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efebeaa86a71c6f27a2b76a4d52092c1675b9cc4878d629b64f890a2a8ddc944 | Text | 3,694 | 40 | # Machine-learning for the prediction of one-year seizure recurrence based on routine electroencephalography
Link to article: [Machine-learning for the prediction of one-year seizure recurrence based on routine electroencephalography](https://www.nature.com/articles/s41598-023-39799-8).
By [Émile Lemoine](https://www... |
7923939caca2a161e5edd654eb6c8e14da2494ef1e2296313d61864e5c2f0aac | Text | 3,727 | 56 | # Data mining of receptor autoradiography data with statistics and machine learning
# Description
The code performs a series of multivariate stats, dimensionaltiy reduction, machine learning (support vector regression) analysis, as well as feature selection (recur... |
a4d9a229d1c3c342850fc08b9da9dac37fd1c603d94e03999c9c8027e70c9ac1 | Text | 3,760 | 64 | <!--
* @Author: ----
* @Date: 2022-04-09 11:57:47
* @LastEditors: GhMa
* @LastEditTime: 2023-05-02 19:35:49
-->
<img src="https://github.com/genema/Noisy-Spiking-Neuron-Nets/raw/master/proj_logo.jpg" width="200px" align="left">
# Noisy Spiking Neural Networks
: van
de Geijn B\*, McVicker G\... |
b3872fb075b4ed367c4c37b00395363200f48249d5dc2a3c4b94cae8b5367cb4 | Text | 3,943 | 98 | [](https://github.com/zining01/gGnome/actions/workflows/check-release.yaml)
[](https://codecov.io/github/mskilab/gGnome?branch=master)
# gGnome
```
... |
837d071b0e6cdfae1eec65faee81d74d50a7824072508bfde9bf26cf7308c901 | Text | 3,946 | 67 | # DSMRI
**DSMRI: Domain Shift Analyzer for Multi-Center MRI Datasets**
The paper has been published in the Journal of Diagnostics.
Link: https://doi.org/10.3390/diagnostics13182947.
```
@article{kushol2023dsmri,
title={Dsmri: Domain shift analyzer for multi-center mri datasets},
author={Kushol, Rafsanjany and Wil... |
d2816046bcd4fdade290869bc00071c9be32441440cda1bf004b2653d8435dce | Text | 3,961 | 99 | [](https://zenodo.org/badge/latestdoi/416769460)
[](https://github.com/darikoneil/Pat-Map/graphs/contributors)
## `code`... |
8777c544e552ddd623097cf963d4a47c0e18fc3bccea78a149df345ffbfb687b | Text | 4,168 | 114 | # GSFA
`GSFA` (Guided Sparse Factor Analysis) is an R package (accelerated by Rcpp)
that performs sparse factor analysis and differential gene expression discovery
simultaneously on single-cell RNA-seq with multiplexed CRISPR screen
(e.g. CROP-seq, Perturb-seq) data.
The method assumes that the perturbation of a t... |
1e0376ddc0d6d321e5681ea38348f134413314ac744e8a42f7c0bd75fd40f013 | Text | 4,200 | 94 | # daart: deep learning for animal action recognition toolbox
[](https://sandbox.zenodo.org/badge/latestdoi/334987729)
A collection of tools for the discrete classification of animal behaviors using low-dimensional representations of videos (such as skeletons provi... |
c6b2d66fc0513ec7fc3e43f4bc2524b4f238f273bdcd52395282d10406955bc0 | Text | 4,200 | 68 | # Transcriptomic-analysis-of-light-induced-genes-in-Nasonia-vitripennis-implications-for-circadian
## Information
This folder contains all the scripts needed to reproduce the analysis of RNAseq data from Nasonia vitripennis, published in the special issue Biological Rhythms and Molecular Clockworks in Physiology and ... |
54b0b0d3bc4f82e888dfe04aa9585df4602de46d485becd43ed744ae48046c98 | Text | 4,209 | 79 | [](https://github.com/rderelle/Broccoli/actions/workflows/build.yml)
[](https://github.com/rderelle/Broccoli/actions/workflows/clip... |
e1366f6e4e709bdb7a3e66da2237b13bcc470017955a2425a92f61246922234d | Text | 4,278 | 30 | # Neurophysiological signatures of cortical micro-architecture
This repository contains processing scripts and data in support of the paper:
Shafiei, G., Fulcher, B. D., Voytek, B., Satterthwaite, T. D., Baillet, S., & Misic, B. (2023). Neurophysiological signatures of cortical micro-architecture. _Nature Communicatio... |
8ac8bc02b09949fb4826ac0ee760e734dae9a55458e70aad2fd174dcd0005228 | Text | 4,303 | 97 | # Focus On Depth - A single DPT encoder for AutoFocus application and Dense Prediction Tasks
 risk-controlling prediction framework. <br>
### Learn Then Test
The [Learn Then Test] method is a post-processing procedure applied to model predictions in order to control a risk, for example
false alarm rate. The prediction m... |
ef948334cf941b3204c3086dbcab47b5cfd06f618702cc1fb530418b3fcc7280 | Text | 4,401 | 79 | # TouchCog
## Hardware Requirements
Computer with 64-bit Windows, MacOS, or Linux Distribution (Debian, Ubuntu, Raspbian, etc.). ChromeOS Linux also supported.
