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93be3324a787ea3969d6be62fde6749b08700035801b3b5131cd43b0f47941a7 | Text | 2,616 | 57 | README for Vertebral Age Estimation Data and Models
===================================================
Files Included
--------------
1. RESULTS.xlsx
└ Contains a spreadsheet with the following columns for each of the 176 subjects
• Subject_ID – Unique identifier for each subject (e.g., “001”,... |
729bed4b6a8b459c46a1cb9434937b5d913378e3df56e71d3b55786e80d80d3b | Text | 2,664 | 27 | # pySpinCapture
a python wrapper to the FLIR PySpin API to capture synchronized video
cameraCapture.py is a minimal program to configure a FLIR BlackFly S monochrome camera to stream compressed video data
to disk and output it to the screen in real-time. It is based on the FLIR Spinnaker PySpin API and its examples,
... |
99182e6cb515fd8b867feb1b0b0a52fb438b1e587e33606e16fbca683f9049c6 | Text | 2,670 | 84 | # hormonaltuning
A collection of the functions used to produce analyses seen in (Fickling et al., 2025, Journal of Neurophysiology).
How do I use hormonaltuning?
-------------
hormonaltuning is used primarily for spike feature extraction (requiring neural spike which are already detected, see github.com/LoganJF/stns),... |
bbe176ac24afd764ae27da50540e47bcf41ad8dea15fa236d0fca3e728613f38 | Text | 2,674 | 58 | # Experience-based-risk-taking-
Part 1: The follwing code files used for the logestic regression analyses:
a. one_category.R: run the model that is based on learning time of risy image/safe image/decision time
b. three_category.R: run the joint model that is based on both learning time of risy image/safe image and dec... |
7cbdb313b2eccdbcffc06fedaae2dfd3f4bd740b60d14528d2db12d891d6a276 | Text | 2,698 | 56 | Part 1: The follwing code files used for the logestic regression analyses:
a. one_category.R: run the model that is based on learning time of risy image/safe image/decision time
b. three_category.R: run the joint model that is based on both learning time of risy image/safe image and decision time
c. one_caegory.st... |
21dbf6ba19ef90ada8d744ab857bf9d3b9a606daae461c9ce156a34ebde4c2c6 | Text | 2,707 | 51 | # Computational materials for pre-transmigratory residence in BBB extravasation
Version 1.2.2
Supporting computational materials for the manuscript **“Pre-transmigratory residence as an estimand in blood--brain barrier extravasation: an interval-observed multi-state framework.”**
Author: André Pereira Marques Trinda... |
7841ef02551d24c4a24abef9a8cc131df53f192203177e5570d6951a05ca26f7 | Text | 2,736 | 73 | <a id="readme-top"></a>
<h3 align="center">Cooperative Coding in Spiking Neural Networks</h3>
<!-- TABLE OF CONTENTS -->
<details>
<summary>Table of Contents</summary>
<ol>
<li><a href="#about-the-project">About The Project</a>
<li><a href="#Prerequisites and Installation">Prerequisites and Installation</... |
19e42808068bc6d7623c274167c41c42ed0b200765885da69f402f1711a7fcec | Text | 2,748 | 104 | # GraphCare
Code for the paper: [GraphCare: Enhancing Healthcare Predictions with Personalized Knowledge Graphs](https://openreview.net/pdf?id=tVTN7Zs0ml) in ICLR'24.
## Requirements:
``` bash
pip install torch==1.12.0
pip install torch-geometric==2.3.0
pip install pyhealth==1.1.2
pip install scikit-learn==1.2.1
pip ... |
441e5e2c8daefbddfbf54c27f565b77d625f4dd072192b58c9a7edf524f32429 | Text | 2,770 | 88 |
# CSLLM (Crystal Synthesis Large Language Models)
An LLM system for the ultra-accurate (TPR=98.8%) prediction of the synthesizability and precursors of crystal structures.
This is the repository for the paper "Is Large Language M... |
f877c2e3bb14099a5769693ea065126e8f7b5f296b049d3ce55c7dc17643f5e3 | Text | 2,792 | 58 | # spheroid_morpho_ML
This project aims to **segment spheroid images**, extract their **morphological properties**, and use **MIIC algorithm** to study the relative importance of the morpholigical features before using **machine learning** to **classify spheroids based on viability** and **predict dose-response curves*... |
05cb8a0fcfe71938e68031820238a1fa6f3d25ec4b80f5b54df62009f8c0ac3c | Text | 2,829 | 77 | <a id="readme-top"></a>
<h3 align="center">Cooperative Coding in Spiking Neural Networks</h3>
[](https://doi.org/10.5281/zenodo.15553757)
<!-- TABLE OF CONTENTS -->
<details>
<summary>Table of Contents</summary>
<ol>
<li><a href="#about-the-project">About The P... |
c1d11e0e647599384165798095ae04cd2ba97d5cf2b5f66b62ac43b43ecc5ff5 | Text | 2,847 | 62 | [](https://opensource.org/licenses/MIT)
# Woven Analysis Repo
Collection of analysis scripts used in "Computational models reveal that intuitive physics underlies visual processing of soft objects"
```bibtex
@article{Bi_Shah_Wong_Scholl_Yildirim,
title=... |
eb0111c8063014609c6c54ed8e5c5cc159fc22a126d2fe9bc350ef37af514dcf | Text | 2,892 | 68 | burstiDAtor
===========
burstiDAtor is a lightweight discharge analysis program for neural extracellular single unit recordings.
