Bayesian Optimization Library for Medical Image Segmentation.

Overview

bayesmedaug: Bayesian Optimization Library for Medical Image Segmentation.

bayesmedaug optimizes your data augmentation hyperparameters for medical image segmentation tasks by using Bayesian Optimization.

bayesmedaug is currently in beta release and still in development.

Authors

  • M. Şafak Bilici
  • Onur Boyar
  • Enes Sadi Uysal
  • Alara Hergün

Simple Usage

import torch
import bayesmedaug
from bayesmedaug import VanillaUNet, Trainer, Listed, BOMed
from bayesmedaug import Rotate, ZoomOut, Gamma

device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

auglist = [
    Rotate,
    ZoomOut,
    Gamma
]

params = {
    'angle': (0,2),
    'zoom_amount': (0.5,0.9),
    'gamma': (0.5,1.5),
}

auglist = Listed(augmentations = auglist)

trainer = Trainer(
    model = VanillaUNet,
    model_args = {"n_channels": 1, "n_classes": 2},
    optimizer = torch.optim.Adam,
    optimizer_args = {"lr": 0.0005},
    device = device,
    epochs = 1,
    train_dir = "/home/safak/Desktop/drive/train/",
    eval_dir = "/home/safak/Desktop/drive/test/",
    augmentations = auglist,
    batch_size = 1
)


optimizer = BOMed(
    f = trainer.train,
    pbounds = params,
    random_state = 1,
)

optimizer.maximize(
    init_points = 15,
    n_iter = 15,
)
Owner
Şafak Bilici
NLP & Bayesian ML.
Şafak Bilici
Time Delayed NN implemented in pytorch

Pytorch Time Delayed NN Time Delayed NN implemented in PyTorch. Usage kernels = [(1, 25), (2, 50), (3, 75), (4, 100), (5, 125), (6, 150)] tdnn = TDNN

Daniil Gavrilov 79 Aug 04, 2022
Facilitating Database Tuning with Hyper-ParameterOptimization: A Comprehensive Experimental Evaluation

A Comprehensive Experimental Evaluation for Database Configuration Tuning This is the source code to the paper "Facilitating Database Tuning with Hype

DAIR Lab 9 Oct 29, 2022
Human segmentation models, training/inference code, and trained weights, implemented in PyTorch

Human-Segmentation-PyTorch Human segmentation models, training/inference code, and trained weights, implemented in PyTorch. Supported networks UNet: b

Thuy Ng 474 Dec 19, 2022
Codes of paper "Unseen Object Amodal Instance Segmentation via Hierarchical Occlusion Modeling"

Unseen Object Amodal Instance Segmentation (UOAIS) Seunghyeok Back, Joosoon Lee, Taewon Kim, Sangjun Noh, Raeyoung Kang, Seongho Bak, Kyoobin Lee This

GIST-AILAB 92 Dec 13, 2022
Code release for DS-NeRF (Depth-supervised Neural Radiance Fields)

Depth-supervised NeRF: Fewer Views and Faster Training for Free Project | Paper | YouTube Pytorch implementation of our method for learning neural rad

524 Jan 08, 2023
Code to reproduce the experiments in the paper "Transformer Based Multi-Source Domain Adaptation" (EMNLP 2020)

Transformer Based Multi-Source Domain Adaptation Dustin Wright and Isabelle Augenstein To appear in EMNLP 2020. Read the preprint: https://arxiv.org/a

CopeNLU 36 Dec 05, 2022
🛠️ SLAMcore SLAM Utilities

slamcore_utils Description This repo contains the slamcore-setup-dataset script. It can be used for installing a sample dataset for offline testing an

SLAMcore 7 Aug 04, 2022
Semi-Supervised Graph Prototypical Networks for Hyperspectral Image Classification, IGARSS, 2021.

Semi-Supervised Graph Prototypical Networks for Hyperspectral Image Classification, IGARSS, 2021. Bobo Xi, Jiaojiao Li, Yunsong Li and Qian Du. Code f

Bobo Xi 7 Nov 03, 2022
Offical code for the paper: "Growing 3D Artefacts and Functional Machines with Neural Cellular Automata" https://arxiv.org/abs/2103.08737

Growing 3D Artefacts and Functional Machines with Neural Cellular Automata Video of more results: https://www.youtube.com/watch?v=-EzztzKoPeo Requirem

Robotics Evolution and Art Lab 51 Jan 01, 2023
Mahadi-Now - This Is Pakistani Just Now Login Tools

PAKISTANI JUST NOW LOGIN TOOLS Install apt update apt upgrade apt install python

MAHADI HASAN AFRIDI 19 Apr 06, 2022
PixelPyramids: Exact Inference Models from Lossless Image Pyramids (ICCV 2021)

PixelPyramids: Exact Inference Models from Lossless Image Pyramids This repository contains the PyTorch implementation of the paper PixelPyramids: Exa

Visual Inference Lab @TU Darmstadt 8 Dec 11, 2022
Time-series-deep-learning - Developing Deep learning LSTM, BiLSTM models, and NeuralProphet for multi-step time-series forecasting of stock price.

Stock Price Prediction Using Deep Learning Univariate Time Series Predicting stock price using historical data of a company using Neural networks for

Abdultawwab Safarji 7 Nov 27, 2022
Teaches a student network from the knowledge obtained via training of a larger teacher network

Distilling-the-knowledge-in-neural-network Teaches a student network from the knowledge obtained via training of a larger teacher network This is an i

Abhishek Sinha 146 Dec 11, 2022
Code for "The Box Size Confidence Bias Harms Your Object Detector"

The Box Size Confidence Bias Harms Your Object Detector - Code Disclaimer: This repository is for research purposes only. It is designed to maintain r

Johannes G. 24 Dec 07, 2022
PyTorch code for the paper: FeatMatch: Feature-Based Augmentation for Semi-Supervised Learning

FeatMatch: Feature-Based Augmentation for Semi-Supervised Learning This is the PyTorch implementation of our paper: FeatMatch: Feature-Based Augmentat

43 Nov 19, 2022
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition

Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition

107 Dec 02, 2022
Zero-shot Synthesis with Group-Supervised Learning (ICLR 2021 paper)

GSL - Zero-shot Synthesis with Group-Supervised Learning Figure: Zero-shot synthesis performance of our method with different dataset (iLab-20M, RaFD,

Andy_Ge 62 Dec 21, 2022
PSML: A Multi-scale Time-series Dataset for Machine Learning in Decarbonized Energy Grids

PSML: A Multi-scale Time-series Dataset for Machine Learning in Decarbonized Energy Grids The electric grid is a key enabling infrastructure for the a

Texas A&M Engineering Research 19 Jan 07, 2023
Vision Transformer for 3D medical image registration (Pytorch).

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

Junyu Chen 192 Dec 20, 2022
Official repository of the paper Learning to Regress 3D Face Shape and Expression from an Image without 3D Supervision

Official repository of the paper Learning to Regress 3D Face Shape and Expression from an Image without 3D Supervision

Soubhik Sanyal 689 Dec 25, 2022