Using artificial intelligence techniques for COVID-19 genome analysis
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ABSTRACT:
SUBMITTER: Nawaz M
PROVIDER: S-EPMC7888282 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We aimed to develop a prediction model for intensive care unit (ICU) hospitalization of Coronavirus disease-19 (COVID-19) patients using artificial neural networks (ANN). We assessed 25 laboratory parameters at first from 248 consecutive adult COVID-19 patients for database creation, training, and development of ANN models. We developed a new alpha-index to assess association of each parameter with outcome. We used 166 records for training of computational simulations (training), 41 for documentation of computational simulations (validation), and 41 for reliability check of computational simulations (testing). The first five laboratory indices ranked by importance were Neutrophil-to-lymphocyte ratio, Lactate Dehydrogenase, Fibrinogen, Albumin, and D-Dimers. The best ANN based on these indices achieved accuracy 95.97%, precision 90.63%, sensitivity 93.55%. and F1-score 92.06%, verified in the validation cohort. Our preliminary findings reveal for the first time an ANN to predict ICU hospitalization accurately and early, using only 5 easily accessible laboratory indices.
| S-EPMC9797218 | biostudies-literature
Project description:In late December 2019, a new type of coronavirus was discovered, which was later named severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). Since its discovery, the virus has spread globally, with 2,975,875 deaths as of 15 April 2021, and has had a huge impact on our health systems and economy. How to suppress the continued spread of new coronary pneumonia is the main task of many scientists and researchers. The introduction of artificial intelligence technology has provided a huge contribution to the suppression of the new coronavirus. This article discusses the main application of artificial intelligence technology in the suppression of coronavirus from three major aspects of identification, prediction, and development through a large amount of literature research, and puts forward the current main challenges and possible development directions. The results show that it is an effective measure to combine artificial intelligence technology with a variety of new technologies to predict and identify COVID-19 patients.
| S-EPMC8720541 | biostudies-literature
Project description:BackgroundThe COVID-19 outbreak has spread rapidly and hospitals are overwhelmed with COVID-19 patients. While analysis of nasal and throat swabs from patients is the main way to detect COVID-19, analyzing chest images could offer an alternative method to hospitals, where health care personnel and testing kits are scarce. Deep learning (DL), in particular, has shown impressive levels of performance when analyzing medical images, including those related to COVID-19 pneumonia.ObjectiveThe goal of this study was to perform a systematic review with a meta-analysis of relevant studies to quantify the performance of DL algorithms in the automatic stratification of COVID-19 patients using chest images.MethodsA search strategy for use in PubMed, Scopus, Google Scholar, and Web of Science was developed, where we searched for articles published between January 1 and April 25, 2020. We used the key terms "COVID-19," or "coronavirus," or "SARS-CoV-2," or "novel corona," or "2019-ncov," and "deep learning," or "artificial intelligence," or "automatic detection." Two authors independently extracted data on study characteristics, methods, risk of bias, and outcomes. Any disagreement between them was resolved by consensus.ResultsA total of 16 studies were included in the meta-analysis, which included 5896 chest images from COVID-19 patients. The pooled sensitivity and specificity of the DL models in detecting COVID-19 were 0.95 (95% CI 0.94-0.95) and 0.96 (95% CI 0.96-0.97), respectively, with an area under the receiver operating characteristic curve of 0.98. The positive likelihood, negative likelihood, and diagnostic odds ratio were 19.02 (95% CI 12.83-28.19), 0.06 (95% CI 0.04-0.10), and 368.07 (95% CI 162.30-834.75), respectively. The pooled sensitivity and specificity for distinguishing other types of pneumonia from COVID-19 were 0.93 (95% CI 0.92-0.94) and 0.95 (95% CI 0.94-0.95), respectively. The performance of radiologists in detecting COVID-19 was lower than that of the DL models; however, the performance of junior radiologists was improved when they used DL-based prediction tools.ConclusionsOur study findings show that DL models have immense potential in accurately stratifying COVID-19 patients and in correctly differentiating them from patients with other types of pneumonia and normal patients. Implementation of DL-based tools can assist radiologists in correctly and quickly detecting COVID-19 and, consequently, in combating the COVID-19 pandemic.