Features
--------
- Compute summary statistics for neural spike recordings (e.g. firing frequency, number of spikes, inter-spike interval, number of burst, burst frequency).
- Burst detectio... |
99049f959fc7a21e62728c04f3671cf13a2406a970dfdab2d83ce209f1f120f9 | Text | 2,894 | 60 | # SCIΦER
SCIΦER is an R package that provides functions to compute expected values of the site frequency spectrum of somatic variants generated by dividing tissues that are either expanding or homeostatic. Modalities for both, neutrally evolving tissues and tissues with selection of a single clone are provided... |
d2f0040345d1cbbacfaafdd25372ddeb71bda20e97a0a9176ff0e456ed53e8ab | Text | 2,901 | 84 | # msalign - signal calibration and alignment
[](https://github.com/lukasz-migas/msalign/actions)
[](https://codecov.io/gh/lukasz-migas/msalign)
[](https://img.shields.io/github/downloads/henriqueslab/SReD/total?style=flat&color=fuchsia)
[](https://github.com/HenriquesLab/SReD... |
f18a6c5f04248ec17748629a80064931adf3e634558562525c89e59c66dd1858 | Text | 2,914 | 61 | # Evidential Deep Learning
<h3 align='center'>"All models are wrong, but some — <i>that know when they can be trusted</i> — are useful!"</h3>
<p align='right'><i>- George Box (Adapted)</i></p>
This repository contains the code to reproduce [Deep Evidential Regression](https://proceedings.neur... |
7302f29f1ab8a572dcbc2a804f4df06a72acc29ef57beb871ab09db28ac7888a | Text | 2,915 | 85 | # F-Phot-Analysis
This Matlab code was created for Michaelides' Lab to analyze fiber photometry across multiple animals with support for saline vs. drug conditions and per-minute AUC analysis.
Fiber Photometry Analysis - MATLAB Toolkit
---------------------------------------------------------------
FILES INCLUDED
... |
3eb5bfa3e29f58e3452808c4b35c02967b4edbec975f73fc3ae84daf049bdd0b | Text | 2,921 | 81 |
.. image:: https://img.shields.io/pypi/v/visualqc.svg
:target: https://pypi.python.org/pypi/visualqc
.. image:: https://app.codacy.com/project/badge/Grade/c67fbfc899d04f5aacd7a0070aeb704d
:target: https://www.codacy.com/gh/raamana/visualqc/dashboard?utm_source=github.com&utm_medium=referral&u... |
094b747f322f46d2469c18238f2ab452e091ba8f281341c14b78079eb0d2479d | Text | 2,922 | 74 | # MOMO-GP
A Multi-Omic Multi-output Gaussian Processes for Integration of Multi Omics Data:
- which learns the nonlinear structure of data by combining the neural network layer with the Gaussian Process layer,
- in the single-view version, it learns separate latent representations for both cells and genes, and
- in th... |
53921eeb84ae672fb3369bd9200751117d06cb9528cb4dcc1a972171a475e5e2 | Text | 2,925 | 74 | # SynMI
A [Keras](keras.io) implementation of a number of Deep Learning tools for the synthesis of Medical Images (mainly MR or CT). Currently, Tensorflow is the required backend, but only one layer (ReflectionPadding) requires it.
## Models
There are 4 different models that can be used for training: **SingleCovNet**,... |
38991eb787967b64e41ad4c4c17edbc4e19a6fccb77a452c57f69ba605a8fe33 | Text | 2,952 | 39 | – README –
This document contains the raw unprocessed data used in the research article "Isolation and Lipidomic Profiling of Neuronal Lipid Droplets to Unveil the Lipid Landscape of Neurodegenerative Disorders"
Note: A previous version of the protocol is available on BioRxiv (DOI: https://doi.org/10.1101/2023.12.13... |
4ea86c3a863dc25e258feccbd2e633cd1ca13981571835bda15a80c4d9920fba | Text | 2,964 | 102 | # RDE-PPI
<img src="./assets/cover.png" alt="cover" style="width:50%;" />
:mountain: Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)
[[Paper]](https://www.biorxiv.org/content/10.1101/2023.02.28.530137)
## Install
### Environment
```bash
con... |
d553d824625a07d7690de93af6f8daf13d6aaed42700929d7ce4e725fa5ef10d | Text | 2,969 | 85 | # three.js
[![NPM Package][npm]][npm-url]
[![Build Size][build-size]][build-size-url]
[![NPM Downloads][npm-downloads]][npmtrends-url]
[![jsDelivr Downloads][jsdelivr-downloads]][jsdelivr-url]
[![Discord][discord]][discord-url]
#### JavaScript 3D library
The aim of the project is to create an easy-to-use, lightweigh... |
2ea33af266b4268a55fd750d0f3265cd3165d61f6be375c5ea3b3ff5c58c7c8c | Text | 2,970 | 19 | [](http://bioconda.github.io/recipes/kraken2/README.html)
[ data after 13C-nutrients administration. The package was originally designed and tested with the lab-built ambien... |
6299af9bc4affb531ee80c803c7ff1a95bad1ba1829c4fe51ac7ea54e01f4d46 | Text | 3,024 | 99 | # AIRPred: A Deep Learning Model for Predicting Peptide Intensity Ratios in Cross-Linking Mass Spectrometry
## Overview
**AIRPred** is a deep learning-based tool designed to enhance Cross-Linking Mass Spectrometry (XL-MS) analysis by predicting intensity ratios of cross-linked peptide pairs. By leveraging Convolutiona... |
8dd9b3088ac976ba911daa66ed65a022d7ba4e33d006756ef18ef49a46f9a5f5 | Text | 3,041 | 37 | # Calcium Transient Analysis Toolbox
This toolbox offers a variety of functionality to meet various post-CNMF analysis of Calcium Imaging Data including:
- **CalTrig** - A single window solution to visualize all data stream outputs from the CNMF process, to assist i... |
3047c799d42bf25c6830a192744dea92f5874fb841ce7891710f0a25d8caf832 | Text | 3,043 | 53 | <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
[](https://github.com/activeloopai/Hub)
# SENSORIUM 2022 Competition
SENSORIUM is a com... |
ae6f738c0e081fae3a9247f79268e344f63c36fc31abbb7d0e7fa729670867ea | Text | 3,053 | 73 | # Requirements
The pipeline is Linux compatible and it was tested under Ubuntu 18 (or newer). We recommend to run the pipeline under Docker in other Linux distributions.
