Search Results for author: Ben Glocker

Found 125 papers, 71 papers with code

The Importance of Model Inspection for Better Understanding Performance Characteristics of Graph Neural Networks

1 code implementation2 May 2024 Nairouz Shehata, Carolina Piçarra, Anees Kazi, Ben Glocker

This study highlights the importance of conducting comprehensive model inspection as part of comparative performance analyses.

Mitigating attribute amplification in counterfactual image generation

no code implementations14 Mar 2024 Tian Xia, Mélanie Roschewitz, Fabio De Sousa Ribeiro, Charles Jones, Ben Glocker

Causal generative modelling is gaining interest in medical imaging due to its ability to answer interventional and counterfactual queries.

Attribute counterfactual +1

Counterfactual contrastive learning: robust representations via causal image synthesis

1 code implementation14 Mar 2024 Melanie Roschewitz, Fabio De Sousa Ribeiro, Tian Xia, Galvin Khara, Ben Glocker

Contrastive pretraining is well-known to improve downstream task performance and model generalisation, especially in limited label settings.

Contrastive Learning counterfactual +2

Average Calibration Error: A Differentiable Loss for Improved Reliability in Image Segmentation

1 code implementation11 Mar 2024 Theodore Barfoot, Luis Garcia-Peraza-Herrera, Ben Glocker, Tom Vercauteren

Using mL1-ACE, we reduce average and maximum calibration error by 45% and 55% respectively, maintaining a Dice score of 87% on the BraTS 2021 dataset.

Image Segmentation Medical Image Segmentation +2

Demystifying Variational Diffusion Models

no code implementations11 Jan 2024 Fabio De Sousa Ribeiro, Ben Glocker

Despite the growing popularity of diffusion models, gaining a deep understanding of the model class remains somewhat elusive for the uninitiated in non-equilibrium statistical physics.

Robust semi-supervised segmentation with timestep ensembling diffusion models

no code implementations13 Nov 2023 Margherita Rosnati, Melanie Roschewitz, Ben Glocker

Medical image segmentation is a challenging task, made more difficult by many datasets' limited size and annotations.

Denoising Image Segmentation +3

Analysing race and sex bias in brain age prediction

no code implementations19 Sep 2023 Carolina Piçarra, Ben Glocker

With the objective of comparing the performance between subgroups, measured by the absolute prediction error, we use a Kruskal-Wallis test followed by two post-hoc Conover-Iman tests to inspect bias across race and biological sex.

Dimensionality Reduction

Distance Matters For Improving Performance Estimation Under Covariate Shift

1 code implementation14 Aug 2023 Mélanie Roschewitz, Ben Glocker

In this work, we show that taking into account distances of test samples to their expected training distribution can significantly improve performance estimation under covariate shift.

Image Classification

Robustness Stress Testing in Medical Image Classification

1 code implementation14 Aug 2023 Mobarakol Islam, Zeju Li, Ben Glocker

We conclude that progressive stress testing is a viable and important tool and should become standard practice in the clinical validation of image-based disease detection models.

Image Classification Medical Image Classification

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

no code implementations11 Aug 2023 Karim Lekadir, Aasa Feragen, Abdul Joseph Fofanah, Alejandro F Frangi, Alena Buyx, Anais Emelie, Andrea Lara, Antonio R Porras, An-Wen Chan, Arcadi Navarro, Ben Glocker, Benard O Botwe, Bishesh Khanal, Brigit Beger, Carol C Wu, Celia Cintas, Curtis P Langlotz, Daniel Rueckert, Deogratias Mzurikwao, Dimitrios I Fotiadis, Doszhan Zhussupov, Enzo Ferrante, Erik Meijering, Eva Weicken, Fabio A González, Folkert W Asselbergs, Fred Prior, Gabriel P Krestin, Gary Collins, Geletaw S Tegenaw, Georgios Kaissis, Gianluca Misuraca, Gianna Tsakou, Girish Dwivedi, Haridimos Kondylakis, Harsha Jayakody, Henry C Woodruf, Hugo JWL Aerts, Ian Walsh, Ioanna Chouvarda, Irène Buvat, Islem Rekik, James Duncan, Jayashree Kalpathy-Cramer, Jihad Zahir, Jinah Park, John Mongan, Judy W Gichoya, Julia A Schnabel, Kaisar Kushibar, Katrine Riklund, Kensaku MORI, Kostas Marias, Lameck M Amugongo, Lauren A Fromont, Lena Maier-Hein, Leonor Cerdá Alberich, Leticia Rittner, Lighton Phiri, Linda Marrakchi-Kacem, Lluís Donoso-Bach, Luis Martí-Bonmatí, M Jorge Cardoso, Maciej Bobowicz, Mahsa Shabani, Manolis Tsiknakis, Maria A Zuluaga, Maria Bielikova, Marie-Christine Fritzsche, Marius George Linguraru, Markus Wenzel, Marleen de Bruijne, Martin G Tolsgaard, Marzyeh Ghassemi, Md Ashrafuzzaman, Melanie Goisauf, Mohammad Yaqub, Mohammed Ammar, Mónica Cano Abadía, Mukhtar M E Mahmoud, Mustafa Elattar, Nicola Rieke, Nikolaos Papanikolaou, Noussair Lazrak, Oliver Díaz, Olivier Salvado, Oriol Pujol, Ousmane Sall, Pamela Guevara, Peter Gordebeke, Philippe Lambin, Pieta Brown, Purang Abolmaesumi, Qi Dou, Qinghua Lu, Richard Osuala, Rose Nakasi, S Kevin Zhou, Sandy Napel, Sara Colantonio, Shadi Albarqouni, Smriti Joshi, Stacy Carter, Stefan Klein, Steffen E Petersen, Susanna Aussó, Suyash Awate, Tammy Riklin Raviv, Tessa Cook, Tinashe E M Mutsvangwa, Wendy A Rogers, Wiro J Niessen, Xènia Puig-Bosch, Yi Zeng, Yunusa G Mohammed, Yves Saint James Aquino, Zohaib Salahuddin, Martijn P A Starmans

This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare.