| S-EPMC8086786 | biostudies-literature
Project description:The application of artificial intelligence (AI) to health has increased, including to COVID-19. This study aimed to provide a clear overview of COVID-19-related AI publication trends using longitudinal bibliometric analysis. A systematic literature search was conducted on the Web of Science for English language peer-reviewed articles related to AI application to COVID-19. A search strategy was developed to collect relevant articles and extracted bibliographic information (e.g., country, research area, sources, and author). VOSviewer (Leiden University) and Bibliometrix (R package) were used to visualize the co-occurrence networks of authors, sources, countries, institutions, global collaborations, citations, co-citations, and keywords. We included 729 research articles on the application of AI to COVID-19 published between 2020 and 2021. PLOS One (33/729, 4.52%), Chaos Solution Fractals (29/729, 3.97%), and Journal of Medical Internet Research (29/729, 3.97%) were the most common journals publishing these articles. The Republic of China (190/729, 26.06%), the USA (173/729, 23.73%), and India (92/729, 12.62%) were the most prolific countries of origin. The Huazhong University of Science and Technology, Wuhan University, and the Chinese Academy of Sciences were the most productive institutions. This is the first study to show a comprehensive picture of the global efforts to address COVID-19 using AI. The findings of this study also provide insights and research directions for academic researchers, policymakers, and healthcare practitioners who wish to collaborate in these domains in the future.
| S-EPMC8070493 | biostudies-literature
Project description:Recent studies show the potential of artificial intelligence (AI) as a screening tool to detect COVID-19 pneumonia based on chest x-ray (CXR) images. However, issues on the datasets and study designs from medical and technical perspectives, as well as questions on the vulnerability and robustness of AI algorithms have emerged. In this study, we address these issues with a more realistic development of AI-driven COVID-19 pneumonia detection models by generating our own data through a retrospective clinical study to augment the dataset aggregated from external sources. We optimized five deep learning architectures, implemented development strategies by manipulating data distribution to quantitatively compare study designs, and introduced several detection scenarios to evaluate the robustness and diagnostic performance of the models. At the current level of data availability, the performance of the detection model depends on the hyperparameter tuning and has less dependency on the quantity of data. InceptionV3 attained the highest performance in distinguishing pneumonia from normal CXR in two-class detection scenario with sensitivity (Sn), specificity (Sp), and positive predictive value (PPV) of 96%. The models attained higher general performance of 91-96% Sn, 94-98% Sp, and 90-96% PPV in three-class compared to four-class detection scenario. InceptionV3 has the highest general performance with accuracy, F1-score, and g-mean of 96% in the three-class detection scenario. For COVID-19 pneumonia detection, InceptionV3 attained the highest performance with 86% Sn, 99% Sp, and 91% PPV with an AUC of 0.99 in distinguishing pneumonia from normal CXR. Its capability of differentiating COVID-19 pneumonia from normal and non-COVID-19 pneumonia attained 0.98 AUC and a micro-average of 0.99 for other classes.
| S-EPMC8516252 | biostudies-literature
Project description:One key task in the early fight against the COVID-19 pandemic was to plan non-pharmaceutical interventions to reduce the spread of the infection while limiting the burden on the society and economy. With more data on the pandemic being generated, it became possible to model both the infection trends and intervention costs, transforming the creation of an intervention plan into a computational optimization problem. This paper proposes a framework developed to help policy-makers plan the best combination of non-pharmaceutical interventions and to change them over time. We developed a hybrid machine-learning epidemiological model to forecast the infection trends, aggregated the socio-economic costs from the literature and expert knowledge, and used a multi-objective optimization algorithm to find and evaluate various intervention plans. The framework is modular and easily adjustable to a real-world situation, it is trained and tested on data collected from almost all countries in the world, and its proposed intervention plans generally outperform those used in real life in terms of both the number of infections and intervention costs.
| S-EPMC9970257 | biostudies-literature
Project description:BackgroundUntil now, there are still a limited number of resources available to predict and diagnose COVID-19 disease. The design of novel drug-drug interaction for COVID-19 patients is an open area of research. Also, the development of the COVID-19 rapid testing kits is still a challenging task.MethodologyThis review focuses on two prime challenges caused by urgent needs to effectively address the challenges of the COVID-19 pandemic, i.e., the development of COVID-19 classification tools and drug discovery models for COVID-19 infected patients with the help of artificial intelligence (AI) based techniques such as machine learning and deep learning models.ResultsIn this paper, various AI-based techniques are studied and evaluated by the means of applying these techniques for the prediction and diagnosis of COVID-19 disease. This study provides recommendations for future research and facilitates knowledge collection and formation on the application of the AI techniques for dealing with the COVID-19 epidemic and its consequences.ConclusionsThe AI techniques can be an effective tool to tackle the epidemic caused by COVID-19. These may be utilized in four main fields such as prediction, diagnosis, drug design, and analyzing social implications for COVID-19 infected patients.