# Workflow
Before executing, it is necessary to generate a STAR (2.6.1b) index directory from the annotation of interest (for more info visit https:... |
55e3088316359caabe152df75e0db08296120223163cbdeda3935edf46f30f4a | Text | 3,086 | 58 | ## Notice Regarding Plagiarism Incident
It has come to my attention that my research paper, titled **"Machine Learning and Deep Learning Methods for Better Anomaly Detection in IoT-23 Dataset Cybersecurity"**, which is available in this repository, has been plagiarized and published without my consent.
The plagiarize... |
be9e5696374b763d70acc19d9f50ae31a4a381140ff7a352c5ad5dc669fe57fc | Text | 3,087 | 52 | # EV-GNN: Scalable Reinforcement Learning for Dynamic Electric Vehicle Charging Optimization Using Graph Neural Networks:
The **Paper** can be found at: [link](https://www.researchsquare.com/article/rs-5504138/v1).
The **trained models** and **results** can be found at: [link](https://drive.google.com/drive/folders... |
0fc7ced58c84daa3b79107a758c94e09ba56dcf7e4001b617615cab1c19ec413 | Text | 3,100 | 53 | # alignvideo
### Overview
This purpose of the alignvideo task is to have participants watch nearly 90 minutes of videos that vary in content.
The videos include scenes intended to feature various kinds of empathic states, appetitive states, aversive states, social relationships,
scenescapes (e.g. mountains, oceans/be... |
a4f162dc416bd9a5eb79740726e27af7a83f263eccd9f5de5a7b1fefb652f417 | Text | 3,115 | 25 | ## Oxford Covid-19 Government Response Tracker (OxCGRT)
<br/>
<br/>
<br/>
| Final OxCGRT dataset available, June 2023 |
| --- |
| *This repository contains old data*. The OxCGRT stopped publishing real-time updates at the end of 2022. A final version of the OxCGRT dataset is available at https://github.com/OxCGRT/cov... |
8558e5d81bf30828239b9f499afab53f959fb55f9b9a6186d2e5d3b849572ad9 | Text | 3,126 | 14 | The following folders contain the data, scripts, models and result for the article "How to train your neuron: Developing a detailed, up-to-date, multipurpose model of hippocampal CA1 pyramidal cells" by Luca Tar, Sára Sáray, Máté Mohácsi, Tamás F. Freund and Szabolcs Káli (2026).
"CA1_data" folder contains the raw ... |
748ee610d299d14dc947848a590d79726aea63c1a7b5fc07d7ca5a6a48aa2438 | Text | 3,170 | 56 | # EV-GNN: Scalable Reinforcement Learning for Dynamic Electric Vehicle Charging Optimization Using Graph Neural Networks:
The **Paper** can be found at: [link](https://www.nature.com/articles/s44172-025-00457-8).
The **trained models** and **results** can be found at: [link](https://drive.google.com/drive/folders/1... |
bed41aa5f71b356f1ddc6334114e6230bb7128c50bbd141d088b12df1c11a2a1 | Text | 3,170 | 41 | README
# 220819_Supplementary_Tables.xlsx
Supplementary Tables for the manuscript:
- Supplementary Table 1: Comparison of CTP deconvolution methods in the ROSMAP dataset. mcc* denotes methylCC deconvolution; sSV* denotes smartSVA; h* indicates Houseman using array reference data; hseq* indicates Houseman with sequen... |
3ce82c1f518428e1c08347870dabd50abcfe2bdacf64d23c22e1399ad27ecb8a | Text | 3,178 | 70 | # LC–MS Dataset for Quantification of Antipyrine (ANP) in Mouse Brain after SeeThrough Protocol
## 1 | Repository Layout
```
MS_data/
├─ README.md ← this file
├─ metadata.tsv ← sample metadata (SampleID, group, conc_uM, bio_rep, tech_rep)
├─ raw/ ← unprocessed Thermo *.RAW files
│ ├─ calibration/ ← calibrat... |
f727435b35835a3d8946b0f8b9dda262d282b6eaed8ecb3b85a6ed1f96c2d41e | Text | 3,180 | 37 | Software accompanying the publication Inman et al. (2023) "A multi-tiered mechanical mechanism shapes the early neural plate" for analysing 3D confocal movies containing partial zebrafish embryos with fluorescent markers for cell membranes and otx.
