Developing a random forest classifier for predicting the depression and managing the health of caregivers supporting patients with Alzheimer's Disease

Quantitative proteomics revealed protein biomarkers to distinguish malignant pleural effusion from benign pleural effusion

To identify protein biomarkers capable of early prediction regarding the distinguishing malignant pleural effusion (MPE) from benign pleural effusion (BPE) in patients with lung disease. A four-dimensional data independent acquisition (4D-DIA) proteomic was performed to determine the differentially expressed proteins in samples from 20 lung adenocarcinoma MPE and 30 BPE. The significantly differential expressed proteins were selected for Gene Ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. Protein biomarkers with high capability to discriminate MPE from BPE patients were identified by Random Forest (RF) algorithm prediction model, whose diagnostic and prognostic efficacy in primary tumors were further explored in public datasets, and were validated by ELISA experiment. 50 important proteins (30 up-regulated and 20 down-regulated) were selected out as potential markers to distinguish the MPE from BPE group. GO analysis revealed that those proteins involving the most important cell component is extracellular space. KEGG analysis identified the involvement of cellular adhesion molecules pathway. Furthermore, the Area Under Curve (AUC) of these proteins were ranged from 0.717 to 1.000，with excellent diagnostic properties to distinguish the MPE. Finally, significant survival and gene and protein expression analysis demonstrated BPIFB1, DPP4, HPRT1 and ABI3BP had high discriminating values. SIGNIFICANCE: We performed a 4D-DIA proteomics to determine the differentially expressed proteins in pleural effusion samples from MPE and BPE. Some potential protein biomarkers were identified to distinguish the MPE from BPE patients., which may provide helpful diagnostic and therapeutic insights for lung cancer. This is significant because the median survival time of patients with MPE is usually 4-12 months, thus, it is particularly important to diagnose MPE early to start treatments promptly. The most common causes of MPE are lung cancers, while pneumonia and tuberculosis are the main causes of BPE. If more diagnostic markers could be identified periodically, there would be an important significance to clinical diagnose and treatment with drugs in lung cancer patients.

A united model for diagnosing pulmonary tuberculosis with random forest and artificial neural network

Background: Pulmonary tuberculosis (PTB) is a chronic infectious disease and is the most common type of TB. Although the sputum smear test is a gold standard for diagnosing PTB, the method has numerous limitations, including low sensitivity, low specificity, and insufficient samples.

Methods: The present study aimed to identify specific biomarkers of PTB and construct a model for diagnosing PTB by combining random forest (RF) and artificial neural network (ANN) algorithms. Two publicly available cohorts of TB, namely, the GSE83456 (training) and GSE42834 (validation) cohorts, were retrieved from the Gene Expression Omnibus (GEO) database. A total of 45 and 61 differentially expressed genes (DEGs) were identified between the PTB and control samples, respectively, by screening the GSE83456 cohort. An RF classifier was used for identifying specific biomarkers, following which an ANN-based classification model was constructed for identifying PTB samples. The accuracy of the ANN model was validated using the receiver operating characteristic (ROC) curve. The proportion of 22 types of immunocytes in the PTB samples was measured using the CIBERSORT algorithm, and the correlations between the immunocytes were determined.

Results: Differential analysis revealed that 11 and 22 DEGs were upregulated and downregulated, respectively, and 11 biomarkers specific to PTB were identified by the RF classifier. The weights of these biomarkers were determined and an ANN-based classification model was subsequently constructed. The model exhibited outstanding performance, as revealed by the area under the curve (AUC), which was 1.000 for the training cohort. The AUC of the validation cohort was 0.946, which further confirmed the accuracy of the model.

Conclusion: Altogether, the present study successfully identified specific genetic biomarkers of PTB and constructed a highly accurate model for the diagnosis of PTB based on blood samples. The model developed herein can serve as a reliable reference for the early detection of PTB and provide novel perspectives into the pathogenesis of PTB.

A hybrid machine learning model of depression estimation in home-based older adults: a 7-year follow-up study

BACKGROUND

Our aim was to explore whether a two-step hybrid machine learning model has the potential to discover the onset of depression in home-based older adults.

METHODS

Depression data (collected in the year 2011, 2013, 2015 and 2018) of home-based older Chinese (n = 2,548) recruited in the China Health and Retirement Longitudinal Study were included in the current analysis. The long short-term memory network (LSTM) was applied to identify the risk factors of participants in 2015 utilizing the first 2 waves of data. Based on the identified predictors, three ML classification algorithms (i.e., gradient boosting decision tree, support vector machine and random forest) were evaluated with a 10-fold cross-validation procedure and a metric of the area under the receiver operating characteristic curve (AUROC) to estimate the depressive outcome.

