Using a multi-staged strategy based on machine learning and mathematical modeling to predict genotype-phenotype risk patterns in diabetic kidney disease: a prospective case-control cohort analysis

Machine Learning-Based Predictive Modeling of Diabetic Nephropathy in Type 2 Diabetes Using Integrated Biomarkers: A Single-Center Retrospective Study

Purpose

Diabetic nephropathy (DN), a major complication of diabetes mellitus, significantly impacts global health. Identifying individuals at risk of developing DN is crucial for early intervention and improving patient outcomes. This study aims to develop and validate a machine learning-based predictive model using integrated biomarkers.

Methods

A cross-sectional analysis was conducted on a baseline dataset involving 2184 participants without DN, categorized based on their development of DN over a follow-up period of 36 months: DN (n=1270) and Non-DN (n=914). Various demographic and clinical parameters were analyzed. The findings were validated using an independent dataset comprising 468 participants, with 273 developing DN and 195 remaining as Non-DN over the follow-up period. Machine learning algorithms, alongside traditional descriptive statistics and logistic regression were used for statistical analyses.

Results

Elevated levels of serum creatinine, urea, and reduced eGFR, alongside an increased prevalence of retinopathy and peripheral neuropathy, were prominently observed in those who developed DN. Validation on the independent dataset further confirmed the model's robustness and consistency. The SVM model demonstrated superior performance in the training set (AUC=0.79, F1-score=0.74) and testing set (AUC=0.83, F1-score=0.82), outperforming other models. Significant predictors of DN included serum creatinine, eGFR, presence of diabetic retinopathy, and peripheral neuropathy.

Conclusion

Integrating machine learning algorithms with clinical and biomarker data at baseline offers a promising avenue for identifying individuals at risk of developing diabetic nephropathy in type 2 diabetes patients over a 36-month period.

Age at natural menopause and its determinants in female population of Kharameh cohort study: Comparison of regression, conditional tree and forests

BACKGROUND

Natural menopause is defined as the permanent cessation of menstruation that occurs after 12 consecutive months of amenorrhea without any obvious pathological or physiological cause. The age of this phenomenon has been reported to be associated with several health outcomes.

OBJECTIVES

This study aimed to estimate the Age at Natural Menopause (ANM) and to identify reproductive and demographic factors affecting ANM.

METHODS

This cross-sectional, population-based study was conducted on 2517 post-menopausal women aged 40-70 years participating in the first phase of the PERSIAN cohort study of Kharameh, Iran, during 2014-2017. To more accurately detect the determinants of ANM, we applied multiple linear regression beside some machine learning algorithms including conditional tree, conditional forest, and random forest. Then, the fitness of these methods was compared using Mean Squared Error (MSE) and Pearson correlation coefficient.

RESULTS

The mean±SD of ANM was 48.95±6.13. Both applied forests provided more accurate results and identified more predictors. However, according to the final comparison, the conditional forest was the most accurate method which recognized that more pregnancies, longer breastfeeding, Fars ethnicity, and urbanization have the greatest impact on later ANM.

CONCLUSIONS

This study found a wide range of reproductive and demographic factors affecting ANM. Considering our findings in decision-making can reduce the complications related to this phenomenon and, consequently, improve the quality of life of post-menopausal women.

The automatic detection of diabetic kidney disease from retinal vascular parameters combined with clinical variables using artificial intelligence in type-2 diabetes patients

BACKGROUND

Diabetic kidney disease (DKD) has become the largest cause of end-stage kidney disease. Early and accurate detection of DKD is beneficial for patients. The present detection depends on the measurement of albuminuria or the estimated glomerular filtration rate, which is invasive and not optimal; therefore, new detection tools are urgently needed. Meanwhile, a close relationship between diabetic retinopathy and DKD has been reported; thus, we aimed to develop a novel detection algorithm for DKD using artificial intelligence technology based on retinal vascular parameters combined with several easily available clinical parameters in patients with type-2 diabetes.

METHODS

A total of 515 consecutive patients with type-2 diabetes mellitus from Xiangyang Central Hospital were included. Patients were stratified by DKD diagnosis and split randomly into either the training set (70%, N = 360) or the testing set (30%, N = 155) (random seed = 1). Data from the training set were used to develop the machine learning algorithm (MLA), while those from the testing set were used to validate the MLA. Model performances were evaluated.

