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
Segment axon and myelin from microscopy data using deep learning

Segment axon and myelin from microscopy data using deep learning. Written in Python. Using the TensorFlow framework. Based on a convolutional neural network architecture. Pixels are classified as eit

NeuroPoly 103 Nov 29, 2022
System Combination for Grammatical Error Correction Based on Integer Programming

System Combination for Grammatical Error Correction Based on Integer Programming This repository contains the code and scripts that implement the syst

NUS NLP Group 0 Mar 29, 2022
PyTorch experiments with the Zalando fashion-mnist dataset

zalando-pytorch PyTorch experiments with the Zalando fashion-mnist dataset Project Organization ├── LICENSE ├── Makefile - Makefile with co

Federico Baldassarre 31 Sep 25, 2021
My implementation of Image Inpainting - A deep learning Inpainting model

Image Inpainting What is Image Inpainting Image inpainting is a restorative process that allows for the fixing or removal of unwanted parts within ima

Joshua V Evans 1 Dec 12, 2021
Training RNNs as Fast as CNNs

News SRU++, a new SRU variant, is released. [tech report] [blog] The experimental code and SRU++ implementation are available on the dev branch which

ASAPP Research 2.1k Jan 01, 2023
Generate fine-tuning samples & Fine-tuning the model & Generate samples by transferring Note On

UPMT Generate fine-tuning samples & Fine-tuning the model & Generate samples by transferring Note On See main.py as an example: from model import PopM

7 Sep 01, 2022
blind SQLIpy sebuah alat injeksi sql yang menggunakan waktu sql untuk mendapatkan sebuah server database.

blind SQLIpy Alat blind SQLIpy ini merupakan alat injeksi sql yang menggunakan metode time based blind sql injection metode tersebut membutuhkan waktu

Galih Anggoro Prasetya 4 Feb 24, 2022
ONNX-PackNet-SfM: Python scripts for performing monocular depth estimation using the PackNet-SfM model in ONNX

Python scripts for performing monocular depth estimation using the PackNet-SfM model in ONNX

Ibai Gorordo 14 Dec 09, 2022
Infrastructure as Code (IaC) for a self-hosted version of Gnosis Safe on AWS

Welcome to Yearn Gnosis Safe! Setting up your local environment Infrastructure Deploying Gnosis Safe Prerequisites 1. Create infrastructure for secret

Numan 16 Jul 18, 2022
Repository for the paper "Online Domain Adaptation for Occupancy Mapping", RSS 2020

RSS 2020 - Online Domain Adaptation for Occupancy Mapping Repository for the paper "Online Domain Adaptation for Occupancy Mapping", Robotics: Science

Anthony 26 Sep 22, 2022
Official PyTorch implementation of Spatial Dependency Networks.

Spatial Dependency Networks: Neural Layers for Improved Generative Image Modeling Đorđe Miladinović   Aleksandar Stanić   Stefan Bauer   Jürgen Schmid

Djordje Miladinovic 34 Jan 19, 2022
Equivariant Imaging: Learning Beyond the Range Space

[Project] Equivariant Imaging: Learning Beyond the Range Space Project about the

Georges Le Bellier 3 Feb 06, 2022
Style-based Neural Drum Synthesis with GAN inversion

Style-based Drum Synthesis with GAN Inversion Demo TensorFlow implementation of a style-based version of the adversarial drum synth (ADS) from the pap

Sound and Music Analysis (SoMA) Group 29 Nov 19, 2022
Implementation of "Learning to Match Features with Seeded Graph Matching Network" ICCV2021

SGMNet Implementation PyTorch implementation of SGMNet for ICCV'21 paper "Learning to Match Features with Seeded Graph Matching Network", by Hongkai C

87 Dec 11, 2022
Grounding Representation Similarity with Statistical Testing

Grounding Representation Similarity with Statistical Testing This repo contains code to replicate the results in our paper, which evaluates representa

26 Dec 02, 2022
UnFlow: Unsupervised Learning of Optical Flow with a Bidirectional Census Loss

UnFlow: Unsupervised Learning of Optical Flow with a Bidirectional Census Loss This repository contains the TensorFlow implementation of the paper UnF

Simon Meister 270 Nov 06, 2022
TensorFlow (v2.7.0) benchmark results on an M1 Macbook Air 2020 laptop (macOS Monterey v12.1).

M1-tensorflow-benchmark TensorFlow (v2.7.0) benchmark results on an M1 Macbook Air 2020 laptop (macOS Monterey v12.1). I was initially testing if Tens

particle 2 Jan 05, 2022
Vehicle detection using machine learning and computer vision techniques for Udacity's Self-Driving Car Engineer Nanodegree.

Vehicle Detection Video demo Overview Vehicle detection using these machine learning and computer vision techniques. Linear SVM HOG(Histogram of Orien

hata 1.1k Dec 18, 2022
PyTorch implementation of adversarial patch

adversarial-patch PyTorch implementation of adversarial patch This is an implementation of the Adversarial Patch paper. Not official and likely to hav

Jamie Hayes 172 Nov 29, 2022
This repository contains code to run experiments in the paper "Signal Strength and Noise Drive Feature Preference in CNN Image Classifiers."

Signal Strength and Noise Drive Feature Preference in CNN Image Classifiers This repository contains code to run experiments in the paper "Signal Stre

0 Jan 19, 2022