| S-EPMC8176528 | biostudies-literature
Project description:Drug repurposing or repositioning is a technique whereby existing drugs are used to treat emerging and challenging diseases, including COVID-19. Drug repurposing has become a promising approach because of the opportunity for reduced development timelines and overall costs. In the big data era, artificial intelligence (AI) and network medicine offer cutting-edge application of information science to defining disease, medicine, therapeutics, and identifying targets with the least error. In this Review, we introduce guidelines on how to use AI for accelerating drug repurposing or repositioning, for which AI approaches are not just formidable but are also necessary. We discuss how to use AI models in precision medicine, and as an example, how AI models can accelerate COVID-19 drug repurposing. Rapidly developing, powerful, and innovative AI and network medicine technologies can expedite therapeutic development. This Review provides a strong rationale for using AI-based assistive tools for drug repurposing medications for human disease, including during the COVID-19 pandemic.
| S-EPMC7500917 | biostudies-literature
Project description:BackgroundThe coronavirus disease (COVID-19) pandemic led to substantial public discussion. Understanding these discussions can help institutions, governments, and individuals navigate the pandemic.ObjectiveThe aim of this study is to analyze discussions on Twitter related to COVID-19 and to investigate the sentiments toward COVID-19.MethodsThis study applied machine learning methods in the field of artificial intelligence to analyze data collected from Twitter. Using tweets originating exclusively in the United States and written in English during the 1-month period from March 20 to April 19, 2020, the study examined COVID-19-related discussions. Social network and sentiment analyses were also conducted to determine the social network of dominant topics and whether the tweets expressed positive, neutral, or negative sentiments. Geographic analysis of the tweets was also conducted.ResultsThere were a total of 14,180,603 likes, 863,411 replies, 3,087,812 retweets, and 641,381 mentions in tweets during the study timeframe. Out of 902,138 tweets analyzed, sentiment analysis classified 434,254 (48.2%) tweets as having a positive sentiment, 187,042 (20.7%) as neutral, and 280,842 (31.1%) as negative. The study identified 5 dominant themes among COVID-19-related tweets: health care environment, emotional support, business economy, social change, and psychological stress. Alaska, Wyoming, New Mexico, Pennsylvania, and Florida were the states expressing the most negative sentiment while Vermont, North Dakota, Utah, Colorado, Tennessee, and North Carolina conveyed the most positive sentiment.ConclusionsThis study identified 5 prevalent themes of COVID-19 discussion with sentiments ranging from positive to negative. These themes and sentiments can clarify the public's response to COVID-19 and help officials navigate the pandemic.
| S-EPMC7438102 | biostudies-literature
Project description:BackgroundThe sublingual microcirculation presumably exhibits disease-specific changes in function and morphology. Algorithm-based quantification of functional microcirculatory hemodynamic variables in handheld vital microscopy (HVM) has recently allowed identification of hemodynamic alterations in the microcirculation associated with COVID-19. In the present study we hypothesized that supervised deep machine learning could be used to identify previously unknown microcirculatory alterations, and combination with algorithmically quantified functional variables increases the model's performance to differentiate critically ill COVID-19 patients from healthy volunteers.MethodsFour international, multi-central cohorts of critically ill COVID-19 patients and healthy volunteers (n = 59/n = 40) were used for neuronal network training and internal validation, alongside quantification of functional microcirculatory hemodynamic variables. Independent verification of the models was performed in a second cohort (n = 25/n = 33).ResultsSix thousand ninety-two image sequences in 157 individuals were included. Bootstrapped internal validation yielded AUROC(CI) for detection of COVID-19 status of 0.75 (0.69-0.79), 0.74 (0.69-0.79) and 0.84 (0.80-0.89) for the algorithm-based, deep learning-based and combined models. Individual model performance in external validation was 0.73 (0.71-0.76) and 0.61 (0.58-0.63). Combined neuronal network and algorithm-based identification yielded the highest externally validated AUROC of 0.75 (0.73-0.78) (P < 0.0001 versus internal validation and individual models).ConclusionsWe successfully trained a deep learning-based model to differentiate critically ill COVID-19 patients from heathy volunteers in sublingual HVM image sequences. Internally validated, deep learning was superior to the algorithmic approach. However, combining the deep learning method with an algorithm-based approach to quantify the functional state of the microcirculation markedly increased the sensitivity and specificity as compared to either approach alone, and enabled successful external validation of the identification of the presence of microcirculatory alterations associated with COVID-19 status.
| S-EPMC9568900 | biostudies-literature