Showing 1–35 of 35 results for author: Zuluaga, M

The MAMA-MIA Challenge: Advancing Generalizability and Fairness in Breast MRI Tumor Segmentation and Treatment Response Prediction

Authors: Lidia Garrucho, Smriti Joshi, Kaisar Kushibar, Richard Osuala, Maciej Bobowicz, Xavier Bargalló, Paulius Jaruševičius, Kai Geissler, Raphael Schäfer, Muhammad Alberb, Tony Xu, Anne Martel, Daniel Sleiman, Navchetan Awasthi, Hadeel Awwad, Joan C. Vilanova, Robert Martí, Daan Schouten, Jeong Hoon Lee, Mirabela Rusu, Eleonora Poeta, Luisa Vargas, Eliana Pastor, Maria A. Zuluaga, Jessica Kächele , et al. (21 additional authors not shown)

Abstract: Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imagi… ▽ More Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are often developed using single-center data and evaluated using aggregate performance metrics, limiting their generalizability and obscuring potential performance disparities across demographic subgroups. The MAMA-MIA Challenge was designed to address these limitations by introducing a large-scale benchmark that jointly evaluates primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under external testing and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging. △ Less

Submitted 1 March, 2026; originally announced March 2026.

An Automated Framework for Large-Scale Graph-Based Cerebrovascular Analysis

Authors: Daniele Falcetta, Liane S. Canas, Lorenzo Suppa, Matteo Pentassuglia, Jon Cleary, Marc Modat, Sébastien Ourselin, Maria A. Zuluaga

Abstract: We present CaravelMetrics, a computational framework for automated cerebrovascular analysis that models vessel morphology through skeletonization-derived graph representations. The framework integrates atlas-based regional parcellation, centerline extraction, and graph construction to compute fifteen morphometric, topological, fractal, and geometric features. The features can be estimated globally… ▽ More We present CaravelMetrics, a computational framework for automated cerebrovascular analysis that models vessel morphology through skeletonization-derived graph representations. The framework integrates atlas-based regional parcellation, centerline extraction, and graph construction to compute fifteen morphometric, topological, fractal, and geometric features. The features can be estimated globally from the complete vascular network or regionally within arterial territories, enabling multiscale characterization of cerebrovascular organization. Applied to 570 3D TOF-MRA scans from the IXI dataset (ages 20-86), CaravelMetrics yields reproducible vessel graphs capturing age- and sex-related variations and education-associated increases in vascular complexity, consistent with findings reported in the literature. The framework provides a scalable and fully automated approach for quantitative cerebrovascular feature extraction, supporting normative modeling and population-level studies of vascular health and aging. △ Less

Submitted 30 January, 2026; v1 submitted 3 December, 2025; originally announced December 2025.

Comments: Submitted to ISBI 2026. 6 pages, 6 figures

MSC Class: 92C55; 68U10 ACM Class: I.4.9; I.5.4

Multi-Domain Brain Vessel Segmentation Through Feature Disentanglement

Authors: Francesco Galati, Daniele Falcetta, Rosa Cortese, Ferran Prados, Ninon Burgos, Maria A. Zuluaga

Abstract: The intricate morphology of brain vessels poses significant challenges for automatic segmentation models, which usually focus on a single imaging modality. However, accurately treating brain-related conditions requires a comprehensive understanding of the cerebrovascular tree, regardless of the specific acquisition procedure. Our framework effectively segments brain arteries and veins in various d… ▽ More The intricate morphology of brain vessels poses significant challenges for automatic segmentation models, which usually focus on a single imaging modality. However, accurately treating brain-related conditions requires a comprehensive understanding of the cerebrovascular tree, regardless of the specific acquisition procedure. Our framework effectively segments brain arteries and veins in various datasets through image-to-image translation while avoiding domain-specific model design and data harmonization between the source and the target domain. This is accomplished by employing disentanglement techniques to independently manipulate different image properties, allowing them to move from one domain to another in a label-preserving manner. Specifically, we focus on manipulating vessel appearances during adaptation while preserving spatial information, such as shapes and locations, which are crucial for correct segmentation. Our evaluation effectively bridges large and varied domain gaps across medical centers, image modalities, and vessel types. Additionally, we conduct ablation studies on the optimal number of required annotations and other architectural choices. The results highlight our framework's robustness and versatility, demonstrating the potential of domain adaptation methodologies to perform cerebrovascular image segmentation in multiple scenarios accurately. Our code is available at https://github.com/i-vesseg/MultiVesSeg. △ Less

Submitted 2 October, 2025; v1 submitted 1 October, 2025; originally announced October 2025.

Comments: 19 pages, 7 figures, 3 tables. Joint first authors: Francesco Galati and Daniele Falcetta. Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2025:021. Code available at https://github.com/i-vesseg/MultiVesSeg

Journal ref: Machine.Learning.for.Biomedical.Imaging. 3 (2025)

Live Music Models

Authors: Lyria Team, Antoine Caillon, Brian McWilliams, Cassie Tarakajian, Ian Simon, Ilaria Manco, Jesse Engel, Noah Constant, Yunpeng Li, Timo I. Denk, Alberto Lalama, Andrea Agostinelli, Cheng-Zhi Anna Huang, Ethan Manilow, George Brower, Hakan Erdogan, Heidi Lei, Itai Rolnick, Ivan Grishchenko, Manu Orsini, Matej Kastelic, Mauricio Zuluaga, Mauro Verzetti, Michael Dooley, Ondrej Skopek , et al. (11 additional authors not shown)

Abstract: We introduce a new class of generative models for music called live music models that produce a continuous stream of music in real-time with synchronized user control. We release Magenta RealTime, an open-weights live music model that can be steered using text or audio prompts to control acoustic style. On automatic metrics of music quality, Magenta RealTime outperforms other open-weights music ge… ▽ More We introduce a new class of generative models for music called live music models that produce a continuous stream of music in real-time with synchronized user control. We release Magenta RealTime, an open-weights live music model that can be steered using text or audio prompts to control acoustic style. On automatic metrics of music quality, Magenta RealTime outperforms other open-weights music generation models, despite using fewer parameters and offering first-of-its-kind live generation capabilities. We also release Lyria RealTime, an API-based model with extended controls, offering access to our most powerful model with wide prompt coverage. These models demonstrate a new paradigm for AI-assisted music creation that emphasizes human-in-the-loop interaction for live music performance. △ Less

Submitted 4 November, 2025; v1 submitted 6 August, 2025; originally announced August 2025.

