Julia package for multiway (inverse) covariance estimation.

Overview

TensorGraphicalModels

TensorGraphicalModels.jl is a suite of Julia tools for estimating high-dimensional multiway (tensor-variate) covariance and inverse covariance matrices.

Installation

] add https://github.com/ywa136/TensorGraphicalModels.jl

Examples

Please check out a Julia colab created for illustration of some functionalities of the package. Here are some basic examples as well:

Example code for fitting a KP inverse covariance model:

using TensorGraphicalModels

model_type = "kp"
sub_model_type = "sb" #this defines the structure of the Kronecker factors, sb = star-block
K = 3
N = 1000
d_list = [5, 10, 15]

X = gen_kronecker_data(model_type, sub_model_type, K, N, d_list) #multi-dimensional array (tensor) of dimension d_1 × … × d_K × N
Ψ_hat_list = kglasso(X)

Example code for fitting a KS inverse covariance model:

using TensorGraphicalModels

model_type = "ks"
sub_model_type = "sb" #this defines the structure of the Kronecker factors, sb = star-block
K = 3
N = 1000
d_list = [5, 10, 15]

X = gen_kronecker_data(model_type, sub_model_type, K, N, d_list, tensorize_out = false) #matrix of dimension d × N

# compute the mode-k Gram matrices (the sufficient statistics for TeraLasso)
X_kGram = [zeros(d_list[k], d_list[k]) for k = 1:K]
Xk = [zeros(d_list[k], Int(prod(d_list) / d_list[k])) for k = 1:K]
for k = 1:K
    for i = 1:N
        copy!(Xk[k], tenmat(reshape(view(X, :, i), d_list), k))
        mul!(X_kGram[k], Xk[k], copy(transpose(Xk[k])), 1.0 / N, 1.0)
    end
end

Ψ_hat_list, _ = teralasso(X_kGram)

Example code for fitting a Sylvester inverse covariance model:

using TensorGraphicalModels

model_type = "sylvester"
sub_model_type = "sb" #this defines the structure of the Kronecker factors, sb = star-block
K = 3
N = 1000
d_list = [5, 10, 15]

X = gen_kronecker_data(model_type, sub_model_type, K, N, d_list, tensorize_out = false) #matrix of dimension d × N

# compute the mode-k Gram matrices (the sufficient statistics for TeraLasso)
X_kGram = [zeros(d_list[k], d_list[k]) for k = 1:K]
Xk = [zeros(d_list[k], Int(prod(d_list) / d_list[k])) for k = 1:K]
for k = 1:K
    for i = 1:N
        copy!(Xk[k], tenmat(reshape(view(X, :, i), d_list), k))
        mul!(X_kGram[k], Xk[k], copy(transpose(Xk[k])), 1.0 / N, 1.0)
    end
end

Psi0 = [sparse(eye(d_list[k])) for k = 1:K]
fun = (iter, Psi) -> [1, time()] # NULL func
lambda = [sqrt(px[k] * log(prod(d_list)) / N) for k = 1:K] 

Ψ_hat_list, _ = syglasso_palm(X, X_kGram, lambda, Psi0, fun = fun)

Example code for fitting a KPCA covariance model:

using TensorGraphicalModels

px = py = 25 #works for K=2 modes only
N = 100
X = zeros((px * py, N))

for i=1:N
    X[:, i] .= vec(rand(MatrixNormal(zeros((px, py)), ScalMat(px, 2.0), ScalMat(py, 4.0))))
end

S = cov(copy(X')) #sample covariance matrix
lambdaL = 20 * (px^2 + py^2 + log(max(px, py, N))) / N
lambdaS = 20 * sqrt(log(px * py)/N)

# robust Kronecker PCA methods using singular value thresholding
Sigma_hat = robust_kron_pca(S, px, py, lambdaL, lambdaS, "SVT"; tau = 0.5, r = 5)
Owner
Wayne Wang
Ph.D. candidate in statistics
Wayne Wang
Pytorch codes for Feature Transfer Learning for Face Recognition with Under-Represented Data

FTLNet_Pytorch Pytorch codes for Feature Transfer Learning for Face Recognition with Under-Represented Data 1. Introduction This repo is an unofficial

1 Nov 04, 2020
Combinatorial model of ligand-receptor binding

Combinatorial model of ligand-receptor binding The binding of ligands to receptors is the starting point for many import signal pathways within a cell

Mobolaji Williams 0 Jan 09, 2022
A program to recognize fruits on pictures or videos using yolov5

Yolov5 Fruits Detector Requirements Either Linux or Windows. We recommend Linux for better performance. Python 3.6+ and PyTorch 1.7+. Installation To

Fateme Zamanian 30 Jan 06, 2023
某学校选课系统GIF验证码数据集 + Baseline模型 + 上下游相关工具

elective-dataset-2021spring 某学校2021春季选课系统GIF验证码数据集(29338张) + 准确率98.4%的Baseline模型 + 上下游相关工具。 数据集采用 知识共享署名-非商业性使用 4.0 国际许可协议 进行许可。 Baseline模型和上下游相关工具采用

xmcp 27 Sep 17, 2021
Face detection using deep learning.

