1,797 | 35 | # Trim Galore
_Trim Galore_ is a wrapper around [Cutadapt](https://github.com/marcelm/cutadapt) and [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
[ is represented as an immobile and uncrossable horseshoe-like barrier (paraboloid).
Cells are distributed along the telencephalon and follow a chemotaxis gra... |
88e62db62f5b6d7b20dc0aac4a913029e1a86dd7bd8803615722c080c163c722 | Text | 1,879 | 55 | Juan F. Santana, Ph.D. (juan-santana@uiowa.edu), University of Iowa, Iowa City, I.A.
# UMI deduplication
This tool is designed to eliminate duplicate of non-stranded paired-end reads in BED files that contain identical unique molecular identifiers (UMIs). It identifies and flags instances where two or more reads shar... |
ae265a206dba4e07a9a2117d6a486322b469213ad7b3b440685a69825fc28772 | Text | 1,894 | 55 | # MetabolismManuscript
R code for Metabolism Manuscript.
## General Info
This repository contains a Data, Script, and Output folder.
### Data
The Data folder contains:
1. Metabolomics data (metab_data) includes micromere inhibitor, 16 cell and 2 day WE inhibitor, and micromere vs nonmicromere experiments.
3. Metabo... |
873ca4547d82fffc005fa3a726da7c711b5e317ce688b2c9fd25b284bf51068a | Text | 1,913 | 29 | # SOLeNNoID
## Solenoid residue detection and classification in protein structures using a U-Net convolutional neural network
## Introduction
SOLeNNoID is a project consisting of scripts and Jupyter notebooks to allow for the detection and classification of solenoid residues in protein structures using a U-Net convol... |
c4528fb54b3f010a545c0d95d6557b1de7ffc4c78f16e4eaf723d54da3afa5a9 | Text | 1,957 | 19 | # Non-negative Matrix Factorization
This code was originally developed and written by the Kaspar Podgorski lab at Janelia.
Non-negative matrix factorization (NMF) is a technique used to find correlated regions in a series of images. The goal is to find a limited number basis set of images that can be combined with di... |
607868dd3e17f152ffbac5937cb7bc2e959b9351537a083060eb62f07276c05f | Text | 1,986 | 42 | # abcd_dl_analysis
This repository contains all analyses associated with our paper "Deep learning reveals that multidimensional social status drives population variation in 11,875 US participant cohort"
Please cite the paper:
## Resources
- The final model is saved in /phase2_outputs/cvae_model_final/ folder, arch... |
324b37f30b28c3560f20986c6b36e883d5e684261f82df3dfe96a54dbf025867 | Text | 2,016 | 22 | # Identifying childhood cancer patients who have receiver care in a mental health-related unit
This folder contains all scripts used in the LERACA project. TurkuNLP neural parser can be found [here](https://github.com/TurkuNLP/Turku-neural-parser-pipeline)
## Pipeline
1. Create base datasets with module `create_datas... |
eb9aa256a13792a81eed738a37e626e69c5e4ce810ad0d77e0dbcff176ab6dd5 | Text | 2,031 | 33 | # CNV detection pipeline from genotyping data
Digital karyotyping pipeline to detect de novo copy number abnormalities arising in cultured cell lines i.e. to determine differences between cell lines and the starting material from which they were derived in term of copy number variation. The genomic screening for chromo... |
4bcba500d5b918366e7f91a81930ae1ec3dd5486e5e90ac4b0579da2c4e12b1e | Text | 2,048 | 36 | Code accompanying Leupin and Britz, in prep.
We here provide the code for preprocessing, epoching, and analysis of EEG data in sensor space. EEG data can be made available upon request.
# Code organization
Each folder is generally organized with a main, helper and constants script.The base folder contains some helper ... |
f2016b1ffb38114cb828e95124fb32c02cd5d069a20ed92712d1a236824bab3f | Text | 2,096 | 51 | ---
title: "Code for Mathios et al."
author: "AA"
date: "01 March, 2024"
output:
html_document:
keep_md: yes
---
# Organization
There are 4 folders of interest in this workflowr.
(1) analysis - contains code needed to generate each figure of the paper.