In the Picture: Medical Imaging Datasets, Artifacts, and their Living Review

Authors: Amelia Jiménez-Sánchez, Natalia-Rozalia Avlona, Sarah de Boer, Víctor M. Campello, Aasa Feragen, Enzo Ferrante, Melanie Ganz, Judy Wawira Gichoya, Camila González, Steff Groefsema, Alessa Hering, Adam Hulman, Leo Joskowicz, Dovile Juodelyte, Melih Kandemir, Thijs Kooi, Jorge del Pozo Lérida, Livie Yumeng Li, Andre Pacheco, Tim Rädsch, Mauricio Reyes, Théo Sourget, Bram van Ginneken, David Wen, Nina Weng , et al. (4 additional authors not shown)

Abstract: Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for s… ▽ More Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://inthepicture.itu.dk/. △ Less

Submitted 2 June, 2025; v1 submitted 18 January, 2025; originally announced January 2025.

Comments: ACM Conference on Fairness, Accountability, and Transparency - FAccT 2025

MVP: Multimodal Emotion Recognition based on Video and Physiological Signals

Authors: Valeriya Strizhkova, Hadi Kachmar, Hava Chaptoukaev, Raphael Kalandadze, Natia Kukhilava, Tatia Tsmindashvili, Nibras Abo-Alzahab, Maria A. Zuluaga, Michal Balazia, Antitza Dantcheva, François Brémond, Laura Ferrari

Abstract: Human emotions entail a complex set of behavioral, physiological and cognitive changes. Current state-of-the-art models fuse the behavioral and physiological components using classic machine learning, rather than recent deep learning techniques. We propose to fill this gap, designing the Multimodal for Video and Physio (MVP) architecture, streamlined to fuse video and physiological signals. Differ… ▽ More Human emotions entail a complex set of behavioral, physiological and cognitive changes. Current state-of-the-art models fuse the behavioral and physiological components using classic machine learning, rather than recent deep learning techniques. We propose to fill this gap, designing the Multimodal for Video and Physio (MVP) architecture, streamlined to fuse video and physiological signals. Differently then others approaches, MVP exploits the benefits of attention to enable the use of long input sequences (1-2 minutes). We have studied video and physiological backbones for inputting long sequences and evaluated our method with respect to the state-of-the-art. Our results show that MVP outperforms former methods for emotion recognition based on facial videos, EDA, and ECG/PPG. △ Less

Submitted 6 January, 2025; originally announced January 2025.

Comments: Preprint. Final paper accepted at Affective Behavior Analysis in-the-Wild (ABAW) at IEEE/CVF European Conference on Computer Vision (ECCV), Milan, September, 2024. 17 pages

MSC Class: 68T05; 68T10 ACM Class: I.5

SMILE-UHURA Challenge -- Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms

Authors: Soumick Chatterjee, Hendrik Mattern, Marc Dörner, Alessandro Sciarra, Florian Dubost, Hannes Schnurre, Rupali Khatun, Chun-Chih Yu, Tsung-Lin Hsieh, Yi-Shan Tsai, Yi-Zeng Fang, Yung-Ching Yang, Juinn-Dar Huang, Marshall Xu, Siyu Liu, Fernanda L. Ribeiro, Saskia Bollmann, Karthikesh Varma Chintalapati, Chethan Mysuru Radhakrishna, Sri Chandana Hudukula Ram Kumara, Raviteja Sutrave, Abdul Qayyum, Moona Mazher, Imran Razzak, Cristobal Rodero , et al. (23 additional authors not shown)

Abstract: The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, maki… ▽ More The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address this, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 $\pm$ 0.066 and 0.716 $\pm$ 0.125 on the respective datasets, with an average performance of up to 0.804 $\pm$ 0.15. △ Less

Submitted 14 November, 2024; originally announced November 2024.

HyperMM : Robust Multimodal Learning with Varying-sized Inputs

Authors: Hava Chaptoukaev, Vincenzo Marcianó, Francesco Galati, Maria A. Zuluaga

Abstract: Combining multiple modalities carrying complementary information through multimodal learning (MML) has shown considerable benefits for diagnosing multiple pathologies. However, the robustness of multimodal models to missing modalities is often overlooked. Most works assume modality completeness in the input data, while in clinical practice, it is common to have incomplete modalities. Existing solu… ▽ More Combining multiple modalities carrying complementary information through multimodal learning (MML) has shown considerable benefits for diagnosing multiple pathologies. However, the robustness of multimodal models to missing modalities is often overlooked. Most works assume modality completeness in the input data, while in clinical practice, it is common to have incomplete modalities. Existing solutions that address this issue rely on modality imputation strategies before using supervised learning models. These strategies, however, are complex, computationally costly and can strongly impact subsequent prediction models. Hence, they should be used with parsimony in sensitive applications such as healthcare. We propose HyperMM, an end-to-end framework designed for learning with varying-sized inputs. Specifically, we focus on the task of supervised MML with missing imaging modalities without using imputation before training. We introduce a novel strategy for training a universal feature extractor using a conditional hypernetwork, and propose a permutation-invariant neural network that can handle inputs of varying dimensions to process the extracted features, in a two-phase task-agnostic framework. We experimentally demonstrate the advantages of our method in two tasks: Alzheimer's disease detection and breast cancer classification. We demonstrate that our strategy is robust to high rates of missing data and that its flexibility allows it to handle varying-sized datasets beyond the scenario of missing modalities. △ Less

Submitted 30 July, 2024; originally announced July 2024.

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

Authors: Kaiyuan Yang, Fabio Musio, Yihui Ma, Norman Juchler, Johannes C. Paetzold, Rami Al-Maskari, Luciano Höher, Hongwei Bran Li, Ibrahim Ethem Hamamci, Anjany Sekuboyina, Suprosanna Shit, Houjing Huang, Chinmay Prabhakar, Ezequiel de la Rosa, Bastian Wittmann, Diana Waldmannstetter, Florian Kofler, Fernando Navarro, Martin Menten, Ivan Ezhov, Daniel Rueckert, Iris N. Vos, Ynte M. Ruigrok, Birgitta K. Velthuis, Hugo J. Kuijf , et al. (88 additional authors not shown)

Abstract: The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imag… ▽ More The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building. △ Less

Submitted 8 July, 2025; v1 submitted 29 December, 2023; originally announced December 2023.

