sha256 stringlengths 64 64 | language stringclasses 27
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|---|---|---|---|---|
8c6015fc074d595b640b5b28bacafdb3246fae355d9b9a3396f1a1f606c134e5 | Text | 2,859 | 56 | # Astrocyte-Ion-Dynamics Model
## Overview
This repository contains Python scripts for simulating ionic homeostasis in an astrocyte.
Running **`ast_modeling.py`** produces a CSV named **`comb_astro_data.csv`** that records:
* Membrane potential ( *V* )
* Intracellular & extracellular ion concentrations (K⁺, Na⁺... |
1c76f5f9458684471cff01e93b3dde07e6b0e124b987e0357e12f2e2294feed2 | Text | 2,861 | 26 | # ADC Performance Survey
*Data collection from the ISSCC & VLSI Circuit Symposium, 1997-2026*
For use in publications and presentations please cite as follows:
B. Murmann, "ADC Performance Survey 1997-2026," [Online]. Available: https://github.com/bmurmann/ADC-survey.
```
@misc{adc_survey,
author = {Murmann, Bor... |
6d50cb64a374bd877bc7cda1a7b05874b306024217f53a7835e5c9356cbbb6a9 | Text | 2,861 | 10 | # gad-sympt-metagwas
This repository contains the scripts for the manuscript: _Genome-wide meta-analysis of quantitatively measured generalized anxiety symptoms in individuals of European ancestry_.
Published in Nature Human Behaviour https://www.nature.com/articles/s41562-026-02476-7
Skelton, M., Mitchell, B. L., A... |
bac25362b21942679ecd91620b11615d8ac7f19e8dfc79cecd9b91bddb0feedb | Text | 2,862 | 39 | # Code accompanying the preprint:
## ["Redundant prefrontal hemispheres adapt storage strategy to working memory demands"](https://www.biorxiv.org/content/10.1101/2025.01.15.633176)
This repository contains the code used to generate the main figures and supplementary analyses presented in the preprint. The code includ... |
9cb0d52601341f8f579c9d3317cc6921a36c91b7572dbb5b10b0f62e8249e345 | Text | 2,867 | 70 | # Compositionally-Restricted Attention-Based Network (CrabNet)
This software package implements the Compositionally-Restricted Attention-Based Network (`CrabNet`) that takes only composition information to predict material properties.
Additionally, it demonstrates several model interpretability techniques that are pos... |
d9365e19e8cf03cdcc3f8b4573327bedf953f54770fc4faaaa7f8889bb8662bd | Text | 2,887 | 64 | # MOSAIC
## Purpose
R script for sequence analysis of nonclonal DNA populations using mapped Nanopore reads.
Specifically used for determining the editing efficiency for mutating DNA at specific target loci by counting the number of modified and wild-type sequences.
This R script was developed as part of the researc... |
05c1b5b70954e387f6cbeb8c6ada63d88c2f8ac96e15d4e90aae562ff2726c9c | Text | 2,891 | 45 | # BakingTray #
<a href="https://raw.githubusercontent.com/wiki/SWC-Advanced-Microscopy/images/example_acq.jpg">
<img src="https://raw.githubusercontent.com/wiki/BaselLaserMouse/BakingTray/images/example_acq_thumb.jpg">
</a>
### What is it?
BakingTray is a complete software platform for 2-photon serial-section microsc... |
c02eab84697061c2822e53fc7df3e1a09af3c48618d98d3061cc633b160f2384 | Text | 2,899 | 30 | # Synthetic super-enhancers enable precision viral immunotherapy
This repository contains steps taken to analyse single cell RNA-seq and SOX2 and SOX9 ChIP-seq data in GBM stem-like cells (GSCs), as used in Koeber and Matjusaitis et al, Nature 2026.
## scRNA-seq
Steps:
8 human GSC lines (E17, E20, E21, E28, E31, E34,... |
5af896ae8f37af34dda62b167bc697af0a293375049ef9d94d2fa86acbcde449 | Text | 2,901 | 30 | # TRACC_PHYSIO
This repository has code to complete TRACC_PHYSIO -- TRACC-PHYSIO performs a cross-correlation between a dynamic MRI signal and a simultaneously recorded physiological signal with a much higher sampling rate to quantify coupling strength and a TimeDelay that reflects the relative arrival time of the phy... |
912e90dbee0e50b50b30f9dfa67bda0a7d7218bf64c2712a16306e3c789bf191 | Text | 2,902 | 116 | # LSNN - Lightweight Liquid Siamese Neural Network
This repository provides a **reproducible implementation** of the Lightweight Liquid Siamese Neural Network (LSNN) for **multimodal satellite image change detection**.
---
## Features
* Pixel-wise semantic change detection (7 classes)
* Dual-branch Siamese architec... |
9546d70eb046497b2ecbcc8e631ac9401166dce0ba67896c07d5de9c4a2215e4 | Text | 2,919 | 77 | # Spheronizator
Spheronizator is a Python research utility designed to voxelize protein structural data from existing PDB files for use in machine learning training sets. The utility is intended to be a part of your data processing pipeline, with an interface that is convenient to use with [IPython](https://ipython.org... |
fd6d64c8c43598b7548bc4e7ba05ab9b4d66cad8959e1f97154a96df7a484c08 | Text | 2,919 | 54 | # MIRAGE
This is the main working branch of MIRAGE. It uses the Stable Cascade diffusion model for reconstructions, and a set of Ridge regression models as the decoding backbone.