Fairness

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

Grounded Object Centric Learning

no code implementations18 Jul 2023 Avinash Kori, Francesco Locatello, Fabio De Sousa Ribeiro, Francesca Toni, Ben Glocker

The extraction of modular object-centric representations for downstream tasks is an emerging area of research.

Object Object Discovery +3

A Causal Ordering Prior for Unsupervised Representation Learning

no code implementations11 Jul 2023 Avinash Kori, Pedro Sanchez, Konstantinos Vilouras, Ben Glocker, Sotirios A. Tsaftaris

Unsupervised representation learning with variational inference relies heavily on independence assumptions over latent variables.

Causal Discovery counterfactual +2

High Fidelity Image Counterfactuals with Probabilistic Causal Models

1 code implementation27 Jun 2023 Fabio De Sousa Ribeiro, Tian Xia, Miguel Monteiro, Nick Pawlowski, Ben Glocker

We present a general causal generative modelling framework for accurate estimation of high fidelity image counterfactuals with deep structural causal models.

counterfactual

Joint Optimization of Class-Specific Training- and Test-Time Data Augmentation in Segmentation

1 code implementation30 May 2023 Zeju Li, Konstantinos Kamnitsas, Qi Dou, Chen Qin, Ben Glocker

We demonstrate the effectiveness of our method on four medical image segmentation tasks across different scenarios with two state-of-the-art segmentation models, DeepMedic and nnU-Net.

Data Augmentation Image Segmentation +4

Understanding metric-related pitfalls in image analysis validation

no code implementations3 Feb 2023 Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul F. Jäger, Lena Maier-Hein

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice.

Paced-Curriculum Distillation with Prediction and Label Uncertainty for Image Segmentation

1 code implementation2 Feb 2023 Mobarakol Islam, Lalithkumar Seenivasan, S. P. Sharan, V. K. Viekash, Bhavesh Gupta, Ben Glocker, Hongliang Ren

Purpose: In curriculum learning, the idea is to train on easier samples first and gradually increase the difficulty, while in self-paced learning, a pacing function defines the speed to adapt the training progress.

Image Segmentation Medical Image Segmentation +3

Image To Tree with Recursive Prompting

no code implementations1 Jan 2023 James Batten, Matthew Sinclair, Ben Glocker, Michiel Schaap

Extracting complex structures from grid-based data is a common key step in automated medical image analysis.

Confidence-Aware Paced-Curriculum Learning by Label Smoothing for Surgical Scene Understanding

1 code implementation22 Dec 2022 Mengya Xu, Mobarakol Islam, Ben Glocker, Hongliang Ren

In this work, we design a paced curriculum by label smoothing (P-CBLS) using paced learning with uniform label smoothing (ULS) for classification tasks and fuse uniform and spatially varying label smoothing (SVLS) for semantic segmentation tasks in a curriculum manner.

Multi-Label Classification Scene Understanding +1

Context Label Learning: Improving Background Class Representations in Semantic Segmentation

1 code implementation16 Dec 2022 Zeju Li, Konstantinos Kamnitsas, Cheng Ouyang, Chen Chen, Ben Glocker

The results demonstrate that CoLab can guide the segmentation model to map the logits of background samples away from the decision boundary, resulting in significantly improved segmentation accuracy.

Segmentation Semantic Segmentation

A Comparative Study of Graph Neural Networks for Shape Classification in Neuroimaging

1 code implementation29 Oct 2022 Nairouz Shehata, Wulfie Bain, Ben Glocker

Graph neural networks have emerged as a promising approach for the analysis of non-Euclidean data such as meshes.

Classification Data Augmentation

Explaining Image Classification with Visual Debates

1 code implementation17 Oct 2022 Avinash Kori, Ben Glocker, Francesca Toni

An effective way to obtain different perspectives on any given topic is by conducting a debate, where participants argue for and against the topic.

Classification Image Classification

Frequency Dropout: Feature-Level Regularization via Randomized Filtering

no code implementations20 Sep 2022 Mobarakol Islam, Ben Glocker

Both high and low frequencies can be characteristic of the underlying noise distribution caused by the image acquisition rather than in relation to the task-relevant information about the image content.

Domain Adaptation Image Classification +1

Risk of Bias in Chest Radiography Deep Learning Foundation Models

2 code implementations7 Sep 2022 Ben Glocker, Charles Jones, Melanie Roschewitz, Stefan Winzeck

Purpose: To analyze a recently published chest radiography foundation model for the presence of biases that could lead to subgroup performance disparities across biological sex and race.

Decision Making Dimensionality Reduction

Deep Structural Causal Shape Models

no code implementations23 Aug 2022 Rajat Rasal, Daniel C. Castro, Nick Pawlowski, Ben Glocker

Causal reasoning provides a language to ask important interventional and counterfactual questions beyond purely statistical association.

counterfactual Image Segmentation +1

Estimating Model Performance under Domain Shifts with Class-Specific Confidence Scores

1 code implementation20 Jul 2022 Zeju Li, Konstantinos Kamnitsas, Mobarakol Islam, Chen Chen, Ben Glocker

If we could estimate the performance that a pre-trained model would achieve on data from a specific deployment setting, for example a certain clinic, we could judge whether the model could safely be deployed or if its performance degrades unacceptably on the specific data.