All software is in the form of Matlab scripts.
Functions included allow... |
0b083347fe076c58d4b41a856926f5f12452634e9778f3d5a7a1087254b3be0b | Text | 3,183 | 71 | # Neural speech tracking in noise reflects the opposing influence of SNR on intelligibility and attentional effort
This repository contains code for reproducing the figures in our study "Neural speech tracking in noise reflects the opposing influence of SNR on intelligibility and attentional effort" published on Imagi... |
b4e11745be4df3b8e6ce696a2bc1d345108caecd055746f3b5027e0cdcfbb091 | Text | 3,241 | 90 | Nearl
=====
|pythonver| |license| |rtdlink|
`Nearl <https://github.com/miemiemmmm/Nearl>`_ is an open-source machine learning framework designed to mine protein dynamics information from molecular dynamics (MD) trajectories.
The current release focuses on a 3D voxel-based representation for use in 3D convolutional ... |
508a112043127c73c5c5a17d64f887d9d107365bca40038d58bd468518cb7e41 | Text | 3,249 | 45 | # Neural Network Error Rate Analysis Script
## 1. Overview
This Python script simulates a simplified model of a neural network to analyze its error rates under different conditions. It specifically investigates how the network's ability to correctly represent input stimuli is affected by:
* **Set Size:** The number ... |
ea2014dab15e9f1a7fe196577bb28c05ae46edeab128fe3e015f675a1715f3fc | Text | 3,275 | 20 | # Cerebellar and Subcortical Contributions to Working Memory Manipulation
This repository contains the code used in my project *"Cerebellar and Subcortical Contributions to Working Memory Manipulation"* (https://doi.org/10.1038/s42003-025-08467-0).
**Code** was written using a combination of MATLAB and Python scripts... |
3a963a0fcf194bd789c5bc5ec1e73d0ac42f7ae1fdf4c23807ea4ccdd70aaf55 | Text | 3,285 | 59 | # clinicalBERT
Repository for [Publicly Available Clinical BERT Embeddings](https://www.aclweb.org/anthology/W19-1909/) (NAACL Clinical NLP Workshop 2019)
## Using Clinical BERT
UPDATE: You can now use ClinicalBERT directly through the [transformers](https://github.com/huggingface/transformers) library. Check out th... |
b363d549de36f82cbcba950637b34e44b861723962aaf93cd974905ee33fa88f | Text | 3,320 | 69 | # igv
Integrative Genomics Viewer - deskt... |
1005918f05b1b87764f5c5df78fa8db2b982bf65078027903de48bca02ad4333 | Text | 3,327 | 55 | # mrQ #
**mrQ** is a software package designed to calculate MR parameters (T1 and PD) using spoiled gradient echo scans (SPGR, FLASH). Using T1 and PD maps, mrQ performs the evaluation of macromolecular tissue volume (MTV) and the apparent volume of the interacting water protons (VIP) as well as the water-surface inte... |
bc71010905e202dc4cddf0194aff915465a2498d276ecb05377ffd67e2874dd8 | Text | 3,328 | 16 | All of the data for this work can be found in the main text and in the Supplementary Information. The COCO 2017 Dataset can be accessed via https://www.kaggle.com/datasets/awsaf49/coco-2017-dataset. The Mapillary Traffic Sign Dataset can be accessed via https://labelbox.com/datasets/mapillary-traffic-sign-dataset/. The... |
e2d19895795f20ab94f24d9e36eac5d269aa7b064c073c91bb397e7b7949630f | Text | 3,351 | 115 | # Multisyn: Accurate prediction of synergistic drug combination using a multi-source information fusion framework
[](https://doi.org/10.5281/zenodo.15194129)
This repository contains the official implementation of our paper:
**Multisyn** integrates pha... |
0a04f000290cb277772cdac2cd247240cf35242f846a0bf03e8c4f53f489f992 | Text | 3,366 | 57 | [](https://zenodo.org/badge/latestdoi/382176345) [](https://gitter.im/LernerLab/GuPPy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![codecov](ht... |
62994987663d3d2c937da834e28dee988653dc1c5637a9606b934873ace25f05 | Text | 3,371 | 69 | # r1_r2s_rel_toolbox #
**r1_r2s_relaxivity** is a software package designed to calculate the r1-r2* relaxivities. The software is described in the following manuscript:
"Uncovering molecular iron compounds in the living human brain."
