Search Results for author: Ozan Oktay

Found 27 papers, 12 papers with code

No Fair Lunch: A Causal Perspective on Dataset Bias in Machine Learning for Medical Imaging

no code implementations31 Jul 2023 Charles Jones, Daniel C. Castro, Fabio De Sousa Ribeiro, Ozan Oktay, Melissa McCradden, Ben Glocker

As machine learning methods gain prominence within clinical decision-making, addressing fairness concerns becomes increasingly urgent.

Decision Making Fairness

Region-based Contrastive Pretraining for Medical Image Retrieval with Anatomic Query

no code implementations9 May 2023 Ho Hin Lee, Alberto Santamaria-Pang, Jameson Merkow, Ozan Oktay, Fernando Pérez-García, Javier Alvarez-Valle, Ivan Tarapov

We introduce a novel Region-based contrastive pretraining for Medical Image Retrieval (RegionMIR) that demonstrates the feasibility of medical image retrieval with similar anatomical regions.

Anatomy Contrastive Learning +2

Making the Most of Text Semantics to Improve Biomedical Vision--Language Processing

1 code implementation21 Apr 2022 Benedikt Boecking, Naoto Usuyama, Shruthi Bannur, Daniel C. Castro, Anton Schwaighofer, Stephanie Hyland, Maria Wetscherek, Tristan Naumann, Aditya Nori, Javier Alvarez-Valle, Hoifung Poon, Ozan Oktay

We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing.

Contrastive Learning Language Modelling +4

Active label cleaning for improved dataset quality under resource constraints

1 code implementation1 Sep 2021 Melanie Bernhardt, Daniel C. Castro, Ryutaro Tanno, Anton Schwaighofer, Kerem C. Tezcan, Miguel Monteiro, Shruthi Bannur, Matthew Lungren, Aditya Nori, Ben Glocker, Javier Alvarez-Valle, Ozan Oktay

Imperfections in data annotation, known as label noise, are detrimental to the training of machine learning models and have an often-overlooked confounding effect on the assessment of model performance.

Hierarchical Analysis of Visual COVID-19 Features from Chest Radiographs

1 code implementation14 Jul 2021 Shruthi Bannur, Ozan Oktay, Melanie Bernhardt, Anton Schwaighofer, Rajesh Jena, Besmira Nushi, Sharan Wadhwani, Aditya Nori, Kal Natarajan, Shazad Ashraf, Javier Alvarez-Valle, Daniel C. Castro

Chest radiography has been a recommended procedure for patient triaging and resource management in intensive care units (ICUs) throughout the COVID-19 pandemic.


Image-and-Spatial Transformer Networks for Structure-Guided Image Registration

1 code implementation22 Jul 2019 Matthew C. H. Lee, Ozan Oktay, Andreas Schuh, Michiel Schaap, Ben Glocker

The goal is to learn a complex function that maps the appearance of input image pairs to parameters of a spatial transformation in order to align corresponding anatomical structures.

Image Registration

Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models

1 code implementation28 Jun 2019 Carlo Biffi, Juan J. Cerrolaza, Giacomo Tarroni, Wenjia Bai, Antonio de Marvao, Ozan Oktay, Christian Ledig, Loic Le Folgoc, Konstantinos Kamnitsas, Georgia Doumou, Jinming Duan, Sanjay K. Prasad, Stuart A. Cook, Declan P. O'Regan, Daniel Rueckert

At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space.


A Comprehensive Approach for Learning-based Fully-Automated Inter-slice Motion Correction for Short-Axis Cine Cardiac MR Image Stacks

no code implementations3 Oct 2018 Giacomo Tarroni, Ozan Oktay, Matthew Sinclair, Wenjia Bai, Andreas Schuh, Hideaki Suzuki, Antonio de Marvao, Declan O'Regan, Stuart Cook, Daniel Rueckert

If long axis (LA) images are available, PSMs are generated for them and combined to create the target PSM; if not, the target PSM is produced from the same stack using a 3D model trained from motion-free stacks.

