A hybrid framework (neural mass model + ML) for SC-to-FC prediction

Overview

🌈 A hybrid framework (neural mass model + ML) for SC-to-FC prediction

The current workflow simulates brain functional connectivity (FC) from structural connectivity (SC) with a neural mass model. Gradient descent is applied to optimize the parameters in the neural mass model.

The pipeline contains the following components:

  • Neural Mass Model (models/torch_neural_mass.py): It is an ODE system that describes the neural activities over time. The Wilson-Cowan model is implemented here with a connected network setting - each neural region is considered as a node in the brain network and connected via SC. The Wilson-Cowan model assumes each node contains two types of neural populations: the excitatory and inhibitory cells. The definition can be found here and here.
  • Hemodynamic Model (models/hrf_torch.py): This module down samples and transforms the neural activities into Blood Oxygen Level Dependence (BOLD) signals. The code is adapted from the Virtual Brain implementation of the Balloon model.

Requirement

PyTorch (my version is 1.10.0)

Usage

An example of running the pipeline can be found at run.sh. Please update path to your data.

Owner
Yilin Liu
PhD Student in Computational Biology at Cornell University
Yilin Liu
PyTorch implementation of SCAFFOLD (Stochastic Controlled Averaging for Federated Learning, ICML 2020).

Scaffold-Federated-Learning PyTorch implementation of SCAFFOLD (Stochastic Controlled Averaging for Federated Learning, ICML 2020). Environment numpy=

KI 30 Dec 29, 2022
This repository contains an implementation of the Permutohedral Attention Module in Pytorch

Permutohedral_attention_module This repository contains an implementation of the Permutohedral Attention Module

Samuel JOUTARD 26 Nov 27, 2022
MMdnn is a set of tools to help users inter-operate among different deep learning frameworks. E.g. model conversion and visualization. Convert models between Caffe, Keras, MXNet, Tensorflow, CNTK, PyTorch Onnx and CoreML.

MMdnn MMdnn is a comprehensive and cross-framework tool to convert, visualize and diagnose deep learning (DL) models. The "MM" stands for model manage

Microsoft 5.7k Jan 09, 2023
This repository for project that can Automate Number Plate Recognition (ANPR) in Morocco Licensed Vehicles. 💻 + 🚙 + 🇲🇦 = 🤖 🕵🏻‍♂️

MoroccoAI Data Challenge (Edition #001) This Reposotory is result of our work in the comepetiton organized by MoroccoAI in the context of the first Mo

SAFOINE EL KHABICH 14 Oct 31, 2022
Rest API Written In Python To Classify NSFW Images.

Rest API Written In Python To Classify NSFW Images.

Wahyusaputra 2 Dec 23, 2021
dualPC.R contains the R code for the main functions.

dualPC.R contains the R code for the main functions. dualPC_sim.R contains an example run with the different PC versions; it calls dualPC_algs.R whic

3 May 30, 2022
Implementation of Stochastic Image-to-Video Synthesis using cINNs.

Stochastic Image-to-Video Synthesis using cINNs Official PyTorch implementation of Stochastic Image-to-Video Synthesis using cINNs accepted to CVPR202

CompVis Heidelberg 135 Dec 28, 2022
Face Library is an open source package for accurate and real-time face detection and recognition

Face Library Face Library is an open source package for accurate and real-time face detection and recognition. The package is built over OpenCV and us

52 Nov 09, 2022
Cereal box identification in store shelves using computer vision and a single train image per model.

Product Recognition on Store Shelves Description You can read the task description here. Report You can read and download our report here. Step A - Mu

Nicholas Baraghini 1 Jan 21, 2022
Perform Linear Classification with Multi-way Data

MultiwayClassification This is an R package to perform linear classification for data with multi-way structure. The distance-weighted discrimination (

Eric F. Lock 2 Dec 15, 2020
A 3D Dense mapping backend library of SLAM based on taichi-Lang designed for the aerial swarm.

TaichiSLAM This project is a 3D Dense mapping backend library of SLAM based Taichi-Lang, designed for the aerial swarm. Intro Taichi is an efficient d

XuHao 230 Dec 19, 2022
A repository for interferometer controller code.

dses-interferometer-controller A repository for interferometer controller code, hardware, and simulations. See dses.science for more information on th

Eli Reed 1 Jan 17, 2022
Python tools for 3D face: 3DMM, Mesh processing(transform, camera, light, render), 3D face representations.

face3d: Python tools for processing 3D face Introduction This project implements some basic functions related to 3D faces. You can use this to process

Yao Feng 2.3k Dec 30, 2022
Ensembling Off-the-shelf Models for GAN Training

Vision-aided GAN video (3m) | website | paper Can the collective knowledge from a large bank of pretrained vision models be leveraged to improve GAN t

345 Dec 28, 2022
ML-Ensemble – high performance ensemble learning

A Python library for high performance ensemble learning ML-Ensemble combines a Scikit-learn high-level API with a low-level computational graph framew

Sebastian Flennerhag 764 Dec 31, 2022
商品推荐系统

商品top50推荐系统 问题建模 本项目的数据集给出了15万左右的用户以及12万左右的商品, 以及对应的经过脱敏处理的用户特征和经过预处理的商品特征,旨在为用户推荐50个其可能购买的商品。 推荐系统架构方案 本项目采用传统的召回+排序的方案。

107 Dec 29, 2022
An exploration of log domain "alternative floating point" for hardware ML/AI accelerators.

This repository contains the SystemVerilog RTL, C++, HLS (Intel FPGA OpenCL to wrap RTL code) and Python needed to reproduce the numerical results in

Facebook Research 373 Dec 31, 2022
Official PyTorch implementation of Joint Object Detection and Multi-Object Tracking with Graph Neural Networks

This is the official PyTorch implementation of our paper: "Joint Object Detection and Multi-Object Tracking with Graph Neural Networks". Our project website and video demos are here.

Richard Wang 443 Dec 06, 2022
Volumetric parameterization of the placenta to a flattened template

placenta-flattening A MATLAB algorithm for volumetric mesh parameterization. Developed for mapping a placenta segmentation derived from an MRI image t

Mazdak Abulnaga 12 Mar 14, 2022