```
example= r1_r2s_relaxivity_run(R1_path,R2s_path,Seg_path,0,[],{'R1_max',1.5,'R1_... |
a990e0b60398a4b2fb82337cdc5ad9f1c5a8231576deb69b4fc3cca2fb1e879e | Text | 3,405 | 98 | # FAMyoS
**Deep Learning Pipeline for Fully Automated Myocardial Infarct Segmentation**
FAMyoS is a deep learning-based pipeline designed to automatically segment myocardial infarcts from cardiac MRI images. The system utilizes a trained neural network to deliver accurate and reproducible segmentation results with min... |
527274f64cb9f6dba5c3a03417f8373d45b02b26604508b73d1b473eba574a00 | Text | 3,408 | 52 | # T1w Fractal Dimension Repository
This repository contains de-identified example data and resources for computing fractal dimensions from T1-weighted MRI scans. It includes code and patient-derived, de-identified data for analysis and processing. The repository is part of ongoing research in the Radiology-Morrison-la... |
9b19147a431e178b55543681561cd5585772ce7bf6cdf65dadc91d4dd8dd8cdb | Text | 3,413 | 76 | # TODO
- [x] Normalize Data
- [x] Add to repository
- [x] Run all experiments
- [x] Verify results
# StrokeAssist
This is the official repository for the paper titled "***STROKE-ASSIST: A novel machine learning framework for stroke type identification in resource-constrained settings resilient to missing data. Publish... |
40f014b4346555eaa425f4c2544f454265505d59d0cf28a93b8f6789bbe413f8 | Text | 3,455 | 44 | # varx_demo
<a href="https://doi.org/10.5281/zenodo.15127333"><img src="https://zenodo.org/badge/832732261.svg" alt="DOI"></a>
Code for analysis in: https://doi.org/10.7554/eLife.104996.3
VARX toolbox: https://github.com/lcparra/varx/tree/main
Figure data: https://doi.org/10.17605/osf.io/vc25t
## Analysis steps
... |
9f259f576b70c160747213e6a155193b4f44221d61077b195fec7e6dba6c3727 | Text | 3,455 | 44 | # varx_demo
<a href="https://doi.org/10.5281/zenodo.15127333"><img src="https://zenodo.org/badge/832732261.svg" alt="DOI"></a>
Code for analysis in: https://doi.org/10.7554/eLife.104996.2
VARX toolbox: https://github.com/lcparra/varx/tree/main
Figure data: https://doi.org/10.17605/osf.io/vc25t
## Analysis steps
... |
e5d7fea17a3e0f1492110c50d8c68db9fa76c3d979fea8dd3fc693a1061af8c1 | Text | 3,455 | 51 | # sEEG-slow-fast-attack <img src="./summary_figure.jpeg" align="right" width="500px">
[](https://doi.org/10.1101/2024.01.16.575785)
[
](ht... |
775d7184b2be7c36bc01c5d6f9e2afb02f1bf94ea21fb85f38daa607031e67a6 | Text | 3,458 | 90 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# About the project:
- this is a repository of an R project containing code and source data
for the Platynereis three-day-old larva connectome paper. Contributed
by [Jékely
lab](https://www.cos.uni-heidelberg.de/en/research-groups/gaspar-je... |
1a4c69b686f1a8ccfaf1c3a133a95fef76e549024098751802fc0d10402a5001 | Text | 3,478 | 53 | # Title
TriCLFF: A multi-modal feature fusion framework using contrastive learning for spatial domain identification
# Overview
TriCLFF is a contrastive learning framework to learn low-dimensional fusion embeddings of gene expression profiles and histological images. We first utilize three different kinds of encoders ... |
b542c66be3f07cbc4c5b9620088da79eeba21ae46decfd1611a829601f11499e | Text | 3,493 | 69 | # 🧠 minimodel
Code to train and test models from the paper: **Fengtong Du, Miguel Angel Núñez-Ochoa, Marius Pachitariu, Carsen Stringer.** *[A simplified minimodel of visual cortical neurons](https://www.biorxiv.org/content/10.1101/2024.06.30.601394v1)*, bioRxiv
## Installation
We recommend using a **clean Python... |
3d68b379eed0b76370c30031da11792b84f391cec54a0458d73e690023dfe541 | Text | 3,520 | 74 | # Classification-and-Interpretation-of-Histopathology-Images
# Breast Cancer Classification Using CNNs and Ensemble Learning
## Overview
This repository contains the implementation of **breast cancer classification** using **Convolutional Neural Networks (CNNs)** and **ensemble learning** techniques. The study employ... |
ec98ebc0c747ce58ae7438a9b12d5cd1ed0098925de9a3cb20aa71ba8831b7fe | Text | 3,530 | 99 | # ConditionCDVAE+
Our study presents an improved deep generative model based on the Crystal Diffusion Variational Autoencoder ([CDVAE](https://github.com/txie-93/cdvae)), ConditionCDVAE+, which enables the inverse design of van der Waals (vdW) heterostructures.