RESULTS

The MLA using the random forest classifier presented optimal performance compared with other classifiers. When validated, the accuracy, sensitivity, specificity, F1 score, and AUC for the optimal model were 84.5%(95% CI 83.3-85.7), 84.5%(82.3-86.7), 84.5%(82.7-86.3), 0.845(0.831-0.859), and 0.914(0.903-0.925), respectively.

CONCLUSIONS

A new machine learning algorithm for DKD diagnosis based on fundus images and 8 easily available clinical parameters was developed, which indicated that retinal vascular changes can assist in DKD screening and detection.

Machine learning based study for the classification of Type 2 diabetes mellitus subtypes

PURPOSE

Data-driven diabetes research has increased its interest in exploring the heterogeneity of the disease, aiming to support in the development of more specific prognoses and treatments within the so-called precision medicine. Recently, one of these studies found five diabetes subgroups with varying risks of complications and treatment responses. Here, we tackle the development and assessment of different models for classifying Type 2 Diabetes (T2DM) subtypes through machine learning approaches, with the aim of providing a performance comparison and new insights on the matter.

METHODS

We developed a three-stage methodology starting with the preprocessing of public databases NHANES (USA) and ENSANUT (Mexico) to construct a dataset with N = 10,077 adult diabetes patient records. We used N = 2,768 records for training/validation of models and left the remaining (N = 7,309) for testing. In the second stage, groups of observations -each one representing a T2DM subtype- were identified. We tested different clustering techniques and strategies and validated them by using internal and external clustering indices; obtaining two annotated datasets Dset A and Dset B. In the third stage, we developed different classification models assaying four algorithms, seven input-data schemes, and two validation settings on each annotated dataset. We also tested the obtained models using a majority-vote approach for classifying unseen patient records in the hold-out dataset.

RESULTS

From the independently obtained bootstrap validation for Dset A and Dset B, mean accuracies across all seven data schemes were [Formula: see text] ([Formula: see text]) and [Formula: see text] ([Formula: see text]), respectively. Best accuracies were [Formula: see text] and [Formula: see text]. Both validation setting results were consistent. For the hold-out dataset, results were consonant with most of those obtained in the literature in terms of class proportions.

CONCLUSION

The development of machine learning systems for the classification of diabetes subtypes constitutes an important task to support physicians for fast and timely decision-making. We expect to deploy this methodology in a data analysis platform to conduct studies for identifying T2DM subtypes in patient records from hospitals.

Artificial intelligence in glomerular diseases

In this narrative review, we focus on the application of artificial intelligence in the clinical history of patients with glomerular disease, digital pathology in kidney biopsy, renal ultrasonography imaging, and prediction of chronic kidney disease (CKD). With the development of natural language processing, the clinical history of a patient can be used to identify a computable phenotype. In kidney pathology, digital imaging has adopted innovative deep learning algorithms (DLAs) that can improve the predictive capability of the examined lesions. However, at this time, these applications can only be used in research because there is no recognized validation to replace the conventional diagnostic applications. Kidney ultrasonography, used in the clinical examination of patients, provides information about the progression of kidney damage. Machine learning algorithms (MLAs) with promising results for the early detection of CKD have been proposed, but, still, they are not solid enough to be incorporated into the clinical practice. A few tools for glomerulonephritis, based on MLAs, are available in clinical practice. They can be downloaded on computers and cellular phones but can only be applied to uniracial cohorts of patients. To improve their performance, it is necessary to organize large consortia with multiracial cohorts. Finally, in many studies MLA development has been carried out using retrospective cohorts. The performance of the models might differ in retrospective cohorts compared to real-world data. Therefore, the models should be validated in prospective external large cohorts.