To install the proper environment, follow `src/setup.sh`.
To use this branch, you must also clone the StableCascade repo from `https://gi... |
3249c3eaf526ef142c3677abc3287b32352651650adc4348f61f6cd35f623669 | Text | 2,928 | 67 | # Mouse Auditory Filter Model
MATLAB implementation of a mouse auditory periphery model based on a zero-phase gammatone filterbank. The code synthesizes several classes of pitch-related stimuli, passes them through a cochlear-inspired filterbank, and estimates temporal pitch strength from the filtered outputs. This re... |
272899eb4fddd9972e3013ab3762746be4142259b818f75867f05455f1156e59 | Text | 2,938 | 34 | # STR GWAS on AD in UKB
This repository contains the code accompanying the paper '**GWAS on short tandem repeats identifies novel genetic mechanisms in Alzheimer’s disease**' ([doi: https://doi.org/10.1101/2025.03.13.25323833](https://doi.org/10.1101/2025.03.13.25323833)).
This code is intended to illustrate the main ... |
8a877cb16e0fdd7f748bb6efeba8ae33dc4ab0080582e05917ab55f91ffd8233 | Text | 2,943 | 100 | # Regression Guided Neural Networks (ReGNN)
This repository contains code for the paper "Unveiling Population Heterogeneity in Health Risks Posed by Environmental Hazards Using Regression-Guided Neural Network".
## Requirements
- Python >= 3.9
- (Optional) [Stata](https://www.stata.com/) — only needed if you want to... |
06577251dbaff37edeecc6e85884728f51be4b755a905ee6763822b22219fdc6 | Text | 2,944 | 47 | # ```StARQ: brainStem Automated Registration and Quantification```
<p><a href="[https://github.com/itsasimiqbal/StARQ](https://colab.research.google.com/drive/19vQyB9K3jokDSuh9qWAbjBJ8sacyQs2M)"><img src="https://github.com/itsasimiqbal/StARQ/blob/main/StARQ_logo.svg" align="center" width="330" height="215" /> </a>
... |
a3d816a3655743346cd48a3b01780fa8b21a1594a2ac6df63b71c9201f52ebdf | Text | 2,959 | 43 | # Geometric-Tm
Protein dynamics-informed multigraphic neural network for melting temperature prediction.
---
# Overview
## Code for data processing and training
The program is written as a Python package located under `/src/ml_modules`.
Code for building the data representation can be found under `data`, while the mod... |
0f8e0bc710afd9d703c1804bb5d26b0538b8be0ac1c1ee85496d48b23ee40478 | Text | 2,966 | 42 | # SensoryGuidedJointLearning
This is a repository of the scripts used for the study:
“A sensory-guided human-machine collaborative learning paradigm for motor imagery brain-computer interfaces.”
Hanwen Wang, Yisha Zhang, Maxim Karrenbach, Yidan Ding, Bin He (2026). Sensory-guided human-machine joint learning accele... |
2382b831c844f86610a7cf60a6e7c93631fe143f7dda27b60b66d8f80150ba8c | Text | 2,966 | 42 | # SensoryGuidedJointLearning
This is a repository of the scripts used for the study:
“A sensory-guided human-machine collaborative learning paradigm for motor imagery brain-computer interfaces.”
Hanwen Wang, Yisha Zhang, Maxim Karrenbach, Yidan Ding, Bin He (2025). Sensory-guided human-machine joint learning accele... |
d6f1ef54ae7b235613c546c1b72f94f99b2263d445af6d4e533b736efc6143d2 | Text | 2,971 | 85 | ## Nextflow pipeline for processing of GPSeq data
Genomic loci positioning by sequencing ([GPSeq](https://doi.org/10.1038/s41587-020-0519-y)): genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius.
<br>
### Getting Started
The whole pipeline can be cloned in your current work... |
38f772903b1de4962052f6b2a7532d6843004cd23d17ae81853393db591b6be1 | Text | 2,977 | 67 | # AAIF-Ethical-CyberDefense
Official repository for the Agentic AI Framework (AAIF): a governance-aware, policy-driven architecture for ethical cyber defense. Includes dataset preprocessing, model training, policy integration, and reproducibility scripts.
# Agentic AI Framework (AAIF) for Ethical Cyber Defense
This r... |
4f8157a927278f97dffd4af239a4aab3e585b91dcf52ef62f8ee32436ecedd75 | Text | 2,984 | 31 | # qunex_run_recipe
Repository for the QuNex recipes manuscript.
The repository has the following structure:
- `example_1`: the first example from the manuscript,
- `example_2`: the second example from the manuscript,
- `recipes`: the recipes library (see below).
