Using machine learning methods to determine a typology of patients with HIV-HCV infection to be treated with antivirals

Several European countries have established criteria for prioritising initiation of treatment in patients infected with the hepatitis C virus (HCV) by grouping patients according to clinical characteristics. Based on neural network techniques, our objective was to identify those factors for HIV/HCV co-infected patients (to which clinicians have given careful consideration before treatment uptake) that have not being included among the prioritisation criteria. This study was based on the Spanish HERACLES cohort (NCT02511496) (April-September 2015, 2940 patients) and involved application of different neural network models with different basis functions (product-unit, sigmoid unit and radial basis function neural networks) for automatic classification of patients for treatment. An evolutionary algorithm was used to determine the architecture and estimate the coefficients of the model. This machine learning methodology found that radial basis neural networks provided a very simple model in terms of the number of patient characteristics to be considered by the classifier (in this case, six), returning a good overall classification accuracy of 0.767 and a minimum sensitivity (for the classification of the minority class, untreated patients) of 0.550. Finally, the area under the ROC curve was 0.802, which proved to be exceptional. The parsimony of the model makes it especially attractive, using just eight connections. The independent variable "recent PWID" is compulsory due to its importance. The simplicity of the model means that it is possible to analyse the relationship between patient characteristics and the probability of belonging to the treated group

Metabolite changes in blood predict the onset of tuberculosis

Immunogenetics and cellular immunology of bacterial infectious disease

Triple Helix, Fall 2018

Table of Contents: Science Agenda: The Politics of Grant Writing / by Kavya Rajesh (p. 4) -- From the Experts / by Katherine Bruner (p. 5) -- 3D Printed Drugs: The Future of Pharmaceuticals / by Ethan Wang (p. 6) -- Computerized Markets: Wall Street Takeover / by James Kiraly (p. 10) -- The Evolution of Fear / by Alisha Ahmed (p. 14) -- ADDing Up / by Victor Liaw (p. 18) -- The Clone Wars / by Jina Zhou (p. 22) -- Physician-Assisted Suicide: Drawing the Line / by Haley Wolf (p. 26) -- Supervised Injection Sites / by Alex Gajewski (p. 30) -- On Emerging Medicalization and Health Care / by Patrick Lee (p. 33) -- The Future of Human Gene Modifications / by Elizabeth Robinson (p. 36)College of Natural SciencesUT LibrariesLiberal Art

Using internet search data to predict new HIV diagnoses in China: a modelling study.

ObjectivesInternet data are important sources of abundant information regarding HIV epidemics and risk factors. A number of case studies found an association between internet searches and outbreaks of infectious diseases, including HIV. In this research, we examined the feasibility of using search query data to predict the number of new HIV diagnoses in China.DesignWe identified a set of search queries that are associated with new HIV diagnoses in China. We developed statistical models (negative binomial generalised linear model and its Bayesian variants) to estimate the number of new HIV diagnoses by using data of search queries (Baidu) and official statistics (for the entire country and for Guangdong province) for 7 years (2010 to 2016).ResultsSearch query data were positively associated with the number of new HIV diagnoses in China and in Guangdong province. Experiments demonstrated that incorporating search query data could improve the prediction performance in nowcasting and forecasting tasks.ConclusionsBaidu data can be used to predict the number of new HIV diagnoses in China up to the province level. This study demonstrates the feasibility of using search query data to predict new HIV diagnoses. Results could potentially facilitate timely evidence-based decision making and complement conventional programmes for HIV prevention

Applying machine learning to predict patient-specific current CD4 cell count in order to determine the progression of human immunodeficiency virus (HIV) infection

This work shows the application of machine learning to predict current CD4 cell count of an HIV-positive patient using genome sequences, viral load and time. A regression model predicting actual CD4 cell counts and a classification model predicting if a patient’s CD4 cell count is less than 200 was built using a support vector machine and neural network. The most accurate regression and classification model took as input the viral load, time, and genome and produced a correlation of co-efficient of 0.9 and an accuracy of 95%, respectively, proving that a CD4 cell count measure may be accurately predicted using machine learning on genotype, viral load and time.Keywords: Human immunodeficiency virus (HIV), antigens, CD4, computational biology, artificial intelligence, data mining, pattern recognition.African Journal of Biotechnology Vol. 12(23), pp. 3724-373

A transfer learning approach to drug resistance classification in mixed HIV dataset

