Search Results for author: Enzo Ferrante

Found 37 papers, 18 papers with code

Unsupervised bias discovery in medical image segmentation

1 code implementation1 Sep 2023 Nicolás Gaggion, Rodrigo Echeveste, Lucas Mansilla, Diego H. Milone, Enzo Ferrante

It has recently been shown that deep learning models for anatomical segmentation in medical images can exhibit biases against certain sub-populations defined in terms of protected attributes like sex or ethnicity.

Fairness Image Segmentation +3

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.


CheXmask: a large-scale dataset of anatomical segmentation masks for multi-center chest x-ray images

1 code implementation6 Jul 2023 Nicolás Gaggion, Candelaria Mosquera, Lucas Mansilla, Martina Aineseder, Diego H. Milone, Enzo Ferrante

To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from six well-known publicly available databases: CANDID-PTX, ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 676, 803 segmentation masks.


Towards unraveling calibration biases in medical image analysis

no code implementations9 May 2023 María Agustina Ricci Lara, Candelaria Mosquera, Enzo Ferrante, Rodrigo Echeveste

In recent years the development of artificial intelligence (AI) systems for automated medical image analysis has gained enormous momentum.


Are demographically invariant models and representations in medical imaging fair?

no code implementations2 May 2023 Eike Petersen, Enzo Ferrante, Melanie Ganz, Aasa Feragen

Medical imaging models have been shown to encode information about patient demographics such as age, race, and sex in their latent representation, raising concerns about their potential for discrimination.

counterfactual Fairness

Multi-center anatomical segmentation with heterogeneous labels via landmark-based models

1 code implementation14 Nov 2022 Nicolás Gaggion, Maria Vakalopoulou, Diego H. Milone, Enzo Ferrante

Learning anatomical segmentation from heterogeneous labels in multi-center datasets is a common situation encountered in clinical scenarios, where certain anatomical structures are only annotated in images coming from particular medical centers, but not in the full database.

Landmark-based segmentation Memorization +1

Improving anatomical plausibility in medical image segmentation via hybrid graph neural networks: applications to chest x-ray analysis

2 code implementations21 Mar 2022 Nicolás Gaggion, Lucas Mansilla, Candelaria Mosquera, Diego H. Milone, Enzo Ferrante

To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures.

Image Segmentation Medical Image Segmentation +2

Supervision by Denoising

no code implementations7 Feb 2022 Sean I. Young, Adrian V. Dalca, Enzo Ferrante, Polina Golland, Christopher A. Metzler, Bruce Fischl, Juan Eugenio Iglesias

SUD unifies stochastic averaging and spatial denoising techniques under a spatio-temporal denoising framework and alternates denoising and model weight update steps in an optimization framework for semi-supervision.

Denoising Image Reconstruction +3

Impact of class imbalance on chest x-ray classifiers: towards better evaluation practices for discrimination and calibration performance

no code implementations23 Dec 2021 Candelaria Mosquera, Luciana Ferrer, Diego Milone, Daniel Luna, Enzo Ferrante

This work aims to analyze standard evaluation practices adopted by the research community when assessing chest x-ray classifiers, particularly focusing on the impact of class imbalance in such appraisals.

Domain Generalization via Gradient Surgery

1 code implementation ICCV 2021 Lucas Mansilla, Rodrigo Echeveste, Diego H. Milone, Enzo Ferrante

In real-life applications, machine learning models often face scenarios where there is a change in data distribution between training and test domains.

Domain Generalization Image Classification

Bridging physiological and perceptual views of autism by means of sampling-based Bayesian inference

no code implementations8 Jun 2021 Rodrigo Echeveste, Enzo Ferrante, Diego H. Milone, Inés Samengo

Theories for autism spectrum disorder (ASD) have been formulated at different levels: ranging from physiological observations to perceptual and behavioral descriptions.

Bayesian Inference Descriptive

Orthogonal Ensemble Networks for Biomedical Image Segmentation

1 code implementation22 May 2021 Agostina J. Larrazabal, César Martínez, Jose Dolz, Enzo Ferrante

Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes.

Decision Making Ensemble Learning +4

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.

Unsupervised Domain Adaptation via CycleGAN for White Matter Hyperintensity Segmentation in Multicenter MR Images

no code implementations10 Sep 2020 Julian Alberto Palladino, Diego Fernandez Slezak, Enzo Ferrante

When such distribution changes but we still aim at performing the same task, we incur in a domain adaptation problem (e. g. using a different MR machine or different acquisition parameters for training and test data).

Image Segmentation Segmentation +2

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.

