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
PyTorch implementation of the end-to-end coreference resolution model with different higher-order inference methods.

End-to-End Coreference Resolution with Different Higher-Order Inference Methods This repository contains the implementation of the paper: Revealing th

Liyan 52 Jan 04, 2023
Help you understand Manual and w/ Clutch point while driving.

简体中文 forza_auto_gear forza_auto_gear is a tool for Forza Horizon 5. It will help us understand the best gear shift point using Manual or w/ Clutch in

15 Oct 08, 2022
Related resources for our EMNLP 2021 paper

Plan-then-Generate: Controlled Data-to-Text Generation via Planning Authors: Yixuan Su, David Vandyke, Sihui Wang, Yimai Fang, and Nigel Collier Code

Yixuan Su 61 Jan 03, 2023
Protect against subdomain takeover

domain-protect scans Amazon Route53 across an AWS Organization for domain records vulnerable to takeover deploy to security audit account scan your en

OVO Technology 0 Nov 17, 2022
Code for Phase diagram of Stochastic Gradient Descent in high-dimensional two-layer neural networks

Phase diagram of Stochastic Gradient Descent in high-dimensional two-layer neural networks Under construction. Description Code for Phase diagram of S

Rodrigo Veiga 3 Nov 24, 2022
DeepVoxels is an object-specific, persistent 3D feature embedding.

DeepVoxels is an object-specific, persistent 3D feature embedding. It is found by globally optimizing over all available 2D observations of

Vincent Sitzmann 196 Dec 25, 2022
Unsupervised Representation Learning via Neural Activation Coding

Neural Activation Coding This repository contains the code for the paper "Unsupervised Representation Learning via Neural Activation Coding" published

yookoon park 5 May 26, 2022
Arquitetura e Desenho de Software.

S203 Este é um repositório dedicado às aulas de Arquitetura e Desenho de Software, cuja sigla é "S203". E agora, José? Como não tenho muito a falar aq

Fabio 7 Oct 23, 2021
Neural Radiance Fields Using PyTorch

This project is a PyTorch implementation of Neural Radiance Fields (NeRF) for reproduction of results whilst running at a faster speed.

Vedant Ghodke 1 Feb 11, 2022
Official source code of Fast Point Transformer, CVPR 2022

Fast Point Transformer Project Page | Paper This repository contains the official source code and data for our paper: Fast Point Transformer Chunghyun

182 Dec 23, 2022
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dea

MIC-DKFZ 1.2k Jan 04, 2023
This repository is for our paper Exploiting Scene Graphs for Human-Object Interaction Detection accepted by ICCV 2021.

SG2HOI This repository is for our paper Exploiting Scene Graphs for Human-Object Interaction Detection accepted by ICCV 2021. Installation Pytorch 1.7

HT 10 Dec 20, 2022
ShinRL: A Library for Evaluating RL Algorithms from Theoretical and Practical Perspectives

Status: Under development (expect bug fixes and huge updates) ShinRL: A Library for Evaluating RL Algorithms from Theoretical and Practical Perspectiv

37 Dec 28, 2022
You Only 👀 One Sequence

You Only 👀 One Sequence TL;DR: We study the transferability of the vanilla ViT pre-trained on mid-sized ImageNet-1k to the more challenging COCO obje

Hust Visual Learning Team 666 Jan 03, 2023
OptNet: Differentiable Optimization as a Layer in Neural Networks

OptNet: Differentiable Optimization as a Layer in Neural Networks This repository is by Brandon Amos and J. Zico Kolter and contains the PyTorch sourc

CMU Locus Lab 428 Dec 24, 2022
Migration of Edge-based Distributed Federated Learning

FedFly: Towards Migration in Edge-based Distributed Federated Learning About the research Due to mobility, a device participating in Federated Learnin

qub-blesson 11 Nov 13, 2022
Specificity-preserving RGB-D Saliency Detection

Specificity-preserving RGB-D Saliency Detection Authors: Tao Zhou, Huazhu Fu, Geng Chen, Yi Zhou, Deng-Ping Fan, and Ling Shao. 1. Preface This reposi

Tao Zhou 35 Jan 08, 2023
A generalized framework for prototyping full-stack cooperative driving automation applications under CARLA+SUMO.

OpenCDA OpenCDA is a SIMULATION tool integrated with a prototype cooperative driving automation (CDA; see SAE J3216) pipeline as well as regular autom

UCLA Mobility Lab 726 Dec 29, 2022
Edison AT is software Depression Assistant personal.

Edison AT Edison AT is software / program Depression Assistant personal. Feature: Analyze emotional real-time from face. Audio Edison(Comingsoon relea

Ananda Rauf 2 Apr 24, 2022
PyTorch Implementation of Google Brain's WaveGrad 2: Iterative Refinement for Text-to-Speech Synthesis

WaveGrad2 - PyTorch Implementation PyTorch Implementation of Google Brain's WaveGrad 2: Iterative Refinement for Text-to-Speech Synthesis. Status (202

Keon Lee 59 Dec 06, 2022