Accuracy of Machine Learning Classification Models for the Prediction of Type 2 Diabetes Mellitus: A Systematic Survey and Meta-Analysis Approach

Soft-computing and statistical learning models have gained substantial momentum in predicting type 2 diabetes mellitus (T2DM) disease. This paper reviews recent soft-computing and statistical learning models in T2DM using a meta-analysis approach. We searched for papers using soft-computing and statistical learning models focused on T2DM published between 2010 and 2021 on three different search engines. Of 1215 studies identified, 34 with 136952 patients met our inclusion criteria. The pooled algorithm's performance was able to predict T2DM with an overall accuracy of 0.86 (95% confidence interval [CI] of [0.82, 0.89]). The classification of diabetes prediction was significantly greater in models with a screening and diagnosis (pooled proportion [95% CI] = 0.91 [0.74, 0.97]) when compared to models with nephropathy (pooled proportion = 0.48 [0.76, 0.89] to 0.88 [0.83, 0.91]). For the prediction of T2DM, the decision trees (DT) models had a pooled accuracy of 0.88 [95% CI: 0.82, 0.92], and the neural network (NN) models had a pooled accuracy of 0.85 [95% CI: 0.79, 0.89]. Meta-regression did not provide any statistically significant findings for the heterogeneous accuracy in studies with different diabetes predictions, sample sizes, and impact factors. Additionally, ML models showed high accuracy for the prediction of T2DM. The predictive accuracy of ML algorithms in T2DM is promising, mainly through DT and NN models. However, there is heterogeneity among ML models. We compared the results and models and concluded that this evidence might help clinicians interpret data and implement optimum models for their dataset for T2DM prediction.

Machine Learning for Renal Pathologies: An Updated Survey

Within the literature concerning modern machine learning techniques applied to the medical field, there is a growing interest in the application of these technologies to the nephrological area, especially regarding the study of renal pathologies, because they are very common and widespread in our society, afflicting a high percentage of the population and leading to various complications, up to death in some cases. For these reasons, the authors have considered it appropriate to collect, using one of the major bibliographic databases available, and analyze the studies carried out until February 2022 on the use of machine learning techniques in the nephrological field, grouping them according to the addressed pathologies: renal masses, acute kidney injury, chronic kidney disease, kidney stone, glomerular disease, kidney transplant, and others less widespread. Of a total of 224 studies, 59 were analyzed according to inclusion and exclusion criteria in this review, considering the method used and the type of data available. Based on the study conducted, it is possible to see a growing trend and interest in the use of machine learning applications in nephrology, becoming an additional tool for physicians, which can enable them to make more accurate and faster diagnoses, although there remains a major limitation given the difficulty in creating public databases that can be used by the scientific community to corroborate and eventually make a positive contribution in this area.

Machine Learning-Based Prediction Method for Tremors Induced by Tacrolimus in the Treatment of Nephrotic Syndrome

Tremors have been reported even with a low dose of tacrolimus in patients with nephrotic syndrome and are responsible for hampering the day-to-day work of young active patients with nephrotic syndrome. This study proposes a neural network model based on seven variables to predict the development of tremors following tacrolimus. The sensitivity and specificity of this algorithm are high. A total of 252 patients were included in this study, out of which 39 (15.5%) experienced tremors, 181 patients (including 32 patients who experienced tremors) were randomly assigned to a training dataset, and the remaining were assigned to an external validation set. We used a recursive feature elimination algorithm to train the training dataset, in turn, through 10-fold cross-validation. The classification performance of the classifer was then used as the evaluation criterion for these subsets to find the subset of optimal features. A neural network was used as a classification algorithm to accurately predict tremors using the subset of optimal features. This model was subsequently tested in the validation dataset. The subset of optimal features contained seven variables (creatinine, D-dimer, total protein, calcium ion, platelet distribution width, serum kalium, and fibrinogen), and the highest accuracy obtained was 0.8288. The neural network model based on these seven variables obtained an area under the curve (AUC) value of 0.9726, an accuracy of 0.9345, a sensitivity of 0.9712, and a specificity of 0.7586 in the training set. Meanwhile, the external validation achieved an accuracy of 0.8214, a sensitivity of 0.8378, and a specificity of 0.7000 in the validation dataset. This model was capable of predicting tremors caused by tacrolimus with an excellent degree of accuracy, which can be beneficial in the treatment of nephrotic syndrome patients.