(2) code - This contains rpcr and rlucas (two packages use... |
52e1738d9fbe6b91e65db7de0baaac3d86fd261eff0e7a9d27fb878b1f6e73ca | Text | 2,106 | 26 | # Studying-Parkinje-cell-heterogeneity
## Abstract
Mammalian cerebellar development is thought to be directed by distinct Purkinje cell (PC) subtypes. However, the degree of PC heterogeneity and its underlying molecular mechanisms remain poorly understood, limiting our ability to manipulate PC diversification and dete... |
5c20ef38b5eba4fee8d98c6f570f46e89ba1272cee14aefeef2db1ee245ccdb8 | Text | 2,143 | 36 | # PI1M: A Benchmark Database for Polymer Informatics
This repository contains a benchmark database for polymer informatics. The details and utility of PI1M are described in our [paper](https://pubs.acs.org/doi/10.1021/acs.jcim.0c00726).
## Abstract
Open source data in large scale are the cornerstones for data-drive... |
a8f20b83cb6c2368b9dfb3f634e0d789e9bb506426928505cfd193aca2a1f8dc | Text | 2,209 | 55 | [](https://paperswithcode.com/sota/retinal-vessel-segmentation-on-drive?p=full-resolution-network-and-dual-threshold)[![PWC](https://img.shields.io/endpoint.svg... |
d2c97d0ca5f381e15a92fd3f1b58a23688e0a10a8fcd48f2144fa3a4331c2fc5 | Text | 2,240 | 69 |
# LiSA-MobileNetV2: an extremely lightweight deep learning model with Swish activation and attention mechanism for accurate rice disease classification.
**"An Enhanced Lightweight CNN Model for Rice Disease Recognition and Deployment"**
<p style="float: center">
<img src="images/LiSA-MobileNetV2-architecture.jpg" a... |
f10cfc7a83e21885e42663fe29d77c8723190dd834b4531357449d7f18a88687 | Text | 2,241 | 25 | # Musicianship
Experiment code for multi-site replication study examining the relationship between musical training and neural and perceptual sound processing. Any folder with a number corresponds to a task. For the full study, the tasks will be run in the order that they are numbered. Each numbered folder contains a w... |
c145413ab11aabe1e14be7e47363ce396b55a9528b16a1c8a65161dee9c6af07 | Text | 2,245 | 51 | # sm_ring_assembly_mrna
These are scripts used to identify and characterize Sm-site containing RNAs within the human and mouse transcriptomes.
a) to identify Sm-sites in human and mouse transcriptomes, use find_smsites.py
Custom R script used to combine the outputs from find_smsites.py into a single file can be acce... |
b0dd07c9af4840193689aee0a88af0680e5744a80a17ecf2415c1b507d0ee55b | Text | 2,257 | 60 | # NeuroCombat-sklearn
[](https://opensource.org/licenses/MIT)
[](https://pypi.org/project/neurocombat-sklearn/)
[
# Learning in PINNs: Phase transition, diffusion equilibrium, and generalization
## Abstract
We investigate the learning dynamics of fully-connected neura... |
7ead97cadd5c90d4540d21de39bdec6808f5775489db24cb3d07d8331060fad5 | Text | 2,327 | 91 | # genderbias_ADHD
This project addresses gender bias in ADHD diagnoses.
The code covers the analyses as described in the publication
"Toward a fair, gender-debiased classifier for the diagnosis of attention deficit/hyperactivity disorder- a Machine-Learning based classification study"
## Description
This project a... |
2c7a81ba45d5fa8d923e7692bf3124408c81f4c1e95d30b384eb9487a41128fa | Text | 2,339 | 34 | # SiphonInvagination_VertexModel
MATLAB code for vertex model simulations of Ciona atrial siphon invagination. Paper: [Bidirectional redistribution of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis](https://doi.org/10.7554/eLife.108588.2), J. Qiao, P. Yu, H. Peng, W. Shi, B. Li, and B. ... |
f516f5af7a7ddfe61b10ab78c0cf6bd1371248364740f2079fe623df5162cdd9 | Text | 2,443 | 50 | # TCGA Breast Cancer Cell Classification Dataset #
This dataset accompanies our paper [Multi-Class Cell Detection Using Spatial Context Representation, ICCV 2021](https://arxiv.org/pdf/2110.04886.pdf). See citation at the end.