Comments: Summary paper for the TopCoW challenge: 15 pages and 6 figures, supplementary material in appendix; Datasets and best performing algorithm Dockers are available at https://zenodo.org/records/15692630 and https://zenodo.org/records/15665435

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

Authors: 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 , et al. (95 additional authors not shown)

Abstract: Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted… ▽ More Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. 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. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI. △ Less

Submitted 8 July, 2024; v1 submitted 11 August, 2023; originally announced September 2023.

ACM Class: I.2.0; I.4.0; I.5.0

A2V: A Semi-Supervised Domain Adaptation Framework for Brain Vessel Segmentation via Two-Phase Training Angiography-to-Venography Translation

Authors: Francesco Galati, Daniele Falcetta, Rosa Cortese, Barbara Casolla, Ferran Prados, Ninon Burgos, Maria A. Zuluaga

Abstract: We present a semi-supervised domain adaptation framework for brain vessel segmentation from different image modalities. Existing state-of-the-art methods focus on a single modality, despite the wide range of available cerebrovascular imaging techniques. This can lead to significant distribution shifts that negatively impact the generalization across modalities. By relying on annotated angiographie… ▽ More We present a semi-supervised domain adaptation framework for brain vessel segmentation from different image modalities. Existing state-of-the-art methods focus on a single modality, despite the wide range of available cerebrovascular imaging techniques. This can lead to significant distribution shifts that negatively impact the generalization across modalities. By relying on annotated angiographies and a limited number of annotated venographies, our framework accomplishes image-to-image translation and semantic segmentation, leveraging a disentangled and semantically rich latent space to represent heterogeneous data and perform image-level adaptation from source to target domains. Moreover, we reduce the typical complexity of cycle-based architectures and minimize the use of adversarial training, which allows us to build an efficient and intuitive model with stable training. We evaluate our method on magnetic resonance angiographies and venographies. While achieving state-of-the-art performance in the source domain, our method attains a Dice score coefficient in the target domain that is only 8.9% lower, highlighting its promising potential for robust cerebrovascular image segmentation across different modalities. △ Less

Submitted 27 March, 2024; v1 submitted 12 September, 2023; originally announced September 2023.

Comments: Accepted at the 34th British Machine Vision Conference (BMVC)

Binary domain generalization for sparsifying binary neural networks

Authors: Riccardo Schiavone, Francesco Galati, Maria A. Zuluaga

Abstract: Binary neural networks (BNNs) are an attractive solution for developing and deploying deep neural network (DNN)-based applications in resource constrained devices. Despite their success, BNNs still suffer from a fixed and limited compression factor that may be explained by the fact that existing pruning methods for full-precision DNNs cannot be directly applied to BNNs. In fact, weight pruning of… ▽ More Binary neural networks (BNNs) are an attractive solution for developing and deploying deep neural network (DNN)-based applications in resource constrained devices. Despite their success, BNNs still suffer from a fixed and limited compression factor that may be explained by the fact that existing pruning methods for full-precision DNNs cannot be directly applied to BNNs. In fact, weight pruning of BNNs leads to performance degradation, which suggests that the standard binarization domain of BNNs is not well adapted for the task. This work proposes a novel more general binary domain that extends the standard binary one that is more robust to pruning techniques, thus guaranteeing improved compression and avoiding severe performance losses. We demonstrate a closed-form solution for quantizing the weights of a full-precision network into the proposed binary domain. Finally, we show the flexibility of our method, which can be combined with other pruning strategies. Experiments over CIFAR-10 and CIFAR-100 demonstrate that the novel approach is able to generate efficient sparse networks with reduced memory usage and run-time latency, while maintaining performance. △ Less

Submitted 23 June, 2023; originally announced June 2023.

Comments: Accepted as conference paper at ECML PKDD 2023

JoB-VS: Joint Brain-Vessel Segmentation in TOF-MRA Images

Authors: Natalia Valderrama, Ioannis Pitsiorlas, Luisa Vargas, Pablo Arbeláez, Maria A. Zuluaga

Abstract: We propose the first joint-task learning framework for brain and vessel segmentation (JoB-VS) from Time-of-Flight Magnetic Resonance images. Unlike state-of-the-art vessel segmentation methods, our approach avoids the pre-processing step of implementing a model to extract the brain from the volumetric input data. Skipping this additional step makes our method an end-to-end vessel segmentation fram… ▽ More We propose the first joint-task learning framework for brain and vessel segmentation (JoB-VS) from Time-of-Flight Magnetic Resonance images. Unlike state-of-the-art vessel segmentation methods, our approach avoids the pre-processing step of implementing a model to extract the brain from the volumetric input data. Skipping this additional step makes our method an end-to-end vessel segmentation framework. JoB-VS uses a lattice architecture that favors the segmentation of structures of different scales (e.g., the brain and vessels). Its segmentation head allows the simultaneous prediction of the brain and vessel mask. Moreover, we generate data augmentation with adversarial examples, which our results demonstrate to enhance the performance. JoB-VS achieves 70.03% mean AP and 69.09% F1-score in the OASIS-3 dataset and is capable of generalizing the segmentation in the IXI dataset. These results show the adequacy of JoB-VS for the challenging task of vessel segmentation in complete TOF-MRA images. △ Less

Submitted 16 April, 2023; originally announced April 2023.

Fairness and bias correction in machine learning for depression prediction: results from four study populations

Authors: Vien Ngoc Dang, Anna Cascarano, Rosa H. Mulder, Charlotte Cecil, Maria A. Zuluaga, Jerónimo Hernández-González, Karim Lekadir

Abstract: A significant level of stigma and inequality exists in mental healthcare, especially in under-served populations. Inequalities are reflected in the data collected for scientific purposes. When not properly accounted for, machine learning (ML) models leart from data can reinforce these structural inequalities or biases. Here, we present a systematic study of bias in ML models designed to predict de… ▽ More A significant level of stigma and inequality exists in mental healthcare, especially in under-served populations. Inequalities are reflected in the data collected for scientific purposes. When not properly accounted for, machine learning (ML) models leart from data can reinforce these structural inequalities or biases. Here, we present a systematic study of bias in ML models designed to predict depression in four different case studies covering different countries and populations. We find that standard ML approaches show regularly biased behaviors. We also show that mitigation techniques, both standard and our own post-hoc method, can be effective in reducing the level of unfair bias. No single best ML model for depression prediction provides equality of outcomes. This emphasizes the importance of analyzing fairness during model selection and transparent reporting about the impact of debiasing interventions. Finally, we provide practical recommendations to develop bias-aware ML models for depression risk prediction. △ Less

Submitted 26 October, 2023; v1 submitted 9 November, 2022; originally announced November 2022.

