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
PPO Lagrangian in JAX

PPO Lagrangian in JAX This repository implements PPO in JAX. Implementation is tested on the safety-gym benchmark. Usage Install dependencies using th

Karush Suri 2 Sep 14, 2022
Airbus Ship Detection Challenge

Airbus Ship Detection Challenge This is an open solution to the Airbus Ship Detection Challenge. Our goals We are building entirely open solution to t

minerva.ml 55 Nov 29, 2022
Credit fraud detection in Python using a Jupyter Notebook

Credit-Fraud-Detection - Credit fraud detection in Python using a Jupyter Notebook , using three classification models (Random Forest, Gaussian Naive Bayes, Logistic Regression) from the sklearn libr

Ali Akram 4 Dec 28, 2021
Replication attempt for the Protein Folding Model

RGN2-Replica (WIP) To eventually become an unofficial working Pytorch implementation of RGN2, an state of the art model for MSA-less Protein Folding f

Eric Alcaide 36 Nov 29, 2022
ROCKET: Exceptionally fast and accurate time series classification using random convolutional kernels

ROCKET + MINIROCKET ROCKET: Exceptionally fast and accurate time series classification using random convolutional kernels. Data Mining and Knowledge D

298 Dec 26, 2022
PyTorch Implementation of Exploring Explicit Domain Supervision for Latent Space Disentanglement in Unpaired Image-to-Image Translation.

DosGAN-PyTorch PyTorch Implementation of Exploring Explicit Domain Supervision for Latent Space Disentanglement in Unpaired Image-to-Image Translation

40 Nov 30, 2022
This is the repository of our article published on MDPI Entropy "Feature Selection for Recommender Systems with Quantum Computing".

Collaborative-driven Quantum Feature Selection This repository was developed by Riccardo Nembrini, PhD student at Politecnico di Milano. See the websi

Quantum Computing Lab @ Politecnico di Milano 10 Apr 21, 2022
PyTorch Language Model for 1-Billion Word (LM1B / GBW) Dataset

PyTorch Large-Scale Language Model A Large-Scale PyTorch Language Model trained on the 1-Billion Word (LM1B) / (GBW) dataset Latest Results 39.98 Perp

Ryan Spring 114 Nov 04, 2022
Official implementation of NeurIPS 2021 paper "Contextual Similarity Aggregation with Self-attention for Visual Re-ranking"

CSA: Contextual Similarity Aggregation with Self-attention for Visual Re-ranking PyTorch training code for CSA (Contextual Similarity Aggregation). We

Hui Wu 19 Oct 21, 2022
PyDEns is a framework for solving Ordinary and Partial Differential Equations (ODEs & PDEs) using neural networks

PyDEns PyDEns is a framework for solving Ordinary and Partial Differential Equations (ODEs & PDEs) using neural networks. With PyDEns one can solve PD

Data Analysis Center 220 Dec 26, 2022
a delightful machine learning tool that allows you to train, test and use models without writing code

igel A delightful machine learning tool that allows you to train/fit, test and use models without writing code Note I'm also working on a GUI desktop

Nidhal Baccouri 3k Jan 05, 2023
Calibrated Hyperspectral Image Reconstruction via Graph-based Self-Tuning Network.

mask-uncertainty-in-HSI This repository contains the testing code and pre-trained models for the paper Calibrated Hyperspectral Image Reconstruction v

JIAMIAN WANG 9 Dec 29, 2022
[LREC] MMChat: Multi-Modal Chat Dataset on Social Media

MMChat This repo contains the code and data for the LREC2022 paper MMChat: Multi-Modal Chat Dataset on Social Media. Dataset MMChat is a large-scale d

Silver 47 Jan 03, 2023
Implement the Pareto Optimizer and pcgrad to make a self-adaptive loss for multi-task

multi-task_losses_optimizer Implement the Pareto Optimizer and pcgrad to make a self-adaptive loss for multi-task 已经实验过了,不会有cuda out of memory情况 ##Par

14 Dec 25, 2022
Copy Paste positive polyp using poisson image blending for medical image segmentation

Copy Paste positive polyp using poisson image blending for medical image segmentation According poisson image blending I've completely used it for bio

Phạm Vũ Hùng 2 Oct 19, 2021
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
[CVPR 2022] Pytorch implementation of "Templates for 3D Object Pose Estimation Revisited: Generalization to New objects and Robustness to Occlusions" paper

template-pose Pytorch implementation of "Templates for 3D Object Pose Estimation Revisited: Generalization to New objects and Robustness to Occlusions

Van Nguyen Nguyen 92 Dec 28, 2022
A machine learning library for spiking neural networks. Supports training with both torch and jax pipelines, and deployment to neuromorphic hardware.

Rockpool Rockpool is a Python package for developing signal processing applications with spiking neural networks. Rockpool allows you to build network

SynSense 21 Dec 14, 2022
Open source simulator for autonomous vehicles built on Unreal Engine / Unity, from Microsoft AI & Research

Welcome to AirSim AirSim is a simulator for drones, cars and more, built on Unreal Engine (we now also have an experimental Unity release). It is open

Microsoft 13.8k Jan 03, 2023
No-Reference Image Quality Assessment via Transformers, Relative Ranking, and Self-Consistency

This repository contains the implementation for the paper: No-Reference Image Quality Assessment via Transformers, Relative Ranking, and Self-Consiste

Alireza Golestaneh 75 Dec 30, 2022