## The recipes library
Under the `recipes` folder yo... |
202354a32f3782678b4cf14801a1d9fa41303d3389ddbe7d38dc22a8a139d795 | Text | 2,991 | 50 | This is the data and code depository for the paper "Generalization of fear learning is shaped by inhibitory sensory processing in mice", NCOMMS-25-57165.
miasma.zip ; contains custom-written imaging analysis software used in this article.
miasma_documentation.docx ; detailed description of files and analysis steps f... |
79d4d87bd41c7fb880774bae65c9a09ca187593883ca573371e7686f48ff0dc4 | Text | 3,006 | 61 | # Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue
## Overview
Translation involves not only canonical main open reading frames (mORFs) but also upstream ORFs (uORFs), which may regulate mORF expression. However, due to technical limitations, syste... |
d26deff051e41de9cf6a2749c44103c73f231cccbfb613dfe505e9bfdc2a61f4 | Text | 3,008 | 56 | # ARC project scripts
Exhaustive codebase to run the pleasantness related analyses on the NEMO dataset
## 1. System Requirements
Operating System: Windows
MATLAB Version: R2023B
### Dependencies:
1. [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/)
2. [GLMSingle](https://github.com/cvnlab/GLMsingle)
3. [L... |
5eb917bc1d25c8c37a87fd988f9601fc07f1a149c22388eba34ba33261bb1841 | Text | 3,010 | 43 | # nonfractal: MATLAB Toolbox for estimating nonfractal connectivity and fractal connectivity
## Description
It is a MATLAB toolbox for estimating both nonfractal connectivity and fractal connectivity from a set of time series with long-range dependence such as resting state fMRI BOLD signals.
## Depends
* Statistic... |
665d6e1b8e4b188f49f0706bdeb2aed74d1967bb64febdd6107f67f6b9f493dd | Text | 3,021 | 23 | # Metabolomic signatures of SSRI exposure during neural differentiation and correlation of lysophosphatidylcholines with early symptoms of neurodevelopmental disorders
Abishek Arora,<sup>a,b,c</sup> Kristina Vacy,<sup>d,e,i</sup> Cátia Marques,<sup>f,i</sup> Mihai-Ovidiu Degeratu,<sup>a,b</sup> Francesca Mastropasqua,<... |
17bbef71a08b3cdefb00229bcf72a6e7fb7c49ec83c8252130a3de3a2993efbf | Text | 3,025 | 77 | # Sigma Receptor Co-Expression Architecture Divergence (WJ-Native)
Weighted Jaccard analysis of continuous genome-wide Spearman correlation vectors reveals that SIGMAR1 (sigma-1) and TMEM97 (sigma-2) share 96.4% of their global co-expression architecture but diverge at their most functionally relevant partners (binary... |
b94c5c628874cf4af00738284f75ca41d0c8da2e2c642657ba30e4ee7c6f38f4 | Text | 3,026 | 72 | # Molecular Fingerprints Are Strong Models for Peptide Function Prediction
Code for paper "Molecular Fingerprints Are Strong Models for Peptide Function Prediction".
ArXiv preprint: https://arxiv.org/abs/2501.17901
## Setup
Dependencies are installed with uv. You can install exact versions used from `uv.lock`
by ru... |
ea810e9c38831e85c6cc3ac4da86cada0587c2faf977e6c81a8656a729a383f7 | Text | 3,034 | 90 | # Neural Surrogate for Real-Time UAV Swarm Flocking in Cluttered Environments
This repository accompanies our paper on replacing online modified-MPIO weight search with a lightweight neural surrogate for distributed UAV swarm control in cluttered environments.
## Release Scope
This repository includes:
- source code... |
d3d4d2b920be708ac5a322e643301e89bf82aff26f78c77d1cce5a969f2b7a80 | Text | 3,038 | 74 | # <img src="https://raw.githubusercontent.com/predictive-clinical-neuroscience/PCNtoolkit/dev/doc/_static/pcn-icon.png" alt="PCNtoolkit logo" height="52" align="top" style="vertical-align: middle; margin-bottom: 20px;" /> PCNtoolkit
[![Downloads][downloads-badge]][downloads-link]
[![DOI][doi-badge]][doi-link]
[
## Description
 Project under Temple University IRB #24452.
NOSC is a multiband, multi-echo, intensively sampled fMRI study of the reward response.
NOSC is described in detail in Mattoni et al., 2025 https://www.biorxiv.org/content/10.1101/2025.09.26.678878v1.
[St... |
c9bc13892dfcb01660972bc50db71caddb7a51b40f2fb8d29ddf32d326479226 | Text | 3,054 | 63 | # RHOSTS-0.2
This is **RHOSTS** (**R**econstructing the **H**igher **O**rder **S**tructure of **T**ime **S**eries), a python implementation of the algorithm for computing the higher-order structure of a multivariate time series
In the folders "High_order_TS" and "High_order_TS_with_scaffold" there are different pytho... |
5c9f97a7f339cde79be8ed9a647c3331a105547bba0835cc3d560b34804e6394 | Text | 3,059 | 82 | # MNDGNN
## Multiplex networks-based directed graph neural network for cancer driver gene identification
Identifying cancer driver genes is crucial in precision oncology. Most existing methods rely on a single interaction network to capture gene relationships. However, with the increasing availability of multi-omics ... |
23dfab2456c25b8fd43a57ae84bc22b73542996872d6fdc18666ec94829ec6d2 | Text | 3,062 | 58 | # GSP_StructuralDecouplingIndex
Code to compute and test structural decoupling index (Preti and Van De Ville 2019)
The code includes two parts: the first part runs in Matlab (folder Matlab), while the second part (Neurosynth analysis) is implemented in Python (folder Python, code adapted from Margulies PNAS 2016).