<p align="center">
<img src="./teaser2.jpg" alt="drawing" width="100%" />
</p>
Thi... |
8ae539772b16dfcf4b15d15380ff300f0c51e97b98063b2f7692b2267d5b1231 | Text | 2,455 | 64 | # EasyMicroPlot: An Efficient and Convenient R package in Microbiome DownStream Analysis and Visualization for Clinical Study
<a href="https://github.com/xielab2017/EasyMicroPlot/wiki"><img src="https://i.loli.net/2021/10/20/u5UfFXvxNyQhWeg.png" width=150 align="right" ></a>
Columns are:
============
Demographics:
-------------
subj: suject id
age: age in years
ses: session (pre=initial or post=follow-up appointment)
gender: Female=1 Male=2
handedness: Right=1, Left=2
Behavioral measures:
--------------------
YBOCS_Tota... |
4af63ee3a3ad4274cf3a4082465636dbf616a04aeff0981019da2729a30f0f3c | Text | 2,537 | 50 | # bacteria-ID
This repo contains demonstrations of using convolutional neural networks (CNNs) to identify the Raman spectra of pathogenic bacteria. This repository is adapted from the codebase used to produce the results in the paper "Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learni... |
dacc5d9fe54907af3d563309ae7e7cf0ad3283058dcf9ace0e6596c056bc86e9 | Text | 2,577 | 53 | # Meninges
[](https://doi.org/10.5281/zenodo.15453825)
## Overview
This repository contains a workflow to study the distribution of tertiary lymphatic structures in
the meninges of rodents. Currently, results are available for the following strains:
- [APOE3](https://gi... |
eceaa2473a323a3c7578d6ec1b441e6f634ec61c9141138b367f5d5651e4274a | Text | 2,660 | 49 | ## "Improving Drug-Induced Liver Injury Prediction Using Graph Neural Networks with Augmented Graph Features from Molecular Optimisation"
[](https://doi.org/10.26434/chemrxiv-2024-d12gk-v2)
<!--
<p align=... |
a1da749dca9fd28f96ef96e8646b4d4bf3a3eb58e8fe1f9ea6d2004499a8f8e9 | Text | 2,668 | 29 | # Matlab code for Osaki et al. Light: Science & Applications 14, 2264 (2025)
Repository for the code that was used to process and analyze data collected for "Multi-photon, Label-free photoacoustic and optical imaging of NADH in neurons",
Osaki et al. Light: Science & Applications (2025), https://doi.org/10.1038/s4137... |
9107e9990d0020ade2107303ef8f20954addd1bb83ec39ef4d12a15a36770eb2 | Text | 2,678 | 55 | # MVP-analysis-tool-box
Multi-Voxel Pattern analysis of Brain imaging data.
This is the code that we used for the Vetter et al. 2020 publication
it is surface based analysis and uses patches of interests (POIs) and Mash-timecourses (MTCs). It is in this sense creating new vertex based data and does not use entire voxe... |
b10a2b48e078f44fbe150b04f6b5c461dbb1d84fa7d9c554df48a1a3e557a14a | Text | 2,678 | 21 | ## Links
* [Cover page](http://zitmen.github.io/thunderstorm/)
* [Documentation wiki](https://github.com/zitmen/thunderstorm/wiki)
* My Ph.D. thesis [Computational methods in single molecule localization microscopy](https://www.researchgate.net/publication/311426573_Computational_methods_in_single_molecule_locali... |
209f3ae80bbd117f80534581cf242ce3f43a3785eb83870d65928097566a1408 | Text | 2,692 | 37 | # GuthPhaseLocking2025
Analysis code for Guth et al., 2025: "Theta-phase locking of single neurons during human spatial memory".
This folder contains the scripts for all analyses in the paper. Different folders contain the scripts for different analyses.
For example, the subfolder "PhaseAnalysis_20230921" contains the ... |
bc6e05578e769529ca0beae4ac278a27664986070b12deda8ff85fedcab8a25b | Text | 2,703 | 45 | # [Taskonomy: Disentangling Task Transfer Learning](https://taskonomy.vision/)
This repository contains:
- [pretrained models (task bank)](https://github.com/StanfordVL/taskonomy/tree/master/taskbank) [PyTorch + TensorFlow].