Motion Compensation

Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images

2 code implementations22 Aug 2018 Jo Schlemper, Ozan Oktay, Michiel Schaap, Mattias Heinrich, Bernhard Kainz, Ben Glocker, Daniel Rueckert

AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy.

General Classification Image Classification +1

Recurrent neural networks for aortic image sequence segmentation with sparse annotations

no code implementations1 Aug 2018 Wenjia Bai, Hideaki Suzuki, Chen Qin, Giacomo Tarroni, Ozan Oktay, Paul M. Matthews, Daniel Rueckert

In this work, we propose an image sequence segmentation algorithm by combining a fully convolutional network with a recurrent neural network, which incorporates both spatial and temporal information into the segmentation task.


Adversarial and Perceptual Refinement for Compressed Sensing MRI Reconstruction

1 code implementation28 Jun 2018 Maximilian Seitzer, Guang Yang, Jo Schlemper, Ozan Oktay, Tobias Würfl, Vincent Christlein, Tom Wong, Raad Mohiaddin, David Firmin, Jennifer Keegan, Daniel Rueckert, Andreas Maier

In addition, we introduce a semantic interpretability score, measuring the visibility of the region of interest in both ground truth and reconstructed images, which allows us to objectively quantify the usefulness of the image quality for image post-processing and analysis.

MRI Reconstruction Open-Ended Question Answering

Attention-Gated Networks for Improving Ultrasound Scan Plane Detection

6 code implementations15 Apr 2018 Jo Schlemper, Ozan Oktay, Liang Chen, Jacqueline Matthew, Caroline Knight, Bernhard Kainz, Ben Glocker, Daniel Rueckert

We show that, when the base network has a high capacity, the incorporated attention mechanism can provide efficient object localisation while improving the overall performance.

Attention U-Net: Learning Where to Look for the Pancreas

31 code implementations11 Apr 2018 Ozan Oktay, Jo Schlemper, Loic Le Folgoc, Matthew Lee, Mattias Heinrich, Kazunari Misawa, Kensaku Mori, Steven McDonagh, Nils Y. Hammerla, Bernhard Kainz, Ben Glocker, Daniel Rueckert

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes.

Brain Tumor Segmentation Image Segmentation +2

Learning-Based Quality Control for Cardiac MR Images

no code implementations25 Mar 2018 Giacomo Tarroni, Ozan Oktay, Wenjia Bai, Andreas Schuh, Hideaki Suzuki, Jonathan Passerat-Palmbach, Antonio de Marvao, Declan P. O'Regan, Stuart Cook, Ben Glocker, Paul M. Matthews, Daniel Rueckert

The results show the capability of the proposed pipeline to correctly detect incomplete or corrupted scans (e. g. on UK Biobank, sensitivity and specificity respectively 88% and 99% for heart coverage estimation, 85% and 95% for motion detection), allowing their exclusion from the analysed dataset or the triggering of a new acquisition.

Motion Detection Specificity

TernaryNet: Faster Deep Model Inference without GPUs for Medical 3D Segmentation using Sparse and Binary Convolutions

1 code implementation29 Jan 2018 Mattias P. Heinrich, Max Blendowski, Ozan Oktay

We propose a new scheme that approximates both trainable weights and neural activations in deep networks by ternary values and tackles the open question of backpropagation when dealing with non-differentiable functions.

Open-Ended Question Answering Pancreas Segmentation +1

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

1 code implementation25 Oct 2017 Wenjia Bai, Matthew Sinclair, Giacomo Tarroni, Ozan Oktay, Martin Rajchl, Ghislain Vaillant, Aaron M. Lee, Nay Aung, Elena Lukaschuk, Mihir M. Sanghvi, Filip Zemrak, Kenneth Fung, Jose Miguel Paiva, Valentina Carapella, Young Jin Kim, Hideaki Suzuki, Bernhard Kainz, Paul M. Matthews, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Ben Glocker, Daniel Rueckert

By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance on par with human experts in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images.

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