RESULTS

Time-varying predictors of the depression were successfully identified by LSTM (mean squared error =0.8). The mean AUCs of the three predictive models had a range from 0.703 to 0.749. Among the prediction variables, self-reported health status, cognition, sleep time, self-reported memory and ADL (activities of daily living) disorder were the top five important variables.

CONCLUSIONS

A two-step hybrid model based on "LSTM+ML" framework can be robust in predicting depression over a 5-year period with easily accessible sociodemographic and health information.

Explainable, trustworthy, and ethical machine learning for healthcare: A survey

With the advent of machine learning (ML) and deep learning (DL) empowered applications for critical applications like healthcare, the questions about liability, trust, and interpretability of their outputs are raising. The black-box nature of various DL models is a roadblock to clinical utilization. Therefore, to gain the trust of clinicians and patients, we need to provide explanations about the decisions of models. With the promise of enhancing the trust and transparency of black-box models, researchers are in the phase of maturing the field of eXplainable ML (XML). In this paper, we provided a comprehensive review of explainable and interpretable ML techniques for various healthcare applications. Along with highlighting security, safety, and robustness challenges that hinder the trustworthiness of ML, we also discussed the ethical issues arising because of the use of ML/DL for healthcare. We also describe how explainable and trustworthy ML can resolve all these ethical problems. Finally, we elaborate on the limitations of existing approaches and highlight various open research problems that require further development.

A Joint Model of Random Forest and Artificial Neural Network for the Diagnosis of Endometriosis

Endometriosis (EM), an estrogen-dependent inflammatory disease with unknown etiology, affects thousands of childbearing-age couples, and its early diagnosis is still very difficult. With the rapid development of sequencing technology in recent years, the accumulation of many sequencing data makes it possible to screen important diagnostic biomarkers from some EM-related genes. In this study, we utilized public datasets in the Gene Expression Omnibus (GEO) and Array-Express database and identified seven important differentially expressed genes (DEGs) (COMT, NAA16, CCDC22, EIF3E, AHI1, DMXL2, and CISD3) through the random forest classifier. Among these DEGs, AHI1, DMXL2, and CISD3 have never been reported to be associated with the pathogenesis of EMs. Our study indicated that these three genes might participate in the pathogenesis of EMs through oxidative stress, epithelial–mesenchymal transition (EMT) with the activation of the Notch signaling pathway, and mitochondrial homeostasis, respectively. Then, we put these seven DEGs into an artificial neural network to construct a novel diagnostic model for EMs and verified its diagnostic efficacy in two public datasets. Furthermore, these seven DEGs were included in 15 hub genes identified from the constructed protein–protein interaction (PPI) network, which confirmed the reliability of the diagnostic model. We hope the diagnostic model can provide novel sights into the understanding of the pathogenesis of EMs and contribute to the clinical diagnosis and treatment of EMs.

Predicting depression among rural and urban disabled elderly in China using a random forest classifier

With global aging, the number of elderly with physical disabilities is also increasing. Compared with the ordinary elderly, the elderly who lose their independence are more likely to have the symptoms of depression. Reducing depression may help to alleviate the disability process of those who find themselves in the disabled stages. Therefore, the purpose of this study is to explore the predictive effects of demographic characteristics, health behavior, health status, family relations, social relations, and subjective attitude on depression in rural and urban disabled elderly to improve early depression symptom recognition.A total of 1460 older adults aged 60 and disabled were selected from China Family Panel Studies (CFPS). Depression was assessed according to The Center for Epidemiologic Studies Depression Scale (CES-D). This paper used the random forest classifier to predict the depression of the disabled elderly from six aspects: demographic characteristics, health status, health behavior, family relationship, and social relationship. The prediction model was established based on 70% of the training set and 30% of the test set. The depression rate of rural disabled elderly was 57.67%, and that of urban disabled elderly was 44.59%. The mean values of the 10-k cross-validated results were 0.71 in rural areas and 0.70 in urban areas. AUC:0.71, specificity: 65.3%, sensitivity: 80.6% for rural disabled elderly with depression; AUC:0.78, specificity: 78.1%, sensitivity: 64.2% for urban disabled elderly with depression, respectively. There are apparent differences in the top ten predictors between rural and urban disabled elderly. The common predictors were self-rated health, changing in perceived health, disease or accidence experience within the past 2 weeks, life satisfaction, trusting people, BMI, and having trust in the future. Non-common predictors were chronic diseases, neighborly relations, total medical expenses within 1 year, community emotion, sleep duration, and family per capita income. Using random forest data to predict the depression of the disabled elderly may lead to early detection of depression.

Analysis of depression in social media texts through the Patient Health Questionnaire-9 and natural language processing

Objective

Although depression in modern people is emerging as a major social problem, it shows a low rate of use of mental health services. The purpose of this study was to classify sentences written by social media users based on the nine symptoms of depression in the Patient Health Questionnaire-9, using natural language processing to assess naturally users’ depression based on their results.