For touch input, the system must utilize touchscreen technology (e.g. capacitive, IR, etc.)
## Software Requirements
In order to run the scripts, you will ne... |
b0ee52a352d169a10f2e36d6d8b79ce92dde9ca17290fa169b37458af9d9383d | Text | 4,423 | 76 | # KNDy-Ca-1
The MATLAB pipeline, the R step that removes inactive ROIs, and the R Shiny app that drew the
before/after plots, behind the calcium-event analysis
in the KNDy manuscript: import and motion correction, hand-drawn ROIs, ΔF/F₀, event detection
(custard, slow, and FAST = custard minus slow), export to CSV, in... |
c74ae026feb6d5dcc64c83c1b04d06599d4e2e06a8842a2d6bfd9a3737aa918b | Text | 4,458 | 125 | DTOR
==============================
DTOR is a project originally designed to assist with the AI-based extraction of features
for treatment response prediction
Project Organization
------------
├── LICENSE
├── README.md <- The top-level README for developers using this project.
├── config ... |
a07dd2e0124a46be50e2613def03a75708cf986cf74082f5bd8977e9a6dde4c0 | Text | 4,478 | 54 | Laminar electrophysiology of primate visual cortex during priming of pop-out visual search
Jake Westerberg
Behavior - Reaction Time, Accuracy
Eye Tracking - Single eye position, x and y coordinates, millisecond precision (x-position/y-position x time x trial)
MUA (Multi... |
7e3f16a68600a81b2820434a001d1855e7e3d13ae16815a60577909b9d484da2 | Text | 4,565 | 61 | # Machine Learning Analysis of Raman Spectra to Quantify the Organic Constituents in Complex Organic-Mineral Mixtures
Welcome to the Raman analysis repository! This repository contains code, data, and documentation related to the analysis of memetic organic-mineral soil composition using Raman spectroscopy. The projec... |
0a006780f4128a61f73adea48d6e582168156e16160da05d904f9ca12c6c915f | Text | 4,572 | 67 | ## Visual Oddity
This repository contains code material for the publication:
S. Woźniak, H. Jónsson, G. Cherubini, A. Pantazi, and E. Eleftheriou, ‘On the visual analytic intelligence of neural networks’.
In particular, the code implements programmatic generation of a dataset for the visual oddity task. The tas... |
edb177b81bb3cac9d3b71b4898ee754a1e72458e3908d8da37726a97d26e9b3f | Text | 4,580 | 123 | # TreFiDe - Trend Filter Denoising
TreFiDe is the software package accompanying the research publication
["Penalized matrix decomposition for denoising, compression, and improved
demixing of functional imaging data"](https://doi.org/10.1101/334706).
TreFiDe is an imporved appproach to compressing and denoising functi... |
69ca31c025cc26690bc020d752f8b1ef46a702c54a0b6cad1b6c9c31c48f747c | Text | 4,627 | 70 | # DISCOVER-EEG: an EEG pipeline for biomarker discovery
This is a workflow that automatically preprocess, analyzes and visualizes resting state EEG data in Matlab using EEGLab and FieldTrip toolboxes. It has been tested on the [LEMON dataset](https://www.nature.com/articles/sdata2018308), the [TD-BRAIN dataset](htt... |
5737b31b4ea4a74e48653128d70a4fee07890f6955f41bd10713ae4bcb07290b | Text | 4,708 | 68 | # TCAG-WGS-CNV-workflow
This repository contains scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods.
If you use any of these scripts, please cite:
B. Trost, S. Walker, Z. Wang, B. Thiruvahindrapuram, J.R. MacDonald, W.W.L. Sung, S.L. Pereira, J. Whitney, A.J.S. Chan, G. P... |
7fe2eb3a915ff6602a9aac76be4143d8e3643f0d6e38910403b719a9c53162cb | Text | 4,724 | 70 | # Brain-Diffuser
Official repository for the paper ["**Brain-Diffuser: Natural scene reconstruction from fMRI signals using generative latent diffusion**"](https://arxiv.org/abs/2303.05334) by Furkan Ozcelik and Rufin VanRullen.