Image Segmentation Semantic Segmentation

Hierarchical Symbolic Reasoning in Hyperbolic Space for Deep Discriminative Models

1 code implementation5 Jul 2022 Ainkaran Santhirasekaram, Avinash Kori, Andrea Rockall, Mathias Winkler, Francesca Toni, Ben Glocker

We achieve this by using the natural properties of \emph{hyperbolic geometry} to more efficiently model a hierarchy of symbolic features and generate \emph{hierarchical symbolic rules} as part of our explanations.

Feature Importance

Vector Quantisation for Robust Segmentation

1 code implementation5 Jul 2022 Ainkaran Santhirasekaram, Avinash Kori, Mathias Winkler, Andrea Rockall, Ben Glocker

The reliability of segmentation models in the medical domain depends on the model's robustness to perturbations in the input space.

Data Augmentation Dictionary Learning +1

GLANCE: Global to Local Architecture-Neutral Concept-based Explanations

no code implementations5 Jul 2022 Avinash Kori, Ben Glocker, Francesca Toni

Specifically, we provide a generator to visualize the `effect' of interactions among features in latent space and draw feature importance therefrom as local explanations.

Disentanglement Feature Importance +1

Distributional Gaussian Processes Layers for Out-of-Distribution Detection

no code implementations27 Jun 2022 Sebastian G. Popescu, David J. Sharp, James H. Cole, Konstantinos Kamnitsas, Ben Glocker

Moreover, by applying the same segmentation model to out-of-distribution data (i. e., images with pathology such as brain tumors), we show that our uncertainty estimates result in out-of-distribution detection that outperforms the capabilities of previous Bayesian networks and reconstruction-based approaches that learn normative distributions.

Gaussian Processes Out-of-Distribution Detection +1

Metrics reloaded: Recommendations for image analysis validation

1 code implementation3 Jun 2022 Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, A. Emre Kavur, Carole H. Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew Blaschko, M. Jorge Cardoso, Veronika Cheplygina, Beth A. Cimini, Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Florian Kofler, Annette Kopp-Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I. Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Paul F. Jäger

The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output.

Instance Segmentation object-detection +2

Structured Uncertainty in the Observation Space of Variational Autoencoders

1 code implementation25 May 2022 James Langley, Miguel Monteiro, Charles Jones, Nick Pawlowski, Ben Glocker

In contrast, improving the model for the observational distribution is rarely considered and typically defaults to a pixel-wise independent categorical or normal distribution.

Decoder Image Generation

Federated Learning Enables Big Data for Rare Cancer Boundary Detection

1 code implementation22 Apr 2022 Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-han Wang, G Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth J Preetha, Felix Sahm, Klaus Maier-Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey Rudie, Javier Villanueva-Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y Huang, Ken Chang, Carmen Balana, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S Alexander, Joseph Lombardo, Joshua D Palmer, Adam E Flanders, Adam P Dicker, Haris I Sair, Craig K Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y So, Cheng Chen, Pheng Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A Vogelbaum, J Ross Mitchell, Joaquim Farinhas, Joseph A Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C Pinho, Divya Reddy, James Holcomb, Benjamin C Wagner, Benjamin M Ellingson, Timothy F Cloughesy, Catalina Raymond, Talia Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh-Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre Xavier Falcão, Samuel B Martins, Bernardo C A Teixeira, Flávia Sprenger, David Menotti, Diego R Lucio, Pamela Lamontagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphael Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John Thompson, David Ryan Ormond, Chaitra Badve, Andrew E Sloan, Vachan Vadmal, Kristin Waite, Rivka R Colen, Linmin Pei, Murat AK, Ashok Srinivasan, J Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Ota Yoshiaki, Toshio Moritani, Sevcan Turk, Joonsang Lee, Snehal Prabhudesai, Fanny Morón, Jacob Mandel, Konstantinos Kamnitsas, Ben Glocker, Luke V M Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I Zacharaki, Konstantinos Moustakas, Christina Kalogeropoulou, Dimitrios M Kardamakis, Yoon Seong Choi, Seung-Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten MJ Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W Schouten, Hendrikus J Dubbink, Arnaud JPE Vincent, Martin J van den Bent, Pim J French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P Niclou, Olivier Keunen, Ann-Christin Hau, Martin Vallières, David Fortin, Martin Lepage, Bennett Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B Chambless, Akshitkumar Mistry, Reid C Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, Sean Benson, Regina G H Beets-Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, Maria Trujillo, William Escobar, Ana Abello, Jose Bernal, Jhon Gómez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan Allen, John M Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiss, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik M Mani, David Payne, Tahsin Kurc, Enrique Pelaez, Heydy Franco-Maldonado, Francis Loayza, Sebastian Quevedo, Pamela Guevara, Esteban Torche, Cristobal Mendoza, Franco Vera, Elvis Ríos, Eduardo López, Sergio A Velastin, Godwin Ogbole, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu'aibu, Adeleye Dorcas, Mayowa Soneye, Farouk Dako, Amber L Simpson, Mohammad Hamghalam, Jacob J Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fabio Y Moraes, Michael A Boss, James Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S Barnholtz-Sloan, Jason Martin, Spyridon Bakas

Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data.

