New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.

BACKGROUND: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. RESULTS: In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. CONCLUSIONS: The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.

SARS-CoV-2 virus classification based on stacked sparse autoencoder.

Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infection diagnosis, metagenomics, phylogenetics, and analysis. Considering that motivation, the authors proposed an efficient viral genome classifier for the SARS-CoV-2 using the deep neural network based on the stacked sparse autoencoder (SSAE). For the best performance of the model, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a classification of the SARS-CoV-2. For that, a dataset based on k-mers image representation was applied. We performed four experiments to provide different levels of taxonomic classification of the SARS-CoV-2. The SSAE technique provided great performance results in all experiments, achieving classification accuracy between 92% and 100% for the validation set and between 98.9% and 100% when the SARS-CoV-2 samples were applied for the test set. In this work, samples of the SARS-CoV-2 were not used during the training process, only during subsequent tests, in which the model was able to infer the correct classification of the samples in the vast majority of cases. This indicates that our model can be adapted to classify other emerging viruses. Finally, the results indicated the applicability of this deep learning technique in genome classification problems.

Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification.

COVID-19, the illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus belonging to the Coronaviridade family, a single-strand positive-sense RNA genome, has been spreading around the world and has been declared a pandemic by the World Health Organization. On 17 January 2022, there were more than 329 million cases, with more than 5.5 million deaths. Although COVID-19 has a low mortality rate, its high capacities for contamination, spread, and mutation worry the authorities, especially after the emergence of the Omicron variant, which has a high transmission capacity and can more easily contaminate even vaccinated people. Such outbreaks require elucidation of the taxonomic classification and origin of the virus (SARS-CoV-2) from the genomic sequence for strategic planning, containment, and treatment of the disease. Thus, this work proposes a high-accuracy technique to classify viruses and other organisms from a genome sequence using a deep learning convolutional neural network (CNN). Unlike the other literature, the proposed approach does not limit the length of the genome sequence. The results show that the novel proposal accurately distinguishes SARS-CoV-2 from the sequences of other viruses. The results were obtained from 1557 instances of SARS-CoV-2 from the National Center for Biotechnology Information (NCBI) and 14,684 different viruses from the Virus-Host DB. As a CNN has several changeable parameters, the tests were performed with forty-eight different architectures; the best of these had an accuracy of 91.94 ± 2.62% in classifying viruses into their realms correctly, in addition to 100% accuracy in classifying SARS-CoV-2 into its respective realm, Riboviria. For the subsequent classifications (family, genera, and subgenus), this accuracy increased, which shows that the proposed architecture may be viable in the classification of the virus that causes COVID-19.

Unsupervised Learning Applied to the Stratification of Preterm Birth Risk in Brazil with Socioeconomic Data.

Preterm birth (PTB) is a phenomenon that brings risks and challenges for the survival of the newborn child. Despite many advances in research, not all the causes of PTB are already clear. It is understood that PTB risk is multi-factorial and can also be associated with socioeconomic factors. Thereby, this article seeks to use unsupervised learning techniques to stratify PTB risk in Brazil using only socioeconomic data. Through the use of datasets made publicly available by the Federal Government of Brazil, a new dataset was generated with municipality-level socioeconomic data and a PTB occurrence rate. This dataset was processed using various unsupervised learning techniques, such as k-means, principal component analysis (PCA), and density-based spatial clustering of applications with noise (DBSCAN). After validation, four clusters with high levels of PTB occurrence were discovered, as well as three with low levels. The clusters with high PTB were comprised mostly of municipalities with lower levels of education, worse quality of public services-such as basic sanitation and garbage collection-and a less white population. The regional distribution of the clusters was also observed, with clusters of high PTB located mostly in the North and Northeast regions of Brazil. The results indicate a positive influence of the quality of life and the offer of public services on the reduction in PTB risk.

Lipid-Polymeric Films: Composition, Production and Applications in Wound Healing and Skin Repair.

The use of lipids in the composition of polymeric-based films for topical administration of bioactive ingredients is a recent research topic; while few products are commercially available, films containing lipids represent a strategic area for the development of new products. Some lipids are usually used in polymeric-based film formulations due to their plasticizing action, with a view to improving the mechanical properties of these films. On the other hand, many lipids have healing, antimicrobial, anti-inflammatory, anti-aging properties, among others, that make them even more interesting for application in the medical-pharmaceutical field. This manuscript discusses the production methods of these films both on a laboratory and at industrial scales, the properties of the developed biopolymers, and their advantages for the development of dermatologic and cosmetic products.

Data stream dataset of SARS-CoV-2 genome.

As of May 25, 2020, the novel coronavirus disease (called COVID-19) spread to more than 185 countries/regions with more than 348,000 deaths and more than 5,550,000 confirmed cases. In the bioinformatics area, one of the crucial points is the analysis of the virus nucleotide sequences using approaches such as data stream techniques and algorithms. However, to make feasible this approach, it is necessary to transform the nucleotide sequences string to numerical stream representation. Thus, the dataset provides four kinds of data stream representation (DSR) of SARS-CoV-2 virus nucleotide sequences. The dataset provides the DSR of 1557 instances of SARS-CoV-2 virus, 11540 other instances of other viruses from the Virus-Host DB dataset, and three instances of Riboviria viruses from NCBI (Betacoronavirus RaTG13, bat-SL-CoVZC45, and bat-SL-CoVZXC21).

Proposal of the CAD System for Melanoma Detection Using Reconfigurable Computing.

This work proposes dedicated hardware to real-time cancer detection using Field-Programmable Gate Arrays (FPGA). The presented hardware combines a Multilayer Perceptron (MLP) Artificial Neural Networks (ANN) with Digital Image Processing (DIP) techniques. The DIP techniques are used to extract the features from the analyzed skin, and the MLP classifies the lesion into melanoma or non-melanoma. The classification results are validated with an open-access database. Finally, analysis regarding execution time, hardware resources usage, and power consumption are performed. The results obtained through this analysis are then compared to an equivalent software implementation embedded in an ARM A9 microprocessor.

Chaos game representation dataset of SARS-CoV-2 genome.

As of April 16, 2020, the novel coronavirus disease (called COVID-19) spread to more than 185 countries/regions with more than 142,000 deaths and more than 2,000,000 confirmed cases. In the bioinformatics area, one of the crucial points is the analysis of the virus nucleotide sequences using approaches such as data stream, digital signal processing, and machine learning techniques and algorithms. However, to make feasible this approach, it is necessary to transform the nucleotide sequences string to numerical values representation. Thus, the dataset provides a chaos game representation (CGR) of SARS-CoV-2 virus nucleotide sequences. The dataset provides the CGR of 100 instances of SARS-CoV-2 virus, 11540 instances of other viruses from the Virus-Host DB dataset, and three instances of Riboviria viruses from NCBI (Betacoronavirus RaTG13, bat-SL-CoVZC45, and bat-SL-CoVZXC21).