Comments: 11 pages, 2 figures

Sparsifying Binary Networks

Authors: Riccardo Schiavone, Maria A. Zuluaga

Abstract: Binary neural networks (BNNs) have demonstrated their ability to solve complex tasks with comparable accuracy as full-precision deep neural networks (DNNs), while also reducing computational power and storage requirements and increasing the processing speed. These properties make them an attractive alternative for the development and deployment of DNN-based applications in Internet-of-Things (IoT)… ▽ More Binary neural networks (BNNs) have demonstrated their ability to solve complex tasks with comparable accuracy as full-precision deep neural networks (DNNs), while also reducing computational power and storage requirements and increasing the processing speed. These properties make them an attractive alternative for the development and deployment of DNN-based applications in Internet-of-Things (IoT) devices. Despite the recent improvements, they suffer from a fixed and limited compression factor that may result insufficient for certain devices with very limited resources. In this work, we propose sparse binary neural networks (SBNNs), a novel model and training scheme which introduces sparsity in BNNs and a new quantization function for binarizing the network's weights. The proposed SBNN is able to achieve high compression factors and it reduces the number of operations and parameters at inference time. We also provide tools to assist the SBNN design, while respecting hardware resource constraints. We study the generalization properties of our method for different compression factors through a set of experiments on linear and convolutional networks on three datasets. Our experiments confirm that SBNNs can achieve high compression rates, without compromising generalization, while further reducing the operations of BNNs, making SBNNs a viable option for deploying DNNs in cheap, low-cost, limited-resources IoT devices and sensors. △ Less

Submitted 11 July, 2022; originally announced July 2022.

Do Deep Neural Networks Contribute to Multivariate Time Series Anomaly Detection?

Authors: Julien Audibert, Pietro Michiardi, Frédéric Guyard, Sébastien Marti, Maria A. Zuluaga

Abstract: Anomaly detection in time series is a complex task that has been widely studied. In recent years, the ability of unsupervised anomaly detection algorithms has received much attention. This trend has led researchers to compare only learning-based methods in their articles, abandoning some more conventional approaches. As a result, the community in this field has been encouraged to propose increasin… ▽ More Anomaly detection in time series is a complex task that has been widely studied. In recent years, the ability of unsupervised anomaly detection algorithms has received much attention. This trend has led researchers to compare only learning-based methods in their articles, abandoning some more conventional approaches. As a result, the community in this field has been encouraged to propose increasingly complex learning-based models mainly based on deep neural networks. To our knowledge, there are no comparative studies between conventional, machine learning-based and, deep neural network methods for the detection of anomalies in multivariate time series. In this work, we study the anomaly detection performance of sixteen conventional, machine learning-based and, deep neural network approaches on five real-world open datasets. By analyzing and comparing the performance of each of the sixteen methods, we show that no family of methods outperforms the others. Therefore, we encourage the community to reincorporate the three categories of methods in the anomaly detection in multivariate time series benchmarks. △ Less

Submitted 4 April, 2022; originally announced April 2022.

Journal ref: Pattern Recognition Volume 132, December 2022,108945

AI-based artistic representation of emotions from EEG signals: a discussion on fairness, inclusion, and aesthetics

Authors: Piera Riccio, Kristin Bergaust, Boel Christensen-Scheel, Juan-Carlos De Martin, Maria A. Zuluaga, Stefano Nichele

Abstract: While Artificial Intelligence (AI) technologies are being progressively developed, artists and researchers are investigating their role in artistic practices. In this work, we present an AI-based Brain-Computer Interface (BCI) in which humans and machines interact to express feelings artistically. This system and its production of images give opportunities to reflect on the complexities and range… ▽ More While Artificial Intelligence (AI) technologies are being progressively developed, artists and researchers are investigating their role in artistic practices. In this work, we present an AI-based Brain-Computer Interface (BCI) in which humans and machines interact to express feelings artistically. This system and its production of images give opportunities to reflect on the complexities and range of human emotions and their expressions. In this discussion, we seek to understand the dynamics of this interaction to reach better co-existence in fairness, inclusion, and aesthetics. △ Less

Submitted 7 February, 2022; originally announced February 2022.

Comments: Accepted to the Politics of the Machines conference 2021 (POM Berlin 2021)

Exploring auditory acoustic features for the diagnosis of the Covid-19

Authors: Madhu R. Kamble, Jose Patino, Maria A. Zuluaga, Massimiliano Todisco

Abstract: The current outbreak of a coronavirus, has quickly escalated to become a serious global problem that has now been declared a Public Health Emergency of International Concern by the World Health Organization. Infectious diseases know no borders, so when it comes to controlling outbreaks, timing is absolutely essential. It is so important to detect threats as early as possible, before they spread. A… ▽ More The current outbreak of a coronavirus, has quickly escalated to become a serious global problem that has now been declared a Public Health Emergency of International Concern by the World Health Organization. Infectious diseases know no borders, so when it comes to controlling outbreaks, timing is absolutely essential. It is so important to detect threats as early as possible, before they spread. After a first successful DiCOVA challenge, the organisers released second DiCOVA challenge with the aim of diagnosing COVID-19 through the use of breath, cough and speech audio samples. This work presents the details of the automatic system for COVID-19 detection using breath, cough and speech recordings. We developed different front-end auditory acoustic features along with a bidirectional Long Short-Term Memory (bi-LSTM) as classifier. The results are promising and have demonstrated the high complementary behaviour among the auditory acoustic features in the Breathing, Cough and Speech tracks giving an AUC of 86.60% on the test set. △ Less

Submitted 22 January, 2022; originally announced January 2022.

