arXiv subjects

Ninon Burgos

Publications and source records attributed to Ninon Burgos.

At least 19 recordsLinked to original sources

arXiv2026

Mitigating the reconstruction-detection trade-off in VAE-based unsupervised anomaly detection

Variational autoencoders are widely used for unsupervised anomaly detection. Model selection however remains an open-question: to remain fully unsupervised, hyperparameters are often chosen to minimize the reconstruction error on normal samples. In this paper, we reveal a trade-off between reconstruction quality and anomaly detection among $\beta$-VAE models. Models with constrained latent space reach higher detection metrics but lower reconstruction quality. We also assess the performance variability across random seeds and show it is linked to the distance between normal and abnormal latent distributions. From this analysis, we justify and investigate two methods to mitigate the reconstructiondetection tradeoff: beta-scheduling and the Sparse VAE. The latter especially shows an improvement in detection while maintaining high reconstruction quality.

cs.LG↗

arXiv2025

Multi-Domain Brain Vessel Segmentation Through Feature Disentanglement

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.

cs.CV↗

arXiv2025

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims

Performance comparisons are fundamental in medical imaging Artificial Intelligence (AI) research, often driving claims of superiority based on relative improvements in common performance metrics. However, such claims frequently rely solely on empirical mean performance. In this paper, we investigate whether newly proposed methods genuinely outperform the state of the art by analyzing a representative cohort of medical imaging papers. We quantify the probability of false claims based on a Bayesian approach that leverages reported results alongside empirically estimated model congruence to estimate whether the relative ranking of methods is likely to have occurred by chance. According to our results, the majority (>80%) of papers claims outperformance when introducing a new method. Our analysis further revealed a high probability (>5%) of false outperformance claims in 86% of classification papers and 53% of segmentation papers. These findings highlight a critical flaw in current benchmarking practices: claims of outperformance in medical imaging AI are frequently unsubstantiated, posing a risk of misdirecting future research efforts.

cs.CV↗

arXiv2025

Unsupervised anomaly detection using Bayesian flow networks: application to brain FDG PET in the context of Alzheimer's disease

Unsupervised anomaly detection (UAD) plays a crucial role in neuroimaging for identifying deviations from healthy subject data and thus facilitating the diagnosis of neurological disorders. In this work, we focus on Bayesian flow networks (BFNs), a novel class of generative models, which have not yet been applied to medical imaging or anomaly detection. BFNs combine the strength of diffusion frameworks and Bayesian inference. We introduce AnoBFN, an extension of BFNs for UAD, designed to: i) perform conditional image generation under high levels of spatially correlated noise, and ii) preserve subject specificity by incorporating a recursive feedback from the input image throughout the generative process. We evaluate AnoBFN on the challenging task of Alzheimer's disease-related anomaly detection in FDG PET images. Our approach outperforms other state-of-the-art methods based on VAEs (beta-VAE), GANs (f-AnoGAN), and diffusion models (AnoDDPM), demonstrating its effectiveness at detecting anomalies while reducing false positive rates.

cs.CV↗

arXiv2024

Confidence intervals uncovered: Are we ready for real-world medical imaging AI?

Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be translated into clinical practice. Frequently, broad conclusions are simply derived from mean performance values. In this paper, we argue that this common practice is often a misleading simplification as it ignores performance variability. Our contribution is threefold. (1) Analyzing all MICCAI segmentation papers (n = 221) published in 2023, we first observe that more than 50% of papers do not assess performance variability at all. Moreover, only one (0.5%) paper reported confidence intervals (CIs) for model performance. (2) To address the reporting bottleneck, we show that the unreported standard deviation (SD) in segmentation papers can be approximated by a second-order polynomial function of the mean Dice similarity coefficient (DSC). Based on external validation data from 56 previous MICCAI challenges, we demonstrate that this approximation can accurately reconstruct the CI of a method using information provided in publications. (3) Finally, we reconstructed 95% CIs around the mean DSC of MICCAI 2023 segmentation papers. The median CI width was 0.03 which is three times larger than the median performance gap between the first and second ranked method. For more than 60% of papers, the mean performance of the second-ranked method was within the CI of the first-ranked method. We conclude that current publications typically do not provide sufficient evidence to support which models could potentially be translated into clinical practice.

cs.CV↗

arXiv2024

Automated MRI Quality Assessment of Brain T1-weighted MRI in Clinical Data Warehouses: A Transfer Learning Approach Relying on Artefact Simulation

