Title: Substitution of numerical models of fluid mechanics by deep learning models.

Applications to aortic dissections.

Supervisors: Badih Ghattas and Valérie Deplano.

Institute of Mathematics of Marseille, I2M, UMR7373 and Institute for Research on Non-Equilibrium Phenomena,
IRPHE, UMR7342.
Contacts: badih.ghattas@univ-amu.fr and Valerie.deplano@univ-amu.fr.

Project description

General Context. This thesis subject is supported by a multidisciplinary consortium made up of researchers
specializing in statistics, fluid mechanics and biomechanics as well as medical imaging. The statistics team of the
Institute of Mathematics of Marseille (UMR7373) and the biomechanics team of the Institute for Research on Non-
Equilibrium Phenomena (UMR7342, Marseille) in collaboration with the medical imaging department of la Timone
Hospital want to develop a clinical diagnostic tool capable of early prediction of the development of pathologies
of the thoracic aorta.

The IRPHE biomechanics team carries out complex digital modeling of some of these pathologies Using data from
medical imaging -CT scan for geometries and 2D MRI for boundary conditions-, the objective is to implement
patient-specific 3D models taking into account fluid-structure interactions for different types of evolution -
favorable and unfavorable - as well as for several postoperative times. This makes it possible to associate physical
quantities linked to the dynamics of flow and structures with certain unfavorable clinical evolutions ([1]) and,
subsequently, to predict certain treatment failures at an early stage. However, the computation time associated
with these complex models constitutes an obstacle to their use in clinical practice.

The main objective of this thesis is therefore to implement deep learning techniques to replace these
numerical models in order to predict early the evolution of pathologies of the thoracic aorta. This
project will focus more specifically on aortic dissections. Indeed, the IRPHE biomechanics team has already carried
out numerical modeling of this pathology as part of F. Khannous' thesis defended in September 2020 ([2], [3]).

Clinical context. Responsible for nearly 18 million deaths each year, cardiovascular diseases are the leading
cause of death in the world. In France, they are the second cause of death per year (behind cancer) with 400
deaths per day. Among them, aortic dissections consist of an intimal tear in the aortic wall, called the portal of
entry, responsible for the creation of a circulating false channel. True and false channels are separated by the
dissected wall, called the neointimal flap.
There are 2 types of dissection: type A dissections located at the level of the
ascending thoracic aorta and type B dissections which concern only the descending
thoracic aorta. Type A dissections are usually treated surgically, uncomplicated type
Bs benefit from medical treatment alone with low morbidity and mortality. However,
despite good immediate results following medical treatment alone, 20 to 50% of
patients develop an aneurysm with a high risk of rupture and mortality Since the
criteria usually used in clinical routine to assess this unfavorable evolution are not
satisfactory, it is a question of determining through numerical modeling and
subsequently by deep learning techniques which physical quantities are likely to be
correlated with an unfavorable outcome, and thus improve patient care.

Methodology. Deep neural networks can be used in this context. It is considered that behind the numerical
model hides a complex latent function 𝑓 which at each input (geometry and boundary conditions from medical
imaging) associates hemodynamic measurements. We note (𝑋𝑖 , 𝑌𝑖 ), 𝑖 = 1, . . , 𝑛 the pairs of inputs and outputs of
the numerical model. We are interested in the approximation of the underlying function 𝑓 by a deep neural
network. The approximation sought is not trivial and raises real challenges for different reasons:

1) the small size of the samples available to train the neural networks due to the small number of simulations
that can be carried out being the long calculation times of the numerical simulations.
2) the high dimension of the data; the inputs 𝑋𝑛 of the model consist not only of CT scans (thoracic scans) i.e.
of volumetric images of approximately 500*250*250 voxels, but also of essential information from 2D MRIs. The
(𝑡)
outputs 𝑌𝑛 = ( 𝑌𝑖𝑗𝑘 ) are composed of several three-dimensional fields (for example blood velocity, three-
dimensional vector) which are spatio-temporal (in each point 𝑖𝑗𝑘 of the aorta and at each instant 𝑡). The volume
of the outputs depends on the spatio-temporal resolution fixed in the numerical model; for example, 3.3 Gigabyte
at each backup time 𝑡. The volume of data increases exponentially with resolution.
3) Data heterogeneity: scanners, MRIs, and three-dimensional spatio-temporal flow fields.
Aix-Marseille Université – Collège Doctoral – 3, Place Victor Hugo – Case 78 – 13003 Marseille – FRANCE
Tél. : (33) 04 13 55 04 51
All these elements illustrate the complexity of the task. For this, we aim to develop and finalize a modeling in
several stages.

