Machine learning for emerging infectious disease field responses.
Ontology highlight
ABSTRACT:
SUBMITTER: Chiu HR
PROVIDER: S-EPMC8748708 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:With the global spread of multidrug resistance in pathogenic microbes, infectious diseases emerge as a key public health concern of the recent time. Identification of host genes associated with infectious diseases will improve our understanding about the mechanisms behind their development and help to identify novel therapeutic targets. RESULTS:We developed a machine learning techniques-based classification approach to identify infectious disease-associated host genes by integrating sequence and protein interaction network features. Among different methods, Deep Neural Networks (DNN) model with 16 selected features for pseudo-amino acid composition (PAAC) and network properties achieved the highest accuracy of 86.33% with sensitivity of 85.61% and specificity of 86.57%. The DNN classifier also attained an accuracy of 83.33% on a blind dataset and a sensitivity of 83.1% on an independent dataset. Furthermore, to predict unknown infectious disease-associated host genes, we applied the proposed DNN model to all reviewed proteins from the database. Seventy-six out of 100 highly-predicted infectious disease-associated genes from our study were also found in experimentally-verified human-pathogen protein-protein interactions (PPIs). Finally, we validated the highly-predicted infectious disease-associated genes by disease and gene ontology enrichment analysis and found that many of them are shared by one or more of the other diseases, such as cancer, metabolic and immune related diseases. CONCLUSIONS:To the best of our knowledge, this is the first computational method to identify infectious disease-associated host genes. The proposed method will help large-scale prediction of host genes associated with infectious-diseases. However, our results indicated that for small datasets, advanced DNN-based method does not offer significant advantage over the simpler supervised machine learning techniques, such as Support Vector Machine (SVM) or Random Forest (RF) for the prediction of infectious disease-associated host genes. Significant overlap of infectious disease with cancer and metabolic disease on disease and gene ontology enrichment analysis suggests that these diseases perturb the functions of the same cellular signaling pathways and may be treated by drugs that tend to reverse these perturbations. Moreover, identification of novel candidate genes associated with infectious diseases would help us to explain disease pathogenesis further and develop novel therapeutics.
| S-EPMC6935192 | biostudies-literature
Project description:Aim. Alzheimer's disease (AD) is a chronic neurodegenerative disease. Recently, computer scientists have developed various methods for early detection based on computer vision and machine learning techniques. Method. In this study, we proposed a novel AD detection method by displacement field (DF) estimation between a normal brain and an AD brain. The DF was treated as the AD-related features, reduced by principal component analysis (PCA), and finally fed into three classifiers: support vector machine (SVM), generalized eigenvalue proximal SVM (GEPSVM), and twin SVM (TSVM). The 10-fold cross validation repeated 50 times. Results. The results showed the "DF + PCA + TSVM" achieved the accuracy of 92.75 ± 1.77, sensitivity of 90.56 ± 1.15, specificity of 93.37 ± 2.05, and precision of 79.61 ± 2.21. This result is better than or comparable with not only the other proposed two methods, but also ten state-of-the-art methods. Besides, our method discovers the AD is related to following brain regions disclosed in recent publications: Angular Gyrus, Anterior Cingulate, Cingulate Gyrus, Culmen, Cuneus, Fusiform Gyrus, Inferior Frontal Gyrus, Inferior Occipital Gyrus, Inferior Parietal Lobule, Inferior Semi-Lunar Lobule, Inferior Temporal Gyrus, Insula, Lateral Ventricle, Lingual Gyrus, Medial Frontal Gyrus, Middle Frontal Gyrus, Middle Occipital Gyrus, Middle Temporal Gyrus, Paracentral Lobule, Parahippocampal Gyrus, Postcentral Gyrus, Posterior Cingulate, Precentral Gyrus, Precuneus, Sub-Gyral, Superior Parietal Lobule, Superior Temporal Gyrus, Supramarginal Gyrus, and Uncus. Conclusion. The displacement filed is effective in detection of AD and related brain-regions.
| S-EPMC4579022 | biostudies-literature
Project description:We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential. The results are in excellent agreement with experimental data and results of full ab initio calculations.