... |
bd5b88017631315e1fafb15f5cc32508cdd1fd266c8b6ca03d961124fb5be4d3 | Text | 3,062 | 47 | # ProtoAgingMCMC
This folder contains the results and codes associated to a computational study aimed at exploring the effect of different neural strategies on the knee joint contact forces during walking in adults, exploiting the data from the ProtoAging study [^1] and the methods proposed by Uhlirch et al [^2] and Ka... |
c2c9fde0ab91576650131490e47f10a7e6b54ed3ea2f3246b7323218fb3e8eff | Text | 3,067 | 45 | # Geometric Intersection Point Computation and Modeling
Supplementary material for "Foot-ground force quantifies impaired balance control mechanisms post-stroke" (Shiozawa et al. 2026)
## Quick Start Guide:
1. Ensure that you have MATLAB R2024a or later installed, along with the following toolboxes:
> Control Syst... |
61faf1e9f91685d886f364eda6b54e7c3f322e9c82fcc04cb4c7c91fe6ef715e | Text | 3,083 | 62 | # Updates
## Create conda env - update.yml uses a python 3.9 environment
```
git clone https://github.com/nih-megcore/MegNET_2020.git
conda env create -n MegNET2020 --file MegNET_2020/conda_environment_update.yml
```
## Alternate install of conda env
```
mamba create megnet2022 python==3.9 pip -y
conda activate megne... |
7618bf66044425b08231def272840926262b66b099f422b4273414d2e749bc36 | Text | 3,086 | 110 | # BioGDR
The official implementation of "Multimodal interpretable deep learning for transcriptome-informed precision oncology and drug mechanism analysis".
<img width="4049" height="4715" alt="figure1" src="https://github.com/user-attachments/assets/40c87c47-297d-4938-8f85-fad98b691103" />
## 1. Requirements
- p... |
8f4ded75292f9ca2c90e7296fd4f0c4cbd9d7f4a29f15d3f1cb0dc67de68db3b | Text | 3,091 | 47 | PsPM-FER01 dataset
===================
Repository Version: 2019.11.27
This dataset includes pupil size response (PSR), skin conductance response (SCR), electrocardiogram (ECG) and respiration measurements. Also included are CS and US information and shock expectancy ratings at the end of the experiment for 30 he... |
1aa811da88dd2c5d3e56ba18f927ab3837b2de39e9feb12e52eb4d4c6b09e9d3 | Text | 3,101 | 47 | # SINTER3D
### SINTER3D is the first implicit neural representation-based framework for joint whole-transcriptome 3D interpolation.
SINTER3D learns the coordinated spatial distribution patterns of all genes within a unified framework, thereby supporting gene expres... |
a3c3cb265c233d6aab96cedb97c60fba181110693163af47ca366d2391454bd1 | Text | 3,113 | 135 | README – Dataset for
A Naturalistic Study on the Combined Neural and Psychological Effects of Psilocybin and Compassion Focused Imagery
This repository contains fully anonymized fMRI-derived functional connectivity data and self-reported questionnaire data supporting the associated manuscript.
fMRI Data
File: fMR... |
e01b19b9334942e43b98be3ffc96e33e4f2fda6a50c37c3c6b0f60e77525c4e6 | Text | 3,116 | 109 | # Basis Set Simulation
This project simulates semi-LASER basis sets using shaped refocusing pulses, producing .basis files compatible with conventional MRS fitting software. Simulated spectra are also generated and exported in PDF format. Core simulation routines leverage functions from FID-A and Osprey for accurate s... |
6c629266c7d54850ccc5f75ee48920798d40500ad5391008bc3a68936a7b976e | Text | 3,121 | 72 | # HSV-Wizard
Interactive HSV color threshold adjuster with calibration and measurement tools for scientific image analysis.
HSV-Wizard is a Python/Tkinter desktop application designed for microscopy and materials science workflows. It allows users to interactively segment images by HSV color thresholds, calibrate a s... |
2e24a73158d9bef7118b8f281b8e8addc9e4140299aa189b5fe03958795916fa | Text | 3,139 | 81 | ### Brain-cancer model v1
This is a Nextflow-based implementation of a predictive model compatible with the [MbCC](https://mbcc.pum.edu.pl/) model registry.
#### Run locally
1. Install Java with SDKMAN
```
curl -s https://get.sdkman.io | bash
sdk install java 17.0.10-tem
java -version
```
2. Install Nextflow
```
cu... |
58f9b73898a20432f7b78214d9dd299b381eccdad19b0f3596e8266281b7f66c | Text | 3,144 | 75 | # KnoMol
This is a Pytorch implementation of the paper: https://pubs.acs.org/doi/10.1021/acs.jcim.4c01092
## Installation
You can just execute following command to create the conda environment.