Alterations in common marmoset gut microbiome associated with duodenal strictures

Chronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets (Callithrix jacchus). Despite standardized housing, diet and husbandry, a recently described gastrointestinal syndrome characterized by duodenal ulcers and strictures was observed in a subset of marmosets sourced from the New England Primate Research Center. As changes in the gut microbiome have been associated with GI diseases, the gut microbiome of 52 healthy, non-stricture marmosets (153 samples) were compared to the gut microbiome of 21 captive marmosets diagnosed with a duodenal ulcer/stricture (57 samples). No significant changes were observed using alpha diversity metrics, and while the community structure was significantly different when comparing beta diversity between healthy and stricture cases, the results were inconclusive due to differences observed in the dispersion of both datasets. Differences in the abundance of individual taxa using ANCOM, as stricture-associated dysbiosis was characterized by Anaerobiospirillum loss and Clostridium perfringens increases. To identify microbial and serum biomarkers that could help classify stricture cases, we developed models using machine learning algorithms (random forest, classification and regression trees, support vector machines and k-nearest neighbors) to classify microbiome, serum chemistry or complete blood count (CBC) data. Random forest (RF) models were the most accurate models and correctly classified strictures using either 9 ASVs (amplicon sequence variants), 4 serum chemistry tests or 6 CBC tests. Based on the RF model and ANCOM results, C. perfringens was identified as a potential causative agent associated with the development of strictures. Clostridium perfringens was also isolated by microbiological culture in 4 of 9 duodenum samples from marmosets with histologically confirmed strictures. Due to the enrichment of C. perfringens in situ, we analyzed frozen duodenal tissues using both 16S microbiome profiling and RNAseq. Microbiome analysis of the duodenal tissues of 29 marmosets from the MIT colony confirmed an increased abundance of Clostridium in stricture cases. Comparison of the duodenal gene expression from stricture and non-stricture marmosets found enrichment of genes associated with intestinal absorption, and lipid metabolism, localization, and transport in stricture cases. Using machine learning, we identified increased abundance of C. perfringens, as a potential causative agent of GI disease and intestinal strictures in marmosets.

Using Machine Learning to Evaluate the Role of Microinflammation in Cardiovascular Events in Patients With Chronic Kidney Disease

Background

Lipid metabolism disorder, as one major complication in patients with chronic kidney disease (CKD), is tied to an increased risk for cardiovascular disease (CVD). Traditional lipid-lowering statins have been found to have limited benefit for the final CVD outcome of CKD patients. Therefore, the purpose of this study was to investigate the effect of microinflammation on CVD in statin-treated CKD patients.

Methods

We retrospectively analysed statin-treated CKD patients from January 2013 to September 2020. Machine learning algorithms were employed to develop models of low-density lipoprotein (LDL) levels and CVD indices. A fivefold cross-validation method was employed against the problem of overfitting. The accuracy and area under the receiver operating characteristic (ROC) curve (AUC) were acquired for evaluation. The Gini impurity index of the predictors for the random forest (RF) model was ranked to perform an analysis of importance.

Results

The RF algorithm performed best for both the LDL and CVD models, with accuracies of 82.27% and 74.15%, respectively, and is therefore the most suitable method for clinical data processing. The Gini impurity ranking of the LDL model revealed that hypersensitive C-reactive protein (hs-CRP) was highly relevant, whereas statin use and sex had the least important effects on the outcomes of both the LDL and CVD models. hs-CRP was the strongest predictor of CVD events.

Conclusion

Microinflammation is closely associated with potential CVD events in CKD patients, suggesting that therapeutic strategies against microinflammation should be implemented to prevent CVD events in CKD patients treated by statin.

Prediction of diabetic kidney disease with machine learning algorithms, upon the initial diagnosis of type 2 diabetes mellitus

INTRODUCTION

Diabetic kidney disease (DKD) accounts for the majority of increased risk of mortality for patients with diabetes, and eventually manifests in approximately half of those patients diagnosed with type 2 diabetes mellitus (T2DM). Although increased screening frequency can avoid delayed diagnoses, this is not uniformly implemented. The purpose of this study was to develop and retrospectively validate a machine learning algorithm (MLA) that predicts stages of DKD within 5 years upon diagnosis of T2DM.

RESEARCH DESIGN AND METHODS

Two MLAs were trained to predict stages of DKD severity, and compared with the Centers for Disease Control and Prevention (CDC) risk score to evaluate performance. The models were validated on a hold-out test set as well as an external dataset sourced from separate facilities.