Boundary Detection Federated Learning

Potential sources of dataset bias complicate investigation of underdiagnosis by machine learning algorithms

no code implementations19 Jan 2022 Mélanie Bernhardt, Charles Jones, Ben Glocker

The models consistently yield higher FPR on subgroups known to be historically underserved, and the study concludes that the models exhibit and potentially even amplify systematic underdiagnosis.

Decision Making Fairness

A Variational Bayesian Method for Similarity Learning in Non-Rigid Image Registration

1 code implementation CVPR 2022 Daniel Grzech, Mohammad Farid Azampour, Ben Glocker, Julia Schnabel, Nassir Navab, Bernhard Kainz, Loïc le Folgoc

We propose a novel variational Bayesian formulation for diffeomorphic non-rigid registration of medical images, which learns in an unsupervised way a data-specific similarity metric.

Image Registration

Matrix Inversion free variational inference in Conditional Student's T Processes

no code implementations pproximateinference AABI Symposium 2022 Sebastian Popescu, Ben Glocker, Mark van der Wilk

We propose a new variational lower bound for performing inference in sparse Student's T Processes that does not require computationally intensive operations such as matrix inversions or log determinants of matrices.

valid Variational Inference

Algorithmic encoding of protected characteristics in image-based models for disease detection

1 code implementation27 Oct 2021 Ben Glocker, Charles Jones, Melanie Bernhardt, Stefan Winzeck

We explore test set resampling, transfer learning, multitask learning, and model inspection to assess the relationship between the encoding of protected characteristics and disease detection performance across subgroups.

Decision Making Transfer Learning

Is MC Dropout Bayesian?

no code implementations8 Oct 2021 Loic Le Folgoc, Vasileios Baltatzis, Sujal Desai, Anand Devaraj, Sam Ellis, Octavio E. Martinez Manzanera, Arjun Nair, Huaqi Qiu, Julia Schnabel, Ben Glocker

We question the properties of MC Dropout for approximate inference, as in fact MC Dropout changes the Bayesian model; its predictive posterior assigns $0$ probability to the true model on closed-form benchmarks; the multimodality of its predictive posterior is not a property of the true predictive posterior but a design artefact.

Uncertainty Quantification Variational Inference

DeepMCAT: Large-Scale Deep Clustering for Medical Image Categorization

no code implementations30 Sep 2021 Turkay Kart, Wenjia Bai, Ben Glocker, Daniel Rueckert

In recent years, the research landscape of machine learning in medical imaging has changed drastically from supervised to semi-, weakly- or unsupervised methods.

Clustering Deep Clustering +1

Class-Distribution-Aware Calibration for Long-Tailed Visual Recognition

1 code implementation11 Sep 2021 Mobarakol Islam, Lalithkumar Seenivasan, Hongliang Ren, Ben Glocker

In CDA-TS, the scalar temperature value is replaced with the CDA temperature vector encoded with class frequency to compensate for the over-confidence.

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.

The Pitfalls of Sample Selection: A Case Study on Lung Nodule Classification

no code implementations11 Aug 2021 Vasileios Baltatzis, Kyriaki-Margarita Bintsi, Loic Le Folgoc, Octavio E. Martinez Manzanera, Sam Ellis, Arjun Nair, Sujal Desai, Ben Glocker, Julia A. Schnabel

Using publicly available data to determine the performance of methodological contributions is important as it facilitates reproducibility and allows scrutiny of the published results.

Lung Nodule Classification

Data synthesis and adversarial networks: A review and meta-analysis in cancer imaging

no code implementations20 Jul 2021 Richard Osuala, Kaisar Kushibar, Lidia Garrucho, Akis Linardos, Zuzanna Szafranowska, Stefan Klein, Ben Glocker, Oliver Diaz, Karim Lekadir

Despite technological and medical advances, the detection, interpretation, and treatment of cancer based on imaging data continue to pose significant challenges.

Image Generation Lesion Detection

Distributional Gaussian Process Layers for Outlier Detection in Image Segmentation

no code implementations28 Apr 2021 Sebastian G. Popescu, David J. Sharp, James H. Cole, Konstantinos Kamnitsas, Ben Glocker

We propose a parameter efficient Bayesian layer for hierarchical convolutional Gaussian Processes that incorporates Gaussian Processes operating in Wasserstein-2 space to reliably propagate uncertainty.

Gaussian Processes Image Segmentation +4

Common Limitations of Image Processing Metrics: A Picture Story

1 code implementation12 Apr 2021 Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Jianxu Chen, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Sandy Engelhardt, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Peter Hirsch, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, A. Emre Kavur, Hannes Kenngott, Jens Kleesiek, Andreas Kleppe, Sven Kohler, Florian Kofler, Annette Kopp-Schneider, Thijs Kooi, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, M. Alican Noyan, Jens Petersen, Gorkem Polat, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clara I. Sánchez, Julien Schroeter, Anindo Saha, M. Alper Selver, Lalith Sharan, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul Jäger, Lena Maier-Hein

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.

Instance Segmentation object-detection +2

Spatially Varying Label Smoothing: Capturing Uncertainty from Expert Annotations

1 code implementation12 Apr 2021 Mobarakol Islam, Ben Glocker

The task of image segmentation is inherently noisy due to ambiguities regarding the exact location of boundaries between anatomical structures.

Image Segmentation Segmentation +1

Analyzing Overfitting under Class Imbalance in Neural Networks for Image Segmentation

1 code implementation20 Feb 2021 Zeju Li, Konstantinos Kamnitsas, Ben Glocker

In particular, in image segmentation neural networks may overfit to the foreground samples from small structures, which are often heavily under-represented in the training set, leading to poor generalization.

