arXiv subjects

Valentin Oreiller

Publications and source records attributed to Valentin Oreiller.

7 recordsLinked to original sources

arXiv2026

Bag-of-Visual-Words for Spatial Mapping of Lung Adenocarcinoma Growth Patterns

Spatial mapping of lung adenocarcinoma (LUAD) growth patterns across whole slide images (WSIs) requires resolving architectural context at the region level, yet existing methods operate at the individual tile level and produce generic morphological clusters rather than clinically defined pattern maps. We propose a weakly supervised Bag-of-Visual-Words (BoVW) pipeline that learns a visual vocabulary from frozen foundation model embeddings extracted from a small set of annotated regions of interest (ROIs). Pattern prototypes are constructed as mean BoVW histograms of same-label ROIs and used for nearest-prototype classification of sliding-window regions under Jensen--Shannon divergence. The resulting predictions are projected onto the WSI tile grid to produce interpretable spatial pattern maps. We evaluate the method on 87 CPTAC-LUAD patients using three foundation model encoders and multiple vocabulary sizes on two clinically motivated tasks. For tumour/healthy classification, the best configuration achieves a balanced accuracy of $0.974$ with H-Optimus-1, approaching the $0.987$ obtained by a supervised SVM trained on mean-pooled WSI embeddings. For binary histologic grade classification, the BoVW pipeline achieves higher balanced accuracy than the supervised baseline for all encoders, suggesting that ROI-level pattern decomposition preserves grade-relevant heterogeneity that is attenuated by global mean pooling.

cs.CV↗

arXiv2025

A Multimodal and Multi-centric Head and Neck Cancer Dataset for Segmentation, Diagnosis and Outcome Prediction

We present a publicly available multimodal dataset for head and neck cancer research, comprising 1123 annotated Positron Emission Tomography/Computed Tomography (PET/CT) studies from patients with histologically confirmed disease, acquired from 10 international medical centers. All studies contain co-registered PET/CT scans with varying acquisition protocols, reflecting real-world clinical diversity from a long-term, multi-institution retrospective collection. Primary gross tumor volumes (GTVp) and involved lymph nodes (GTVn) were manually segmented by experienced radiation oncologists and radiologists following established guidelines. We provide anonymized NifTi files, expert-annotated segmentation masks, comprehensive clinical metadata, and radiotherapy dose distributions for a patient subset. The metadata include TNM staging, HPV status, demographics, long-term follow-up outcomes, survival times, censoring indicators, and treatment information. To demonstrate its utility, we benchmark three key clinical tasks: automated tumor segmentation, recurrence-free survival prediction, and HPV status classification, using state-of-the-art deep learning models like UNet, SegResNet, and multimodal prognostic frameworks.

cs.CV↗

arXiv2023

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

cs.CV↗

arXiv2022

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

cs.CV↗

arXiv2022

Overview of the HECKTOR Challenge at MICCAI 2021: Automatic Head and Neck Tumor Segmentation and Outcome Prediction in PET/CT Images

This paper presents an overview of the second edition of the HEad and neCK TumOR (HECKTOR) challenge, organized as a satellite event of the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2021. The challenge is composed of three tasks related to the automatic analysis of PET/CT images for patients with Head and Neck cancer (H&N), focusing on the oropharynx region. Task 1 is the automatic segmentation of H&N primary Gross Tumor Volume (GTVt) in FDG-PET/CT images. Task 2 is the automatic prediction of Progression Free Survival (PFS) from the same FDG-PET/CT. Finally, Task 3 is the same as Task 2 with ground truth GTVt annotations provided to the participants. The data were collected from six centers for a total of 325 images, split into 224 training and 101 testing cases. The interest in the challenge was highlighted by the important participation with 103 registered teams and 448 result submissions. The best methods obtained a Dice Similarity Coefficient (DSC) of 0.7591 in the first task, and a Concordance index (C-index) of 0.7196 and 0.6978 in Tasks 2 and 3, respectively. In all tasks, simplicity of the approach was found to be key to ensure generalization performance. The comparison of the PFS prediction performance in Tasks 2 and 3 suggests that providing the GTVt contour was not crucial to achieve best results, which indicates that fully automatic methods can be used. This potentially obviates the need for GTVt contouring, opening avenues for reproducible and large scale radiomics studies including thousands potential subjects.

eess.IV↗

arXiv2020

3D Solid Spherical Bispectrum CNNs for Biomedical Texture Analysis

Locally Rotation Invariant (LRI) operators have shown great potential in biomedical texture analysis where patterns appear at random positions and orientations. LRI operators can be obtained by computing the responses to the discrete rotation of local descriptors, such as Local Binary Patterns (LBP) or the Scale Invariant Feature Transform (SIFT). Other strategies achieve this invariance using Laplacian of Gaussian or steerable wavelets for instance, preventing the introduction of sampling errors during the discretization of the rotations. In this work, we obtain LRI operators via the local projection of the image on the spherical harmonics basis, followed by the computation of the bispectrum, which shares and extends the invariance properties of the spectrum. We investigate the benefits of using the bispectrum over the spectrum in the design of a LRI layer embedded in a shallow Convolutional Neural Network (CNN) for 3D image analysis. The performance of each design is evaluated on two datasets and compared against a standard 3D CNN. The first dataset is made of 3D volumes composed of synthetically generated rotated patterns, while the second contains malignant and benign pulmonary nodules in Computed Tomography (CT) images. The results indicate that bispectrum CNNs allows for a significantly better characterization of 3D textures than both the spectral and standard CNN. In addition, it can efficiently learn with fewer training examples and trainable parameters when compared to a standard convolutional layer.

cs.CV↗

arXiv2020

Local Rotation Invariance in 3D CNNs

Locally Rotation Invariant (LRI) image analysis was shown to be fundamental in many applications and in particular in medical imaging where local structures of tissues occur at arbitrary rotations. LRI constituted the cornerstone of several breakthroughs in texture analysis, including Local Binary Patterns (LBP), Maximum Response 8 (MR8) and steerable filterbanks. Whereas globally rotation invariant Convolutional Neural Networks (CNN) were recently proposed, LRI was very little investigated in the context of deep learning. LRI designs allow learning filters accounting for all orientations, which enables a drastic reduction of trainable parameters and training data when compared to standard 3D CNNs. In this paper, we propose and compare several methods to obtain LRI CNNs with directional sensitivity. Two methods use orientation channels (responses to rotated kernels), either by explicitly rotating the kernels or using steerable filters. These orientation channels constitute a locally rotation equivariant representation of the data. Local pooling across orientations yields LRI image analysis. Steerable filters are used to achieve a fine and efficient sampling of 3D rotations as well as a reduction of trainable parameters and operations, thanks to a parametric representations involving solid Spherical Harmonics (SH), which are products of SH with associated learned radial profiles.Finally, we investigate a third strategy to obtain LRI based on rotational invariants calculated from responses to a learned set of solid SHs. The proposed methods are evaluated and compared to standard CNNs on 3D datasets including synthetic textured volumes composed of rotated patterns, and pulmonary nodule classification in CT. The results show the importance of LRI image analysis while resulting in a drastic reduction of trainable parameters, outperforming standard 3D CNNs trained with data augmentation.

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