## Results
The following are a few reconstructions obtained :
<p align="center"><img src=... |
32c34df1de1bdb54d41bbd5e4213f8b69fcb0a9772fe16a529bdc289054cc8f0 | Text | 4,730 | 149 | # LatentVelo
Estimating RNA velocity in a learned latent space, enabling batch correction and dynamics based embeddings.
Pre-print available at https://www.biorxiv.org/content/10.1101/2022.08.22.504858v2
# Reproducing results
The paper_notebooks/ directory run... |
20b2ca3e3fab5ff59948a7c41ca71391cd1189693fe1a36761fc6463b4ee8bee | Text | 4,778 | 85 | # Bidirectional-PDP
This repo implements our paper:
[Lim, O'Brien, & Onnis (2023)](https://doi.org/10.3758/s13428-023-02094-5), “Orthography-phonology consistency in English: Theory- and data-driven measures and their impact on auditory vs. visual word recognition,” in Behavior Research Methods.
Please cite our paper... |
d6e4964b84e1795eb6192a6be721edc2b9f023ad5fafd31d1ff671de9a8a3ec5 | Text | 4,786 | 109 | # GM-AE
The repository of [GM-AE](https://github.com/liaw05/GM-AE) is an implementation of the paper '[Parameterized Gompertz-guided Morphological AutoEncoder for Predicting Pulmonary Nodule Growth](https://ieeexplore.ieee.org/document/10189348)', accepted by TMI.
Nodules used for [GM-AE](https://github.com/liaw05/GM-... |
519b436ec1c9829b657b0824ad113c97dd8667be8eb8abb2048d0eb78d5ff751 | Text | 4,860 | 131 | [](https://zenodo.org/badge/latestdoi/341508464)
[](https://coveralls.io/github/Tevien/dtor?branch=main)
DTOR
====... |
441c4c722a80da3bb98306e29cf5321b66fbe60a21e641542d69352307f4c58e | Text | 4,864 | 151 | # Keras Attention Layer
[](https://pepy.tech/project/attention)
[](https://pepy.tech/project/attention)
[](https://github.com/philipperemy/keras... |
cda56453c957d6f733ce0e218b0d45ad2858f399a1927fc05c54358c1f7dedfb | Text | 4,878 | 119 | #######
keras2c
#######
|Python-Publish| |Python-Versions| |Codecov|
|License| |DOI|
keras2c is a library for deploying keras neural networks in C99, using only standard libraries. It is designed to be as simple as possible for real-time applications.
Please cite `this paper <https://doi.org/10.1016/j.engappai.202... |
e8366429ea63333dd56394784fc5d408d275262e918809788d17d94282914637 | Text | 4,907 | 133 | #### This toolbox is no longer supported by its author. The code is working on the last 2015 Matlab version, but may not be compatible with future versions. Consider using [pyRiemann](http://pythonhosted.org/pyriemann/) as a (python) alternative.
Fee free to fork the toolbox and start your own support :)
# Covariance... |
c74faf8a07a9252e3bbb21611ca506ee0df105b5576d24e6cb51d5b36f67a218 | Text | 4,949 | 76 | # How can SHAP values help to shape metabolic stability of chemical compounds?
This repository accompanies article [How can SHAP values help to shape metabolic stability of chemical compounds?](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00542-y) by Agnieszka Wojtuch, Rafał Jankowski, and Sabina Pod... |
ade7d79098e68caaa2fe22f3435a6c732d0774310268c3ff743421e462775cb6 | Text | 4,972 | 81 | 
Automatic **EX**traction, **S**eparation, and **C**aption-based natural **L**anguage **A**nnotation of **IM**ages from scientific figures
[[wiki](https://github.com/MaterialEyes/exsclaim/wiki)] [[paper](https://arxiv.org/abs/2103.1... |
47b60c1665d3570cd26aadd68c01b528f085456d91cff76104bff29051b30b57 | Text | 5,042 | 55 | # Phase to Rate Coding
This is the code underlying a research project where we investigate how spatial phase information in grid cells is processed in a biophysically
realistic model of the dentate gyrus. The main purpose of this repository is to make the code we wrote for the project available and reproduce our findin... |
18d18e7ad1ff14731de22cf1f3df3fe668cba80660b59f47c287ba7e471b6fef | Text | 5,093 | 140 | # AscatNGS
| Master | Develop |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
AscatNG... |
28e6bc974273fc4fc4c8bbbb303c6192dc43e5dbfa3881ff695cafd8ba1894d6 | Text | 5,389 | 140 | # Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
This repository accompanies article [*Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction*](https://arxiv.org/abs/2012.04444) by Agnieszka Pocha, Tomasz Danel, Sabina Podlewska, Jac... |
6b2ac59c29e2055f3fca39048525d120d81d6439b53c1cb446ec939113945343 | Text | 5,424 | 154 | # Biologically Informed Neural Network (BINN)
[](https://github.com/InfectionMedicineProteomics/BINN/actions/workflows/pages/pages-build-deployment)
[](https://paperswithcode.com/sota/univariate-time-series-forecasting-on-aep?p=multi-horizon-short-term-load-forecasting)
[](https://pypi.org/project/pydapsys/)
PyDapsys is a package to read neurography recordings made with [DAPSYS](http://dapsys.net/) (Data Acquisition Processor System). It is based on a reverse-engineered... |
f1dc612c90e7f568c93055ec46e2c096b0dafab11b391b38bccea2f08efe6f95 | Text | 5,596 | 107 | Welcome to DASH
==============================
|**Status**| [](https://github.com/rinikerlab/DASH-tree/actions/workflows/CI.yaml) [](https://githu... |
4b7dbdd85e763e6d829b168c3fbdfc81b198788a99cda2cd10e74d0a2ab92b79 | Text | 5,650 | 94 | # BARNACLE
RNA Contact prediction with deep learning
## Running scripts
- Scripts for running different methods are in the `scripts` folder
- NOTE: these scripts will likely take a very long time on a desktop computer without a datacenter grade GPU.