'''
conda create --name KnoMol --file requirements.txt
'''
## Usage
#### 1. Dataset ... |
0406d4ca38a8097cd3ef745c2ee6b00cf73194e177cb992c1b310ad9bd47be84 | Text | 3,152 | 78 | Overview
This MATLAB script performs calculations related to Unified Structural and Functional Connectivity (USFC) modeling for brain connectivity analysis. It processes subject-specific functional (FC) and structural (SC) connectivity matrices to compute various metrics and save the results for further analysis.
Prer... |
6701625e5b0228108cb3e217e9b4464f676cba48dcede3a7c9cad426e7178c9f | Text | 3,156 | 90 | # DeepCas12a: A Deep Learning Model for AsCas12a On-Target Efficiency Prediction
DeepCas12a predicts AsCas12a on-target guide efficiency from a 34 bp target-context sequence and two epigenetic feature channels: DNA methylation and chromatin accessibility. The model encodes the input as a multi-channel sequence represe... |
03a1935b8a4ea598616f48b4b1fe8a2871d8d1c06d38c19eb6b280dcde2a8f6d | Text | 3,162 | 47 | # optimap
[](https://optimap.readthedocs.org)
[](https://github.com/cardiacvision/optimap/actions/workflows/main.yml)
[
If you are using DL+DiReCT in your research, please cite ([bibtex](citations.bib)... |
ebc60220428adb9147681e220c2c030017e655f057a3ee016711efcb1a3339a0 | Text | 3,176 | 145 | # MLMarker
MLMarker is a Python package for tissue-specific proteomics prediction using machine learning, with integrated SHAP-based explainability features.
## Key Features
- **Dual Model Support**: Binary and quantitative tissue prediction models
- **SHAP-Based Predictions**: Uses SHAP values for more interpretabl... |
c70104996880ee74c5358a3ccffce9fa8b283083e41d8a6eec3544c732042fab | Text | 3,199 | 26 | # Requitements
All requirements are listed in the requirements.txt file which can be installed via *pip install requirements.txt*
# Deep Normative Modeling Scripts
| Folder | File Name | Description |
|---------------------|-... |
752fe85fb71f9b85a59aabf1fbc55c83241762b163e6e2a790e0f71f5cbe93a9 | Text | 3,207 | 78 | # VEEG-A-U-Net — Attention-Enhanced U-Net for Sensor-Efficient High-Density EEG Reconstruction
## Description
This repository serves as the journal appendix / reproducibility package for the manuscript:
**“Attention-Enhanced U-Net for Sensor-Efficient High-Density EEG Reconstruction in Wearable Brain Monitoring Syste... |
87712608125a88cf0b75a3b374669137a940bc7cbfbae1c467466865102a99c2 | Text | 3,207 | 98 | # Heart failure detection in electrocardiograms using artificial intelligence and pragmatic labelling
[](https://www.nature.com/articles/s41746-026-02774-4)
---
## ️ Project Structure
Code is located under the `src/` folder with the... |
9a5c2f2f97b240b06da9bf13c874c9deff0e6449eedd522e27334ca65f0e5966 | Text | 3,209 | 66 | # `ComptoxAI`
[](https://zenodo.org/badge/latestdoi/202416245)
[](https://github.com/jdromano2/comptox_ai/actions/workflows/ci-python-test.yml)
[, ICML 2024.
### Installation
To clone this repository:
```
git clone https://github.com/cheliu-computation/MERL.git
```
### Dataset download... |
8158a7879226885c351dbeddc0cc78509e25ae231a7c4cb6f0159237203a3ccc | Text | 3,236 | 55 | # AutoCurationKilosort: Automated Curation for Kilosort Output
[](https://github.com/jiumao2/AutoCurationKilosort)
**AutoCurationKilosort** is a MATLAB-based pipeline designed to streamline and automate the curati... |
2ee77f047ab705ba94be4e58c4438a4864fc73ad54d1f086b325d64f5903b0cc | Text | 3,242 | 60 | This repo contains code for training response optimized models and dissecting their hidden unit activations.
Methodological details and results are described in this paper: https://www.biorxiv.org/content/10.1101/2022.03.16.484578v1
A note on dataloaders:
Dataloaders expect the following data:
stimuli_all_subs.np... |
214bcd851df74688ca2bcab1a8eed9b697d5518a2f31e40532ec24e73a1e8899 | Text | 3,256 | 44 | # Enhanced Locally low-rank Imaging for Tissue contrast Enhancement (ELITE)
This repository contains MATLAB and Python scripts to replicate our reconstruction framework for dynamic MRI radial k-space data, specifically designed for Dynamic Contrast-Enhanced (DCE) breast MRI. The reconstruction framework incorporates a... |
2585f70446eedc16bf094feea8c0c71599a9af5724b58243267bef2d4a12a42f | Text | 3,275 | 52 | # Rapid and Energy-Efficient Ultra-Large Library Screening for Drug Discovery on a SpiNNaker2 Neuromorphic Chip
Software stack for the scientific work "Rapid and Energy-Efficient Ultra-Large Library Screening for
Drug Discovery on a SpiNNaker2 Neuromorphic Chip".
