Category Archives: Journals

BB-UNet: U-Net with Bounding Box Prior (in IEEE Journal of Selected Topics in Signal Processing 2020)

By Rosana El Jurdi, Caroline Petitjean, Paul Honeine, Fahed Abdallah.

in IEEE Journal of Selected Topics in Signal Processing, 14(6): 1189-1198. October 2020.

BB-UNet: U-Net with Bounding Box Prior [pdf] paper   doi:10.1109/JSTSP.2020.3001502

Abstract. Medical image segmentation is the process of anatomically isolating organs for analysis and treatment. Leading works within this domain emerged with the well-known U-Net. Despite its success, recent works have shown the limitations of U-Net to conduct segmentation given image particularities such as noise, corruption or lack of contrast. Prior knowledge integration allows to overcome segmentation ambiguities. This paper introduces BB-UNet (Bounding Box U-Net), a deep learning model that integrates location as well as shape prior onto model training. The proposed model is inspired by U-Net and incorporates priors through a novel convolutional layer introduced at the level of skip connections. The proposed architecture helps in presenting attention kernels onto the neural training in order to guide the model on where to look for the organs. Moreover, it fine-tunes the encoder layers based on positional constraints. The proposed model is exploited within two main paradigms: as a solo model given a fully supervised framework and as an ancillary model, in a weakly supervised setting. In the current experiments, manual bounding boxes are fed at inference and as such BB-Unet is exploited in a semi-automatic setting; however, BB-Unet has the potential of being part of a fully automated process, if it relies on a preliminary step of object detection. To validate the performance of the proposed model, experiments are conducted on two public datasets: the SegTHOR dataset which focuses on the segmentation of thoracic organs at risk in computed tomography (CT) images, and the Cardiac dataset which is a mono-modal MRI dataset released as part of the Decathlon challenge and dedicated to segmentation of the left atrium. Results show that the proposed method outperforms state-of-the-art methods in fully supervised learning frameworks and registers relevant results given the weakly supervised domain.

Interpretable time series kernel analytics by pre-image estimation (in Artificial Intelligence 2020)

by Thi Phuong Thao Tran, Ahlame Douzal-Chouakria, Saeed Varasteh Yazdi, Paul Honeine, Patrick Gallinari.

Paper published in Artificial Intelligence (Volume 286, September 2020, 103342):

Abstract. Kernel methods are known to be effective to analyse complex objects by implicitly embedding them into some feature space. To interpret and analyse the obtained results, it is often required to restore in the input space the results obtained in the feature space, by using pre-image estimation methods. This work proposes a new closed-form pre-image estimation method for time series kernel analytics that consists of two steps. In the first step, a time warp function, driven by distance constraints in the feature space, is defined to embed time series in a metric space where analytics can be performed conveniently. In the second step, the time series pre-image estimation is cast as learning a linear (or a nonlinear) transformation that ensures a local isometry between the time series embedding space and the feature space. The proposed method is compared to the state of the art through three major tasks that require pre-image estimation: 1) time series averaging, 2) time series reconstruction and denoising and 3) time series representation learning. The extensive experiments conducted on 33 publicly-available datasets show the benefits of the pre-image estimation for time series kernel analytics.