- train.py runs the self-supervised pre-training. On four A100 ... |
885424e599e692e4ac13c5b8b94913925dc770f09e2387832bcd4865b473c217 | Text | 5,686 | 118 | # Autoformer (NeurIPS 2021)
Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting
Time series forecasting is a critical demand for real applications. Enlighted by the classic time series analysis and stochastic process theory, we propose the Autoformer as a general series forec... |
40f6ac460d04e4664fe9e52b40475178645970a7779eaced0b924ee890ee3014 | Text | 5,726 | 146 | # Sequence assignment validation in cryo-EM models with checkMySequence
- [How to cite](#how-to-cite)
- [Installation](#installation)
- [installing from source](#source-installation)
- [troubleshooting](#troubleshooting)
- [Test your installation](#test-your-installation)
- [How to use checkMySequence](#how-to-u... |
d94ad1d98fefbab9274b22c950bef3c9ab0b3eaa60cea1af3f33ac52b788c1bc | Text | 5,818 | 158 | # GMTransformer for molecular design
-a probablistic generative transformer neural network model for molecular design
This repository contains the datasets and link to the code for our paper:
[**GENERATIVE TRANSFORMER LANGUAGE MODELS FOR GENERATIVE AND TINKERING DESIGN OF MOLECULES**](https://jcheminf.biomedcentral.... |
6942c517e29be89c759ed8e5395ca43267ec0c8c6f2a32b5cbcd82cd407ba984 | Text | 6,059 | 110 | 
Automatic **EX**traction, **S**eparation, and **C**aption-based natural **L**anguage **A**nnotation of **IM**ages from scientific figures
[[wiki](https://github.com/MaterialEyes/exsclaim/wiki)] [[paper](https://arxiv.org/abs/2103.10... |
c77fac95ee3287cc9e9aaac57c2c25eb50d382cb8bac4c8122c3ea1cb793a142 | Text | 6,138 | 75 | # In-Context Operator Networks (ICON)
This repository contains the code for the following papers. Feel free to star this repository and cite our papers if you find it useful for your research. You can find the citation details below.
This repository serves solely as an archive and is not actively maintained. For tuto... |
d5c7bd2427990063495339811c8b6e7bdf07040c0f402b033dbc00bd358d5cfd | Text | 6,148 | 112 | # computeUI
This repository provides code to compute the information decomposition defined in [*Quantifying Unique Information*](http://dx.doi.org/10.3390/e16042161).
The code implements the admUI algorithm proposed by Banerjee, et al. in [*Computing the Unique Information*](https://arxiv.org/abs/1709.07487).