Methods

First, train two sentence classifiers: the Y/N sentence classifier, which categorizes whether a user’s sentence is related to depression, and the 0–9 sentence classifier, which further categorizes the user sentence based on the depression symptomology of the Patient Health Questionnaire-9. Then the depression classifier, which is a logistic regression model, was generated to classify the sentence writer’s depression. These trained sentence classifiers and the depression classifier were used to analyze the social media textual data of users and establish their depression.

Results

Our experimental results showed that the proposed depression classifier showed 68.3% average accuracy, which was better than the baseline depression classifier that used only the Y/N sentence classifier and had 53.3% average accuracy.

Conclusions

This study is significant in that it demonstrates the possibility of determining depression from only social media users’ textual data.

Comparing Ensemble-Based Machine Learning Classifiers Developed for Distinguishing Hypokinetic Dysarthria from Presbyphonia

It is essential to understand the voice characteristics in the normal aging process to accurately distinguish presbyphonia from neurological voice disorders. This study developed the best ensemble-based machine learning classifier that could distinguish hypokinetic dysarthria from presbyphonia using classification and regression tree (CART), random forest, gradient boosting algorithm (GBM), and XGBoost and compared the prediction performance of models. The subjects of this study were 76 elderly patients diagnosed with hypokinetic dysarthria and 174 patients with presbyopia. This study developed prediction models for distinguishing hypokinetic dysarthria from presbyphonia by using CART, GBM, XGBoost, and random forest and compared the accuracy, sensitivity, and specificity of the development models to identify the prediction performance of them. The results of this study showed that random forest had the best prediction performance when it was tested with the test dataset (accuracy = 0.83, sensitivity = 0.90, and specificity = 0.80, and area under the curve (AUC) = 0.85). The main predictors for detecting hypokinetic dysarthria were Cepstral peak prominence (CPP), jitter, shimmer, L/H ratio, L/H ratio_SD, CPP max (dB), CPP min (dB), and CPPF0 in the order of magnitude. Among them, CPP was the most important predictor for identifying hypokinetic dysarthria.

Key Experimental Factors of Machine Learning-Based Identification of Surgery Cancellations

This study aimed to provide effective methods for the identification of surgeries with high cancellation risk based on machine learning models and analyze the key factors that affect the identification performance. The data covered the period from January 1, 2013, to December 31, 2014, at West China Hospital in China, which focus on elective urologic surgeries. All surgeries were scheduled one day in advance, and all cancellations were of institutional resource- and capacity-related types. Feature selection strategies, machine learning models, and sampling methods are the most discussed topic in general machine learning researches and have a direct impact on the performance of machine learning models. Hence, they were considered to systematically generate complete schemes in machine learning-based identification of surgery cancellations. The results proved the feasibility and robustness of identifying surgeries with high cancellation risk, with the considerable maximum of area under the curve (AUC) (0.7199) for random forest model with original sampling using backward selection strategy. In addition, one-side Delong test and sum of square error analysis were conducted to measure the effects of feature selection strategy, machine learning model, and sampling method on the identification of surgeries with high cancellation risk, and the selection of machine learning model was identified as the key factors that affect the identification of surgeries with high cancellation risk. This study offers methodology and insights for identifying the key experimental factors for identifying surgery cancellations, and it is helpful to further research on machine learning-based identification of surgeries with high cancellation risk.

Prediction of the development of depression and post-traumatic stress disorder in sexually abused children using a random forest classifier

BACKGROUND

Depression and post-traumatic stress disorder (PTSD) are among the most common psychiatric disorders observed in children and adolescents exposed to sexual abuse.

OBJECTIVE

The present study aimed to investigate the effects of many factors such as the characteristics of a child, abuse, and the abuser, family type of the child, and the role of social support in the development of psychiatric disorders using machine learning techniques.

PARTICIPANTS AND SETTINGS

The records of 482 children and adolescents who were determined to have been sexually abused were examined to predict the development of depression and PTSD.

METHODS

Each child was evaluated by a child and adolescent psychiatrist in the psychiatric aspect according to the DSM-V. Through the data of both groups, a predictive model was established based on a random forest classifier.

RESULTS

The mean values and standard deviation of the 10-k cross-validated results were obtained as accuracy: 0.82% (+/- 0.19%), F1: 0.81% (+/- 0.19%), precision: 0.81% (+/- 0.19%), recall: 0.80% (+/- 0.19%) for children with depression; and accuracy: 0.72% (+/- 0.12%), F1: 0.71% (+/- 0.12%), precision: 0.72% (+/- 0.12%), recall: 0.71% (+/- 0.12%) for children with PTSD, respectively. ROC curves were drawn for both, and the AUC results were obtained as 0.88 for major depressive disorder and 0.76 for PTSD.