Data Augmentation Image Segmentation +2

Atlas-ISTN: Joint Segmentation, Registration and Atlas Construction with Image-and-Spatial Transformer Networks

no code implementations18 Dec 2020 Matthew Sinclair, Andreas Schuh, Karl Hahn, Kersten Petersen, Ying Bai, James Batten, Michiel Schaap, Ben Glocker

We propose Atlas-ISTN, a framework that jointly learns segmentation and registration on 2D and 3D image data, and constructs a population-derived atlas in the process.

Image Registration Segmentation +1

Hierarchical Gaussian Processes with Wasserstein-2 Kernels

no code implementations28 Oct 2020 Sebastian Popescu, David Sharp, James Cole, Ben Glocker

Stacking Gaussian Processes severely diminishes the model's ability to detect outliers, which when combined with non-zero mean functions, further extrapolates low non-parametric variance to low training data density regions.

Gaussian Processes Out-of-Distribution Detection

Cranial Implant Design via Virtual Craniectomy with Shape Priors

no code implementations29 Sep 2020 Franco Matzkin, Virginia Newcombe, Ben Glocker, Enzo Ferrante

Our direct estimation method outperforms the baselines provided by the organizers, while the model with shape priors shows superior performance when dealing with out-of-distribution cases.

Self-supervised Skull Reconstruction in Brain CT Images with Decompressive Craniectomy

1 code implementation7 Jul 2020 Franco Matzkin, Virginia Newcombe, Susan Stevenson, Aneesh Khetani, Tom Newman, Richard Digby, Andrew Stevens, Ben Glocker, Enzo Ferrante

Decompressive craniectomy (DC) is a common surgical procedure consisting of the removal of a portion of the skull that is performed after incidents such as stroke, traumatic brain injury (TBI) or other events that could result in acute subdural hemorrhage and/or increasing intracranial pressure.

Decoder Self-Supervised Learning

Post-DAE: Anatomically Plausible Segmentation via Post-Processing with Denoising Autoencoders

1 code implementation24 Jun 2020 Agostina J. Larrazabal, César Martínez, Ben Glocker, Enzo Ferrante

We introduce Post-DAE, a post-processing method based on denoising autoencoders (DAE) to improve the anatomical plausibility of arbitrary biomedical image segmentation algorithms.

Denoising Image Segmentation +3

Deep Generative Model-based Quality Control for Cardiac MRI Segmentation

no code implementations23 Jun 2020 Shuo Wang, Giacomo Tarroni, Chen Qin, Yuanhan Mo, Chengliang Dai, Chen Chen, Ben Glocker, Yike Guo, Daniel Rueckert, Wenjia Bai

Our approach provides a real-time and model-agnostic quality control for cardiac MRI segmentation, which has the potential to be integrated into clinical image analysis workflows.

Image Segmentation MRI segmentation +2

Unpaired Multi-modal Segmentation via Knowledge Distillation

1 code implementation6 Jan 2020 Qi Dou, Quande Liu, Pheng Ann Heng, Ben Glocker

We propose a novel learning scheme for unpaired cross-modality image segmentation, with a highly compact architecture achieving superior segmentation accuracy.

Image Segmentation Knowledge Distillation +3

Causality matters in medical imaging

no code implementations17 Dec 2019 Daniel C. Castro, Ian Walker, Ben Glocker

This article discusses how the language of causality can shed new light on the major challenges in machine learning for medical imaging: 1) data scarcity, which is the limited availability of high-quality annotations, and 2) data mismatch, whereby a trained algorithm may fail to generalize in clinical practice.

BIG-bench Machine Learning Image Segmentation +3

Universal Adversarial Robustness of Texture and Shape-Biased Models

1 code implementation23 Nov 2019 Kenneth T. Co, Luis Muñoz-González, Leslie Kanthan, Ben Glocker, Emil C. Lupu

Increasing shape-bias in deep neural networks has been shown to improve robustness to common corruptions and noise.

Adversarial Robustness Image Classification

Vertebrae Detection and Localization in CT with Two-Stage CNNs and Dense Annotations

1 code implementation14 Oct 2019 James McCouat, Ben Glocker

We propose a new, two-stage approach to the vertebrae centroid detection and localization problem.

Machine Learning with Multi-Site Imaging Data: An Empirical Study on the Impact of Scanner Effects

no code implementations10 Oct 2019 Ben Glocker, Robert Robinson, Daniel C. Castro, Qi Dou, Ender Konukoglu

This is an empirical study to investigate the impact of scanner effects when using machine learning on multi-site neuroimaging data.

BIG-bench Machine Learning

Needles in Haystacks: On Classifying Tiny Objects in Large Images

1 code implementation16 Aug 2019 Nick Pawlowski, Suvrat Bhooshan, Nicolas Ballas, Francesco Ciompi, Ben Glocker, Michal Drozdzal

In some important computer vision domains, such as medical or hyperspectral imaging, we care about the classification of tiny objects in large images.

Classification General Classification +2

Overfitting of neural nets under class imbalance: Analysis and improvements for segmentation

1 code implementation25 Jul 2019 Zeju Li, Konstantinos Kamnitsas, Ben Glocker

Overfitting in deep learning has been the focus of a number of recent works, yet its exact impact on the behavior of neural networks is not well understood.

Image Segmentation Segmentation +1

Is Texture Predictive for Age and Sex in Brain MRI?

1 code implementation25 Jul 2019 Nick Pawlowski, Ben Glocker

Deep learning builds the foundation for many medical image analysis tasks where neuralnetworks are often designed to have a large receptive field to incorporate long spatialdependencies.