The rep... |
2e762dae7dfb0a82fc06c12bc2c3a6374eee287227fbad4693540740f47148c4 | Text | 6,340 | 137 | .. raw:: html
<a href="https://foolbox.jonasrauber.de"><img src="https://raw.githubusercontent.com/bethgelab/foolbox/master/guide/.vuepress/public/logo_small.png" align="right" /></a>
.. image:: https://badge.fury.io/py/foolbox.svg
:target: https://badge.fury.io/py/foolbox
.. image:: https://readthedocs.org/pr... |
30763c6ded6267aca33afb6c9f978775568abd233f996632f0ac0a8dc4c4e1e8 | Text | 6,356 | 111 | <div align="center">
<img src="assets/accum_grad_v5.png" width="30%" alt='gradient-accumulator'>
<h1 align="center">GradientAccumulator</h1>
<h3 align="center">Seemless gradient accumulation for TensorFlow 2</h3>
[](... |
d092d995a9ef2a58f75fb60d659d04425c20b9a68a29bf923065ed78e8b5385f | Text | 6,463 | 40 | # Archived
This repo is no longer maintained. For questions on this reop please email Honghan directly (honghan.wu@gmail.com), or for broader CogStack enquiries please reach out to contact@cogstack.org
# SemEHR
Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitme... |
7fd203c1a7e0ef50aa4a22fee43fe1406b0517c4cc171bf54124fed32ee5851c | Text | 6,520 | 153 | # DSL
Official implementation of paper "Mining Multi-Center Heterogeneous Medical Data with Distributed Synthetic Learning"
## System Requirements
- Hardware:
- One Nvidia GPU with video memory 12GB+
- Software:
- Linux(we use Ubuntu 18.04.5)
- Python 3.6
- pytorch 1.3.1+
- CUDA10.0
## Installati... |
d84520eb9a3273b21b67c0f84053d26e0344b2fb7ae4c7c55192ce53439519bc | Text | 6,586 | 78 | # Evaluation of Medical Image Segmentation Models for UncertainSmallEmpty Reference Annotations
[paper](https://doi.org/10.1016/j.media.2023.102927) ([preprint](https://doi.org/10.48550/arXiv.2209.13008))
Uncertain: inter-**expert** variability (can be quantified by comparing segmentations of two experts with this eva... |
134c367ab31a2b1b2b7af6ab46fdee27170bdb3944911c5e5f157674e0a5ebb8 | Text | 6,617 | 156 | # DSL
[](https://zenodo.org/badge/latestdoi/531561838)
Official implementation of paper "Mining Multi-Center Heterogeneous Medical Data with Distributed Synthetic Learning"
## System Requirements
- Hardware:
- One Nvidia GPU with video memory 12GB+
- Software:
-... |
c65cd1a3ff18b7a0121ef6ad04ba1bf50f0de2954ea51e96c29e13b8e29acade | Text | 6,686 | 129 | # PyDapsys - Read DAPSYS recordings with Python
[](https://pypi.org/project/pydapsys/) [](https://doi.org/10.3389/fninf.2023.1250260)
[.
## 目录
* [简介](#一简介)
* [任务说明](#二任务说明)
* [FAQ](#faq)
## 一、简介
法律智能旨在赋予机器阅读理解法律文本与定量分析案例的能力，完成罪名预测、法律条款推荐、刑期预测等具有实际应用需求的任务，有望辅助法官、律师等人士更加高效地进行法律判决。近年来，以深度学习和自然语言处理为代表的人工智能技术取得巨大突破，也开始在法律智能领域崭露头角，受到学术界和产业... |
ec5f58d414c4eaddd571e9be222937172617a301473f3d45d44bc95c01cfe7e6 | Text | 6,761 | 168 | <p align="center">
<a href="https://github.com/jlsteenwyk/clipkit">
<img src="https://raw.githubusercontent.com/JLSteenwyk/ClipKIT/master/docs/_static/img/logo.jpg" alt="Logo" width="400">
</a>
<p align="center">
<a href="https://jlsteenwyk.com/ClipKIT/">Docs</a>
·
<a href="https://github.com/jlst... |
8e25052f01bb4748ca7b090d95da68ba15ab4d19a858af9af3921378780cd9cd | Text | 6,808 | 93 | # SFC_Nature_Comm_2023
**Author:** Panagiotis Fotiadis, 2021-2023
This repository contains code that was created to conduct the main analyses described in our paper:
**"Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex,"
currently accepted for pub... |
36b80a1da66adfdcf66322f0f1764d2dcda5827cdd6ca75f6d7b5fc6153eea1c | Text | 6,810 | 200 | ### DynamicST introduction
---
DynamicST is a command-line tool developed by DynamicBiosystems for processing spatial transcriptomics data generated by the DynaSpatial system. It enables researchers to convert raw image data and sequencing data into valuable gene expression information with spatial context.
The key ... |
bdae8a0b715d4568e0623bc5a3ffd69ed605ec62eee1ec86d57757f53a805f53 | Text | 6,810 | 200 | ### DynamicST introduction
---
DynamicST is a command-line tool developed by DynamicBiosystems for processing spatial transcriptomics data generated by the DynaSpatial system. It enables researchers to convert raw image data and sequencing data into valuable gene expression information with spatial context.
The key ... |
d932e414cb8c623ecd55255d25159f52268af988ed72d50d2e4c81c1bc35f873 | Text | 6,853 | 180 | # Connectivity pipeline
Here is the pipeline for the analysis of Deep Brain Stimulation (DBS) connectivity for patients with Treatment Resistant Depression.