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

Anatomical Priors for Image Segmentation via Post-Processing with Denoising Autoencoders

1 code implementation5 Jun 2019 Agostina J. Larrazabal, Cesar Martinez, Enzo Ferrante

We learn a low-dimensional space of anatomically plausible segmentations, and use it as a post-processing step to impose shape constraints on the resulting masks obtained with arbitrary segmentation methods.

Denoising Image Segmentation +3

Joint Learning of Brain Lesion and Anatomy Segmentation from Heterogeneous Datasets

no code implementations8 Mar 2019 Nicolas Roulet, Diego Fernandez Slezak, Enzo Ferrante

However, to date, little work has been done regarding simultaneous learning of brain lesion and anatomy segmentation from disjoint datasets.

Anatomy Benchmarking

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

Weakly-Supervised Learning of Metric Aggregations for Deformable Image Registration

no code implementations24 Sep 2018 Enzo Ferrante, Puneet K. Dokania, Rafael Marini Silva, Nikos Paragios

Conventional approaches refer to the definition of a similarity criterion that, once endowed with a deformation model and a smoothness constraint, determines the optimal transformation to align two given images.

Image Registration Weakly-supervised Learning

Left ventricle quantification through spatio-temporal CNNs

3 code implementations23 Aug 2018 Alejandro Debus, Enzo Ferrante

Cardiovascular diseases are among the leading causes of death globally.

Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation

no code implementations4 Nov 2017 Konstantinos Kamnitsas, Wenjia Bai, Enzo Ferrante, Steven McDonagh, Matthew Sinclair, Nick Pawlowski, Martin Rajchl, Matthew Lee, Bernhard Kainz, Daniel Rueckert, Ben Glocker

Deep learning approaches such as convolutional neural nets have consistently outperformed previous methods on challenging tasks such as dense, semantic segmentation.

Semantic Segmentation

Deformable Registration through Learning of Context-Specific Metric Aggregation

no code implementations19 Jul 2017 Enzo Ferrante, Puneet K. Dokania, Rafael Marini, Nikos Paragios

We propose a novel weakly supervised discriminative algorithm for learning context specific registration metrics as a linear combination of conventional similarity measures.

Arabidopsis roots segmentation based on morphological operations and CRFs

no code implementations25 Apr 2017 José Ignacio Orlando, Hugo Luis Manterola, Enzo Ferrante, Federico Ariel

Arabidopsis thaliana is a plant species widely utilized by scientists to estimate the impact of genetic differences in root morphological features.

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

Distance Metric Learning using Graph Convolutional Networks: Application to Functional Brain Networks

3 code implementations7 Mar 2017 Sofia Ira Ktena, Sarah Parisot, Enzo Ferrante, Martin Rajchl, Matthew Lee, Ben Glocker, Daniel Rueckert

Evaluating similarity between graphs is of major importance in several computer vision and pattern recognition problems, where graph representations are often used to model objects or interactions between elements.

Graph Similarity Metric Learning

Slice-to-volume medical image registration: a survey

no code implementations6 Feb 2017 Enzo Ferrante, Nikos Paragios

During the last decades, the research community of medical imaging has witnessed continuous advances in image registration methods, which pushed the limits of the state-of-the-art and enabled the development of novel medical procedures.

Image Reconstruction Image Registration +1

Rigid Slice-To-Volume Medical Image Registration through Markov Random Fields

1 code implementation19 Aug 2016 Roque Porchetto, Franco Stramana, Nikos Paragios, Enzo Ferrante

Rigid slice-to-volume registration is a challenging task, which finds application in medical imaging problems like image fusion for image guided surgeries and motion correction for volume reconstruction.

Image Registration Medical Image Registration

Prior-based Coregistration and Cosegmentation

no code implementations22 Jul 2016 Mahsa Shakeri, Enzo Ferrante, Stavros Tsogkas, Sarah Lippe, Samuel Kadoury, Iasonas Kokkinos, Nikos Paragios

We propose a modular and scalable framework for dense coregistration and cosegmentation with two key characteristics: first, we substitute ground truth data with the semantic map output of a classifier; second, we combine this output with population deformable registration to improve both alignment and segmentation.

Sub-cortical brain structure segmentation using F-CNN's

no code implementations5 Feb 2016 Mahsa Shakeri, Stavros Tsogkas, Enzo Ferrante, Sarah Lippe, Samuel Kadoury, Nikos Paragios, Iasonas Kokkinos

In this paper we propose a deep learning approach for segmenting sub-cortical structures of the human brain in Magnetic Resonance (MR) image data.

Segmentation Semantic Segmentation

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