For the code version used to generate the published re... |
83a690fcf0739dd24f5848a67ed648c9c3a5b38c16e686682a0534ce15b67ab8 | Text | 3,276 | 62 | <p align="center">
<img src="archvelo_LOGO.jpg" alt="ArchVelo Logo" width="200"/>
</p>
ArchVelo is a method for modeling gene regulation and inferring cell trajectories using simultaneous single-cell chromatin accessibility and transcriptomic profiling (scRNA+ATAC-seq). ArchVelo extracts a set of shared **archetypal... |
548ce9b801e033f64a8824d3c46f9705c3a8dd9140c08ca6c959b256cea8a6e8 | Text | 3,281 | 110 | # TACMAN
## Overview
## Create runtime environment
```bash
# create environment
conda create --name TACMAN --file require_TACMAN_conda --yes
conda activate TACMAN
### for interactive mode in Jupytor
python -m ipykernel install --user --name 'TACMAN' --display-name 'TACMAN'
```
## Demo scrip... |
9b2363e3e08cf948119392e08df77a77b3b5b58f7d16778b7dd5278a452b29be | Text | 3,292 | 59 | # Multiple sclerosis cortical and WM lesion segmentation at 3T MRI: a deep learning method based on FLAIR and MP2RAGE
This is the code repository of the Neuroimage: Clinical [paper](https://doi.org/10.1016/j.nicl.2020.102335).
## Overview
This software provide a multiple sclerosis cortical and white matter lesion seg... |
dd75032dc140cf5bf14e271b30637288741ab6b1797cb26625bcc3ed147e7cec | Text | 3,293 | 59 | # Multiple sclerosis cortical and WM lesion segmentation at 3T MRI: a deep learning method based on FLAIR and MP2RAGE
This is the code repository of the Neuroimage: Clinical [paper](https://doi.org/10.1016/j.nicl.2020.102335).
## Overview
This software provide a multiple sclerosis cortical and white matter lesion seg... |
c8874da63d28c0ddfc2d80257dd6353430a4af5199922f0df154287df32e892d | Text | 3,295 | 72 | # Leveraging Geometric Deep Learning for Epidemic Network Reconstruction
This repository contains the code and supporting materials for the manuscript **"Leveraging Geometric Deep Learning for Epidemic Network Reconstruction"**. The project demonstrates a novel approach using Graph Neural Networks (GNNs) to impute soc... |
f91f6a23537f67b095741f421c0a5056f656730c487cfe40ae77e14ff9f9d9da | Text | 3,296 | 37 | # Lingpred
Code and preprocessed data used for the analysis in the following journal article:
Schönmann, I., Szewczyk, J., de Lange, F. P., & Heilbron, M. (2025). Stimulus dependencies—rather than next-word prediction—can explain pre-onset brain encoding during natural listening. _ELife_.
**For access to the neural,... |
c9078a35ede8a24a39b6d3b54ea74525d5c243c51aa4b1dc089bcbf2475f8d6d | Text | 3,297 | 81 | # Sigma Receptor Co-Expression Architecture Divergence (WJ-Native)
Weighted Jaccard analysis of continuous genome-wide Spearman correlation vectors reveals that SIGMAR1 (sigma-1) and TMEM97 (sigma-2) share 96.4% of their global co-expression architecture but diverge at their most functionally relevant partners (binary... |
9bdf8aff2b9ddc17141b71692456c8a2f143742d2fc2a544ee1e2645ab67c9b2 | Text | 3,298 | 38 | # CBC-Based Ferritin Estimation using Machine Learning
This repository contains the official Python implementation and Jupyter Notebooks for the data preprocessing, hyperparameter optimization, and model training processes associated with our manuscript on predicting continuous and binary ferritin levels using Complet... |
a40d57234971640f9817d6763ffff4696ea63646b5ce006ceb446a376bdda12c | Text | 3,313 | 57 | # Notebook Documentation: Intrinsic Dimension Estimation with lFCI
## Overview
This documentation describes two Jupyter notebooks designed for **Intrinsic Dimension (ID) estimation** using the **Local Full Correlation Integral (lFCI)** method, as proposed in the paper *"Exploring neural manifolds across a wide range o... |
2498bd1b33d52eb96e7fd98513cf504d5755dc72435a93bf97cacb3a14f0ffac | Text | 3,322 | 44 | **Authors:** Meriam Zid, Veldon-James Laurie, Jorge Ramírez-Ruiz, Alix Lavigne-Champagne, Akram Shourkeshti, Dameon Harrell, Alexander B. Herman, R. Becket Ebitz.
**Link to paper:** [Version 2](https://www.biorxiv.org/content/10.1101/2024.07.08.602539v2)
**Link to official version:** to be added.
## Overview
This r... |
c45ade38e6c6baa04963d72d424c275ee03c9acbbff953ce8c0f626d7e0fa9bd | Text | 3,322 | 65 | # Sensory-association-training-behavior
This usage of this algorithm has been outlined below.