It contains the code for my master thesis at the ['Brain Stimulation Mapping group at Inselspital and ARTORG Bern'](https://www.brainstimmapping.science/)
Startin... |
af396564f75ed841ee6c7e0fddabd27229e2700c4d4d0d80b2e14f94f0115ce7 | Text | 6,905 | 114 | # BayesDesign
<img src="https://github.com/dellacortelab/bayes_design/blob/master/data/figs/bayes_design.png?raw=true" alt="drawing" width="700"/>
BayesDesign is an algorithm for designing proteins with high stability and conformational specificity. See [preprint here](https://www.biorxiv.org/content/10.1101/2022.12.2... |
f549d5ac356c3f25dcacfe682d80a6b1f118749b0c7c4147383fd97f5a6ecb12 | Text | 6,963 | 83 | # Triangle-Mesh-Rasterization-Projection
This program converts 3D point clouds in PLY file format to 2D image data in [BBF](doc/BBF.md) or PNG file format.<br>
It includes two different methods:
- **Triangle-Mesh-Rasterization-Projection (TMRP):** A new way to project point clouds into a dense accurate 2D raster image... |
2db6c455750c66e9dc62ae55995d5bf3ea4d4b8c2cff96e402a9837da6f4c553 | Text | 6,970 | 102 | [](https://zenodo.org/badge/latestdoi/504649998)
# Fast Autonomous Scanning Toolkit (FAST)
This repository contains the code for the Fast Autonomous Scanning Toolkit (FAST) reported
in the manuscript:
"Demonstration of an AI-driven workflow for autonomous high-resol... |
2b434ce3a8d22f8d0d4ccaf265b238a37e60033cabd4a3f96cca790e3d5fc23f | Text | 7,032 | 55 | # Multi-template MRI mouse brain atlas (both _in vivo_ and _ex vivo_)
[](https://zenodo.org/badge/latestdoi/166476589)
Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the [original webpage](http://cmic.cs.ucl.ac.uk/staff/da_ma/multi_atlas/))
##... |
5ff7c66a6c78f9bd88c59e5773ec9dfcc26fc68d8357d32d71684ed9e2edeb05 | Text | 7,056 | 141 | # PCInvariance
Train a **Hebbian Predictive Coding Network** on short sequences of moving objects. Both invariant representations and a generative model are learned.
This repository provides the code for the experiments in our paper:
Matthias Brucklacher*, Sander M. Bohte, Jorge F. Mejias, Cyriel M. A. Pennartz - [L... |
cd3dd35e165e991b14f31e8d65c9c5aab5965d85012d7c1fab4e7b10a54485b6 | Text | 7,178 | 148 | # SSDLiteX
## Introduction
SSDLite is an improved version of SSD and being widely used.
However, it is not well discussed which difference they have.
In SSDLiteX, the difference is discussed,
and better model will be suggested.
## Citing SSDLiteX
Please cite SSDLiteX in your publications if it helps your research:
... |
7af2628c43ee4c516d1c948eb38507adf4552e5ed0c6e51e7406ac3fa29b4fb6 | Text | 7,179 | 64 | # DeepPCB
DeepPCB: a dataset contains 1,500 image pairs, each of which consists of a defect-free template image and an aligned tested image with annotations including positions of 6 most common types of PCB defects: open, short, mousebite, spur, pin hole and spurious copper.
## Dataset Description
### Image Collection... |
6ab425f4cee6324d38f60717bbeeb59cf07b3e52cd2a6e421959560122a0f741 | Text | 7,335 | 142 | # TDT (Tucker-Davis Technologies) Fiber Photometry Analysis GUI 🐁
Please cite (Drakopoulos, V., Reichenbach, A., Stark, R., Foldi, C. J., Jean-Richard-Dit-Bressel, P., & Andrews, Z. B. (2025). FiPhoPHA-A Fiber Photometry Python Package for Post Hoc Analysis. eNeuro, 12(8), ENEURO.0221-25.2025. https://doi.org/10.1523... |
e740cb502b21b8f11a11d1ccb028cd5f6044dc266642ffdc28aa8cc14dfddb90 | Text | 7,362 | 146 | # Zeffiro Interface
© 2018- Sampsa Pursiainen & ZI Development Team
[](https://se.mathworks.com/matlabcentral/fileexchange/68285-zeffiro-forward-and-inverse-int... |
b184d4bab06b2a0c27d3b39392b618c3042687dd90615177c5a91ad17e11b637 | Text | 7,383 | 151 | # QIIME 2 Provenance Replay
Software to support scientific reproducibility, attribution, and collaboration on the QIIME 2 platform.