The emergence of clinical data warehouses (CDWs), which contain the medical data of millions of patients, has paved the way for vast data sharing for research. The quality of MRIs gathered in CDWs differs greatly from what is observed in research settings and reflects a certain clinical reality. Consequently, a significant proportion of these images turns out to be unusable due to their poor quality. Given the massive volume of MRIs contained in CDWs, the manual rating of image quality is impossible. Thus, it is necessary to develop an automated solution capable of effectively identifying corrupted images in CDWs. This study presents an innovative transfer learning method for automated quality control of 3D gradient echo T1-weighted brain MRIs within a CDW, leveraging artefact simulation. We first intentionally corrupt images from research datasets by inducing poorer contrast, adding noise and introducing motion artefacts. Subsequently, three artefact-specific models are pre-trained using these corrupted images to detect distinct types of artefacts. Finally, the models are generalised to routine clinical data through a transfer learning technique, utilising 3660 manually annotated images. The overall image quality is inferred from the results of the three models, each designed to detect a specific type of artefact. Our method was validated on an independent test set of 385 3D gradient echo T1-weighted MRIs. Our proposed approach achieved excellent results for the detection of bad quality MRIs, with a balanced accuracy of over 87%, surpassing our previous approach by 3.5 percent points. Additionally, we achieved a satisfactory balanced accuracy of 79% for the detection of moderate quality MRIs, outperforming our previous performance by 5 percent points. Our framework provides a valuable tool for exploiting the potential of MRIs in CDWs.

eess.IV↗

arXiv2024

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

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.

eess.IV↗

arXiv2024

Evaluation of pseudo-healthy image reconstruction for anomaly detection with deep generative models: Application to brain FDG PET

Over the past years, pseudo-healthy reconstruction for unsupervised anomaly detection has gained in popularity. This approach has the great advantage of not requiring tedious pixel-wise data annotation and offers possibility to generalize to any kind of anomalies, including that corresponding to rare diseases. By training a deep generative model with only images from healthy subjects, the model will learn to reconstruct pseudo-healthy images. This pseudo-healthy reconstruction is then compared to the input to detect and localize anomalies. The evaluation of such methods often relies on a ground truth lesion mask that is available for test data, which may not exist depending on the application. We propose an evaluation procedure based on the simulation of realistic abnormal images to validate pseudo-healthy reconstruction methods when no ground truth is available. This allows us to extensively test generative models on different kinds of anomalies and measuring their performance using the pair of normal and abnormal images corresponding to the same subject. It can be used as a preliminary automatic step to validate the capacity of a generative model to reconstruct pseudo-healthy images, before a more advanced validation step that would require clinician's expertise. We apply this framework to the reconstruction of 3D brain FDG PET using a convolutional variational autoencoder with the aim to detect as early as possible the neurodegeneration markers that are specific to dementia such as Alzheimer's disease.

eess.IV↗

arXiv2023

Leveraging healthy population variability in deep learning unsupervised anomaly detection in brain FDG PET

Unsupervised anomaly detection is a popular approach for the analysis of neuroimaging data as it allows to identify a wide variety of anomalies from unlabelled data. It relies on building a subject-specific model of healthy appearance to which a subject's image can be compared to detect anomalies. In the literature, it is common for anomaly detection to rely on analysing the residual image between the subject's image and its pseudo-healthy reconstruction. This approach however has limitations partly due to the pseudo-healthy reconstructions being imperfect and to the lack of natural thresholding mechanism. Our proposed method, inspired by Z-scores, leverages the healthy population variability to overcome these limitations. Our experiments conducted on FDG PET scans from the ADNI database demonstrate the effectiveness of our approach in accurately identifying Alzheimer's disease related anomalies.

eess.IV↗

arXiv2023

Frequency Disentangled Learning for Segmentation of Midbrain Structures from Quantitative Susceptibility Mapping Data

One often lacks sufficient annotated samples for training deep segmentation models. This is in particular the case for less common imaging modalities such as Quantitative Susceptibility Mapping (QSM). It has been shown that deep models tend to fit the target function from low to high frequencies. One may hypothesize that such property can be leveraged for better training of deep learning models. In this paper, we exploit this property to propose a new training method based on frequency-domain disentanglement. It consists of two main steps: i) disentangling the image into high- and low-frequency parts and feature learning; ii) frequency-domain fusion to complete the task. The approach can be used with any backbone segmentation network. We apply the approach to the segmentation of the red and dentate nuclei from QSM data which is particularly relevant for the study of parkinsonian syndromes. We demonstrate that the proposed method provides considerable performance improvements for these tasks. We further applied it to three public datasets from the Medical Segmentation Decathlon (MSD) challenge. For two MSD tasks, it provided smaller but still substantial improvements (up to 7 points of Dice), especially under small training set situations.