- [dataset](https://github.com/StanfordVL/taskonomy/tree/master/data)
- [reference code](https... |
a6e24b05bd0e569ddee6d11231efd47a58d89d985f4331111a0b6476e5e6e8e8 | Text | 2,704 | 20 | # Neural-Similarity-Predicts-Whether-Strangers-Become-Friends
To comply with the guidelines outlined in the Journal’s Code and Software Submission Checklist, a small, simulated dataset (with 10 subjects and timeseries across 100 TRs in 5 brain regions) is provided to demo the code. The source code uses the simulated d... |
7fde93ca7d7d54f8981a43bf25a5a722a024065a395123e4ee81f8a63749768a | Text | 2,706 | 27 | <img src="docs/SAMBAR_Logo.png" width="200">
Logo generated using DALL-E 2
# SAMBAR-Net
<ins>S</ins>equence <ins>A</ins>nalysis of <ins>M</ins>urine <ins>B</ins>2 <ins>A</ins>ccumulated <ins>R</ins>NAs: A CNN model to predict expressed B2 SINE genes in 3T3 cells across the mm10 genome
*Sahil B. Shah, Priyanka Sanghra... |
9d9ef667f1c2cc9a113f7dcbab4e4bc69d37a5a3d87dbf88945af3f0b06f4211 | Text | 2,716 | 37 | # GuthPhaseLocking2025
Analysis code for Guth et al., Nature Communications, 2025: "Theta-phase locking of single neurons during human spatial memory".
This folder contains the scripts for all analyses in the paper. Different folders contain the scripts for different analyses.
For example, the subfolder "PhaseAnalysis_... |
038045da67d4dd029a521936f61b5063bb18caba1983287db8c3f07c700563ab | Text | 2,728 | 68 | # Modeling of cerebrospinal fluid (CSF) flow and solute transport in zebrafish brain ventricles
CSF flow is modeled by the Stokes equations, and solute transport is modeled by an advection-diffusion
equation. The equations are discretized and solved numerically with finite element methods using
DOLFINx. The code is par... |
4401019528098b45835c98c252704406049e2c4204f92b09e7c918be937035b2 | Text | 2,790 | 50 | # ANI-1 dataset support repository
This repository contains the scripts needed to access the ANI-1 data set.
##### If you use ANI-1 dataset please cite the following two papers:
Justin S. Smith, Olexandr Isayev, Adrian E. Roitberg. *ANI-1: An extensible neural network potential with DFT accuracy at force field compu... |
7b51250d07fdf81e656dee6878a05c2e4230781d8e9196361331b4f3f6b6ba71 | Text | 2,823 | 49 | # Cholinergic Pre-Phrenic Plethysmography README
# Purpose
This script will take raw plethysmography recordings from emka iox2 software and sample information from the user.\
If these plethysmography experiments contained multiple cycles in gas, it will break the file into multiple trials.\
It will use manual and auto... |
97f1b2cff61d2eb8dc09f8d01d9112895d4f023447c7ffe43db9b92e91d7d948 | Text | 2,833 | 69 | # CNN-TLSM
Asynchronous training of ResNet-18 and Time-aware LSTM
This repository contains full training code for a 3D ResNet18 CNN backbone in Keras for survival prediction on preprocessed, spatially registered volumetric MRI data, along with GradCAM/SHAP explainability tools.
Our own implementation of the Time-awar... |
375019f89e89bba1a71211912914cdb6abce3df983c4d5f82c60fdd3cb56eb5b | Text | 2,842 | 61 | # Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS+
Xiufei Chen<sup>1,2,3,10</sup>, Jingfei Cheng<sup>2,3,10</sup>, Linzhen Kong<sup>2,3,10</sup>, Xiao Shu<sup>2,3</sup>, Haiqi Xu<sup>2,3</sup>, Masato Inoue<sup>2,3</sup>, Marion Silva... |
25ebf519c29ed8da95c6b701efbb686291667a0c141fe826c1aa5d89869ef476 | Text | 2,862 | 60 | # julearn
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/julearn/badges/ve... |
2a3a14a1dce81a9baa53104c5a16921051595fbef0d0f2174998595695a8cfbb | Text | 2,896 | 45 | # RNA-seq Analysis Code for Immune Checkpoint Study in Humans and Dogs
This repository contains R code associated with the publication: **"Barking Up the Right Tree: Immune Checkpoint Signatures of Human and Dog Cancers"**, preprint DOI: [10.1101/2024.06.26.600825](https://doi.org/10.1101/2024.06.26.600825). Currently... |
962827e6039ebc5acfb1414856c9f6ab58af69fc26db396271aecb5f1958d154 | Text | 2,899 | 76 | # pyEntropy (pyEntrp)
, [GPU](./environment_gpu.yml)).