## About
The provenance-lib software provides the QIIME 2 Provenance Replay functionality, which parses the computational history ( or "provenance") of QIIME 2 results into a directed gra... |
be32e5ad7feb4f90849f4f9d33baf4cb49f5493af0004040af83378df4a23f2f | Text | 7,439 | 104 | [](https://zenodo.org/badge/latestdoi/504649998)
# Fast Autonomous Scanning Toolkit (FAST)
This repository contains the code for the Fast Autonomous Scanning Toolkit (FAST) reported
in the manuscript:
"Demonstration of an AI-driven workflow for autonomous high-resol... |
473b7c0207ad9e465c47cdc969edfc74e9f21bbc47b924536b69819ed9af345a | Text | 7,444 | 162 |
[](https://www.python.org/downloads/release/python-376/)
[](https://pytorch.org/)
[](https://github.com/kumar-shridhar/... |
223db66582722fdf3d700a101fb9d4de6075c5acb33a35183cdba9eb24f33f2c | Text | 7,579 | 151 | # SNFpy
This package provides a Python implementation of similarity network fusion (SNF), a technique for combining multiple data sources into a single graph representing sample relationships.
[](https://travis-ci.org/rmarkello/snfpy)
[![Codecov]... |
c5b75fd7715639977bbc92ddb4982aa9c2b3fb7aa7df56a5233ab4ccc3fbdd48 | Text | 7,586 | 124 | =====ROSE: RANK ORDERING OF SUPER-ENHANCERS=====
ROSE IS RELEASED UNDER THE MIT X11 LICENSE
EXAMPLE DATA AND ADDTIONAL INFORMATION CAN BE FOUND HERE:
http://younglab.wi.mit.edu/super_enhancer_code.html
N.B. LICENSE.txt
For details of this analysis see:
Master Transcription Factors and Mediator Establish Super-Enha... |
0ea4b6f645f943d616bd8ae805f08a8e2e8def17d7d404caacf7e33288a19b4e | Text | 8,174 | 114 | # Examination of PDGFRβ reactivity and KLF4 expression following cerebral ischemia
This repository was organised by Daniel Manrique-Castano, former postdoctoral fellow and current research data curation officer at the Digital Research Alliance of Canada.
**Website:** https://daniel-manrique.github.io/
**GitHub:** h... |
6f5089bdc0882813e54df6fbac1c93176d42727316bdfde050b9632e1dfa9812 | Text | 8,485 | 131 | powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions
=====================================================================
.. image:: https://github.com/jeffalstott/powerlaw/workflows/Tests/badge.svg
:target: https://github.com/jeffalstott/powerlaw/actions
:alt: Tests
``powerlaw`` is a toolbox ... |
7106a7f5ca68236d314b60a8095ae35f31a0406fc153646e2e0077aa77155e54 | Text | 8,536 | 122 |
[](https://doi.org/10.5281/zenodo.15747309)
DeepSlice is a p... |
7fe14a230944b576a324ac4b320619a11631eafd18e6cf47f2113f2ab2de91a0 | Text | 8,660 | 151 | ROSE: RANK ORDERING OF SUPER-ENHANCERS
============================================================
ROSE IS RELEASED UNDER THE MIT X11 LICENSE
EXAMPLE DATA AND ADDTIONAL INFORMATION CAN BE FOUND HERE:
http://younglab.wi.mit.edu/super_enhancer_code.html
N.B. LICENSE.txt
For details of this analysis see:
>Master Tra... |
23493e4a8c74d55ea786279b7e96639ea798e74cc123226b2766c1b185b0079b | Text | 8,826 | 131 | # Wall Segmentation 
Implementation of a wall segmentation algorithm in PyTorch.
Accompanying papers:
- [Getting Started with Wall Segmentation](https://www.researchgate.net/publication/363059238_Getting_Started_with_Wall_Segmentation)
- [Wall segmentat... |
066cbce3363111d45ed4cc28d8bb81c7061556a9cd7bc581ae116ef7afcf625e | Text | 9,147 | 224 | <h1 align="center">taxopy</h1>
<p align="center">
<a href="https://apcamargo.github.io/taxopy"><b>Documentation</b></a> | <a href="https://doi.org/10.5281/zenodo.6993580"><b>DOI</b></a>
</p>
`taxopy` is a Python package that provides an interface for assessing NCBI-formatted taxonomic databases. It enables various ... |
1369033ad2f01bf6b8afe7419148b1da3637ccedd38fca07ebbf3e85fa7afddd | Text | 9,162 | 121 | # VFTModels
Verbal Fluency Task Analysis Tool using traditional rule-based, list-based and a novel **semantic relatedness method**.
This Github repository contains the code of the publication **Hähnel et al 2023 (DOI: 10.2196/46021)**. Please refer to this publication for further details.