RESULTS

The MLAs outperformed the CDC risk score in both the hold-out test and external datasets. Our algorithms achieved an area under the receiver operating characteristic curve (AUROC) of 0.75 on the hold-out set for prediction of any-stage DKD and an AUROC of over 0.82 for more severe endpoints, compared with the CDC risk score with an AUROC <0.70 on all test sets and endpoints.

CONCLUSION

This retrospective study shows that an MLA can provide timely predictions of DKD among patients with recently diagnosed T2DM.

New Diagnostic Model for the Differentiation of Diabetic Nephropathy From Non-Diabetic Nephropathy in Chinese Patients

BACKGROUND

The disease pathology for diabetes mellitus patients with chronic kidney disease (CKD) may be diabetic nephropathy (DN), non-diabetic renal disease (NDRD), or DN combined with NDRD. Considering that the prognosis and treatment of DN and NDRD differ, their differential diagnosis is of significance. Renal pathological biopsy is the gold standard for diagnosing DN and NDRD. However, it is invasive and cannot be implemented in many patients due to contraindications. This article constructed a new noninvasive evaluation model for differentiating DN and NDRD.

METHODS

We retrospectively screened 1,030 patients with type 2 diabetes who has undergone kidney biopsy from January 2005 to March 2017 in a single center. Variables were ranked according to importance, and the machine learning methods (random forest, RF, and support vector machine, SVM) were then used to construct the model. The final model was validated with an external group (338 patients, April 2017-April 2019).

RESULTS

In total, 929 patients were assigned. Ten variables were selected for model development. The areas under the receiver operating characteristic curves (AUCROCs) for the RF and SVM methods were 0.953 and 0.947, respectively. Additionally, 329 patients were analyzed for external validation. The AUCROCs for the external validation of the RF and SVM methods were 0.920 and 0.911, respectively.

CONCLUSION

We successfully constructed a predictive model for DN and NDRD using machine learning methods, which were better than our regression methods.

CLINICAL TRIAL REGISTRATION

ClinicalTrial.gov, NCT03865914.

Mining real-world high dimensional structured data in medicine and its use in decision support. Some different perspectives on unknowns, interdependency, and distinguishability

There are many difficulties in extracting and using knowledge for medical analytic and predictive purposes from Real-World Data, even when the data is already well structured in the manner of a large spreadsheet. Preparative curation and standardization or "normalization" of such data involves a variety of chores but underlying them is an interrelated set of fundamental problems that can in part be dealt with automatically during the datamining and inference processes. These fundamental problems are reviewed here and illustrated and investigated with examples. They concern the treatment of unknowns, the need to avoid independency assumptions, and the appearance of entries that may not be fully distinguished from each other. Unknowns include errors detected as implausible (e.g., out of range) values that are subsequently converted to unknowns. These problems are further impacted by high dimensionality and problems of sparse data that inevitably arise from high-dimensional datamining even if the data is extensive. All these considerations are different aspects of incomplete information, though they also relate to problems that arise if care is not taken to avoid or ameliorate consequences of including the same information twice or more, or if misleading or inconsistent information is combined. This paper addresses these aspects from a slightly different perspective using the Q-UEL language and inference methods based on it by borrowing some ideas from the mathematics of quantum mechanics and information theory. It takes the view that detection and correction of probabilistic elements of knowledge subsequently used in inference need only involve testing and correction so that they satisfy certain extended notions of coherence between probabilities. This is by no means the only possible view, and it is explored here and later compared with a related notion of consistency.

The evolution and future of diabetic kidney disease research: a bibliometric analysis

BACKGROUND

Diabetic kidney disease (DKD) is one of the most important complications of diabetic mellitus. It is essential for nephrologists to understand the evolution and development trends of DKD.

METHODS

Based on the total cited numbers in the Web of Science Core Collection, which was searched through September 28th, 2020, we performed a bibliometric analysis of the top 100 most cited full-length original articles on the subject of DKD. The timespans, authors, contributions, subcategories, and topics of those 100 articles were analysed. In addition, the evolution of topics in DKD research was investigated.