eess.IV↗

arXiv2022

Fourier Disentangled Multimodal Prior Knowledge Fusion for Red Nucleus Segmentation in Brain MRI

Early and accurate diagnosis of parkinsonian syndromes is critical to provide appropriate care to patients and for inclusion in therapeutic trials. The red nucleus is a structure of the midbrain that plays an important role in these disorders. It can be visualized using iron-sensitive magnetic resonance imaging (MRI) sequences. Different iron-sensitive contrasts can be produced with MRI. Combining such multimodal data has the potential to improve segmentation of the red nucleus. Current multimodal segmentation algorithms are computationally consuming, cannot deal with missing modalities and need annotations for all modalities. In this paper, we propose a new model that integrates prior knowledge from different contrasts for red nucleus segmentation. The method consists of three main stages. First, it disentangles the image into high-level information representing the brain structure, and low-frequency information representing the contrast. The high-frequency information is then fed into a network to learn anatomical features, while the list of multimodal low-frequency information is processed by another module. Finally, feature fusion is performed to complete the segmentation task. The proposed method was used with several iron-sensitive contrasts (iMag, QSM, R2*, SWI). Experiments demonstrate that our proposed model substantially outperforms a baseline UNet model when the training set size is very small.

eess.IV↗

arXiv2022

Reproducibility in machine learning for medical imaging

Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the publications of various guidelines in order to improve research reproducibility. This didactic chapter intends at being an introduction to reproducibility for researchers in the field of machine learning for medical imaging. We first distinguish between different types of reproducibility. For each of them, we aim at defining it, at describing the requirements to achieve it and at discussing its utility. The chapter ends with a discussion on the benefits of reproducibility and with a plea for a non-dogmatic approach to this concept and its implementation in research practice.

cs.CV↗

arXiv2022

Data Augmentation in High Dimensional Low Sample Size Setting Using a Geometry-Based Variational Autoencoder

In this paper, we propose a new method to perform data augmentation in a reliable way in the High Dimensional Low Sample Size (HDLSS) setting using a geometry-based variational autoencoder. Our approach combines a proper latent space modeling of the VAE seen as a Riemannian manifold with a new generation scheme which produces more meaningful samples especially in the context of small data sets. The proposed method is tested through a wide experimental study where its robustness to data sets, classifiers and training samples size is stressed. It is also validated on a medical imaging classification task on the challenging ADNI database where a small number of 3D brain MRIs are considered and augmented using the proposed VAE framework. In each case, the proposed method allows for a significant and reliable gain in the classification metrics. For instance, balanced accuracy jumps from 66.3% to 74.3% for a state-of-the-art CNN classifier trained with 50 MRIs of cognitively normal (CN) and 50 Alzheimer disease (AD) patients and from 77.7% to 86.3% when trained with 243 CN and 210 AD while improving greatly sensitivity and specificity metrics.

stat.ML↗

arXiv2022

Interpretability of Machine Learning Methods Applied to Neuroimaging

Deep learning methods have become very popular for the processing of natural images, and were then successfully adapted to the neuroimaging field. As these methods are non-transparent, interpretability methods are needed to validate them and ensure their reliability. Indeed, it has been shown that deep learning models may obtain high performance even when using irrelevant features, by exploiting biases in the training set. Such undesirable situations can potentially be detected by using interpretability methods. Recently, many methods have been proposed to interpret neural networks. However, this domain is not mature yet. Machine learning users face two major issues when aiming to interpret their models: which method to choose, and how to assess its reliability? Here, we aim at providing answers to these questions by presenting the most common interpretability methods and metrics developed to assess their reliability, as well as their applications and benchmarks in the neuroimaging context. Note that this is not an exhaustive survey: we aimed to focus on the studies which we found to be the most representative and relevant.

cs.CV↗

arXiv2021

Clinica: an open source software platform for reproducible clinical neuroscience studies

