RESUMEN
This research aims to review and evaluate the most relevant scientific studies about deep learning (DL) models in the omics field. It also aims to realize the potential of DL techniques in omics data analysis fully by demonstrating this potential and identifying the key challenges that must be addressed. Numerous elements are essential for comprehending numerous studies by surveying the existing literature. For example, the clinical applications and datasets from the literature are essential elements. The published literature highlights the difficulties encountered by other researchers. In addition to looking for other studies, such as guidelines, comparative studies, and review papers, a systematic approach is used to search all relevant publications on omics and DL using different keyword variants. From 2018 to 2022, the search procedure was conducted on four Internet search engines: IEEE Xplore, Web of Science, ScienceDirect, and PubMed. These indexes were chosen because they offer enough coverage and linkages to numerous papers in the biological field. A total of 65 articles were added to the final list. The inclusion and exclusion criteria were specified. Of the 65 publications, 42 are clinical applications of DL in omics data. Furthermore, 16 out of 65 articles comprised the review publications based on single- and multi-omics data from the proposed taxonomy. Finally, only a small number of articles (7/65) were included in papers focusing on comparative analysis and guidelines. The use of DL in studying omics data presented several obstacles related to DL itself, preprocessing procedures, datasets, model validation, and testbed applications. Numerous relevant investigations were performed to address these issues. Unlike other review papers, our study distinctly reflects different observations on omics with DL model areas. We believe that the result of this study can be a useful guideline for practitioners who look for a comprehensive view of the role of DL in omics data analysis.
RESUMEN
Biomarkers including fasting blood sugar, heart rate, electrocardiogram (ECG), blood pressure, etc. are essential in the heart disease (HD) diagnosing. Using wearable sensors, these measures are collected and applied as inputs to a deep learning (DL) model for HD diagnosis. However, it is observed that model accuracy weakens when the data gathered are scarce or imbalanced. Therefore, this work proposes two DL-based frameworks, GAN-1D-CNN, and GAN-Bi-LSTM. These frameworks contain: (1) a generative adversarial network (GAN) and (2) a one-dimensional convolutional neural network (1D-CNN) or bi-directional long short-term memory (Bi-LSTM). The GAN model is utilized to augment the small and imbalanced dataset, which is the Cleveland dataset. The 1D-CNN and Bi-LSTM models are then trained using the enlarged dataset to diagnose HD. Unlike previous works, the proposed frameworks increase the dataset first to avoid the prediction bias caused by the limited data. The GAN-1D-CNN achieved 99.1% accuracy, specificity, sensitivity, F1-score, and 100% area under the curve (AUC). Similarly, the GAN-Bi-LSTM obtained 99.3% accuracy, 99.2% specificity, 99.3% sensitivity, 99.2% F1-score, and 100% AUC. Furthermore, time complexity of proposed frameworks is investigated with and without principal component analysis (PCA). The PCA method reduced prediction times for 61 samples using GAN-1D-CNN and GAN-Bi-LSTM to 68.8 and 74.8 ms, respectively. These results show that it is reliable to use our frameworks for augmenting limited data and predicting heart disease.
RESUMEN
Effective prioritization plays critical roles in precision medicine. Healthcare decisions are complex, involving trade-offs among numerous frequently contradictory priorities. Considering the numerous difficulties associated with COVID-19, approaches that could triage COVID-19 patients may help in prioritizing treatment and provide precise medicine for those who are at risk of serious disease. Prioritizing a patient with COVID-19 depends on a variety of examination criteria, but due to the large number of these biomarkers, it may be hard for medical practitioners and emergency systems to decide which cases should be given priority for treatment. The aim of this paper is to propose a Multidimensional Examination Framework (MEF) for the prioritization of COVID-19 severe patients on the basis of combined multi-criteria decision-making (MCDM) methods. In contrast to the existing literature, the MEF has not considered only a single dimension of the examination factors; instead, the proposed framework included different multidimensional examination criteria such as demographic, laboratory findings, vital signs, symptoms, and chronic conditions. A real dataset that consists of data from 78 patients with different examination criteria was used as a base in the construction of Multidimensional Evaluation Matrix (MEM). The proposed framework employs the CRITIC (CRiteria Importance Through Intercriteria Correlation) method to identify objective weights and importance for multidimensional examination criteria. Furthermore, the VIKOR (VIekriterijumsko KOmpromisno Rangiranje) method is utilized to prioritize COVID-19 severe patients. The results based on the CRITIC method showed that the most important examination criterion for prioritization is COVID-19 patients with heart disease, followed by cough and nasal congestion symptoms. Moreover, the VIKOR method showed that Patients 8, 3, 9, 59, and 1 are the most urgent cases that required the highest priority among the other 78 patients. Finally, the proposed framework can be used by medical organizations to prioritize the most critical COVID-19 patient that has multidimensional examination criteria and to promptly give appropriate care for more precise medicine.