## Installation
Git clone the web URL or download ZIP.
Change your current working directory to the location where you want the cloned directory to be made.
```bash
git clone https://github.com/barthlab/Sensory-associati... |
b30f4c1ebbd897697b23e148cf207dda930636bf6e1284e7d3797a7d950a8974 | Text | 3,338 | 102 | # DeepDendrite-modularization
Extension to [DeepDendrite](https://github.com/pkuzyc/DeepDendrite) with modularized layer APIs for constructing & data-driven training of multi-layer, detailed multi-compartment neural networks.
Code associated with the paper "[Gan He, Kai Du and Tiejun Huang, (2026). Going deeper with m... |
56f81a13cbe39b564981b09e3a03c3b32979a66e191c7a7b337c026e62683a29 | Text | 3,340 | 136 | # Uni-Mol-MeCAP
Uni-Mol-backbone Methyl Cation/Anion Affinity Predictor
<p align="left">
<img src="fig/toc.jpg" width="500"/>
</p>
## Environment
All requirements are listed in`./envs/environments.yml`.
Create the conda environment with:
```bash
conda env create -f ./envs/environment.yml -n mecap
```
## Training... |
b10cf233c2a16029c0853583c2229cad6a434c36dd5ffd2c1e83348e8db0ee42 | Text | 3,347 | 48 | This README is a short introduction to the analytical pipeline used in the paper "Respiratory pauses highlight sleep architecture in mice" - Casali et al., 2026, Nature Communications.
For technical info please contact
Dr. Giulio Casali (giulio.casali.proATgmail.com)
Tim Gervois (tim.gervoisATu-bordeaux.fr)
Dr. Nicol... |
c96c5ab8a11fea24f0a3ae615b0750c804c66adfb0ec8a2c55fb11e0734019d3 | Text | 3,348 | 47 | # SemMol
Augmenting molecular structure representation learning using semantic biomedical knowledge
[](https://doi.org/10.5281/zenodo.20710533)
### Requirements
- Python ≥ 3.8.0;
- ```requirements.txt``` contains the Python packages requirements.
### Data
The data used a... |
60a78686bd8dc6428f0d7fa42a10e8c8388d46fd9ab7d9cb42d9de989cecf023 | Text | 3,366 | 47 | # SemMol
Augmenting molecular structure representation learning using semantic biomedical knowledge
[](https://doi.org/10.5281/zenodo.13946620)
### Requirements
- Python ≥ 3.8.0;
- ```requirements.txt``` contains the Python packages requirements.
### Da... |
ad05d47df3d76546a87e20b38cf9993f1dca91257bd050fb00877525c44b5c86 | Text | 3,370 | 52 | # memoryaha
Preprint can be found [here](https://www.biorxiv.org/content/10.1101/2025.03.12.642853v1).
Raw and processed fMRI data are shared in [OpenNeuro](https://openneuro.org/datasets/ds005658).
## installation
To run the codes, which reproduce results in the manuscript, it is necessary to install the Python pack... |
e5d211796c01fd8387c87e97f9f6518fb1924a54105875ccd74d5c3165448f9a | Text | 3,378 | 82 | # What makes a lonely child: Environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study
## Overview
This project investigates multilevel correlates of **prospective loneliness** in late childhood using data from the Adolescent Brain Cognitive Development (ABCD) Study. The... |
fb81161f79f382489572e1c6008fe2c4f36836db2071f4f45ea7c26c3c04081b | Text | 3,380 | 49 | PsPM-PCF3 dataset
=================
Repository Version: 2024.04.11
This dataset contains skin conductance responses (SCR), heart beat time stamps from a pulse oxymeter (HB), respiration, pupil size (PSR), and gaze coordinates measurements for 31 healthy individuals (15 females, mean age +- standard deviation: 31... |
3a306461375734417dd0d66297a8e226c9855a6a7fdb46774c47842b65159a83 | Text | 3,381 | 90 | # Cellular Signatures of Melanocortin Pathway Genes Across the Locus Coeruleus
This repository contains the analysis code accompanying the manuscript:
> **Cellular Signatures of Melanocortin Pathway Genes Across the Locus Coeruleus**
> Basak A, Erol FMB, De Rosa MC, et al. *Acta Neuropathologica Communications* (20... |
b67efd35c66996838066a44aa9b0faa9ee1231969849a8dda8bf57cec9d9c109 | Text | 3,388 | 73 | # Unsupervised Aspect Extraction
Codes and Dataset for ACL2017 paper ‘‘An unsupervised neural attention model for aspect extraction’’. [(pdf)](http://aclweb.org/anthology/P/P17/P17-1036.pdf)
## Data
You can find the pre-processed datasets and the pre-trained word embeddings in [[Download]](https://drive.google.com/ope... |
543b8cf94ac45d1afa14873f8a65ad9131cc40a4b09f76e536d3ba5a0d040082 | Text | 3,392 | 88 | # AI-Based Analysis of Key Predictors of CO₂ Emissions Across Income Groups
Code accompanying the iScience article *"AI-Based Analysis of Key Predictors
of CO₂ Emissions Across Income Groups"* (Fannouch & Tounsi, Laboratory of
Applied Economics, Mohammed V University, Rabat, Morocco).