When using this software, p... |
87a40d5794db0a84a1aa12dedcf6230cd71a6ad38fb5bc5d2dcfcc1067dd942b | Text | 9,163 | 122 | [](https://doi.org/10.5281/zenodo.10865908)
[](https://doi.org/10.3389/fbioe.2023.1238130)
# Perfect prosthetic heart valve: generative design with machine learning, modeling, and o... |
7e071dec82240e1f08b97ac19101f0a437851f96ac1fa7b1010d0e0d778c67e4 | Text | 9,242 | 123 | #
[](https://doi.org/10.5281/zenodo.7933484)
[](https://opensource.org/licenses/MIT)
Background: When using deep learning models, one of the most critical vulnerabilities is their exp... |
4f12783274ec921ba3f768b863a7629cbf8cda7bba44787f652d4b04e9d9f222 | Text | 9,696 | 118 | ## This repo is DEPRECATED and no longer supported - We recommend that you do not use the content in this repo for any production or sensitive purpose
## BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation
## Announcement: BLIP is now officially integrated into [LA... |
695f67868f561280ec2b0124ce180ff40831f13e258d9428a5faa281c5a0cb93 | Text | 10,089 | 228 | [](https://pypi.org/project/aimnet/) [](https://github.com/isayevlab/aimnetcentral/releases) [](https://w... |
e387a4476e29ba3f0830dd52442ea95be282fa6f280e3ee6d1bd006f8c3bf9ac | Text | 10,119 | 263 | DynamicST Assist
====
# Introduction
<div align=center><img src='./images/dynamicstassist-logo.png' width =80%, height=80%></div>
DynamicST Assist is an interactive software designed to help users manually identify fiducial points in DynaSpatial images, select spots under tissue, and align DynaBlot images with micr... |
6b742a17fafae4b28e5bc440e4c824c4f4d856c83c6e69bcc9755f05922f5ec0 | Text | 10,203 | 254 | # Deep learning for risk-based stratification of cognitively impaired individuals
This work is accepted in *iScience*.
## Introduction
We present here code for the above paper. This code has principally been organized in the **main.py** file under mri_surv/
<img src="figures/structure.png" width="2000"/>
## Result... |
f6d9aa1a87b7899228589db2f546914c579c2e70b568e468dcc4b93c43d7bc52 | Text | 10,666 | 229 | <!--
MIT License
Copyright (c) 2018 Othneil Drew
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish,... |
86114a917852eba0dbac06dd32e3cb3af780b2fdeb6e53df95ac2f18d6b126fb | Text | 10,701 | 239 | <div align="center">
# *Oligo Designer Toolsuite* - Lightweight Development of Custom Oligo Design Pipelines
[](https://oligo-designer-toolsuite.readthedocs.io/en/latest/)
[ output the 2D positi... |
daa2821bc07ff7486f77bb7df62198ddf66239a2f887a108b84b7154f267ba51 | Text | 12,661 | 258 | ## *SvABA* — Structural variation and indel analysis by assembly
SvABA (formerly *Snowman*) is an SV and indel caller for short-read BAMs.
It performs genome-wide local assembly, realigns contigs with BWA-MEM, and
scores variants by reassembled read support. Tumor/normal, trios, and
single-sample modes are supported; ... |
c6a92463930cc88e5fbb22509b4dfd379074ec46af68889075758e4024444d73 | Text | 12,740 | 255 | # doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models
- [How to cite](#how-to-cite)
- [Installation](#installation)
- [Troubleshooting](#troubleshooting)
- [How to use doubleHelix](#how-to-use-doublehelix)
- [Generating base-pairing restrai... |
f32621efb0ff1735cda959c44081595ab9d6f63b92016863127b2791316ccc3f | Text | 12,819 | 216 | ## Repository Status
<b>This repository is no longer actively maintained.
Active development has moved to the Clement Lab:
https://github.com/clementlab/AmpUMI </b>
We encourage users to use the new repository for the latest features and updates.
# AmpUMI
<img src='https://github.com/user-attachments/assets/c92717d... |
53de122a2ea4cf4b6a619d319e3271442be92a23cccb3e7bb7c8322951e2a67c | Text | 13,119 | 357 | # AnySleep
⚠️ Due to their size, we are moving the experiment results from this repository into a dedicated Zenodo archive. Downloading the Git LFS files might currently fail. The Zenodo archive with our experiment results is now available at: https://doi.org/10.5281/zenodo.23764134 ⚠️
Research codebase for automatic... |
feedc0257c95650d67416c4f0f420f837e9ea8a146ef789d03a5291f1de4d661 | Text | 13,157 | 260 | [](https://badge.fury.io/py/sbi)
[](https://github.com/conda-forge/sbi-feedstock)
[](https://sbi.re... |
7ae809c1b2c6ed0dbb38117e6c1c5b6c01059466d0d305d337038504258eb694 | Text | 13,327 | 240 | # Linear Sync Toolkit (linsync)
Copyright (C) 2012- [Joseph T. Lizier](http://lizier.me/joseph/)
The `linsync` toolkit provides Matlab tools for analysing **synchronization** in networks of linearly coupled nodes.
Specifically, it provides implementations of the maths to measure and explore
the expected mean square d... |
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