This is an implemented code from a paper titled "Deep ge... |
70d06a07686965b7720ab5440b54a1631a9aab745ca20d29876a9415870b0515 | Text | 3,539 | 66 |
# Latent Variable Sequence Identification for Cognitive Models with Neural Network Estimators
This repository is the official implementation of [LaseNet: Latent Variable Sequence Identification for Cognitive Models with Neural Network Estimators](https://doi.org/10.3758/s13428-025-02794-0)
If you want to run the cod... |
d0b3353217e625c06180143b7a407401767d8552bb9b8cd5c0900391a0762e4f | Text | 3,562 | 97 | # LabelFusion
<p align="center">
<a href="https://github.com/FeTS-AI/LabelFusion/actions/workflows/test.yml"><img src="https://github.com/FeTS-AI/LabelFusion/actions/workflows/test.yml/badge.svg" alt="Build Status"></a>
<a href="https://doi.org/10.5281/zenodo.4534122"><img src="https://zenodo.org/badge/DOI/10.... |
266e44aa02d6c19c0bf4ea7b72f3917b60267ee10652236170c079160a0e6d49 | Text | 3,604 | 65 | # MDM #
**MDM** is a software package designed to calculate the derivative of a qMRI parameter relative to
MTV (MDM signature). The software and the sensetivity of MDM measurments to molecular composition are described in the following article:
"Disentangling molecular alterations from water-content changes in the agi... |
7bc7a42addbacafff0ac3ac60f7327d3da188e1d9c52057530da999ae5e72a71 | Text | 3,691 | 63 | Code for "Generation of surrogate brain maps preserving spatial autocorrelation through random rotation of geometric eigenmodes"
--------------------------------------------------------------------------------------------------------------------------------
.. image:: ./_static/main_figure.jpg
:scale: 20%
:align: ... |
68f3ac3ca950dc43bb0e008320593af2216bdf5ed22d920f68726fff5e95d275 | Text | 3,708 | 100 |
|
.. image:: https://img.shields.io/pypi/v/eigenstrapping
:target: https://pypi.python.org/pypi/eigenstrapping/
:alt: Latest PyPI version
.. image:: https://zenodo.org/badge/710175458.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10218973
:alt: Zenodo DOI
.. image:: https://github.com/SNG-newy/eig... |
7f68a16dfc6f8882b4b36ba7c9acf3f64c93480da528fd5cea1facaae29e8d2c | Text | 3,729 | 132 | # Generative GaitNet (Simple Version)
The updated version is available in https://github.com/namjohn10/BidirectionalGaitNet.
## Abstract
Understanding the relation between anatomy and gait is key to successful predictive gait simulation. In this paper, we present Generative GaitNet, which is a novel network archite... |
a742d33951bafb1370ed5b8877632dc7e92b9ab93778e7989826745d56bb3304 | Text | 3,730 | 74 | # ABC-DLS (Approximate Bayesian Computation with Deep Learning and Sequential monte carlo)
This software is a python pipeline where you can use simulated summary statistics to predict which underlying model can better explain the observed or real-world results (classification) and can guess which parameters can produce... |
74d85957733ddcd3e2642a650697ab57a56ffe3ab9ed9ad2ebff89d296f9dd1d | Text | 3,755 | 74 | # ABC-DLS (Approximate Bayesian Computation with Deep Learning and Sequential monte carlo)
This software is a python pipeline where you can use simulated summary statistics to predict which underlying model can better explain the observed or real-world results (classification) and can guess which parameters can produce... |
3e417226c354cd191613cf73f81e8b24d2ec95eb31b90e91692876b56fb4ff86 | Text | 3,767 | 79 |
# Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
## Introduction
This repository aims to share the raw data processing and visualization code used in the **"Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues"** paper.
![github_spatial... |
43438deaf2235dbf29fbfbf08d103907ca9b8e82f1d37c682daf97df39d94cac | Text | 3,776 | 95 | Microglial Ramification Analysis
Author: [Dr Aravind Sivakumar]
Date: [10/1/2025]
Overview
This MATLAB script analyzes microglial morphology in .tif images to assess ramification index, a key feature of microglial activation. It extracts connected microglial structures and quantifies morphological complexity.
Workflow... |
46b92c8d062ca5f2f13f05c29fa21e45b6e307a0b45f514b9afe4f2bcb377cb1 | Text | 3,811 | 101 | # PIEZO1-HaloTag Analysis Pipeline
This repository contains a collection of Python scripts and FLIKA plugins for analyzing PIEZO1 protein dynamics in microscopy data, as described in [Bertaccini et al. 2024](https://doi.org/10.1101/2023.12.22.573117). The tools enable tracking, visualization, and analysis of PIEZO1 pr... |
a5dc778eb9f247b921d79307f1fd2399337c9af8db0da975640e1edd5076dd68 | Text | 3,811 | 85 | # Analysis code for registered report: Wakefulness can be distinguished from general anesthesia and sleep in flies using a massive library of univariate time series analyses
OSF project DOI 10.17605/OSF.IO/8WVSQ (stage 2)
## Data files
Data files available at https://osf.io/8wvsq/?view_only=8a056d1c573b4f23a6cf6cea8b... |
85259859bba7ae7d6e7fa3b12779a411123a21d7a68d8dee9539c96d51b8798d | Text | 3,863 | 87 | # iSeq (Ohno et al. from Inokuchi Lab.)