CONCLUSIONS

Machine learning techniques are powerful methods that can be used to predict disorders that may develop after sexual abuse. The results should be supported by studies with larger samples, which are repeated and applied to other risk groups.

Exploring the Predictors of Rapid Eye Movement Sleep Behavior Disorder for Parkinson's Disease Patients Using Classifier Ensemble

The rapid eye movement sleep behavior disorder (RBD) of Parkinson's disease (PD) patients can be improved with medications such as donepezil as long as it is diagnosed with a thorough medical examination, since identifying a high-risk group of RBD is a critical issue to treat PD. This study develops a model for predicting the high-risk groups of RBD using random forest (RF) and provides baseline information for selecting subjects for polysomnography. Subjects consisted of 350 PD patients (Parkinson's disease with normal cognition (PD-NC) = 48; Parkinson's disease with mild cognitive impairment (PD-MCI) = 199; Parkinson's disease dementia (PDD) = 103) aged 60 years and older. This study compares the prediction performance of RF, discriminant analysis, classification and regression tree (CART), radial basis function (RBF) neural network, and logistic regression model to select a final model with the best model performance and presents the variable importance of the final model's variable. As a result of analysis, the sensitivity of RF (79%) was superior to other models (discriminant analysis = 14%, CART = 32%, RBF neural network = 25%, and logistic regression = 51%). It was confirmed that age, the motor score of Untitled Parkinson's Disease Rating (UPDRS), the total score of UPDRS, the age when a subject was diagnosed with PD first time, the Korean Mini Mental State Examination, and Korean Instrumental Activities of Daily Living, were major variables with high weight for predicting RBD. Among them, age was the most important factor. The model for predicting Parkinson's disease RBD developed in this study will contribute to the screening of patients who should receive a video-polysomnography.

Is the Random Forest Algorithm Suitable for Predicting Parkinson's Disease with Mild Cognitive Impairment out of Parkinson's Disease with Normal Cognition?

Because it is possible to delay the progression of dementia if it is detected and treated in an early stage, identifying mild cognitive impairment (MCI) is an important primary goal of dementia treatment. The objectives of this study were to develop a random forest-based Parkinson's disease with mild cognitive impairment (PD-MCI) prediction model considering health behaviors, environmental factors, medical history, physical functions, depression, and cognitive functions using the Parkinson's Dementia Clinical Epidemiology Data (a national survey conducted by the Korea Centers for Disease Control and Prevention) and to compare the prediction accuracy of our model with those of decision tree and multiple logistic regression models. We analyzed 96 subjects (PD-MCI = 45; Parkinson's disease with normal cognition (PD-NC) = 51 subjects). The prediction accuracy of the model was calculated using the overall accuracy, sensitivity, and specificity. Based on the random forest analysis, the major risk factors of PD-MCI were, in descending order of magnitude, Clinical Dementia Rating (CDR) sum of boxes, Untitled Parkinson's Disease Rating (UPDRS) motor score, the Korean Mini Mental State Examination (K-MMSE) total score, and the K- Korean Montreal Cognitive Assessment (K-MoCA) total score. The random forest method achieved a higher sensitivity than the decision tree model. Thus, it is advisable to develop a protocol to easily identify early stage PDD based on the PD-MCI prediction model developed in this study, in order to establish individualized monitoring to track high-risk groups.

Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine

Precision medicine is one of the recent and powerful developments in medical care, which has the potential to improve the traditional symptom-driven practice of medicine, allowing earlier interventions using advanced diagnostics and tailoring better and economically personalized treatments. Identifying the best pathway to personalized and population medicine involves the ability to analyze comprehensive patient information together with broader aspects to monitor and distinguish between sick and relatively healthy people, which will lead to a better understanding of biological indicators that can signal shifts in health. While the complexities of disease at the individual level have made it difficult to utilize healthcare information in clinical decision-making, some of the existing constraints have been greatly minimized by technological advancements. To implement effective precision medicine with enhanced ability to positively impact patient outcomes and provide real-time decision support, it is important to harness the power of electronic health records by integrating disparate data sources and discovering patient-specific patterns of disease progression. Useful analytic tools, technologies, databases, and approaches are required to augment networking and interoperability of clinical, laboratory and public health systems, as well as addressing ethical and social issues related to the privacy and protection of healthcare data with effective balance. Developing multifunctional machine learning platforms for clinical data extraction, aggregation, management and analysis can support clinicians by efficiently stratifying subjects to understand specific scenarios and optimize decision-making. Implementation of artificial intelligence in healthcare is a compelling vision that has the potential in leading to the significant improvements for achieving the goals of providing real-time, better personalized and population medicine at lower costs. In this study, we focused on analyzing and discussing various published artificial intelligence and machine learning solutions, approaches and perspectives, aiming to advance academic solutions in paving the way for a new data-centric era of discovery in healthcare.