Thibault Marin

Xiaofeng Liu, Qianru Zhang, Thibault Marin et al.

The synergistic interpretation of anatomical information from computed tomography (CT) and metabolic information from positron emission tomography (PET) is important to oncologic imaging. However, existing deep learning methods for PET/CT remain largely task-specific, are often trained on single-center cohorts, or adopt dual-branch fusion schemes that delay cross-modal interaction and underutilize early spatial correspondence between PET and CT. To address these limitations, we present an open-source, multi-center, whole-body FDG PET/CT foundation model utilizing 4,997 harmonized scans from four public datasets. Our framework employs hierarchical UNet-shaped backbones with early channel-wise concatenation, enabling anatomical and metabolic features to interact from the first embedding layer onward. We further introduce a masked autoencoding objective based on zero-mean imputation, combined with a weighted global reconstruction loss. This design avoids non-physical intensity discontinuities at masked-region boundaries that arise from learnable mask tokens. On downstream AutoPET lesion segmentation, the proposed models demonstrate strong label efficiency: with only 10\% of the labeled training data, they achieve performance comparable to models trained from scratch on the full dataset. Under extreme 5-shot linear probing, joint PET/CT pretraining also achieves higher Dice scores than separated-modality pretraining. This multi-center foundation model demonstrates label efficiency and cross-modality representation learning for PET/CT tumor segmentation. It provides a robust, open-source basis for advancing automated oncologic imaging, significantly reducing the need for large-scale manual annotations in clinical practice.

Xiaofeng Liu, Thibault Marin, Tiss Amal et al.

Background: In medical imaging, images are usually treated as deterministic, while their uncertainties are largely underexplored. Purpose: This work aims at using deep learning to efficiently estimate posterior distributions of imaging parameters, which in turn can be used to derive the most probable parameters as well as their uncertainties. Methods: Our deep learning-based approaches are based on a variational Bayesian inference framework, which is implemented using two different deep neural networks based on conditional variational auto-encoder (CVAE), CVAE-dual-encoder and CVAE-dual-decoder. The conventional CVAE framework, i.e., CVAE-vanilla, can be regarded as a simplified case of these two neural networks. We applied these approaches to a simulation study of dynamic brain PET imaging using a reference region-based kinetic model. Results: In the simulation study, we estimated posterior distributions of PET kinetic parameters given a measurement of time-activity curve. Our proposed CVAE-dual-encoder and CVAE-dual-decoder yield results that are in good agreement with the asymptotically unbiased posterior distributions sampled by Markov Chain Monte Carlo (MCMC). The CVAE-vanilla can also be used for estimating posterior distributions, although it has an inferior performance to both CVAE-dual-encoder and CVAE-dual-decoder. Conclusions: We have evaluated the performance of our deep learning approaches for estimating posterior distributions in dynamic brain PET. Our deep learning approaches yield posterior distributions, which are in good agreement with unbiased distributions estimated by MCMC. All these neural networks have different characteristics and can be chosen by the user for specific applications. The proposed methods are general and can be adapted to other problems.

Xiaofeng Liu, Thibault Marin, Tiss Amal et al.

This work aims efficiently estimating the posterior distribution of kinetic parameters for dynamic positron emission tomography (PET) imaging given a measurement of time of activity curve. Considering the inherent information loss from parametric imaging to measurement space with the forward kinetic model, the inverse mapping is ambiguous. The conventional (but expensive) solution can be the Markov Chain Monte Carlo (MCMC) sampling, which is known to produce unbiased asymptotical estimation. We propose a deep-learning-based framework for efficient posterior estimation. Specifically, we counteract the information loss in the forward process by introducing latent variables. Then, we use a conditional variational autoencoder (CVAE) and optimize its evidence lower bound. The well-trained decoder is able to infer the posterior with a given measurement and the sampled latent variables following a simple multivariate Gaussian distribution. We validate our CVAE-based method using unbiased MCMC as the reference for low-dimensional data (a single brain region) with the simplified reference tissue model.

Xiaofeng Liu, Yongsong Huang, Thibault Marin et al.

The to-be-denoised positron emission tomography (PET) volumes are inherent with diverse count levels, which imposes challenges for a unified model to tackle varied cases. In this work, we resort to the recently flourished prompt learning to achieve generalizable PET denoising with different count levels. Specifically, we propose dual prompts to guide the PET denoising in a divide-and-conquer manner, i.e., an explicitly count-level prompt to provide the specific prior information and an implicitly general denoising prompt to encode the essential PET denoising knowledge. Then, a novel prompt fusion module is developed to unify the heterogeneous prompts, followed by a prompt-feature interaction module to inject prompts into the features. The prompts are able to dynamically guide the noise-conditioned denoising process. Therefore, we are able to efficiently train a unified denoising model for various count levels, and deploy it to different cases with personalized prompts. We evaluated on 1940 low-count PET 3D volumes with uniformly randomly selected 13-22\% fractions of events from 97 $^{18}$F-MK6240 tau PET studies. It shows our dual prompting can largely improve the performance with informed count-level and outperform the count-conditional model.

Xiaofeng Liu, Fangxu Xing, Thibault Marin et al.

Lesions or organ boundaries visible through medical imaging data are often ambiguous, thus resulting in significant variations in multi-reader delineations, i.e., the source of aleatoric uncertainty. In particular, quantifying the inter-observer variability of manual annotations with Magnetic Resonance (MR) Imaging data plays a crucial role in establishing a reference standard for various diagnosis and treatment tasks. Most segmentation methods, however, simply model a mapping from an image to its single segmentation map and do not take the disagreement of annotators into consideration. In order to account for inter-observer variability, without sacrificing accuracy, we propose a novel variational inference framework to model the distribution of plausible segmentation maps, given a specific MR image, which explicitly represents the multi-reader variability. Specifically, we resort to a latent vector to encode the multi-reader variability and counteract the inherent information loss in the imaging data. Then, we apply a variational autoencoder network and optimize its evidence lower bound (ELBO) to efficiently approximate the distribution of the segmentation map, given an MR image. Experimental results, carried out with the QUBIQ brain growth MRI segmentation datasets with seven annotators, demonstrate the effectiveness of our approach.