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Project description:The complex, unpredictable nature of pathogen occurrence has required substantial efforts to accurately predict infectious diseases (IDs). With rising popularity of Machine Learning (ML) and Deep Learning (DL) techniques combined with their unique ability to uncover connections between large amounts of diverse data, we conducted a PRISMA systematic review to investigate advances in ID prediction for human and animal diseases using ML and DL. This review included the type of IDs modeled, ML and DL techniques utilized, geographical distribution, prediction tasks performed, input features utilized, spatial and temporal scales, error metrics used, computational efficiency, uncertainty quantification, and missing data handling methods. Among 237 relevant articles published between January 2001 and May 2021, highly contagious diseases in humans were most often represented, including COVID-19 (37.1%), influenza/influenza-like illnesses (9.3%), dengue (8.9%), and malaria (5.1%). Out of 37 diseases identified, 51.4% were zoonotic, 37.8% were human-only, and 8.1% were animal-only, with only 1.6% economically significant, non-zoonotic livestock diseases. Despite the number of zoonoses, 86.5% of articles modeled humans whereas only a few articles (5.1%) contained more than one host species. Eastern Asia (32.5%), North America (17.7%), and Southern Asia (13.1%) were the most represented locations. Frequent approaches included tree-based ML (38.4%) and feed-forward neural networks (26.6%). Articles predicted temporal incidence (66.7%), disease risk (38.0%), and/or spatial movement (31.2%). Less than 10% of studies addressed uncertainty quantification, computational efficiency, and missing data, which are essential to operational use and deployment. This study highlights trends and gaps in ML and DL for ID prediction, providing guidelines for future works to better support biopreparedness and response. To fully utilize ML and DL for improved ID forecasting, models should include the full disease ecology in a One-Health context, important food and agricultural diseases, underrepresented hotspots, and important metrics required for operational deployment.
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Project description:The increasing number of emerging infectious disease events that have spread internationally, such as severe acute respiratory syndrome (SARS) and the 2009 pandemic A/H1N1, highlight the need for improvements in global outbreak surveillance. It is expected that the proliferation of Internet-based reports has resulted in greater communication and improved surveillance and reporting frameworks, especially with the revision of the World Health Organization's (WHO) International Health Regulations (IHR 2005), which went into force in 2007. However, there has been no global quantitative assessment of whether and how outbreak detection and communication processes have actually changed over time. In this study, we analyzed the entire WHO public record of Disease Outbreak News reports from 1996 to 2009 to characterize spatial-temporal trends in the timeliness of outbreak discovery and public communication about the outbreak relative to the estimated outbreak start date. Cox proportional hazards regression analyses show that overall, the timeliness of outbreak discovery improved by 7.3% [hazard ratio (HR) = 1.073, 95% CI (1.038; 1.110)] per year, and public communication improved by 6.2% [HR = 1.062, 95% CI (1.028; 1.096)] per year. However, the degree of improvement varied by geographic region; the only WHO region with statistically significant (? = 0.05) improvement in outbreak discovery was the Western Pacific region [HR = 1.102 per year, 95% CI (1.008; 1.205)], whereas the Eastern Mediterranean [HR = 1.201 per year, 95% CI (1.066; 1.353)] and Western Pacific regions [HR = 1.119 per year, 95% CI (1.025; 1.221)] showed improvement in public communication. These findings provide quantitative historical assessment of timeliness in infectious disease detection and public reporting of outbreaks.
| S-EPMC3003006 | biostudies-literature
Project description:In the last decade, high-content screening based on multivariate single-cell imaging has been proven effective in drug discovery to evaluate drug-induced phenotypic variations. Unfortunately, this method inherently requires fluorescent labeling which has several drawbacks. Here we present a label-free method for evaluating cellular drug responses only by high-throughput bright-field imaging with the aid of machine learning algorithms. Specifically, we performed high-throughput bright-field imaging of numerous drug-treated and -untreated cells (N?=?~240,000) by optofluidic time-stretch microscopy with high throughput up to 10,000?cells/s and applied machine learning to the cell images to identify their morphological variations which are too subtle for human eyes to detect. Consequently, we achieved a high accuracy of 92% in distinguishing drug-treated and -untreated cells without the need for labeling. Furthermore, we also demonstrated that dose-dependent, drug-induced morphological change from different experiments can be inferred from the classification accuracy of a single classification model. Our work lays the groundwork for label-free drug screening in pharmaceutical science and industry.
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Project description:Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA) for another indication is a more rapid and less expensive option. In this study, we profile 80 FDA-approved and clinically tested drugs in neural cell cultures, with the goal of producing a ranked list of possible repurposing candidates.
