arXiv subjects

Antoine Olivier

Publications and source records attributed to Antoine Olivier.

6 recordsLinked to original sources

arXiv2026

CytoSyn: a Foundation Diffusion Model for Histopathology -- Tech Report

Computational pathology has made significant progress in recent years, fueling advances in both fundamental disease understanding and clinically ready tools. This evolution is driven by the availability of large amounts of digitized slides and specialized deep learning methods and models. Multiple self-supervised foundation feature extractors have been developed, enabling downstream predictive applications from cell segmentation to tumor sub-typing and survival analysis. In contrast, generative foundation models designed specifically for histopathology remain scarce. Such models could address tasks that are beyond the capabilities of feature extractors, such as virtual staining. In this paper, we introduce CytoSyn, a state-of-the-art foundation latent diffusion model that enables the guided generation of highly realistic and diverse histopathology H&E-stained images, as shown in an extensive benchmark. We explored methodological improvements, training set scaling, sampling strategies and slide-level overfitting, culminating in the improved CytoSyn-v2, and compared our work to PixCell, a state-of-the-art model, in an in-depth manner. This comparison highlighted the strong sensitivity of both diffusion models and performance metrics to preprocessing-specific details such as JPEG compression. Our model has been trained on a dataset obtained from more than 10,000 TCGA diagnostic whole-slide images of 32 different cancer types. Despite being trained only on oncology slides, it maintains state-of-the-art performance generating inflammatory bowel disease images. To support the research community, we publicly release CytoSyn's weights, its training and validation datasets, and a sample of synthetic images in this repository: https://huggingface.co/Owkin-Bioptimus/CytoSyn.

cs.CV↗

arXiv2025

IMILIA: interpretable multiple instance learning for inflammation prediction in IBD from H&E whole slide images

As the therapeutic target for Inflammatory Bowel Disease (IBD) shifts toward histologic remission, the accurate assessment of microscopic inflammation has become increasingly central for evaluating disease activity and response to treatment. In this work, we introduce IMILIA (Interpretable Multiple Instance Learning for Inflammation Analysis), an end-to-end framework designed for the prediction of inflammation presence in IBD digitized slides stained with hematoxylin and eosin (H&E), followed by the automated computation of markers characterizing tissue regions driving the predictions. IMILIA is composed of an inflammation prediction module, consisting of a Multiple Instance Learning (MIL) model, and an interpretability module, divided in two blocks: HistoPLUS, for cell instance detection, segmentation and classification; and EpiSeg, for epithelium segmentation. IMILIA achieves a cross-validation ROC-AUC of 0.83 on the discovery cohort, and a ROC-AUC of 0.99 and 0.84 on two external validation cohorts. The interpretability module yields biologically consistent insights: tiles with higher predicted scores show increased densities of immune cells (lymphocytes, plasmocytes, neutrophils and eosinophils), whereas lower-scored tiles predominantly contain normal epithelial cells. Notably, these patterns were consistent across all datasets. Code and models to partially replicate the results on the public IBDColEpi dataset can be found at https://github.com/owkin/imilia.

cs.CV↗

arXiv2025

Robust sensitivity control in digital pathology via tile score distribution matching

Deploying digital pathology models across medical centers is challenging due to distribution shifts. Recent advances in domain generalization improve model transferability in terms of aggregated performance measured by the Area Under Curve (AUC). However, clinical regulations often require to control the transferability of other metrics, such as prescribed sensitivity levels. We introduce a novel approach to control the sensitivity of whole slide image (WSI) classification models, based on optimal transport and Multiple Instance Learning (MIL). Validated across multiple cohorts and tasks, our method enables robust sensitivity control with only a handful of calibration samples, providing a practical solution for reliable deployment of computational pathology systems.

cs.CV↗

arXiv2025

Distilling foundation models for robust and efficient models in digital pathology

In recent years, the advent of foundation models (FM) for digital pathology has relied heavily on scaling the pre-training datasets and the model size, yielding large and powerful models. While it resulted in improving the performance on diverse downstream tasks, it also introduced increased computational cost and inference time. In this work, we explore the distillation of a large foundation model into a smaller one, reducing the number of parameters by several orders of magnitude. Leveraging distillation techniques, our distilled model, H0-mini, achieves nearly comparable performance to large FMs at a significantly reduced inference cost. It is evaluated on several public benchmarks, achieving 3rd place on the HEST benchmark and 5th place on the EVA benchmark. Additionally, a robustness analysis conducted on the PLISM dataset demonstrates that our distilled model reaches excellent robustness to variations in staining and scanning conditions, significantly outperforming other state-of-the art models. This opens new perspectives to design lightweight and robust models for digital pathology, without compromising on performance.

cs.CV↗

arXiv2018

Combination of direct methods and homotopy in numerical optimal control: application to the optimization of chemotherapy in cancer

We consider a state-constrained optimal control problem of a system of two non-local partial-differential equations, which is an extension of the one introduced in a previous work in mathematical oncology. The aim is to minimize the tumor size through chemotherapy while avoiding the emergence of resistance to the drugs. The numerical approach to solve the problem was the combination of direct methods and continuation on discretization parameters, which happen to be insufficient for the more complicated model, where diffusion is added to account for mutations. In the present paper, we propose an approach relying on changing the problem so that it can theoretically be solved thanks to a Pontryagin Maximum Principle in infinite dimension. This provides an excellent starting point for a much more reliable and efficient algorithm combining direct methods and continuations. The global idea is new and can be thought of as an alternative to other numerical optimal control techniques.

math.OC↗

arXiv2017

Redundancy implies robustness for bang-bang strategies

We develop in this paper a method ensuring robustness properties to bang-bang strategies , for general nonlinear control systems. Our main idea is to add bang arcs in the form of needle-like variations of the control. With such bang-bang controls having additional degrees of freedom, steering the control system to some given target amounts to solving an overdeter-mined nonlinear shooting problem, what we do by developing a least-square approach. In turn, we design a criterion to measure the quality of robustness of the bang-bang strategy, based on the singular values of the end-point mapping, and which we optimize. Our approach thus shows that redundancy implies robustness, and we show how to achieve some compromises in practice, by applying it to the attitude control of a 3d rigid body.

math.OC↗