Comments: Accepted in ICASSP 2022

Class-wise Thresholding for Robust Out-of-Distribution Detection

Authors: Matteo Guarrera, Baihong Jin, Tung-Wei Lin, Maria Zuluaga, Yuxin Chen, Alberto Sangiovanni-Vincentelli

Abstract: We consider the problem of detecting OoD(Out-of-Distribution) input data when using deep neural networks, and we propose a simple yet effective way to improve the robustness of several popular OoD detection methods against label shift. Our work is motivated by the observation that most existing OoD detection algorithms consider all training/test data as a whole, regardless of which class entry eac… ▽ More We consider the problem of detecting OoD(Out-of-Distribution) input data when using deep neural networks, and we propose a simple yet effective way to improve the robustness of several popular OoD detection methods against label shift. Our work is motivated by the observation that most existing OoD detection algorithms consider all training/test data as a whole, regardless of which class entry each input activates (inter-class differences). Through extensive experimentation, we have found that such practice leads to a detector whose performance is sensitive and vulnerable to label shift. To address this issue, we propose a class-wise thresholding scheme that can apply to most existing OoD detection algorithms and can maintain similar OoD detection performance even in the presence of label shift in the test distribution. △ Less

Submitted 1 July, 2022; v1 submitted 28 October, 2021; originally announced October 2021.

Comments: 12 pages, 7 figures, 7 tables

Journal ref: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops, 2022, pp. 2837-2846

Improved optimization strategies for deep Multi-Task Networks

Authors: Lucas Pascal, Pietro Michiardi, Xavier Bost, Benoit Huet, Maria A. Zuluaga

Abstract: In Multi-Task Learning (MTL), it is a common practice to train multi-task networks by optimizing an objective function, which is a weighted average of the task-specific objective functions. Although the computational advantages of this strategy are clear, the complexity of the resulting loss landscape has not been studied in the literature. Arguably, its optimization may be more difficult than a s… ▽ More In Multi-Task Learning (MTL), it is a common practice to train multi-task networks by optimizing an objective function, which is a weighted average of the task-specific objective functions. Although the computational advantages of this strategy are clear, the complexity of the resulting loss landscape has not been studied in the literature. Arguably, its optimization may be more difficult than a separate optimization of the constituting task-specific objectives. In this work, we investigate the benefits of such an alternative, by alternating independent gradient descent steps on the different task-specific objective functions and we formulate a novel way to combine this approach with state-of-the-art optimizers. As the separation of task-specific objectives comes at the cost of increased computational time, we propose a random task grouping as a trade-off between better optimization and computational efficiency. Experimental results over three well-known visual MTL datasets show better overall absolute performance on losses and standard metrics compared to an averaged objective function and other state-of-the-art MTL methods. In particular, our method shows the most benefits when dealing with tasks of different nature and it enables a wider exploration of the shared parameter space. We also show that our random grouping strategy allows to trade-off between these benefits and computational efficiency. △ Less

Submitted 18 July, 2022; v1 submitted 21 September, 2021; originally announced September 2021.

PANACEA cough sound-based diagnosis of COVID-19 for the DiCOVA 2021 Challenge

Authors: Madhu R. Kamble, Jose A. Gonzalez-Lopez, Teresa Grau, Juan M. Espin, Lorenzo Cascioli, Yiqing Huang, Alejandro Gomez-Alanis, Jose Patino, Roberto Font, Antonio M. Peinado, Angel M. Gomez, Nicholas Evans, Maria A. Zuluaga, Massimiliano Todisco

Abstract: The COVID-19 pandemic has led to the saturation of public health services worldwide. In this scenario, the early diagnosis of SARS-Cov-2 infections can help to stop or slow the spread of the virus and to manage the demand upon health services. This is especially important when resources are also being stretched by heightened demand linked to other seasonal diseases, such as the flu. In this contex… ▽ More The COVID-19 pandemic has led to the saturation of public health services worldwide. In this scenario, the early diagnosis of SARS-Cov-2 infections can help to stop or slow the spread of the virus and to manage the demand upon health services. This is especially important when resources are also being stretched by heightened demand linked to other seasonal diseases, such as the flu. In this context, the organisers of the DiCOVA 2021 challenge have collected a database with the aim of diagnosing COVID-19 through the use of coughing audio samples. This work presents the details of the automatic system for COVID-19 detection from cough recordings presented by team PANACEA. This team consists of researchers from two European academic institutions and one company: EURECOM (France), University of Granada (Spain), and Biometric Vox S.L. (Spain). We developed several systems based on established signal processing and machine learning methods. Our best system employs a Teager energy operator cepstral coefficients (TECCs) based frontend and Light gradient boosting machine (LightGBM) backend. The AUC obtained by this system on the test set is 76.31% which corresponds to a 10% improvement over the official baseline. △ Less

Submitted 7 June, 2021; originally announced June 2021.

Comments: Accepted in INTERSPEECH 2021

Efficient Model Monitoring for Quality Control in Cardiac Image Segmentation

Authors: Francesco Galati, Maria A. Zuluaga

Abstract: Deep learning methods have reached state-of-the-art performance in cardiac image segmentation. Currently, the main bottleneck towards their effective translation into clinics requires assuring continuous high model performance and segmentation results. In this work, we present a novel learning framework to monitor the performance of heart segmentation models in the absence of ground truth. Formula… ▽ More Deep learning methods have reached state-of-the-art performance in cardiac image segmentation. Currently, the main bottleneck towards their effective translation into clinics requires assuring continuous high model performance and segmentation results. In this work, we present a novel learning framework to monitor the performance of heart segmentation models in the absence of ground truth. Formulated as an anomaly detection problem, the monitoring framework allows deriving surrogate quality measures for a segmentation and allows flagging suspicious results. We propose two different types of quality measures, a global score and a pixel-wise map. We demonstrate their use by reproducing the final rankings of a cardiac segmentation challenge in the absence of ground truth. Results show that our framework is accurate, fast, and scalable, confirming it is a viable option for quality control monitoring in clinical practice and large population studies. △ Less

Submitted 12 April, 2021; originally announced April 2021.