* Updated technical report of the framework on [ArXiv](https://arxiv.org/... |
957a4b5f28e74d389fad8b48e8dce3edf5a10669f596f92dc908e5cb40b9ae0d | Text | 2,933 | 34 | <h2 align="center">Multimodal Integration of Longitudinal Noninvasive Diagnostics for Survival Prediction in Immunotherapy Using Deep Learning</h2>
<p align="center"><b>Published in JAMIA-2025</b> | <a href="https://doi.org/10.1093/jamia/ocaf074">[Paper]</a> | <a href="https://github.com/MeldaYeghaian/MMTSimTANet">[Cod... |
1dff00f002fae45fdd219c0bfa8ac2a8b44b6d1becdf260286487a78ca2a70e4 | Text | 2,936 | 60 | # salmonella-serovar-classification-foods
This repository is for the article **"Rapid *Salmonella* Serovar Classification Using AI-Enabled Hyperspectral Microscopy with Enhanced Data Preprocessing and Multimodal Fusion"**, published in Foods.
- Preprint: [doi: 10.20944/preprints202507.1691.v1](https://doi.org/10.20944... |
9de17170e7209e79bd8ca8131ba8ab174d88ef74106e3fee0a6453d462ee5d78 | Text | 3,001 | 57 | <p align="center">
</p>
[](https://github.com/miniscope/minian/actions/workflows/testandcov.yml)
[. <a href="https://www.jneurosci.org/content/41/25/5553">Liqiang Chu et al (2021)</a> have shown that layer 5 pyramidal trac... |
0572e99460274c9fd578a9dde883342116ae2bc01e0c326bc80a634c79f46abb | Text | 3,099 | 52 | # FiPHoPHA - A Fiber Photometry Python Package for Post-Hoc Analysis
This Python tool allows for the analysis of photometry data, enabling the user to upload Excel files, select baseline and comparison periods, and calculate significant differences within and between-groups. The tool performs both bootstrapping to d... |
571670747d516f44dcafac26e3a2041c68a5242b2cb238ff9051b982e601c240 | Text | 3,100 | 94 | <h1 align="center"><strong>MetaVelo</strong></h1>
<p align="center">
<img src="assets/overview.jpg" alt="Overview of MetaVelo">
</p>
Code for the paper "Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations" (KDD 2025).
Our code is implemented using PyTorch an... |
72aed14cbc66a191de2ebcca106b6b2a1ebf1421c85bafce714b937696ec7681 | Text | 3,114 | 38 | # MO-GCAN: Multi Omics integration based on Graph Convolutional and Attention Networks
## What is it?
MO-GCAN is a framework that leverages supervised feature learning and classification based on a graph-based learning approach with attention mechanism for subtype detection. The work is inspired by MOGONET[1], MoGCN [... |
29f0d99041b2bd9589137006dcb47068b587f0dfa7064ea63c5599e6541622ff | Text | 3,152 | 47 | # General Macros for Fiji (ImageJ)
This collection of macros is to help with tricky or interesting problems using the image analysis package Fiji (ImageJ). For more information about Dominic and his projects please refer to his main [homepage](https://dwaithe.github.io/home/).