Funding: This research is funded by the Tertiary Education Trust Fund (TETFund), Nigeria.As we advance towards individualized therapy, the ‘one-size-fits-all’ regimen is gradually paving the way for adaptive techniques that address the complexities of failed treatments. Treatment failure is associated with factors such as poor drug adherence, adverse side effect/reaction, co-infection, lack of follow-up, drug-drug interaction and more. This paper implements a transfer learning approach that classifies patients' response to failed treatments due to adverse drug reactions. The research is motivated by the need for early detection of patients' response to treatments and the generation of domain-specific datasets to balance under-represented classification data, typical of low-income countries located in Sub-Saharan Africa. A soft computing model was pre-trained to cluster CD4+ counts and viral loads of treatment change episodes (TCEs) processed from two disparate sources: the Stanford HIV drug resistant database (https://hivdb.stanford.edu), or control dataset, and locally sourced patients' records from selected health centers in Akwa Ibom State, Nigeria, or mixed dataset. Both datasets were experimented on a traditional 2-layer neural network (NN) and a 5-layer deep neural network (DNN), with odd dropout neurons distribution resulting in the following configurations: NN (Parienti et al., 2004) [32], NN (Deniz et al., 2018) [53] and DNN [9 7 5 3 1]. To discern knowledge of failed treatment, DNN1 [9 7 5 3 1] and DNN2 [9 7 5 3 1] were introduced to model both datasets and only TCEs of patients at risk of drug resistance, respectively. Classification results revealed fewer misclassifications, with the DNN architecture yielding best performance measures. However, the transfer learning approach with DNN2 [9 7 3 1] configuration produced superior classification results when compared to other variants/configurations, with classification accuracy of 99.40%, and RMSE values of 0.0056, 0.0510, and 0.0362, for test, train, and overall datasets, respectively. The proposed system therefore indicates good generalization and is vital as decision-making support to clinicians/physicians for predicting patients at risk of adverse drug reactions. Although imbalanced features classification is typical of disease problems and diminishes dependence on classification accuracy, the proposed system still compared favorably with the literature and can be hybridized to improve its precision and recall rates.Publisher PDFPeer reviewe

An Intelligent Multicriteria Model for Diagnosing Dementia in People Infected with Human Immunodeficiency Virus

Hybrid models to detect dementia based on Machine Learning can provide accurate diagnoses in individuals with neurological disorders and cognitive complications caused by Human Immunodeficiency Virus (HIV) infection. This study proposes a hybrid approach, using Machine Learning algorithms associated with the multicriteria method of Verbal Decision Analysis (VDA). Dementia, which affects many HIV-infected individuals, refers to neurodevelopmental and mental disorders. Some manuals standardize the information used in the correct detection of neurological disorders with cognitive complications. Among the most common manuals used are the DSM-5 (Diagnostic and Statistical Manual of Mental Disorders, 5th edition) of the American Psychiatric Association and the International Classification of Diseases, 10th edition (ICD-10)—both published byWorld Health Organization (WHO). The model is designed to explore the predictive of specific data. Furthermore, a well-defined database data set improves and optimizes the diagnostic models sought in the research.info:eu-repo/semantics/publishedVersio

Machine learning outperformed logistic regression classification even with limit sample size: A model to predict pediatric HIV mortality and clinical progression to AIDS

Logistic regression (LR) is the most common prediction model in medicine. In recent years, supervised machine learning (ML) methods have gained popularity. However, there are many concerns about ML utility for small sample sizes. In this study, we aim to compare the performance of 7 algorithms in the prediction of 1-year mortality and clinical progression to AIDS in a small cohort of infants living with HIV from South Africa and Mozambique. The data set (n = 100) was randomly split into 70% training and 30% validation set. Seven algorithms (LR, Random Forest (RF), Support Vector Machine (SVM), K-Nearest Neighbor (KNN), Naive Bayes (NB), Artificial Neural Network (ANN), and Elastic Net) were compared. The variables included as predictors were the same across the models including sociodemographic, virologic, immunologic, and maternal status features. For each of the models, a parameter tuning was performed to select the best-performing hyperparameters using 5 times repeated 10-fold cross-validation. A confusion-matrix was built to assess their accuracy, sensitivity, and specificity. RF ranked as the best algorithm in terms of accuracy (82,8%), sensitivity (78%), and AUC (0,73). Regarding specificity and sensitivity, RF showed better performance than the other algorithms in the external validation and the highest AUC. LR showed lower performance compared with RF, SVM, or KNN. The outcome of children living with perinatally acquired HIV can be predicted with considerable accuracy using ML algorithms. Better models would benefit less specialized staff in limited resources countries to improve prompt referral in case of high-risk clinical progression