## Overview
iSeq (or its GPU implementation, `igpu`) automatically extracts 'neural sequences,' which are patterns of neuronal population activity with specific temporal order relationships, from raster data with neuron × time dimensions. This program is specifically tuned for ... |
ecf7a2f9967095345fb04ea8553fa0eff305caf80efa07eeb4d4f2221df342ac | Text | 3,886 | 70 | # Plagiarism Detection Across Languages: A Comprehensive Study of Arabic and English-to-Arabic Long Documents
## Overview
Plagiarism detection in Arabic texts remains a significant challenge due to the complex morphological structure, rich linguistic diversity, and scarcity of high-quality labeled datasets. This stud... |
fcc6a79f3cada15ff391981fdfafa64868d6088758aff4b88f648f58bb43fb03 | Text | 3,891 | 44 | # Wissing_and_Eschholz_LC-transduction
This repository contains custom MATLAB-code that allows reproduction of the analysis of data presented in the manuscript
"A comparison of viral strategies and model systems to target norepinephrine neurons in the locus coeruleus reveals high variability in transgene expression p... |
f162834b22ee64acfbb6f90c79743b6be2ce9f31fef9574b100ad5eaed8f7b0c | Text | 3,901 | 75 | # R-general
Reusable R functions and scripts for general data analysis and visualizations
## Functions
### PermtestsEBM.R
```
permtest_mean(list1, list2, tails, showgraph)
```
Performs a permutation test comparing the means of the 2 lists of data. It shuffles the data 100000 times without replacement.
Prints t... |
ec1b9d359ac71d05d1e5f7a7d5d53a4b93597d7b57024d62a2fd1235d4d490df | Text | 3,902 | 101 | # MassCube
[](https://pypi.org/project/masscube/)
**masscube** is an integrated Python package for liquid chromatography-mass spectrometry (LC-MS) data processing.
- **Documentation:** https://huaxuyu.github.io/masscubedocs/
- **Source ... |
bf51d81ab5735c571f73c22d4fa6c4048344d46542551f2be68741d2c5af6f4b | Text | 3,903 | 110 | [](https://arxiv.org/abs/2402.08708)
# Similarity based Molecular Generation (SiMGen)
<a href="https://zndraw.icp.uni-stuttgart.de">
<img src="banner_animation.gif" height="350"/>
</a>
SiMGen is a local similarity based molecular generation method. It uses... |
6f5e778ce913ea36529fba905599d8891e12e5495c0122362a65d21af3495d78 | Text | 3,928 | 45 | # Wissing_and_Eschholz_LC-transduction
This repository contains custom MATLAB-code that allows reproduction of the analysis of data presented in the manuscript
"A comparison of viral strategies and model systems to target norepinephrine neurons in the locus coeruleus reveals high variability in transgene expression p... |
108e277eaa77a89e4fdb7becf5c25099f7ee94510893c0a98b5ac5f12acd1107 | Text | 3,933 | 66 | <a href="https://arxiv.org/abs/2105.05874" alt="Citation"><img src="https://img.shields.io/badge/cite-citation-blue" /></a>
<a href="https://twitter.com/FeTS_Challenge" alt="Citation"><img src="https://img.shields.io/twitter/follow/fets_challenge?style=social" /></a>
# Federated Tumor Segmentation Challenge
The repo ... |
3209087e67f0905776842a70afc11158427692b860149ac731600cb17ec40ec8 | Text | 3,961 | 153 | # EDKA:Efficient Knowledge Distillation and Alignment forImproved KB-VQA: Enhancing Multimodal Understanding
[](LICENSE)
[](https://www.python.org/)
[ of neurons.
The code can be run either on a single core or multiple c... |
78a3622bb5a088a84b241764a0d31e86f022dc6bbb30c411a2a73e89f483061b | Text | 3,995 | 94 | # TS2Vec
This repository contains the official implementation for the paper [TS2Vec: Towards Universal Representation of Time Series](https://arxiv.org/abs/2106.10466) (AAAI-22).
## Requirements
The recommended requirements for TS2Vec are specified as follows:
* Python 3.8
* torch==1.8.1
* scipy==1.6.1
* numpy==1.19... |
1a76538688b040db61636967a9d2c1c53bbe73ee351cbfc9109baa450ee568d1 | Text | 4,037 | 114 | # ReactBench: Benchmarking MLIP Performance in Transition State Search on a Reactive Dataset
ReactBench is an automated transition state(TS) search workflow for benchmarking various MLIPs on a reactive dataset.
Through customizing new calculators or uploading new datasets, ReactBench can be used to evaluate the perfor... |
9a3815404098e0b58199302bf4821cbb03b5bb6a1522bd8a66d5fd05aa062d62 | Text | 4,054 | 82 | # A standardized and reproducible method to measure decision-making in mice: Data
*Beta Disclaimer. Please note that this is a beta version of the IBL dataset, which is still undergoing final quality checks. If you find any issues or inconsistencies in the data, please contact us at info+behavior@internationalbrainlab... |
194a1091a5945691716aa188a79eb721107fc57d8919be1a36f4a04e0dc49144 | Text | 4,063 | 68 | # CellPower [](https://zenodo.org/doi/10.5281/zenodo.10125075)
Most epigenetic studies generate genome-wide profiles from bulk tissues (e.g. brain) however, this prevents identification of the cell type associated with the observed difference. Technologies such as [fluo... |
1b8f93fde9d6412226cc62b56ec333285ef7c7494a73f0e33300c43be1f48ee4 | Text | 4,085 | 105 | README: ANN Training & Evaluation Data for MI Prediction
This README file describes the complete dataset collection used in the study *"Deep learning prediction of noise-driven nonlinear instabilities in fibre optics"*.