Comments: Accepted to the 11th Biennial Meeting on Functional Imaging and Modeling of the Heart (FIMH-2021)

One-class Autoencoder Approach for Optimal Electrode Set-up Identification in Wearable EEG Event Monitoring

Authors: Laura M. Ferrari, Guy Abi Hanna, Paolo Volpe, Esma Ismailova, François Bremond, Maria A. Zuluaga

Abstract: A limiting factor towards the wide routine use of wearables devices for continuous healthcare monitoring is their cumbersome and obtrusive nature. This is particularly true for electroencephalography (EEG) recordings, which require the placement of multiple electrodes in contact with the scalp. In this work, we propose to identify the optimal wearable EEG electrode set-up, in terms of minimal numb… ▽ More A limiting factor towards the wide routine use of wearables devices for continuous healthcare monitoring is their cumbersome and obtrusive nature. This is particularly true for electroencephalography (EEG) recordings, which require the placement of multiple electrodes in contact with the scalp. In this work, we propose to identify the optimal wearable EEG electrode set-up, in terms of minimal number of electrodes, comfortable location and performance, for EEG-based event detection and monitoring. By relying on the demonstrated power of autoencoder (AE) networks to learn latent representations from high-dimensional data, our proposed strategy trains an AE architecture in a one-class classification setup with different electrode set-ups as input data. The resulting models are assessed using the F-score and the best set-up is chosen according to the established optimal criteria. Using alpha wave detection as use case, we demonstrate that the proposed method allows to detect an alpha state from an optimal set-up consisting of electrodes in the forehead and behind the ear, with an average F-score of 0.78. Our results suggest that a learning-based approach can be used to enable the design and implementation of optimized wearable devices for real-life healthcare monitoring. △ Less

Submitted 19 May, 2021; v1 submitted 9 April, 2021; originally announced April 2021.

Multi-Atlas Based Pathological Stratification of d-TGA Congenital Heart Disease

Authors: Maria A. Zuluaga, Alex F. Mendelson, M. Jorge Cardoso, Andrew M. Taylor, Sébastien Ourselin

Abstract: One of the main sources of error in multi-atlas segmentation propagation approaches comes from the use of atlas databases that are morphologically dissimilar to the target image. In this work, we exploit the segmentation errors associated with poor atlas selection to build a computer aided diagnosis (CAD) system for pathological classification in post-operative dextro-transposition of the great ar… ▽ More One of the main sources of error in multi-atlas segmentation propagation approaches comes from the use of atlas databases that are morphologically dissimilar to the target image. In this work, we exploit the segmentation errors associated with poor atlas selection to build a computer aided diagnosis (CAD) system for pathological classification in post-operative dextro-transposition of the great arteries (d-TGA). The proposed approach extracts a set of features, which describe the quality of a segmentation, and introduces them into a logical decision tree that provides the final diagnosis. We have validated our method on a set of 60 whole heart MR images containing healthy cases and two different forms of post-operative d-TGA. The reported overall CAD system accuracy was of 93.33%. △ Less

Submitted 5 April, 2021; originally announced April 2021.

Comments: In: IEEE International Symposium on Biomedical Imaging 2014

Vessel-CAPTCHA: an efficient learning framework for vessel annotation and segmentation

Authors: Vien Ngoc Dang, Francesco Galati, Rosa Cortese, Giuseppe Di Giacomo, Viola Marconetto, Prateek Mathur, Karim Lekadir, Marco Lorenzi, Ferran Prados, Maria A. Zuluaga

Abstract: Deep learning techniques for 3D brain vessel image segmentation have not been as successful as in the segmentation of other organs and tissues. This can be explained by two factors. First, deep learning techniques tend to show poor performances at the segmentation of relatively small objects compared to the size of the full image. Second, due to the complexity of vascular trees and the small size… ▽ More Deep learning techniques for 3D brain vessel image segmentation have not been as successful as in the segmentation of other organs and tissues. This can be explained by two factors. First, deep learning techniques tend to show poor performances at the segmentation of relatively small objects compared to the size of the full image. Second, due to the complexity of vascular trees and the small size of vessels, it is challenging to obtain the amount of annotated training data typically needed by deep learning methods. To address these problems, we propose a novel annotation-efficient deep learning vessel segmentation framework. The framework avoids pixel-wise annotations, only requiring weak patch-level labels to discriminate between vessel and non-vessel 2D patches in the training set, in a setup similar to the CAPTCHAs used to differentiate humans from bots in web applications. The user-provided weak annotations are used for two tasks: 1) to synthesize pixel-wise pseudo-labels for vessels and background in each patch, which are used to train a segmentation network, and 2) to train a classifier network. The classifier network allows to generate additional weak patch labels, further reducing the annotation burden, and it acts as a noise filter for poor quality images. We use this framework for the segmentation of the cerebrovascular tree in Time-of-Flight angiography (TOF) and Susceptibility-Weighted Images (SWI). The results show that the framework achieves state-of-the-art accuracy, while reducing the annotation time by ~77% w.r.t. learning-based segmentation methods using pixel-wise labels for training. △ Less

Submitted 20 July, 2021; v1 submitted 22 January, 2021; originally announced January 2021.

Maximum Roaming Multi-Task Learning

Authors: Lucas Pascal, Pietro Michiardi, Xavier Bost, Benoit Huet, Maria A. Zuluaga

Abstract: Multi-task learning has gained popularity due to the advantages it provides with respect to resource usage and performance. Nonetheless, the joint optimization of parameters with respect to multiple tasks remains an active research topic. Sub-partitioning the parameters between different tasks has proven to be an efficient way to relax the optimization constraints over the shared weights, may the… ▽ More Multi-task learning has gained popularity due to the advantages it provides with respect to resource usage and performance. Nonetheless, the joint optimization of parameters with respect to multiple tasks remains an active research topic. Sub-partitioning the parameters between different tasks has proven to be an efficient way to relax the optimization constraints over the shared weights, may the partitions be disjoint or overlapping. However, one drawback of this approach is that it can weaken the inductive bias generally set up by the joint task optimization. In this work, we present a novel way to partition the parameter space without weakening the inductive bias. Specifically, we propose Maximum Roaming, a method inspired by dropout that randomly varies the parameter partitioning, while forcing them to visit as many tasks as possible at a regulated frequency, so that the network fully adapts to each update. We study the properties of our method through experiments on a variety of visual multi-task data sets. Experimental results suggest that the regularization brought by roaming has more impact on performance than usual partitioning optimization strategies. The overall method is flexible, easily applicable, provides superior regularization and consistently achieves improved performances compared to recent multi-task learning formulations. △ Less

Submitted 19 May, 2021; v1 submitted 17 June, 2020; originally announced June 2020.

