Assessment and classification of COVID-19 DNA sequence using pairwise features concatenation from multi-transformer and deep features with machine learning models.

The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such a major viral outbreak demands early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. The emerging global infectious COVID-19 disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. Due to the continued evolution of the SARS-CoV-2 pandemic, researchers worldwide are working to mitigate, suppress its spread, and better understand it by deploying deep learning and machine learning approaches. In a general computational context for biomedical data analysis, DNA sequence classification is a crucial challenge. Several machine and deep learning techniques have been used in recent years to complete this task with some success. The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art deep learning-based models are proposed using two DNA sequence conversion methods. We also proposed a novel multi-transformer deep learning model and pairwise features fusion technique for DNA sequence classification. Furthermore, deep features are extracted from the last layer of the multi-transformer and used in machine-learning models for DNA sequence classification. The k-mer and one-hot encoding sequence conversion techniques have been presented. The proposed multi-transformer achieved the highest performance in COVID DNA sequence classification. Automatic identification and classification of viruses are essential to avoid an outbreak like COVID-19. It also helps in detecting the effect of viruses and drug design.

3D-IncNet: Head and Neck (H&N) Primary Tumors Segmentation and Survival Prediction.

Cancer begins when healthy cells change and grow out of control, forming a mass called a tumor. Head and neck (H&N) cancers usually develop in or around the head and neck, including the mouth (oral cavity), nose and sinuses, throat (pharynx), and voice box (larynx). 4% of all cancers are H&N cancers with a very low survival rate (a five-year survival rate of 64.7%). FDG-PET/CT imaging is often used for early diagnosis and staging of H&N tumors, thus improving these patients' survival rates. This work presents a novel 3D-Inception-Residual aided with 3D depth-wise convolution and squeeze and excitation block. We introduce a 3D depth-wise convolution-inception encoder consisting of an additional 3D squeeze and excitation block and a 3D depth-wise convolution-based residual learning decoder (3D-IncNet), which not only helps to recalibrate the channel-wise features but adaptively through explicit inter-dependencies modeling but also integrate the coarse and fine features resulting in accurate tumor segmentation. We further demonstrate the effectiveness of inception-residual encoder-decoder architecture in achieving better dice scores and the impact of depth-wise convolution in lowering the computational cost. We applied random forest for survival prediction on deep, clinical, and radiomics features. Experiments are conducted on the benchmark HECKTOR21 challenge, which showed significantly better performance by surpassing the state-of-the-artwork and achieved 0.836 and 0.811 concordance index and dice scores, respectively. We made the model and code publicly available.

Placental vessel segmentation and registration in fetoscopy: Literature review and MICCAI FetReg2021 challenge findings.

Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to restore a physiological blood exchange among twins. The procedure is particularly challenging, from the surgeon's side, due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to amniotic fluid turbidity, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation of pathological anastomoses, resulting in persistent TTTS. Computer-assisted intervention (CAI) can provide TTTS surgeons with decision support and context awareness by identifying key structures in the scene and expanding the fetoscopic field of view through video mosaicking. Research in this domain has been hampered by the lack of high-quality data to design, develop and test CAI algorithms. Through the Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge, which was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge, we released the first large-scale multi-center TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms with a focus on creating drift-free mosaics from long duration fetoscopy videos. For this challenge, we released a dataset of 2060 images, pixel-annotated for vessels, tool, fetus and background classes, from 18 in-vivo TTTS fetoscopy procedures and 18 short video clips of an average length of 411 frames for developing placental scene segmentation and frame registration for mosaicking techniques. Seven teams participated in this challenge and their model performance was assessed on an unseen test dataset of 658 pixel-annotated images from 6 fetoscopic procedures and 6 short clips. For the segmentation task, overall baseline performed was the top performing (aggregated mIoU of 0.6763) and was the best on the vessel class (mIoU of 0.5817) while team RREB was the best on the tool (mIoU of 0.6335) and fetus (mIoU of 0.5178) classes. For the registration task, overall the baseline performed better than team SANO with an overall mean 5-frame SSIM of 0.9348. Qualitatively, it was observed that team SANO performed better in planar scenarios, while baseline was better in non-planner scenarios. The detailed analysis showed that no single team outperformed on all 6 test fetoscopic videos. The challenge provided an opportunity to create generalized solutions for fetoscopic scene understanding and mosaicking. In this paper, we present the findings of the FetReg2021 challenge, alongside reporting a detailed literature review for CAI in TTTS fetoscopy. Through this challenge, its analysis and the release of multi-center fetoscopic data, we provide a benchmark for future research in this field.

Fuzzy Model for the Automatic Recognition of Human Dendritic Cells.