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

Improving RetinaNet for CT Lesion Detection with Dense Masks from Weak RECIST Labels

3 code implementations5 Jun 2019 Martin Zlocha, Qi Dou, Ben Glocker

We propose a highly accurate and efficient one-stage lesion detector, by re-designing a RetinaNet to meet the particular challenges in medical imaging.

Computed Tomography (CT) Lesion Detection +3

Medical Imaging with Deep Learning: MIDL 2019 -- Extended Abstract Track

no code implementations21 May 2019 M. Jorge Cardoso, Aasa Feragen, Ben Glocker, Ender Konukoglu, Ipek Oguz, Gozde Unal, Tom Vercauteren

This compendium gathers all the accepted extended abstracts from the Second International Conference on Medical Imaging with Deep Learning (MIDL 2019), held in London, UK, 8-10 July 2019.

BIG-bench Machine Learning

Graph Convolutional Gaussian Processes

no code implementations14 May 2019 Ian Walker, Ben Glocker

We propose a novel Bayesian nonparametric method to learn translation-invariant relationships on non-Euclidean domains.

BIG-bench Machine Learning Gaussian Processes +2

PnP-AdaNet: Plug-and-Play Adversarial Domain Adaptation Network with a Benchmark at Cross-modality Cardiac Segmentation

2 code implementations19 Dec 2018 Qi Dou, Cheng Ouyang, Cheng Chen, Hao Chen, Ben Glocker, Xiahai Zhuang, Pheng-Ann Heng

In this paper, we propose the PnPAdaNet (plug-and-play adversarial domain adaptation network) for adapting segmentation networks between different modalities of medical images, e. g., MRI and CT. We propose to tackle the significant domain shift by aligning the feature spaces of source and target domains in an unsupervised manner.

Cardiac Segmentation Domain Adaptation +2

Towards continual learning in medical imaging

no code implementations6 Nov 2018 Chaitanya Baweja, Ben Glocker, Konstantinos Kamnitsas

This work investigates continual learning of two segmentation tasks in brain MRI with neural networks.