Comments: Accepted at the 35th AAAI Conference on Artificial Intelligence (AAAI 2021)

Journal ref: Proceedings of the AAAI Conference on Artificial Intelligence: 35(10), 9331-9341 (2021)

Automatic Right Ventricle Segmentation using Multi-Label Fusion in Cardiac MRI

Authors: Maria A. Zuluaga, M. Jorge Cardoso, Sébastien Ourselin

Abstract: Accurate segmentation of the right ventricle (RV) is a crucial step in the assessment of the ventricular structure and function. Yet, due to its complex anatomy and motion segmentation of the RV has not been as largely studied as the left ventricle. This paper presents a fully automatic method for the segmentation of the RV in cardiac magnetic resonance images (MRI). The method uses a coarse-to-fi… ▽ More Accurate segmentation of the right ventricle (RV) is a crucial step in the assessment of the ventricular structure and function. Yet, due to its complex anatomy and motion segmentation of the RV has not been as largely studied as the left ventricle. This paper presents a fully automatic method for the segmentation of the RV in cardiac magnetic resonance images (MRI). The method uses a coarse-to-fine segmentation strategy in combination with a multi-atlas propagation segmentation framework. Based on a cross correlation metric, our method selects the best atlases for propagation allowing the refinement of the segmentation at each iteration of the propagation. The proposed method was evaluated on 32 cardiac MRI datasets provided by the RV Segmentation Challenge in Cardiac MRI. △ Less

Submitted 5 April, 2020; originally announced April 2020.

Journal ref: Workshop on RV Segmentation Challenge in Cardiac MRI in conjunction with Medical Image Computing and Computer-Assisted Intervention 2012

Multi-objective Consensus Clustering Framework for Flight Search Recommendation

Authors: Sujoy Chatterjee, Nicolas Pasquier, Simon Nanty, Maria A. Zuluaga

Abstract: In the travel industry, online customers book their travel itinerary according to several features, like cost and duration of the travel or the quality of amenities. To provide personalized recommendations for travel searches, an appropriate segmentation of customers is required. Clustering ensemble approaches were developed to overcome well-known problems of classical clustering approaches, that… ▽ More In the travel industry, online customers book their travel itinerary according to several features, like cost and duration of the travel or the quality of amenities. To provide personalized recommendations for travel searches, an appropriate segmentation of customers is required. Clustering ensemble approaches were developed to overcome well-known problems of classical clustering approaches, that each rely on a different theoretical model and can thus identify in the data space only clusters corresponding to this model. Clustering ensemble approaches combine multiple clustering results, each from a different algorithmic configuration, for generating more robust consensus clusters corresponding to agreements between initial clusters. We present a new clustering ensemble multi-objective optimization-based framework developed for analyzing Amadeus customer search data and improve personalized recommendations. This framework optimizes diversity in the clustering ensemble search space and automatically determines an appropriate number of clusters without requiring user's input. Experimental results compare the efficiency of this approach with other existing approaches on Amadeus customer search data in terms of internal (Adjusted Rand Index) and external (Amadeus business metric) validations. △ Less

Submitted 26 February, 2020; v1 submitted 19 February, 2020; originally announced February 2020.

Towards Quantifying Neurovascular Resilience

Authors: Stefano Moriconi, Rafael Rehwald, Maria A. Zuluaga, H. Rolf Jäger, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso

Abstract: Whilst grading neurovascular abnormalities is critical for prompt surgical repair, no statistical markers are currently available for predicting the risk of adverse events, such as stroke, and the overall resilience of a network to vascular complications. The lack of compact, fast, and scalable simulations with network perturbations impedes the analysis of the vascular resilience to life-threateni… ▽ More Whilst grading neurovascular abnormalities is critical for prompt surgical repair, no statistical markers are currently available for predicting the risk of adverse events, such as stroke, and the overall resilience of a network to vascular complications. The lack of compact, fast, and scalable simulations with network perturbations impedes the analysis of the vascular resilience to life-threatening conditions, surgical interventions and long-term follow-up. We introduce a graph-based approach for efficient simulations, which statistically estimates biomarkers from a series of perturbations on the patient-specific vascular network. Analog-equivalent circuits are derived from clinical angiographies. Vascular graphs embed mechanical attributes modelling the impedance of a tubular structure with stenosis, tortuosity and complete occlusions. We evaluate pressure and flow distributions, simulating healthy topologies and abnormal variants with perturbations in key pathological scenarios. These describe the intrinsic network resilience to pathology, and delineate the underlying cerebrovascular autoregulation mechanisms. Lastly, a putative graph sampling strategy is devised on the same formulation, to support the topological inference of uncertain neurovascular graphs. △ Less

Submitted 29 October, 2019; originally announced October 2019.

Journal ref: Machine Learning and Medical Engineering for Cardiovascular Health and Intravascular Imaging and Computer Assisted Stenting. MLMECH 2019, CVII-STENT 2019. Lecture Notes in Computer Science, vol 11794. Springer, Cham

Grey matter sublayer thickness estimation in themouse cerebellum

Authors: Da Ma, Manuel J. Cardoso, Maria A. Zuluaga, Marc Modat, Nick. Powell, Frances Wiseman, Victor Tybulewicz, Elizabeth Fisher, Mark. F. Lythgoe, Sebastien Ourselin

Abstract: The cerebellar grey matter morphology is an important feature to study neurodegenerative diseases such as Alzheimer's disease or Down's syndrome. Its volume or thickness is commonly used as a surrogate imaging biomarker for such diseases. Most studies about grey matter thickness estimation focused on the cortex, and little attention has been drawn on the morphology of the cerebellum. Using ex vivo… ▽ More The cerebellar grey matter morphology is an important feature to study neurodegenerative diseases such as Alzheimer's disease or Down's syndrome. Its volume or thickness is commonly used as a surrogate imaging biomarker for such diseases. Most studies about grey matter thickness estimation focused on the cortex, and little attention has been drawn on the morphology of the cerebellum. Using ex vivo high-resolution MRI, it is now possible to visualise the different cell layers in the mouse cerebellum. In this work, we introduce a framework to extract the Purkinje layer within the grey matter, enabling the estimation of the thickness of the cerebellar grey matter, the granular layer and molecular layer from gadolinium-enhanced ex vivo mouse brain MRI. Application to mouse model of Down's syndrome found reduced cortical and layer thicknesses in the transchromosomic group. △ Less

Submitted 8 January, 2019; originally announced January 2019.