RESULTS

There were 23,968 items under the subject of DKD in the Web of Science Core Collection. The top 100 cited articles, published from 1999 to 2017, were cited 38,855 times in total. Researchers from the USA contributed the most publications. The number of articles included in 'Experimental studies (EG)', 'Clinical studies (CS)', 'Epidemiological studies (ES)', and 'Pathological and pathophysiological studies (PP)' were 65, 26, 7, and 2, respectively. Among the 15 topics, the most popular topic is the renin-angiotensin-aldosterone system (RAAS), occurring in 26 articles, including 6 of the top 10 most cited articles. The evolution of topics reveals that the role of RAAS inhibitor is a continuous hotspot, and sodium-glucose cotransporter 2 (SGLT-2) inhibitor and glucagon-like peptide 1 (GLP-1) agonist are two renoprotective agents which represent novel therapeutic methods in DKD. In addition, the 26 clinical studies among the top 100 most cited articles were highlighted, as they help guide clinical practice to better serve patients.

CONCLUSIONS

This bibliometric analysis of the top 100 most cited articles revealed important studies, popular topics, and trends in DKD research to assist researchers in further understanding the subject.

A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach

Tolerance to stress conditions is vital for organismal survival, including bacteria under specific environmental conditions, antibiotics, and other perturbations. Some studies have described common modulation and shared genes during stress response to different types of disturbances (termed as perturbome), leading to the idea of central control at the molecular level. We implemented a robust machine learning approach to identify and describe genes associated with multiple perturbations or perturbome in a Pseudomonas aeruginosa PAO1 model. Using microarray datasets from the Gene Expression Omnibus (GEO), we evaluated six approaches to rank and select genes: using two methodologies, data single partition (SP method) or multiple partitions (MP method) for training and testing datasets, we evaluated three classification algorithms (SVM Support Vector Machine, KNN K-Nearest neighbor and RF Random Forest). Gene expression patterns and topological features at the systems level were included to describe the perturbome elements. We were able to select and describe 46 core response genes associated with multiple perturbations in P. aeruginosa PAO1 and it can be considered a first report of the P. aeruginosa perturbome. Molecular annotations, patterns in expression levels, and topological features in molecular networks revealed biological functions of biosynthesis, binding, and metabolism, many of them related to DNA damage repair and aerobic respiration in the context of tolerance to stress. We also discuss different issues related to implemented and assessed algorithms, including data partitioning, classification approaches, and metrics. Altogether, this work offers a different and robust framework to select genes using a machine learning approach.

Machine learning in nephrology: scratching the surface

Machine learning shows enormous potential in facilitating decision-making regarding kidney diseases. With the development of data preservation and processing, as well as the advancement of machine learning algorithms, machine learning is expected to make remarkable breakthroughs in nephrology. Machine learning models have yielded many preliminaries to moderate and several excellent achievements in the fields, including analysis of renal pathological images, diagnosis and prognosis of chronic kidney diseases and acute kidney injury, as well as management of dialysis treatments. However, it is just scratching the surface of the field; at the same time, machine learning and its applications in renal diseases are facing a number of challenges. In this review, we discuss the application status, challenges and future prospects of machine learning in nephrology to help people further understand and improve the capacity for prediction, detection, and care quality in kidney diseases.

IgA Nephropathy Prediction in Children with Machine Learning Algorithms

Immunoglobulin A nephropathy (IgAN) is the most common primary glomerular disease all over the world and it is a major cause of renal failure. IgAN prediction in children with machine learning algorithms has been rarely studied. We retrospectively analyzed the electronic medical records from the Nanjing Eastern War Zone Hospital, chose eXtreme Gradient Boosting (XGBoost), random forest (RF), CatBoost, support vector machines (SVM), k-nearest neighbor (KNN), and extreme learning machine (ELM) models in order to predict the probability that the patient would not reach or reach end-stage renal disease (ESRD) within five years, used the chi-square test to select the most relevant 16 features as the input of the model, and designed a decision-making system (DMS) of IgAN prediction in children that is based on XGBoost and Django framework. The receiver operating characteristic (ROC) curve was used in order to evaluate the performance of the models and XGBoost had the best performance by comparison. The AUC value, accuracy, precision, recall, and f1-score of XGBoost were 85.11%, 78.60%, 75.96%, 76.70%, and 76.33%, respectively. The XGBoost model is useful for physicians and pediatric patients in providing predictions regarding IgAN. As an advantage, a DMS can be designed based on the XGBoost model to assist a physician to effectively treat IgAN in children for preventing deterioration.

