Section: Research Program

Biomedical Image Analysis & Machine Learning

The long-term objective of biomedical image analysis is to extract, from biomedical images, pertinent information for the construction of the e-patient and for the development of e-medicine. This relates to the development of advanced segmentation and registration of images, the extraction of image biomarkers of pathologies, the detection and classification of image abnormalities, the construction of temporal models of motion or evolution from time-series of images, etc.

A good illustration of the current state of the art and of the remaining challenges can be found in these recent publications which address for instance the extraction of quantitative biomarkers on static or time varying images, as well as image registration and deformation analysis problems. This also applies to the analysis of microscopic and multi-scale images.

In addition, the growing availability of very large databases of biomedical images, the growing power of computers and the progress of machine learning (ML) approaches have opened up new opportunities for biomedical image analysis.

This is the reason why we decided to revisit a number of biomedical image analysis problems with ML approaches, including segmentation and registration problems, automatic detection of abnormalities, prediction of a missing imaging modality, etc. Not only those ML approaches often outperform the previous state-of-the-art solutions in terms of performances (accuracy of the results, computing times), but they also tend to offer a higher flexibility like the possibility to be transferred from one problem to another one with a similar framework. However, even when successful, ML approaches tend to suffer from a lack of explanatory power, which is particularly annoying for medical applications. We also plan to work on methods that can interpret the results of the ML algorithms that we develop.

• Revisiting Segmentation problems with Machine Learning: Through a partnership with Microsoft Research in Cambridge (UK), we are studying new segmentation methods based on deep learning with weakly annotated data. In effect, a complete segmentation ground truth is costly to collect in medical image analysis, as it requires the tedious task of contouring regions of interest and their validation by an expert. On the other hand, the label "presence" or "absence" of a lesion for instance (weak annotation) can be obtained at a much lower cost.

  We also plan to explore the application of deep learning methods to the fast segmentation of static or deformable organs. For instance we plan to use deep learning methods for the 3D consistent segmentation of the myocardium tissue of the 2 cardiac ventricles, an important preliminary step to mesh the cardiac muscle for computational anatomy, physiology and cardiology projects.

• Revisiting Registration problems with Machine Learning: We are studying, through a partnership with Siemens (Princeton), the possibility to apply robust non-rigid registration through agent-based action learning. We propose a decision process where the objective simplifies to iteratively finding the strategically next best step. An artificial agent is driven to solve the task of non-rigid registration through exploring the parametric space of a statistical deformation model built from training data. Since it is difficult to extract trustworthy ground-truth deformation fields we propose a training scheme with synthetically deformed cases and few real inter-subject cases.

• Prediction of an imaging modality from other imaging modalities with machine learning: Through a partnership with the Brain and Stem Institute in Paris, we plan to develop deep learning approaches to quantify some brain alterations currently measured by an invasive nuclear medicine imaging modality (PET imaging with specific tracers), directly from a multi-sequence acquisition of a non-invasive imaging modality (MRI). This requires innovative approaches taking into account the relatively small size of the ground truth database (patients having undergone both PET and MR Image acquisitions) and exploiting the a priori knowledge on the brain anatomy. We believe that this approach could apply to other image prediction problems in the longer term.

• Prediction of cardiac pathologies with machine learning and image simulation: Following the important work on cardiac image simulation done during the ERC project MedYMA, we are currently able to simulate time-series of images of various cardiac pathologies for which we can vary the parameters of a generative electro-mechanical model. We plan to develop new deep learning methods exploiting both the shape and motion phenotypes present in the time-series of images to detect and characterize a number of cardiac pathologies, including subtle assynchronies, local ischemia or infarcts.

• Measuring Brain, Cognition, Behaviour: We developed a collaborative project MNC3 which is supported by the excellence initiative Idex $UC{A}^{Jedi}$. This project gathers partners from Inria, Nice Hospitals (physicians), Nice University, and IPMC (biologists). The goal is to provide a joint analysis of heterogenous data collected on patients with neurological and psychiatric diseases. Those data include medical imaging (mainly MRI), activity (measured by connected wrists or video or microphones), biology/genomics, and clinical information. We want to show the increase in the statistical power of a joint analysis of the data to classify a pathology and to quantify its evolution.

In addition to these mid-term goals, we have applied to two important projects with local clinicians. A project on "Lung cancer", headed by anatomopathologist P. Hofman, to better exploit the joint information coming from imaging and circulating tumoral cells (in collaboration with Median Tech company); and a project "Cluster headache", headed by neurosurgeon D. Fontaine, to better integrate and exploit information coming from imaging, genetics and clinic (in collaboration with Inria Team Athena).