Face Detection Docker Solution Using Faster R-CNN Dockerface is a deep learning face detector. It deploys a trained Faster R-CNN network on Caffe thro

Nataniel Ruiz 181 Dec 19, 2022
Element selection for functional materials discovery by integrated machine learning of atomic contributions to properties

Element selection for functional materials discovery by integrated machine learning of atomic contributions to properties 8.11.2021 Andrij Vasylenko I

Leverhulme Research Centre for Functional Materials Design 4 Dec 20, 2022
A Differentiable Recipe for Learning Visual Non-Prehensile Planar Manipulation

A Differentiable Recipe for Learning Visual Non-Prehensile Planar Manipulation This repository contains the source code of the paper A Differentiable

Bernardo Aceituno 2 May 05, 2022
The code for MM2021 paper "Multi-Level Counterfactual Contrast for Visual Commonsense Reasoning"

The Code for MM2021 paper "Multi-Level Counterfactual Contrast for Visual Commonsense Reasoning" Setting up and using the repo Get the dataset. Follow

4 Apr 20, 2022
Unofficial keras(tensorflow) implementation of MAE model from Masked Autoencoders Are Scalable Vision Learners

MAE-keras Unofficial keras(tensorflow) implementation of MAE model described in 'Masked Autoencoders Are Scalable Vision Learners'. This work has been

Yewon 11 Jun 12, 2022
Code for the paper "SmoothMix: Training Confidence-calibrated Smoothed Classifiers for Certified Robustness" (NeurIPS 2021)

SmoothMix: Training Confidence-calibrated Smoothed Classifiers for Certified Robustness (NeurIPS2021) This repository contains code for the paper "Smo

Jongheon Jeong 17 Dec 27, 2022
Attentional Focus Modulates Automatic Finger‑tapping Movements

"Attentional Focus Modulates Automatic Finger‑tapping Movements", in Scientific Reports

Xingxun Jiang 1 Dec 02, 2021
This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA)

Description This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA), described in the publication [1]. Directory

MAMMASMIAS Consortium 6 Nov 14, 2022
Implementation of Neural Style Transfer in Pytorch

PytorchNeuralStyleTransfer Code to run Neural Style Transfer from our paper Image Style Transfer Using Convolutional Neural Networks. Also includes co

Leon Gatys 396 Dec 01, 2022
A Comprehensive Study on Learning-Based PE Malware Family Classification Methods

A Comprehensive Study on Learning-Based PE Malware Family Classification Methods Datasets Because of copyright issues, both the MalwareBazaar dataset

8 Oct 21, 2022
Gesture recognition on Event Data

Event based Gesture Recognition Gesture recognition on Event Data usually involv

2 Feb 14, 2022
Graph Convolutional Networks in PyTorch

Graph Convolutional Networks in PyTorch PyTorch implementation of Graph Convolutional Networks (GCNs) for semi-supervised classification [1]. For a hi

Thomas Kipf 4.5k Dec 31, 2022
RobustVideoMatting and background composing in one model by using onnxruntime.

RVM_onnx_compose RobustVideoMatting and background composing in one model by using onnxruntime. Usage pip install -r requirements.txt python infer_cam

Quantum Liu 4 Apr 07, 2022
A framework that constructs deep neural networks, autoencoders, logistic regressors, and linear networks

A framework that constructs deep neural networks, autoencoders, logistic regressors, and linear networks without the use of any outside machine learning libraries - all from scratch.

Kordel K. France 2 Nov 14, 2022
Segmentation vgg16 fcn - cityscapes

VGGSegmentation Segmentation vgg16 fcn - cityscapes Priprema skupa skripta prepare_dataset_downsampled.py Iz slika cityscapesa izrezuje haubu automobi

6 Oct 24, 2020
Code for EMNLP'21 paper "Types of Out-of-Distribution Texts and How to Detect Them"

ood-text-emnlp Code for EMNLP'21 paper "Types of Out-of-Distribution Texts and How to Detect Them" Files fine_tune.py is used to finetune the GPT-2 mo

Udit Arora 19 Oct 28, 2022