The dataset consists of both **numerical (GNLSE simulations)** and **experimental (real-time DFT)*... |
086684b67f3053d94a0920491643542afde86d061f810511c5bf56aaf0ec8502 | Text | 4,107 | 99 | # GBMPurity
## Table of Contents
- [GBMPurity](#gbmpurity)
- [Table of Contents](#table-of-contents)
- [Overview](#overview)
- [Installation](#installation)
- [Usage](#usage)
- [Data Preparation](#data-preparation)
- [Inference on bulk samples](#inference-on-bulk-samples)
- [Access GBMPurity model]... |
9aa3f0c55c57797c7517bcea78db4d92c51c26077082382c6e9e7130ca1012ac | Text | 4,135 | 132 | # BenchmarkCycPeptMP
PyTorch implementation for *__Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability__* <br />
Wei Liu, Jianguo Li, Chandra S. Verma and Hwee Kuan Lee*
## 🧬 Overview
Cyclic peptides are promising drug candidates due to their ability to target protein–prote... |
5294c8ec1de6b98e806d949f30c6e3bb0f7585b65b10a58348044bb67344eb61 | Text | 4,162 | 74 | # BayHunter v2.1
BayHunter is an open source Python tool to perform an McMC transdimensional Bayesian inversion of surface wave dispersion and/or receiver functions. The algorithm follows a data-driven strategy and solves for the velocity-depth structure, the number of layers, Vp/Vs ratio and noise parameters, i.e., d... |
fd8e9afb57bb0f99cc0fc8efe137f9f62bd4bf79d8de01a1b7c753d8d7dc516f | Text | 4,179 | 86 | # DeepEthoProfile
Software to automatically annotate mouse behaviours inside a home cage.
The solution is based on a CNN that processes video recordings and classifies each frame with one of eight first order behaviours
<img src="./pics/behaviours_H.jpg" width="700"/>
The system was tested to work on a computer run... |
331412951167d994d9de2f7b40e7ab6ddf80c0058481c405f9d455da5d166bf0 | Text | 4,202 | 64 | Analysis code and results for the study
# Childhood Mild Traumatic Brain Injury is Reliably Associated with Anxiety but Not Other Examined Psychiatric Outcomes at Two-Year Follow-up, After Adjusting for Prior Mental Health
<p align="center">
<a href="https://en.wikipedia.org/wiki/R_(programming_language)"><img
a... |
ea30511f5637701924fdd80baed8839b32ee47a713c98e6b41617f4a0487fbc2 | Text | 4,235 | 43 | # An Expanded Subventricular Zone Supports Postnatal Cortical Interneuron Migration in Gyrencephalic Brains
Repository hosting code used for transcriptomics analysis used in **An Expanded Subventricular Zone Supports Postnatal Cortical Interneuron Migration in Gyrencephalic Brains.**
JaeYeon Kim<sup>1</sup>, Aunoy Podd... |
95c94b1bf6dd90235bcf359df9308ec8ae9493f64af607340fcc82a7fad88f3d | Text | 4,239 | 121 | # DANTE: Deep Active Optimization with Neural-surrogate-guided Tree Exploration
## Introduction
DANTE is a deep active optimization pipeline that combines deep neural surrogate models and a novel tree search explorationalgorithm to find superior solutions in high-dimensional complex problems characterized by limited ... |
651383a827a1da4aa323b110f1dee4e4d3a6a68d10b090f1605a2518d37ec681 | Text | 4,248 | 79 | # SBCDataAnalysis
## Table of Contents
|content |
|---------------------------------|
|[1. Abstract](#overview) |
|[2. Publication](#publication) |
|[3. Installation](#installation) |
|[4. Description](#description) |
|[5. Fundings](#fundings) |
|[6. Competing intrests](#com... |
db4c937613d377ba40d49eaa7014b09a09c2edc92c6b5aa8c6a566e99c4afa0e | Text | 4,262 | 69 | # SysISTD
A demultiplexer for SysFate Illumina spatial transcriptomic.
## Description
### How to run
```
require arguments:
--f1 file1
The fastq file 1 you want analyse. (It can be compress with extension .gz)
--f2 file2
The fastq file 2 you want analyse. (I... |
56772a74e24738bdea6efc9190469f1e117f537e90c46ab71765604b397c92bc | Text | 4,265 | 115 | # Short‑Horizon Neonatal Seizure Prediction (neoSeer)
Deep‑learning code, configs, and utilities for our paper ⬇️
> **Short‑Horizon Neonatal Seizure Prediction Using EEG‑Based Deep Learning**
> Jonathan Kim MD, Edilberto Amorim MD, Vikram R. Rao MD PhD, Hannah C. Glass MD MAS, Danilo Bernardo MD\*
> (Submitt... |
d9aa04f043b4256750de45331620267a7adc78ee2c59ae9af5994ebe0de68919 | Text | 4,284 | 64 | # BioML
In this project, we present an application of graph neural networks for constructing mechanistic models for time-dependent gene expression. Our result highlights not only the flexibility of GAEs, but also their limitations, appearing in the form of spurious edges. Furthermore, we demonstrate how a good fit of ... |
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