Section: Research Program

Computational Physiology & Image-Guided Therapy

Computational Physiology aims at developing computational models of human organ functions, an important component of the e-patient, with applications in e-medicine and more specifically in computer-aided prevention, diagnosis, therapy planning and therapy guidance. The focus of our research is on descriptive (allowing to reproduce available observations), discriminative (allowing to separate two populations), and above all predictive models which can be personalized from patient data including medical images, biosignals, biological information and other available metadata. A key aspect of this scientific axis is therefore the coupling of biophysical models with patient data which implies that we are mostly considering models with relatively few and identifiable parameters. To this end, data assimilation methods aiming at estimating biophysical model parameters in order to reproduce available patient data are preferably developed as they potentially lead to predictive models suitable for therapy planning.

Previous research projects in computational physiology have led us to develop biomechanical models representing quasi-static small or large soft tissue deformations (e.g. liver or breast deformation after surgery), mechanical growth or atrophy models (e.g. simulating brain atrophy related to neurodegenerative diseases), heat transfer models (e.g. simulating radiofrequency ablation of tumors), and tumor growth models (e.g. brain or lung tumor growth).

To improve the data assimilation of biophysical models from patient data, a long term objective of our research will be to develop joint imaging and biophysical generative models in a probabilistic framework which simultaneously describe the appearance and function of an organ (or its pathologies) in medical images. Indeed, current approaches for the personalization of biophysical models often proceed in two separate steps. In a first stage, geometric, kinematic or functional features are first extracted from medical images. In a second stage, they are used by personalization methods to optimize model parameters in order to match the extracted features. In this process, subtle information present in the image which could be informative for biophysical models is often lost which may lead to limited personalization results. Instead, we propose to develop more integrative approaches where the extraction of image features would be performed jointly with the model parameter fitting. Those imaging and biophysical generative models should lead to a better understanding of the content of images, to a better personalization of model parameters and also better estimates of their uncertainty.

This improved coupling between images and model should help solving various practical problems driven by clinical applications. Depending on available resources, datasets, and clinical problems, we wish to develop a new expertise for the simulation of tissue perfusion (e.g. to capture the uptake of contrast agent or radioactive tracers), or blood flow in medium / small vessels (e.g. to capture the transport of drugs or radioactive materials in interventional radiology).

• Reduced Computational Biophysical Models. Clinical constraint and uncertainty estimation inevitably lead to the requirement of relatively fast computation of biophysical models. In addition to hardware acceleration (GPU, multithreading) we will explore various ways to accelerate the computation of models through intrusive (e.g. proper orthogonal decomposition, computation of condensed stiffness matrices in non-linear mechanics) or non intrusive methods (e.g. polynomial chaos expansion, Gaussian processes).

• Uncertainty estimation of Biophysical Models. We will pursue our research on this topic by developing Bayesian methods to estimate the posterior probability of model parameters, initial and boundary conditions from image features or image voxels. Such approaches rely on the definition of relevant likelihood terms relating the model state variables to the observable quantities in images. When possible joint imaging and biophysical generative models will be developed to avoid to rely on intermediate image features. Approximate inference of uncertainty will be estimated through Variational Bayes approaches whose accuracy will be evaluated through a comparison with stochastic sampling methods (e.g. MCMC). Through this uncertainty estimation, we also aim at developing a reliable framework to select the most sensitive and discriminative parameters of a given model but also to select the biophysical model best suited to solve a given problem (e.g. prediction of therapy outcome).

• High Order Finite Element Modeling. Soft tissue biomechanical models have until now been formulated as linear elastic or hyperelastic materials discretized as linear tetrahedra finite elements. While being very generic, those elements are known to suffer from numerical locking for nearly incompressible materials and lead to poor estimate of stress field. We will develop efficient implementation and assembly methods using high order tetrahedral (and possibly hexahedral) elements. To maintain the number of nodes relatively low while keeping a good accuracy, we intend to develop elements of adaptive degree ($p$-refinement) driven by local error indices. Solution for meshing surfaces or volumes with curved high order elements will be developed in collaboration with the Titane and Aromath Inria teams.

• Clinical Applications. We plan to develop new applications of therapy planning and therapy guidance through existing or emerging collaborations related to the following problems : breast reconstruction following insertion of breast implants (with Anatoscope), planning of cochlear electrodes implantation (with CHU Nice and Oticon Medical), lung deformation following COPD or pulmonary fibrosis (with CHU Nice), echography based elastometry (with CHU Nice).