Step 1: Data preprocessing. Data from heterogeneous sources and formats require significant preparation,
cleaning, shaping and encoding work in order to be used in deep learning models. During this phase, important
technical choices will be made on the format and mode of access to data in order to avoid blockages in the
learning phases. This step will be carried out in close collaboration with the IRPHE, which will carry out the
numerical simulations and provide the data necessary for the following steps.
Step 2: Instantaneous model to predict flows in high spatial resolution. A first model will work only on the spatial
component of the data at a time 𝑡. This will make it possible to predict at a given moment the hemodynamic
fields (ie the 3D components of flow velocity at all points) from the 3D mask of a patient (which represents the
geometry of the aorta) and parameters from the 2D MRI at the same time. The 3D masks used as input to this
first model result from the automatic semantic segmentation of the scans of the thoracic aorta obtained with a
model developed and validated within the framework of J. Fournel's thesis ([4]).
The model used will probably be of the convolutional type ([5]), but important technical choices will have to be
studied beforehand (2D or 3D, type of architecture, etc.). The output of this first model will correspond to the
predicted field for a time 𝑡 at any point of the aorta (in high spatial resolution). The temporal resolution of this
first model is limited by the temporal resolution of 2D MRIs, which is generally quite low (between 20 and 30ms).
Step 3 : Model to improve the temporal resolution of hemodynamic results in high spatial resolution. The objective
of the second model is to increase the temporal resolution of the forecasts given by the first model. For this we
will adopt an approach similar to that exposed in Fukami et al ([6]). A deep neural network could be trained to
predict the spatial field 𝑌 at time 𝑡 + 1 from the fields available at times instants 𝑡 and 𝑡 + 2, thus estimate a
model 𝑌𝑡+1 = 𝑔(𝑌𝑡 , 𝑌𝑡+2 ). The estimation of this model could be done with a learning database built from the outputs
of the numerical models. The figure below schematizes the models proposed in steps 2 and 3 of this project.

Figure 1 Pipeline describing the deep learning models used in the project.

Candidate profile
The candidate must have academic knowledge in the disciplinary fields relating to the subject: Deep learning in
priority and digital modelling. He (she) must have a proven appetite for interdisciplinarity. Python programming
experience is essential, in particular; tensorflow, keras, pandas and numpy.

Candidacy
Candidates must send their application before May 15, 2022. Application consists of a Curriculum Vitae, a cover
letter, transcripts and copies of diplomas (Bachelor and Master) and a letter of recommendation, for example
from the internship supervisor or the master's thesis supervisor. The application folder must be sent in the form
of a .zip archive to the project supervisors at the addresses badih.ghattas@univ-amu.fr and
valerie.deplano@univ-amu.fr.

[1] Deplano et al, (2021) Vascular geometric singularities, hemodynamic markers and pathologies, WILEY. In
press
[2] Khannous et al, (2020) Residual type B aortic dissection FSI modeling. CMBBE, 23(1).
[3] khannous et al, (2022) Numerical modeling of residual type B aortic dissection: longitudinal analysis of
favorable and unfavorable evolution". Medical & Biological Engineering & Computing, DOI: 10.1007/s11517-
021-02480-1.
[4] Fournel J (2020). Deep Learning for thoracic imaging segmentation to improve cardiovascular risk
prediction. Thèse coencadrée par B. Ghattas et A. Jacquier (CRMBM)
[5] Liang et al, (2020) A Feasibility Study of Deep Learning for Predicting Hemodynamics of Human Thoracic
Aorta J. of Biomech., 99.
[6] Fukami et al, (2019) Super resolution reconstruction of turbulent flows with machine learning, J. Fluid
Mech., 870