Atari Games Continual Learning +3

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

1 code implementation5 Nov 2018 Spyridon Bakas, Mauricio Reyes, Andras Jakab, Stefan Bauer, Markus Rempfler, Alessandro Crimi, Russell Takeshi Shinohara, Christoph Berger, Sung Min Ha, Martin Rozycki, Marcel Prastawa, Esther Alberts, Jana Lipkova, John Freymann, Justin Kirby, Michel Bilello, Hassan Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Benedikt Wiestler, Rivka Colen, Aikaterini Kotrotsou, Pamela Lamontagne, Daniel Marcus, Mikhail Milchenko, Arash Nazeri, Marc-Andre Weber, Abhishek Mahajan, Ujjwal Baid, Elizabeth Gerstner, Dongjin Kwon, Gagan Acharya, Manu Agarwal, Mahbubul Alam, Alberto Albiol, Antonio Albiol, Francisco J. Albiol, Varghese Alex, Nigel Allinson, Pedro H. A. Amorim, Abhijit Amrutkar, Ganesh Anand, Simon Andermatt, Tal Arbel, Pablo Arbelaez, Aaron Avery, Muneeza Azmat, Pranjal B., W Bai, Subhashis Banerjee, Bill Barth, Thomas Batchelder, Kayhan Batmanghelich, Enzo Battistella, Andrew Beers, Mikhail Belyaev, Martin Bendszus, Eze Benson, Jose Bernal, Halandur Nagaraja Bharath, George Biros, Sotirios Bisdas, James Brown, Mariano Cabezas, Shilei Cao, Jorge M. Cardoso, Eric N Carver, Adrià Casamitjana, Laura Silvana Castillo, Marcel Catà, Philippe Cattin, Albert Cerigues, Vinicius S. Chagas, Siddhartha Chandra, Yi-Ju Chang, Shiyu Chang, Ken Chang, Joseph Chazalon, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Chen, Kun Cheng, Ahana Roy Choudhury, Roger Chylla, Albert Clérigues, Steven Colleman, Ramiro German Rodriguez Colmeiro, Marc Combalia, Anthony Costa, Xiaomeng Cui, Zhenzhen Dai, Lutao Dai, Laura Alexandra Daza, Eric Deutsch, Changxing Ding, Chao Dong, Shidu Dong, Wojciech Dudzik, Zach Eaton-Rosen, Gary Egan, Guilherme Escudero, Théo Estienne, Richard Everson, Jonathan Fabrizio, Yong Fan, Longwei Fang, Xue Feng, Enzo Ferrante, Lucas Fidon, Martin Fischer, Andrew P. French, Naomi Fridman, Huan Fu, David Fuentes, Yaozong Gao, Evan Gates, David Gering, Amir Gholami, Willi Gierke, Ben Glocker, Mingming Gong, Sandra González-Villá, T. Grosges, Yuanfang Guan, Sheng Guo, Sudeep Gupta, Woo-Sup Han, Il Song Han, Konstantin Harmuth, Huiguang He, Aura Hernández-Sabaté, Evelyn Herrmann, Naveen Himthani, Winston Hsu, Cheyu Hsu, Xiaojun Hu, Xiaobin Hu, Yan Hu, Yifan Hu, Rui Hua, Teng-Yi Huang, Weilin Huang, Sabine Van Huffel, Quan Huo, Vivek HV, Khan M. Iftekharuddin, Fabian Isensee, Mobarakol Islam, Aaron S. Jackson, Sachin R. Jambawalikar, Andrew Jesson, Weijian Jian, Peter Jin, V Jeya Maria Jose, Alain Jungo, B Kainz, Konstantinos Kamnitsas, Po-Yu Kao, Ayush Karnawat, Thomas Kellermeier, Adel Kermi, Kurt Keutzer, Mohamed Tarek Khadir, Mahendra Khened, Philipp Kickingereder, Geena Kim, Nik King, Haley Knapp, Urspeter Knecht, Lisa Kohli, Deren Kong, Xiangmao Kong, Simon Koppers, Avinash Kori, Ganapathy Krishnamurthi, Egor Krivov, Piyush Kumar, Kaisar Kushibar, Dmitrii Lachinov, Tryphon Lambrou, Joon Lee, Chengen Lee, Yuehchou Lee, M Lee, Szidonia Lefkovits, Laszlo Lefkovits, James Levitt, Tengfei Li, Hongwei Li, Hongyang Li, Xiaochuan Li, Yuexiang Li, Heng Li, Zhenye Li, Xiaoyu Li, Zeju Li, Xiaogang Li, Wenqi Li, Zheng-Shen Lin, Fengming Lin, Pietro Lio, Chang Liu, Boqiang Liu, Xiang Liu, Mingyuan Liu, Ju Liu, Luyan Liu, Xavier Llado, Marc Moreno Lopez, Pablo Ribalta Lorenzo, Zhentai Lu, Lin Luo, Zhigang Luo, Jun Ma, Kai Ma, Thomas Mackie, Anant Madabushi, Issam Mahmoudi, Klaus H. Maier-Hein, Pradipta Maji, CP Mammen, Andreas Mang, B. S. Manjunath, Michal Marcinkiewicz, S McDonagh, Stephen McKenna, Richard McKinley, Miriam Mehl, Sachin Mehta, Raghav Mehta, Raphael Meier, Christoph Meinel, Dorit Merhof, Craig Meyer, Robert Miller, Sushmita Mitra, Aliasgar Moiyadi, David Molina-Garcia, Miguel A. B. Monteiro, Grzegorz Mrukwa, Andriy Myronenko, Jakub Nalepa, Thuyen Ngo, Dong Nie, Holly Ning, Chen Niu, Nicholas K Nuechterlein, Eric Oermann, Arlindo Oliveira, Diego D. C. Oliveira, Arnau Oliver, Alexander F. I. Osman, Yu-Nian Ou, Sebastien Ourselin, Nikos Paragios, Moo Sung Park, Brad Paschke, J. Gregory Pauloski, Kamlesh Pawar, Nick Pawlowski, Linmin Pei, Suting Peng, Silvio M. Pereira, Julian Perez-Beteta, Victor M. Perez-Garcia, Simon Pezold, Bao Pham, Ashish Phophalia, Gemma Piella, G. N. Pillai, Marie Piraud, Maxim Pisov, Anmol Popli, Michael P. Pound, Reza Pourreza, Prateek Prasanna, Vesna Prkovska, Tony P. Pridmore, Santi Puch, Élodie Puybareau, Buyue Qian, Xu Qiao, Martin Rajchl, Swapnil Rane, Michael Rebsamen, Hongliang Ren, Xuhua Ren, Karthik Revanuru, Mina Rezaei, Oliver Rippel, Luis Carlos Rivera, Charlotte Robert, Bruce Rosen, Daniel Rueckert, Mohammed Safwan, Mostafa Salem, Joaquim Salvi, Irina Sanchez, Irina Sánchez, Heitor M. Santos, Emmett Sartor, Dawid Schellingerhout, Klaudius Scheufele, Matthew R. Scott, Artur A. Scussel, Sara Sedlar, Juan Pablo Serrano-Rubio, N. Jon Shah, Nameetha Shah, Mazhar Shaikh, B. Uma Shankar, Zeina Shboul, Haipeng Shen, Dinggang Shen, Linlin Shen, Haocheng Shen, Varun Shenoy, Feng Shi, Hyung Eun Shin, Hai Shu, Diana Sima, M Sinclair, Orjan Smedby, James M. Snyder, Mohammadreza Soltaninejad, Guidong Song, Mehul Soni, Jean Stawiaski, Shashank Subramanian, Li Sun, Roger Sun, Jiawei Sun, Kay Sun, Yu Sun, Guoxia Sun, Shuang Sun, Yannick R Suter, Laszlo Szilagyi, Sanjay Talbar, DaCheng Tao, Zhongzhao Teng, Siddhesh Thakur, Meenakshi H Thakur, Sameer Tharakan, Pallavi Tiwari, Guillaume Tochon, Tuan Tran, Yuhsiang M. Tsai, Kuan-Lun Tseng, Tran Anh Tuan, Vadim Turlapov, Nicholas Tustison, Maria Vakalopoulou, Sergi Valverde, Rami Vanguri, Evgeny Vasiliev, Jonathan Ventura, Luis Vera, Tom Vercauteren, C. A. Verrastro, Lasitha Vidyaratne, Veronica Vilaplana, Ajeet Vivekanandan, Qian Wang, Chiatse J. Wang, Wei-Chung Wang, Duo Wang, Ruixuan Wang, Yuanyuan Wang, Chunliang Wang, Guotai Wang, Ning Wen, Xin Wen, Leon Weninger, Wolfgang Wick, Shaocheng Wu, Qiang Wu, Yihong Wu, Yong Xia, Yanwu Xu, Xiaowen Xu, Peiyuan Xu, Tsai-Ling Yang, Xiaoping Yang, Hao-Yu Yang, Junlin Yang, Haojin Yang, Guang Yang, Hongdou Yao, Xujiong Ye, Changchang Yin, Brett Young-Moxon, Jinhua Yu, Xiangyu Yue, Songtao Zhang, Angela Zhang, Kun Zhang, Xue-jie Zhang, Lichi Zhang, Xiaoyue Zhang, Yazhuo Zhang, Lei Zhang, Jian-Guo Zhang, Xiang Zhang, Tianhao Zhang, Sicheng Zhao, Yu Zhao, Xiaomei Zhao, Liang Zhao, Yefeng Zheng, Liming Zhong, Chenhong Zhou, Xiaobing Zhou, Fan Zhou, Hongtu Zhu, Jin Zhu, Ying Zhuge, Weiwei Zong, Jayashree Kalpathy-Cramer, Keyvan Farahani, Christos Davatzikos, Koen van Leemput, Bjoern Menze

