Tensor-based approaches for fMRI classification

Overview

tensor-fmri

Using tensor-based approaches to classify fMRI data from StarPLUS.

Citation

If you use any code in this repository, please cite the following work.

Here is where we will add the citation to the paper.

Installation and Requirements

git clone https://github.com/elizabethnewman/tensor-fmri.git
cd tensor-fmri
pip install -r requirements.txt

Additional Requirements: python version 3.7 or newer

Additional Advice: before installing the requirements, create a virtual environment via

virtualenv -p python3 <env_name>

To use the environment, activate via

source env_name/bin/activate
pip install -r requirements.txt

When finished, deactivate while in the virtual environment via

deactivate

StarPlus Data

The StarPlus fMRI dataset is publicly-available and fairly small. This dataset consists of fMRIs of study subjects who are shown either a sentence or an image, and we aim to classify them into these two categories. We represent the data in a fifth order tensor containing pixel data of the 3D brain images over time over each trial.

Download from the website to the data folder before running StarPlus scripts.

Organization

  • data: contains two datasets, the toy synthetic dataset and the MNIST datasets.

  • tensor: contains functions for all the needed tensor products and tensor SVD. This is the core of the repository and is written for general use, not just for fMRI data.

  • tests: contains internal code to test the tensor-tensor products and can be used in the development of new code.

  • utils: contains visualization and preprocessing tools.

Introductary Notebooks in Google Colab

To illustrate the utility of the code and our algorithm, we have create two Google Colab notebooks.

  • Synthetic Data Example: Open In Colab

  • MNIST Example: Open In Colab

Resources

Projecting interval uncertainty through the discrete Fourier transform

Projecting interval uncertainty through the discrete Fourier transform This repo

1 Mar 02, 2022
Repo for CVPR2021 paper "QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information"

QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information by Masato Tamura, Hiroki Ohashi, and Tomoaki Yosh

105 Dec 23, 2022
Official implementation of Unfolded Deep Kernel Estimation for Blind Image Super-resolution.

Unfolded Deep Kernel Estimation for Blind Image Super-resolution Hongyi Zheng, Hongwei Yong, Lei Zhang, "Unfolded Deep Kernel Estimation for Blind Ima

Z80 15 Dec 26, 2022
Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

Troyanskaya Laboratory 323 Jan 01, 2023
Official implementation for CVPR 2021 paper: Adaptive Class Suppression Loss for Long-Tail Object Detection

Adaptive Class Suppression Loss for Long-Tail Object Detection This repo is the official implementation for CVPR 2021 paper: Adaptive Class Suppressio

CASIA-IVA-Lab 67 Dec 04, 2022
Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic

Pytorch Implementation of Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic [Paper] [Colab is coming soon] Approach Example Usage To r

170 Jan 03, 2023
Official PyTorch implementation of "IntegralAction: Pose-driven Feature Integration for Robust Human Action Recognition in Videos", CVPRW 2021

IntegralAction: Pose-driven Feature Integration for Robust Human Action Recognition in Videos Introduction This repo is official PyTorch implementatio

Gyeongsik Moon 29 Sep 24, 2022
darija <-> english dictionary

darija-dictionary Having advanced IT solutions that are well adapted to the Moroccan context passes inevitably through understanding Moroccan dialect.

DODa 102 Jan 01, 2023
A curated list of awesome resources related to Semantic Search🔎 and Semantic Similarity tasks.

A curated list of awesome resources related to Semantic Search🔎 and Semantic Similarity tasks.

224 Jan 04, 2023
Implementation of ETSformer, state of the art time-series Transformer, in Pytorch

ETSformer - Pytorch Implementation of ETSformer, state of the art time-series Transformer, in Pytorch Install $ pip install etsformer-pytorch Usage im

Phil Wang 121 Dec 30, 2022
Official repository for the paper "GN-Transformer: Fusing AST and Source Code information in Graph Networks".

GN-Transformer AST This is the official repository for the paper "GN-Transformer: Fusing AST and Source Code information in Graph Networks". Data Prep

Cheng Jun-Yan 10 Nov 26, 2022
PyTorch module to use OpenFace's nn4.small2.v1.t7 model

OpenFace for Pytorch Disclaimer: This codes require the input face-images that are aligned and cropped in the same way of the original OpenFace. * I m

Pete Tae-hoon Kim 176 Dec 12, 2022
ELECTRA: Pre-training Text Encoders as Discriminators Rather Than Generators

ELECTRA Introduction ELECTRA is a method for self-supervised language representation learning. It can be used to pre-train transformer networks using

Google Research 2.1k Dec 28, 2022
LaBERT - A length-controllable and non-autoregressive image captioning model.

Length-Controllable Image Captioning (ECCV2020) This repo provides the implemetation of the paper Length-Controllable Image Captioning. Install conda

bearcatt 53 Nov 13, 2022
This is an official implementation of the CVPR2022 paper "Blind2Unblind: Self-Supervised Image Denoising with Visible Blind Spots".

Blind2Unblind: Self-Supervised Image Denoising with Visible Blind Spots Blind2Unblind Citing Blind2Unblind @inproceedings{wang2022blind2unblind, tit

demonsjin 58 Dec 06, 2022
Img-process-manual - Utilize Python Numpy and Matplotlib to realize OpenCV baisc image processing function

Img-process-manual - Opencv Library basic graphic processing algorithm coding reproduction based on Numpy and Matplotlib library

Jack_Shaw 2 Dec 12, 2022
The Implicit Bias of Gradient Descent on Generalized Gated Linear Networks

The Implicit Bias of Gradient Descent on Generalized Gated Linear Networks This folder contains the code to reproduce the data in "The Implicit Bias o

Samuel Lippl 0 Feb 05, 2022
Unsupervised Foreground Extraction via Deep Region Competition

Unsupervised Foreground Extraction via Deep Region Competition [Paper] [Code] The official code repository for NeurIPS 2021 paper "Unsupervised Foregr

28 Nov 06, 2022
A deep learning object detector framework written in Python for supporting Land Search and Rescue Missions.

AIR: Aerial Inspection RetinaNet for supporting Land Search and Rescue Missions AIR is a deep learning based object detection solution to automate the

Accenture 13 Dec 22, 2022
A PyTorch implementation of "Multi-Scale Contrastive Siamese Networks for Self-Supervised Graph Representation Learning", IJCAI-21

MERIT A PyTorch implementation of our IJCAI-21 paper Multi-Scale Contrastive Siamese Networks for Self-Supervised Graph Representation Learning. Depen

Graph Analysis & Deep Learning Laboratory, GRAND 32 Jan 02, 2023