This repository contains the ful... |
92ffc6729196d9012286384f918681ac8bdd257e7ac4e806bcce44bfdb767074 | Text | 3,396 | 110 | Graph Convolutional Networks for Inferring
Cell-Cell Communication from Spatial
Transcriptomics Data
========================================
SPatial Inference of Communication Effects (SPICE)
========================================
<!-- 
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[](https://github.com/cardiacvision/optimap/actions/workflows/main.yml)
[** by Fe... |
54fd2a527dd4a36c7d38b3cb45dd722518ce7354a0312ae3b9af00391da3b0b5 | Text | 3,406 | 107 | # CNN-ENCODER-XGBOOST Genotype-Tissue Expression Profile Simulator
This notebook provides the source code for the CEX pipeline, a genotype-tissue expression profile simulator.
It consists of the following module.
1. Vicinity Set Cover Algorithm for Solving Reference Genes in the Human Genome
2. Build the CNN Module
3... |
9bf5f56e2e8699f8cfa73a8fa66578e7ad840b4fad2b73370f828fd3314e5024 | Text | 3,408 | 98 | # LiteSensor-Net MDPI Reproducibility Package
This folder is prepared for GitHub upload with the code, raw data, and raw result files supporting the revised manuscript:
**Drift-Robust Lightweight Deep Learning for CBRN-Motivated Edge Gas-Sensor Classification: A Benchmark Study Using Open Gas Sensor Data**
Manuscrip... |
1e9e683fe5b10b0fa593de714a985022b88cce154ecc1402ec48d7e6af2aa99c | Text | 3,417 | 70 | # Stan models for reward/punishment-learning interference
Computational-modeling code accompanying:
> Lin WW, Lee PY, Tsai HY, Lin YH, Lin MM, Lu ZL, Yeh MY, Tseng MT.
> "Competing value signals impair reward-learning via dopaminergic mechanisms and increase exploration" *PLOS Biology* (2026).
This repository contai... |
6afd1d58d6f9d8e7d1b7153bf7d72d4a1b21b2edbb288df9ccdd7c8ef2ad354e | Text | 3,420 | 62 | # Cross-species alignment
- Ref: [Xu, Nenning et al., (2020). Cross-species functional alignment reveals evolutionary hierarchy within the connectome. NeuroImage, 223,117346](https://www.sciencedirect.com/science/article/pii/S1053811920308326)
- Download [https://github.com/TingsterX/alignment_macaque-human](https://g... |
185e2a05fd6f37f84ae3614aafadba226d4cf53f4bcae615a527dc365d3158a2 | Text | 3,427 | 73 | # Robust Disease Prognosis via Diagnostic Knowledge Preservation
This repository contains the official PyTorch implementation of the paper:
**"Robust Disease Prognosis via Diagnostic Knowledge Preservation: A Sequential Learning Approach"**.
The code implements a **Sequential Learning with Experience Replay** framewo... |
bd68ba9d85decb9a24cc1b5d6dc6bfbbb94cdc537dfaac2d7a1d734215c6b0b3 | Text | 3,430 | 81 | # Towards Reliable Transient Stability Prediction of Power Systems: A CNN-based Deep Ensemble Model with Optimized Class-Specific Thresholds
This repository provides the MATLAB implementation associated with the paper:
**Towards Reliable Transient Stability Prediction of Power Systems: A CNN-based Deep Ensemble Model... |
c246e4097d25f04c60549b7be9731aceea8c5b66ddd24dfd72c764ab1d801125 | Text | 3,434 | 52 | # ConnectivityAdaptation
Matlab code to reproduce figures for "Adaptation modulates effective connectivity and network stability" by Thomas J. Richner, Martynas Dervinis, and Brian N. Lundstrom
This repo is an organized subset and fixed snapshot of two other repos:
https://github.com/TomRichner/RandomMatrixTheory
http... |
672848ab579e7fb038a437a096940192bbca5b542cf304579f0c7547bcc1e18e | Text | 3,437 | 107 | # PyMeshLab
[](https://doi.org/10.5281/zenodo.4438750)
[](https://github.com/cnr-isti-vclab/PyMeshLab/actions/workflows/BuildAndTest.yml)
[](https://doi.org/10.5281/zenodo.14040699)
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<u>S</u>emi-<u>a</u>utomated <u>H</u>and <u>A</u>nnotation for Single
Cell and Spati... |
e8cda21732c5ba482be8a66af44f3ec4a57aef48c32a0841b8dbf45f266fc86a | Text | 3,454 | 57 | # Scalable Boltzmann Generators for equilibrium sampling of large-scale materials
Maximilian Schebek, Frank Noé, Jutta Rogal
[](https://arxiv.org/abs/2509.25486)
[![Nature Communications](https://img.shields.io/badge/Nature_Communications-published-1D... |
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