This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i. e., 2012-2018.

Brain Tumor Segmentation Survival Prediction +1

Morpho-MNIST: Quantitative Assessment and Diagnostics for Representation Learning

1 code implementation ICLR 2019 Daniel C. Castro, Jeremy Tan, Bernhard Kainz, Ender Konukoglu, Ben Glocker

Revealing latent structure in data is an active field of research, having introduced exciting technologies such as variational autoencoders and adversarial networks, and is essential to push machine learning towards unsupervised knowledge discovery.

Domain Adaptation Outlier Detection +1

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.

Computational Efficiency General Classification +2

Deep Generative Models in the Real-World: An Open Challenge from Medical Imaging

no code implementations14 Jun 2018 Xiaoran Chen, Nick Pawlowski, Martin Rajchl, Ben Glocker, Ender Konukoglu

In this paper, we explore the feasibility of using state-of-the-art auto-encoder-based deep generative models, such as variational and adversarial auto-encoders, for one such task: abnormality detection in medical imaging.

Anomaly Detection

NeuroNet: Fast and Robust Reproduction of Multiple Brain Image Segmentation Pipelines

1 code implementation11 Jun 2018 Martin Rajchl, Nick Pawlowski, Daniel Rueckert, Paul M. Matthews, Ben Glocker

NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM.

Brain Image Segmentation Brain Segmentation +3

Semi-Supervised Learning via Compact Latent Space Clustering

no code implementations ICML 2018 Konstantinos Kamnitsas, Daniel C. Castro, Loic Le Folgoc, Ian Walker, Ryutaro Tanno, Daniel Rueckert, Ben Glocker, Antonio Criminisi, Aditya Nori

We present a novel cost function for semi-supervised learning of neural networks that encourages compact clustering of the latent space to facilitate separation.

Clustering

Nonparametric Density Flows for MRI Intensity Normalisation

1 code implementation7 Jun 2018 Daniel C. Castro, Ben Glocker

With the adoption of powerful machine learning methods in medical image analysis, it is becoming increasingly desirable to aggregate data that is acquired across multiple sites.

Graph Saliency Maps through Spectral Convolutional Networks: Application to Sex Classification with Brain Connectivity

no code implementations5 Jun 2018 Salim Arslan, Sofia Ira Ktena, Ben Glocker, Daniel Rueckert

Graph convolutional networks (GCNs) allow to apply traditional convolution operations in non-Euclidean domains, where data are commonly modelled as irregular graphs.

General Classification

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.

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

DLTK: State of the Art Reference Implementations for Deep Learning on Medical Images

1 code implementation18 Nov 2017 Nick Pawlowski, Sofia Ira Ktena, Matthew C. H. Lee, Bernhard Kainz, Daniel Rueckert, Ben Glocker, Martin Rajchl

We present DLTK, a toolkit providing baseline implementations for efficient experimentation with deep learning methods on biomedical images.

Image Segmentation Semantic Segmentation

Implicit Weight Uncertainty in Neural Networks

2 code implementations3 Nov 2017 Nick Pawlowski, Andrew Brock, Matthew C. H. Lee, Martin Rajchl, Ben Glocker

Modern neural networks tend to be overconfident on unseen, noisy or incorrectly labelled data and do not produce meaningful uncertainty measures.

Normalising Flows

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.

3D Reconstruction in Canonical Co-ordinate Space from Arbitrarily Oriented 2D Images

no code implementations19 Sep 2017 Benjamin Hou, Bishesh Khanal, Amir Alansary, Steven McDonagh, Alice Davidson, Mary Rutherford, Jo V. Hajnal, Daniel Rueckert, Ben Glocker, Bernhard Kainz

We extensively evaluate the effectiveness of our approach quantitatively on simulated Magnetic Resonance Imaging (MRI), fetal brain imagery with synthetic motion and further demonstrate qualitative results on real fetal MRI data where our method is integrated into a full reconstruction and motion compensation pipeline.

3D Reconstruction Image Reconstruction +2

Efficient variational Bayesian neural network ensembles for outlier detection

1 code implementation20 Mar 2017 Nick Pawlowski, Miguel Jaques, Ben Glocker

In this work we perform outlier detection using ensembles of neural networks obtained by variational approximation of the posterior in a Bayesian neural network setting.

Outlier Detection

Spectral Graph Convolutions for Population-based Disease Prediction

1 code implementation8 Mar 2017 Sarah Parisot, Sofia Ira Ktena, Enzo Ferrante, Matthew Lee, Ricardo Guerrerro Moreno, Ben Glocker, Daniel Rueckert

We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks.

Disease Prediction