##### General Requirements:
Macros writ... |
981f8aef5a105d57f26c64635b5bf7b71bdc2c9f6d67f3fc6bd21f6598d06d27 | Text | 3,287 | 58 | # REACHER — Operant Experiment Control Server
**Hardware control, session coordination, and live data capture for Arduino-driven rodent operant behavior experiments.**
[](https://github.com/Otis-Lab-MUSC/reacher/releases)
[
This repository contains the code accompanying the paper:
***Topological and geometric signatures of brain network dynamics in Alzheimer’s disease***
🔗 Read the full open‐access paper here: http... |
121e148ed9dcd5e43f278bcabfb02b8e8b052b735999a31f9c648cb61737b298 | Text | 3,339 | 50 | # Multitask Prompt Learning for Vision-Language Models
This repo contains the codebase of a series of research projects focused on adapting vision-language models like [CLIP](https://arxiv.org/abs/2103.00020) to downstream datasets via *multitask prompt learning*:
* [Multitask Vision-Language Prompt Tuning](https://a... |
8a572c20860fa0181aebb11472f957e05db79abfb6bf0d7dfdd3ad4e55ab7f03 | Text | 3,366 | 48 | # Musicianship EEG Dataset (BIDS)
Frequency-following response (FFR) EEG to a /da/ syllable from a large multi-site study of musical training.
This BIDS version: Zenodo, doi:10.5281/zenodo.22967622.
Original data: Whiteford et al. (2025), Harvard Dataverse, doi:10.7910/DVN/SKOWNK.
Paper: Whiteford, K.L., Baltzell, L.S... |
943a3619ea22b58508daa662f12b24f28f40c6c72bb109715ed8d48e3b8112c0 | Text | 3,379 | 78 | # CBMPy
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2010-2023 Brett G. Olivier, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free ... |
5dee6df7a14f6c9f6de0dce301181539efef8c563729fcb84ce9d147f074b71d | Text | 3,452 | 42 | Data and code supporting '[Functional Coupling and Longitudinal Outcome Prediction in First-Episode Psychosis](https://doi.org/10.1016/j.bpsgos.2025.100589)'
We used resting-state functional magnetic resonance imaging (fMRI) to evaluate whether baseline functional coupling (FC), or 3-month changes (ΔFC), could predict... |
a0b8c5e64ce03ac3d36db86c3bd4a0bbda4aeedfd47b31906b12607c2043a3eb | Text | 3,458 | 44 | ## Maintenance Status
This project is currently not actively maintained due to the author's health-related sick leave.
Updates will resume when possible.
##
# 
**Cartool** is a software primarily design... |
d7e6959dddae2258b36757b404225dcc4c6fb47f7834815e2e75e74b1ffc0e7f | Text | 3,486 | 112 | # GeoALBEF
## About
This repository contains the code and resources of the following paper:
Multimodal modeling for polymer property prediction
## Overview of the framework
By integrating the chemical semantic sequence information with the intrinsic and spatial information of polymers, a deep neural network architect... |
ecf116290a5e3ededc3c7dee2a67f41dbf510dccbe8a12ff708b1877b9b2bb71 | Text | 3,505 | 113 |
# Paper figures and data
This folder includes the code used for the data processing for the paper. Three models were used:
1) Omnipose
2) PAF
3) DT_C
## Omnipose
To process the Omnipose data, you will need to download the omnipose github:
https://github.com/kevinjohncutler/omnipose.git
the code that create t... |
684cdf38d74f51684a57fb04278f1d50e597200c5c56ce1aa8d468a2eecabb8b | Text | 3,556 | 42 | # mGluRpaper
Collection of the code used for analysis and plotting of the figures for the Ostenrath et al 2024 titled "Inhibition mediated by group III mGluRs regulates habenula activity and defensive behaviors"
Each Figure has it's own matlab script and the implemented functions are collected in the "Subfunction" fol... |
05ec93fe0f602c6bedb652e7bc292e44cb06c31769c8bc1390dcac6a913e5a02 | Text | 3,572 | 90 | ## Automatic detection of arterial input function for brain DCE-MRI in multi-site cohorts
This is the Keras/TensorFlow implementation for automatic detection of the arterial input function in brain DCE-MRI. Pretrained model weights are provided and linked below.
Article to Cite:
Saca, L., et al. [Automatic detection... |
61ebd2c954c7e5506a48190a45ca4ba0c285fb83c84cdc50c24a469b2e00ebe3 | Text | 3,665 | 104 | Juan F. Santana, Ph.D. (juan-santana@uiowa.edu), University of Iowa, Iowa City, I.A.
The workflow has been published in [Santana et al., 2024](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1253/7513806).
# DFF-Seq snakemake pipeline
This DFF-Seq Snakemake pipeline processes paired-end FASTQ files ... |
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