2021-01-14 | GSE164788 | GEO
Project description:Emerging infectious diseases such as Ebola Virus Disease (EVD), Nipah Virus Encephalitis and Lassa fever pose significant epidemic threats. Responses to emerging infectious disease outbreaks frequently occur in resource-constrained regions and under high pressure to quickly contain the outbreak prior to potential spread. As seen in the 2020 EVD outbreaks in the Democratic Republic of Congo and the current COVID-19 pandemic, there is a continued need to evaluate and address the ethical challenges that arise in the high stakes environment of an emerging infectious disease outbreak response. The research presented here provides analysis of the ethical challenges with regard to allocation of limited resources, particularly experimental therapeutics, using the 2013-2016 EVD outbreak in West Africa as a case study. In-depth semi-structured interviews were conducted with senior healthcare personnel (n = 16) from international humanitarian aid organizations intimately engaged in the 2013-2016 EVD outbreak response in West Africa. Interviews were recorded in private setting, transcribed, and iteratively coded using grounded theory methodology. A majority of respondents indicated a clear propensity to adopt an ethical framework of guiding principles for international responses to emerging infectious disease outbreaks. Respondents agreed that prioritization of frontline workers' access to experimental therapeutics was warranted based on a principle of reciprocity. There was widespread acceptance of adaptive trial designs and greater trial transparency in providing access to experimental therapeutics. Many respondents also emphasized the importance of community engagement in limited resource allocation scheme design and culturally appropriate informed consent procedures. The study results inform a potential ethical framework of guiding principles based on the interview participants' insights to be adopted by international response organizations and their healthcare workers in the face of allocating limited resources such as experimental therapeutics in future emerging infectious disease outbreaks to ease the moral burden of individual healthcare providers.
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Project description:Tularemia is a bacterial disease of humans, wild, and domestic animals. Francisella tularensis, which is a Gram-negative coccobacillus-shaped bacterium, is the causative agent of tularemia. Recently, an increase in the number of human tularemia cases has been noticed in several countries around the world. It has been reported mostly from North America, several Scandinavian countries, and certain Asian countries. The disease spreads through vectors such as mosquitoes, horseflies, deer flies, and ticks. Humans can acquire the disease through direct contact of sick animals, consumption of infected animals, drinking or direct contact of contaminated water, and inhalation of bacteria-loaded aerosols. Low infectious dose, aerosol route of infection, and its ability to induce fatal disease make it a potential agent of biological warfare. Tularemia leads to several clinical forms, such as glandular, ulceroglandular, oculoglandular, oropharyngeal, respiratory, and typhoidal forms. The disease is diagnosed through the use of culture, serology, or molecular methods. Quinolones, tetracyclines, or aminoglycosides are frequently used in the treatment of tularemia. No licensed vaccine is available in the prophylaxis of tularemia and this is need of the time and high-priority research area. This review mostly focuses on general features, importance, current status, and preventive measures of this disease.
| S-EPMC7521936 | biostudies-literature
Project description:The disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has caused dramatic amphibian population declines and extinctions in Australia, Central and North America, and Europe. Bd is associated with >200 species extinctions of amphibians, but not all species that become infected are susceptible to the disease. Specifically, Bd has rapidly emerged in some areas of the world, such as in Australia, USA, and throughout Central and South America, causing population and species collapse. The mechanism behind the rapid global emergence of the disease is poorly understood, in part due to an incomplete picture of the global distribution of Bd. At present, there is a considerable amount of geographic bias in survey effort for Bd, with Asia being the most neglected continent. To date, Bd surveys have been published for few Asian countries, and infected amphibians have been reported only from Indonesia, South Korea, China and Japan. Thus far, there have been no substantiated reports of enigmatic or suspected disease-caused population declines of the kind that has been attributed to Bd in other areas. In order to gain a more detailed picture of the distribution of Bd in Asia, we undertook a widespread, opportunistic survey of over 3,000 amphibians for Bd throughout Asia and adjoining Papua New Guinea. Survey sites spanned 15 countries, approximately 36° latitude, 111° longitude, and over 2000 m in elevation. Bd prevalence was very low throughout our survey area (2.35% overall) and infected animals were not clumped as would be expected in epizootic events. This suggests that Bd is either newly emerging in Asia, endemic at low prevalence, or that some other ecological factor is preventing Bd from fully invading Asian amphibians. The current observed pattern in Asia differs from that in many other parts of the world.
| S-EPMC3156717 | biostudies-literature