Comments: 8 pages, 7 figures, International Conference on Medical Image Computing and Computer-Assisted Intervention 2015

Journal ref: International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Cham, 2015

Fréchet Audio Distance: A Metric for Evaluating Music Enhancement Algorithms

Authors: Kevin Kilgour, Mauricio Zuluaga, Dominik Roblek, Matthew Sharifi

Abstract: We propose the Fréchet Audio Distance (FAD), a novel, reference-free evaluation metric for music enhancement algorithms. We demonstrate how typical evaluation metrics for speech enhancement and blind source separation can fail to accurately measure the perceived effect of a wide variety of distortions. As an alternative, we propose adapting the Fréchet Inception Distance (FID) metric used to evalu… ▽ More We propose the Fréchet Audio Distance (FAD), a novel, reference-free evaluation metric for music enhancement algorithms. We demonstrate how typical evaluation metrics for speech enhancement and blind source separation can fail to accurately measure the perceived effect of a wide variety of distortions. As an alternative, we propose adapting the Fréchet Inception Distance (FID) metric used to evaluate generative image models to the audio domain. FAD is validated using a wide variety of artificial distortions and is compared to the signal based metrics signal to distortion ratio (SDR), cosine distance and magnitude L2 distance. We show that, with a correlation coefficient of 0.52, FAD correlates more closely with human perception than either SDR, cosine distance or magnitude L2 distance, with correlation coefficients of 0.39, -0.15 and -0.01 respectively. △ Less

Submitted 17 January, 2019; v1 submitted 20 December, 2018; originally announced December 2018.

Elastic Registration of Geodesic Vascular Graphs

Authors: Stefano Moriconi, Maria A. Zuluaga, H. Rolf Jager, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso

Abstract: Vascular graphs can embed a number of high-level features, from morphological parameters, to functional biomarkers, and represent an invaluable tool for longitudinal and cross-sectional clinical inference. This, however, is only feasible when graphs are co-registered together, allowing coherent multiple comparisons. The robust registration of vascular topologies stands therefore as key enabling te… ▽ More Vascular graphs can embed a number of high-level features, from morphological parameters, to functional biomarkers, and represent an invaluable tool for longitudinal and cross-sectional clinical inference. This, however, is only feasible when graphs are co-registered together, allowing coherent multiple comparisons. The robust registration of vascular topologies stands therefore as key enabling technology for group-wise analyses. In this work, we present an end-to-end vascular graph registration approach, that aligns networks with non-linear geometries and topological deformations, by introducing a novel overconnected geodesic vascular graph formulation, and without enforcing any anatomical prior constraint. The 3D elastic graph registration is then performed with state-of-the-art graph matching methods used in computer vision. Promising results of vascular matching are found using graphs from synthetic and real angiographies. Observations and future designs are discussed towards potential clinical applications. △ Less

Submitted 14 September, 2018; originally announced September 2018.

Journal ref: Medical Image Computing and Computer Assisted Intervention -- MICCAI 2018

VTrails: Inferring Vessels with Geodesic Connectivity Trees

Authors: Stefano Moriconi, Maria A. Zuluaga, H. Rolf Jäger, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso

Abstract: The analysis of vessel morphology and connectivity has an impact on a number of cardiovascular and neurovascular applications by providing patient-specific high-level quantitative features such as spatial location, direction and scale. In this paper we present an end-to-end approach to extract an acyclic vascular tree from angiographic data by solving a connectivity-enforcing anisotropic fast marc… ▽ More The analysis of vessel morphology and connectivity has an impact on a number of cardiovascular and neurovascular applications by providing patient-specific high-level quantitative features such as spatial location, direction and scale. In this paper we present an end-to-end approach to extract an acyclic vascular tree from angiographic data by solving a connectivity-enforcing anisotropic fast marching over a voxel-wise tensor field representing the orientation of the underlying vascular tree. The method is validated using synthetic and real vascular images. We compare VTrails against classical and state-of-the-art ridge detectors for tubular structures by assessing the connectedness of the vesselness map and inspecting the synthesized tensor field as proof of concept. VTrails performance is evaluated on images with different levels of degradation: we verify that the extracted vascular network is an acyclic graph (i.e. a tree), and we report the extraction accuracy, precision and recall. △ Less

Submitted 8 June, 2018; originally announced June 2018.

Journal ref: IPMI 2017: Information Processing in Medical Imaging pp 672-684

Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning

Authors: Guotai Wang, Wenqi Li, Maria A. Zuluaga, Rosalind Pratt, Premal A. Patel, Michael Aertsen, Tom Doel, Anna L. David, Jan Deprest, Sebastien Ourselin, Tom Vercauteren

Abstract: Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a no… ▽ More Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a novel deep learning-based framework for interactive segmentation by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine-tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine-tuning. We applied this framework to two applications: 2D segmentation of multiple organs from fetal MR slices, where only two types of these organs were annotated for training; and 3D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only tumor cores in one MR sequence were annotated for training. Experimental results show that 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine-tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods. △ Less

Submitted 11 October, 2017; originally announced October 2017.

Comments: 11 pages, 11 figures

DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation

Authors: Guotai Wang, Maria A. Zuluaga, Wenqi Li, Rosalind Pratt, Premal A. Patel, Michael Aertsen, Tom Doel, Anna L. David, Jan Deprest, Sebastien Ourselin, Tom Vercauteren

Abstract: Accurate medical image segmentation is essential for diagnosis, surgical planning and many other applications. Convolutional Neural Networks (CNNs) have become the state-of-the-art automatic segmentation methods. However, fully automatic results may still need to be refined to become accurate and robust enough for clinical use. We propose a deep learning-based interactive segmentation method to im… ▽ More Accurate medical image segmentation is essential for diagnosis, surgical planning and many other applications. Convolutional Neural Networks (CNNs) have become the state-of-the-art automatic segmentation methods. However, fully automatic results may still need to be refined to become accurate and robust enough for clinical use. We propose a deep learning-based interactive segmentation method to improve the results obtained by an automatic CNN and to reduce user interactions during refinement for higher accuracy. We use one CNN to obtain an initial automatic segmentation, on which user interactions are added to indicate mis-segmentations. Another CNN takes as input the user interactions with the initial segmentation and gives a refined result. We propose to combine user interactions with CNNs through geodesic distance transforms, and propose a resolution-preserving network that gives a better dense prediction. In addition, we integrate user interactions as hard constraints into a back-propagatable Conditional Random Field. We validated the proposed framework in the context of 2D placenta segmentation from fetal MRI and 3D brain tumor segmentation from FLAIR images. Experimental results show our method achieves a large improvement from automatic CNNs, and obtains comparable and even higher accuracy with fewer user interventions and less time compared with traditional interactive methods. △ Less

Submitted 19 September, 2017; v1 submitted 3 July, 2017; originally announced July 2017.

Comments: 14 pages, 15 figures