Michel Salomon

Alain Lalande, Zhihao Chen, Thibaut Pommier et al.

A key factor for assessing the state of the heart after myocardial infarction (MI) is to measure whether the myocardium segment is viable after reperfusion or revascularization therapy. Delayed enhancement-MRI or DE-MRI, which is performed several minutes after injection of the contrast agent, provides high contrast between viable and nonviable myocardium and is therefore a method of choice to evaluate the extent of MI. To automatically assess myocardial status, the results of the EMIDEC challenge that focused on this task are presented in this paper. The challenge's main objectives were twofold. First, to evaluate if deep learning methods can distinguish between normal and pathological cases. Second, to automatically calculate the extent of myocardial infarction. The publicly available database consists of 150 exams divided into 50 cases with normal MRI after injection of a contrast agent and 100 cases with myocardial infarction (and then with a hyperenhanced area on DE-MRI), whatever their inclusion in the cardiac emergency department. Along with MRI, clinical characteristics are also provided. The obtained results issued from several works show that the automatic classification of an exam is a reachable task (the best method providing an accuracy of 0.92), and the automatic segmentation of the myocardium is possible. However, the segmentation of the diseased area needs to be improved, mainly due to the small size of these areas and the lack of contrast with the surrounding structures.

Jean-Francois Couchot, Raphaël Couturier, Michel Salomon

Conventional state-of-the-art image steganalysis approaches usually consist of a classifier trained with features provided by rich image models. As both features extraction and classification steps are perfectly embodied in the deep learning architecture called Convolutional Neural Network (CNN), different studies have tried to design a CNN-based steganalyzer. The network designed by Xu et al. is the first competitive CNN with the combination Spatial Rich Models (SRM) and Ensemble Classifier (EC) providing detection performances of the same order. In this work we propose a criterion to choose either the CNN or the SRM+EC method for a given input image. Our approach is studied with three different steganographic spatial domain algorithms: S-UNIWARD, MiPOD, and HILL, using the Tensorflow computing platform, and exhibits detection capabilities better than each method alone. Furthermore, as SRM+EC and the CNN are both only trained with a single embedding algorithm, namely MiPOD, the proposed method can be seen as an approach for blind steganalysis. In blind detection, error rates are respectively of 16% for S-UNIWARD, 16% for MiPOD, and 17% for HILL on the BOSSBase with a payload of 0.4 bpp. For 0.1 bpp, the respective corresponding error rates are of 39%, 38%, and 41%, and are always better than the ones provided by SRM+EC.

Bassam AlKindy, Bashar Al-Nuaimi, Christophe Guyeux et al.

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of problematic genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur the phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained provided such a number of blurring genes is reduced. The problem is thus to determine the largest subset of core genes that produces the best-supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a distributed Binary Particle Swarm Optimization (BPSO) is proposed in sequential and distributed fashions. Obtained results from both versions of the BPSO are compared with those computed using an hybrid approach embedding both genetic algorithms and statistical tests. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.

Jacques M. Bahi, Jean-François Couchot, Christophe Guyeux et al.

Many research works deal with chaotic neural networks for various fields of application. Unfortunately, up to now these networks are usually claimed to be chaotic without any mathematical proof. The purpose of this paper is to establish, based on a rigorous theoretical framework, an equivalence between chaotic iterations according to Devaney and a particular class of neural networks. On the one hand we show how to build such a network, on the other hand we provide a method to check if a neural network is a chaotic one. Finally, the ability of classical feedforward multilayer perceptrons to learn sets of data obtained from a dynamical system is regarded. Various Boolean functions are iterated on finite states. Iterations of some of them are proven to be chaotic as it is defined by Devaney. In that context, important differences occur in the training process, establishing with various neural networks that chaotic behaviors are far more difficult to learn.

Jean-François Couchot, Raphaël Couturier, Christophe Guyeux et al.

For the past few years, in the race between image steganography and steganalysis, deep learning has emerged as a very promising alternative to steganalyzer approaches based on rich image models combined with ensemble classifiers. A key knowledge of image steganalyzer, which combines relevant image features and innovative classification procedures, can be deduced by a deep learning approach called Convolutional Neural Networks (CNN). These kind of deep learning networks is so well-suited for classification tasks based on the detection of variations in 2D shapes that it is the state-of-the-art in many image recognition problems. In this article, we design a CNN-based steganalyzer for images obtained by applying steganography with a unique embedding key. This one is quite different from the previous study of {\em Qian et al.} and its successor, namely {\em Pibre et al.} The proposed architecture embeds less convolutions, with much larger filters in the final convolutional layer, and is more general: it is able to deal with larger images and lower payloads. For the "same embedding key" scenario, our proposal outperforms all other steganalyzers, in particular the existing CNN-based ones, and defeats many state-of-the-art image steganography schemes.

Bassam AlKindy, Christophe Guyeux, Jean-François Couchot et al.

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of problematic genes is low, the problem being to determine the largest subset of core genes that produces the best supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, we propose an hybrid approach that embeds both genetic algorithms and statistical tests. Given a set of organisms, the result is a pipeline of many stages for the production of well supported phylogenetic trees. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.

Bassam AlKindy, Christophe Guyeux, Jean-François Couchot et al.

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.