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
😇A pyTorch implementation of the DeepMoji model: state-of-the-art deep learning model for analyzing sentiment, emotion, sarcasm etc

------ Update September 2018 ------ It's been a year since TorchMoji and DeepMoji were released. We're trying to understand how it's being used such t

Hugging Face 865 Dec 24, 2022
AutoDeeplab / auto-deeplab / AutoML for semantic segmentation, implemented in Pytorch

AutoML for Image Semantic Segmentation Currently this repo contains the only working open-source implementation of Auto-Deeplab which, by the way out-

AI Necromancer 299 Dec 17, 2022
Deep Networks with Recurrent Layer Aggregation

RLA-Net: Recurrent Layer Aggregation Recurrence along Depth: Deep Networks with Recurrent Layer Aggregation This is an implementation of RLA-Net (acce

Joy Fang 21 Aug 16, 2022
This repository includes the official project for the paper: TransMix: Attend to Mix for Vision Transformers.

TransMix: Attend to Mix for Vision Transformers This repository includes the official project for the paper: TransMix: Attend to Mix for Vision Transf

Jie-Neng Chen 130 Jan 01, 2023
Machine learning, in numpy

numpy-ml Ever wish you had an inefficient but somewhat legible collection of machine learning algorithms implemented exclusively in NumPy? No? Install

David Bourgin 11.6k Dec 30, 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
A PyTorch implementation of deep-learning-based registration

DiffuseMorph Implementation A PyTorch implementation of deep-learning-based registration. Requirements OS : Ubuntu / Windows Python 3.6 PyTorch 1.4.0

24 Jan 03, 2023
VoxHRNet - Whole Brain Segmentation with Full Volume Neural Network

VoxHRNet This is the official implementation of the following paper: Whole Brain Segmentation with Full Volume Neural Network Yeshu Li, Jonathan Cui,

Microsoft 12 Nov 24, 2022
Space-invaders - Simple Game created using Python & PyGame, as my Beginner Python Project

Space Invaders This is a simple SPACE INVADER game create using PYGAME whihc hav

Gaurav Pandey 2 Jan 08, 2022
Evaluating Privacy-Preserving Machine Learning in Critical Infrastructures: A Case Study on Time-Series Classification

PPML-TSA This repository provides all code necessary to reproduce the results reported in our paper Evaluating Privacy-Preserving Machine Learning in

Dominik 1 Mar 08, 2022
Python scripts form performing stereo depth estimation using the HITNET model in ONNX.

ONNX-HITNET-Stereo-Depth-estimation Python scripts form performing stereo depth estimation using the HITNET model in ONNX. Stereo depth estimation on

Ibai Gorordo 30 Nov 08, 2022
DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021)

DPT This repo is the official implementation of DPT: Deformable Patch-based Transformer for Visual Recognition (ACM MM2021). We provide code and model

CASIA-IVA-Lab 111 Dec 21, 2022
This project implements "virtual speed" from heart rate monito

ANT+ Virtual Stride Based Speed and Distance Monitor Overview This project imple

2 May 20, 2022
Kinetics-Data-Preprocessing

Kinetics-Data-Preprocessing Kinetics-400 and Kinetics-600 are common video recognition datasets used by popular video understanding projects like Slow

Kaihua Tang 7 Oct 27, 2022
Code accompanying paper: Meta-Learning to Improve Pre-Training

Meta-Learning to Improve Pre-Training This folder contains code to run experiments in the paper Meta-Learning to Improve Pre-Training, NeurIPS 2021. P

28 Dec 31, 2022
CRNN With PyTorch

CRNN-PyTorch Implementation of https://arxiv.org/abs/1507.05717

Vadim 4 Sep 01, 2022
PyTorch implementation of DirectCLR from paper Understanding Dimensional Collapse in Contrastive Self-supervised Learning

DirectCLR DirectCLR is a simple contrastive learning model for visual representation learning. It does not require a trainable projector as SimCLR. It

Meta Research 49 Dec 21, 2022
Rule Based Classification Project

Kural Tabanlı Sınıflandırma ile Potansiyel Müşteri Getirisi Hesaplama İş Problemi: Bir oyun şirketi müşterilerinin bazı özelliklerini kullanaraknseviy

Şafak 1 Jan 12, 2022
DeepRec is a recommendation engine based on TensorFlow.

DeepRec Introduction DeepRec is a recommendation engine based on TensorFlow 1.15, Intel-TensorFlow and NVIDIA-TensorFlow. Background Sparse model is a

Alibaba 676 Jan 03, 2023
ManiSkill-Learn is a framework for training agents on SAPIEN Open-Source Manipulation Skill Challenge (ManiSkill Challenge), a large-scale learning-from-demonstrations benchmark for object manipulation.

ManiSkill-Learn ManiSkill-Learn is a framework for training agents on SAPIEN Open-Source Manipulation Skill Challenge, a large-scale learning-from-dem

Hao Su's Lab, UCSD 48 Dec 30, 2022