Background and objective: Nowadays, foodborne illness is considered one of the most outgrowing diseases in the world, and studies show that its rate increases sharply each year. Foodborne illness is considered a public health problem which is caused by numerous factors, such as food intoxications, allergies, intolerances, etc. Mycotoxin is one of the food contaminants which is caused by various species of molds (or fungi), which, in turn, causes intoxications that can be chronic or acute. Thus, even low concentrations of Mycotoxin have a severely harmful impact on human health. It is, therefore, necessary to develop an assessment tool for evaluating their impact on the immune response. Recently, researchers have approved a new method of investigation using human dendritic cells, yet the analysis of the geometric properties of these cells is still visual. Moreover, this type of analysis is subjective, time-consuming, and difficult to perform manually. In this paper, we address the automation of this evaluation using image-processing techniques. Methods: Automatic classification approaches of microscopic dendritic cell images are developed to provide a fast and objective evaluation. The first proposed classifier is based on support vector machines (SVM) and Fisher's linear discriminant analysis (FLD) method. The FLD-SVM classifier does not provide satisfactory results due to the significant confusion between the inhibited cells on one hand, and the other two cell types (mature and immature) on the other hand. Then, another strategy was suggested to enhance dendritic cell recognition results that are emitted from microscopic images. This strategy is mainly based on fuzzy logic which allows us to consider the uncertainties and inaccuracies of the given data. Results: These proposed methods are tested on a real dataset consisting of 421 images of microscopic dendritic cells, where the fuzzy classification scheme efficiently improved the classification results by successfully classifying 96.77% of the dendritic cells. Conclusions: The fuzzy classification-based tools provide cell maturity and inhibition rates which help biologists evaluate severe health impacts caused by food contaminants.

Targeted Data Augmentation and Hierarchical Classification with Deep Learning for Fish Species Identification in Underwater Images.

In this paper, we address fish species identification in underwater video for marine monitoring applications such as the study of marine biodiversity. Video is the least disruptive monitoring method for fish but requires efficient techniques of image processing and analysis to overcome challenging underwater environments. We propose two Deep Convolutional Neural Network (CNN) approaches for fish species classification in unconstrained underwater environment. In the first approach, we use a traditional transfer learning framework and we investigate a new technique based on training/validation loss curves for targeted data augmentation. In the second approach, we propose a hierarchical CNN classification to classify fish first into family levels and then into species categories. To demonstrate the effectiveness of the proposed approaches, experiments are carried out on two benchmark datasets for automatic fish identification in unconstrained underwater environment. The proposed approaches yield accuracies of 99.86% and 81.53% on the Fish Recognition Ground-Truth dataset and LifeClef 2015 Fish dataset, respectively.

Automatic Human Dendritic Cells Segmentation Using K-Means Clustering and Chan-Vese Active Contour Model.

BACKGROUND AND OBJECTIVE: Nowadays, the number of pathologies related to food are multiplied. Mycotoxins are one of the most severe food contaminants that cause serious effects on the human health. Therefore, it is necessary to develop an assessment tool for evaluating their impact on the immune response. Recently, a new investigational method using human dendritic cells was endorsed by biologists. Nevertheless, analysis of the morphological features and the behavior of these cells remains merely visual. In addition, this manual analysis is difficult and time-consuming. Here, we focus mainly on automating the evaluation process by using advanced image processing technology. METHODS: An automatic segmentation approach of microscopic dendritic cell images is developed to provide a fast and objective evaluation. First, a combination of K-means clustering and mathematical morphology is used to detect dendritic cells. Second, a region-based Chan-Vese active contour model is used to segment the detected cells more precisely. Finally, dendritic cells are extracted by a filtering based on eccentricity measure. RESULTS: The proposed scheme is tested on an actual dataset containing 421 microscopic dendritic cell images. The experimental results show high conformity between the results of the proposed scheme and ground-truth elaborated by biological expert. Moreover, a comparative study with other state-of-art segmentation schemes demonstrates the efficiency of the proposed method. It gives the highest average accuracy rate (99.42 %) compared to recent studied approaches. CONCLUSIONS: The proposed image segmentation method for morphological analysis of dendrite inhibition can consistently be used as an assessment tool for biologists to facilitate the evaluation of serious health impacts of mycotoxins.

Geodesics-based image registration: applications to biological and medical images depicting concentric ring patterns.

In many biological or medical applications, images that contain sequences of shapes are common. The existence of high inter-individual variability makes their interpretation complex. In this paper, we address the computer-assisted interpretation of such images and we investigate how we can remove or reduce these image variabilities. The proposed approach relies on the development of an efficient image registration technique. We first show the inadequacy of state-of-the-art intensity-based and feature-based registration techniques for the considered image datasets. Then, we propose a robust variational method which benefits from the geometrical information present in this type of images. In the proposed non-rigid geodesics-based registration, the successive shapes are represented by a level-set representation, which we rely on to carry out the registration. The successive level sets are regarded as elements in a shape space and the corresponding matching is that of the optimal geodesic path. The proposed registration scheme is tested on synthetic and real images. The comparison against results of state-of-the-art methods proves the relevance of the proposed method for this type of images.