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii) perform reproducible evaluations of their methods, and iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI and PET data), as well as tools for statistics, machine learning and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS and NIFD). Processed data include image-valued scalar fields (e.g. tissue probability maps), meshes, surface-based scalar fields (e.g. cortical thickness maps) or scalar outputs (e.g. regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.

q-bio.QM↗

arXiv2021

Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse

Many studies on machine learning (ML) for computer-aided diagnosis have so far been mostly restricted to high-quality research data. Clinical data warehouses, gathering routine examinations from hospitals, offer great promises for training and validation of ML models in a realistic setting. However, the use of such clinical data warehouses requires quality control (QC) tools. Visual QC by experts is time-consuming and does not scale to large datasets. In this paper, we propose a convolutional neural network (CNN) for the automatic QC of 3D T1-weighted brain MRI for a large heterogeneous clinical data warehouse. To that purpose, we used the data warehouse of the hospitals of the Greater Paris area (Assistance Publique-Hôpitaux de Paris [AP-HP]). Specifically, the objectives were: 1) to identify images which are not proper T1-weighted brain MRIs; 2) to identify acquisitions for which gadolinium was injected; 3) to rate the overall image quality. We used 5000 images for training and validation and a separate set of 500 images for testing. In order to train/validate the CNN, the data were annotated by two trained raters according to a visual QC protocol that we specifically designed for application in the setting of a data warehouse. For objectives 1 and 2, our approach achieved excellent accuracy (balanced accuracy and F1-score \textgreater 90\%), similar to the human raters. For objective 3, the performance was good but substantially lower than that of human raters. Nevertheless, the automatic approach accurately identified (balanced accuracy and F1-score \textgreater 80\%) low quality images, which would typically need to be excluded. Overall, our approach shall be useful for exploiting hospital data warehouses in medical image computing.

eess.IV↗

arXiv2020

Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimers disease

Diffusion MRI is the modality of choice to study alterations of white matter. In past years, various works have used diffusion MRI for automatic classification of AD. However, classification performance obtained with different approaches is difficult to compare and these studies are also difficult to reproduce. In the present paper, we first extend a previously proposed framework to diffusion MRI data for AD classification. Specifically, we add: conversion of diffusion MRI ADNI data into the BIDS standard and pipelines for diffusion MRI preprocessing and feature extraction. We then apply the framework to compare different components. First, FS has a positive impact on classification results: highest balanced accuracy (BA) improved from 0.76 to 0.82 for task CN vs AD. Secondly, voxel-wise features generally gives better performance than regional features. Fractional anisotropy (FA) and mean diffusivity (MD) provided comparable results for voxel-wise features. Moreover, we observe that the poor performance obtained in tasks involving MCI were potentially caused by the small data samples, rather than by the data imbalance. Furthermore, no extensive classification difference exists for different degree of smoothing and registration methods. Besides, we demonstrate that using non-nested validation of FS leads to unreliable and over-optimistic results: 0.05 up to 0.40 relative increase in BA. Lastly, with proper FR and FS, the performance of diffusion MRI features is comparable to that of T1w MRI. All the code of the framework and the experiments are publicly available: general-purpose tools have been integrated into the Clinica software package (www.clinica.run) and the paper-specific code is available at: https://github.com/aramis-lab/AD-ML.

q-bio.QM↗

arXiv2020

Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation

Over 30 papers have proposed to use convolutional neural network (CNN) for AD classification from anatomical MRI. However, the classification performance is difficult to compare across studies due to variations in components such as participant selection, image preprocessing or validation procedure. Moreover, these studies are hardly reproducible because their frameworks are not publicly accessible and because implementation details are lacking. Lastly, some of these papers may report a biased performance due to inadequate or unclear validation or model selection procedures. In the present work, we aim to address these limitations through three main contributions. First, we performed a systematic literature review and found that more than half of the surveyed papers may have suffered from data leakage. Our second contribution is the extension of our open-source framework for classification of AD using CNN and T1-weighted MRI. Finally, we used this framework to rigorously compare different CNN architectures. The data was split into training/validation/test sets at the very beginning and only the training/validation sets were used for model selection. To avoid any overfitting, the test sets were left untouched until the end of the peer-review process. Overall, the different 3D approaches (3D-subject, 3D-ROI, 3D-patch) achieved similar performances while that of the 2D slice approach was lower. Of note, the different CNN approaches did not perform better than a SVM with voxel-based features. The different approaches generalized well to similar populations but not to datasets with different inclusion criteria or demographical characteristics.

cs.LG↗