Abel Díaz Berenguer

Luuk H. Boulogne, Julian Lorenz, Daniel Kienzle et al.

Challenges drive the state-of-the-art of automated medical image analysis. The quantity of public training data that they provide can limit the performance of their solutions. Public access to the training methodology for these solutions remains absent. This study implements the Type Three (T3) challenge format, which allows for training solutions on private data and guarantees reusable training methodologies. With T3, challenge organizers train a codebase provided by the participants on sequestered training data. T3 was implemented in the STOIC2021 challenge, with the goal of predicting from a computed tomography (CT) scan whether subjects had a severe COVID-19 infection, defined as intubation or death within one month. STOIC2021 consisted of a Qualification phase, where participants developed challenge solutions using 2000 publicly available CT scans, and a Final phase, where participants submitted their training methodologies with which solutions were trained on CT scans of 9724 subjects. The organizers successfully trained six of the eight Final phase submissions. The submitted codebases for training and running inference were released publicly. The winning solution obtained an area under the receiver operating characteristic curve for discerning between severe and non-severe COVID-19 of 0.815. The Final phase solutions of all finalists improved upon their Qualification phase solutions.HSUXJM-TNZF9CHSUXJM-TNZF9C

Abel Díaz Berenguer, Tanmoy Mukherjee, Matias Bossa et al.

Successful data representation is a fundamental factor in machine learning based medical imaging analysis. Deep Learning (DL) has taken an essential role in robust representation learning. However, the inability of deep models to generalize to unseen data can quickly overfit intricate patterns. Thereby, we can conveniently implement strategies to aid deep models in discovering useful priors from data to learn their intrinsic properties. Our model, which we call a dual role network (DRN), uses a dependency maximization approach based on Least Squared Mutual Information (LSMI). The LSMI leverages dependency measures to ensure representation invariance and local smoothness. While prior works have used information theory measures like mutual information, known to be computationally expensive due to a density estimation step, our LSMI formulation alleviates the issues of intractable mutual information estimation and can be used to approximate it. Experiments on CT based COVID-19 Detection and COVID-19 Severity Detection benchmarks demonstrate the effectiveness of our method.

Abel Díaz Berenguer, Hichem Sahli, Boris Joukovsky et al.

Our motivating application is a real-world problem: COVID-19 classification from CT imaging, for which we present an explainable Deep Learning approach based on a semi-supervised classification pipeline that employs variational autoencoders to extract efficient feature embedding. We have optimized the architecture of two different networks for CT images: (i) a novel conditional variational autoencoder (CVAE) with a specific architecture that integrates the class labels inside the encoder layers and uses side information with shared attention layers for the encoder, which make the most of the contextual clues for representation learning, and (ii) a downstream convolutional neural network for supervised classification using the encoder structure of the CVAE. With the explainable classification results, the proposed diagnosis system is very effective for COVID-19 classification. Based on the promising results obtained qualitatively and quantitatively, we envisage a wide deployment of our developed technique in large-scale clinical studies.Code is available at https://git.etrovub.be/AVSP/ct-based-covid-19-diagnostic-tool.git.