Analysis for warning factors of type 2 diabetes mellitus complications with Markov blanket based on a Bayesian network model

BACKGROUND AND OBJECTIVE

Type 2 diabetes mellitus (T2DM) complications seriously affect the quality of life and could not be cured completely. Actions should be taken for prevention and self-management. Analysis of warning factors is beneficial for patients, on which some previous studies focused. They generally used the professional medical test factors or complete factors to predict and prevent, but it was inconvenient and impractical for patients to self-manage. With this in mind, this study built a Bayesian network (BN) model, from the perspective of diabetic patients' self-management and prevention, to predict six complications of T2DM using the selected warning factors which patients could have access from medical examination. Furthermore, the model was analyzed to explore the relationships between physiological variables and T2DM complications, as well as the complications themselves. The model aims to help patients with T2DM self-manage and prevent themselves from complications.

METHODS

The dataset was collected from a well-known data center called the National Health Clinical Center between 1st January 2009 and 31st December 2009. After preprocess and impute the data, a BN model merging expert knowledge was built with Bootstrap and Tabu search algorithm. Markov Blanket (MB) was used to select the warning factors and predict T2DM complications. Moreover, a Bayesian network without prior information (BN-wopi) model learned using 10-fold cross-validation both in structure and in parameters was added to compare with other classifiers learned using 10-fold cross-validation fairly. The warning factors were selected according the structure learned in each fold and were used to predict. Finally, the performance of two BN models using warning features were compared with Naïve Bayes model, Random Forest model, and C5.0 Decision Tree model, which used all features to predict. Besides, the validation parameters of the proposed model were also compared with those in existing studies using some other variables in clinical data or biomedical data to predict T2DM complications.

RESULTS

Experimental results indicated that the BN models using warning factors performed statistically better than their counterparts using all other variables in predicting T2DM complications. In addition, the proposed BN model were effective and significant in predicting diabetic nephropathy (DN) (AUC: 0.831), diabetic foot (DF) (AUC: 0.905), diabetic macrovascular complications (DMV) (AUC: 0.753) and diabetic ketoacidosis (DK) (AUC: 0.877) with the selected warning factors compared with other experiments.

CONCLUSIONS

The warning factors of DN, DF, DMV, and DK selected by MB in this research might be able to help predict certain T2DM complications effectively, and the proposed BN model might be used as a general tool for prevention, monitoring, and self-management.

Role of Artificial Intelligence in Kidney Disease

Artificial intelligence (AI), as an advanced science technology, has been widely used in medical fields to promote medical development, mainly applied to early detections, disease diagnoses, and management. Owing to the huge number of patients, kidney disease remains a global health problem. Challenges remain in its diagnosis and treatment. AI could take individual conditions into account, produce suitable decisions and promise to make great strides in kidney disease management. Here, we review the current studies of AI applications in kidney disease in alerting systems, diagnostic assistance, guiding treatment and evaluating prognosis. Although the number of studies related to AI applications in kidney disease is small, the potential of AI in the management of kidney disease is well recognized by clinicians; AI will greatly enhance clinicians' capacity in their clinical practice in the future.

Artificial Intelligence Applications in Type 2 Diabetes Mellitus Care: Focus on Machine Learning Methods

Objectives

The incidence of type 2 diabetes mellitus has increased significantly in recent years. With the development of artificial intelligence applications in healthcare, they are used for diagnosis, therapeutic decision making, and outcome prediction, especially in type 2 diabetes mellitus. This study aimed to identify the artificial intelligence (AI) applications for type 2 diabetes mellitus care.

Methods

This is a review conducted in 2018. We searched the PubMed, Web of Science, and Embase scientific databases, based on a combination of related mesh terms. The article selection process was based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Finally, 31 articles were selected after inclusion and exclusion criteria were applied. Data gathering was done by using a data extraction form. Data were summarized and reported based on the study objectives.

Results

The main applications of AI for type 2 diabetes mellitus care were screening and diagnosis in different stages. Among all of the reviewed AI methods, machine learning methods with 71% (n = 22) were the most commonly applied techniques. Many applications were in multi method forms (23%). Among the machine learning algorithms applications, support vector machine (21%) and naive Bayesian (19%) were the most commonly used methods. The most important variables that were used in the selected studies were body mass index, fasting blood sugar, blood pressure, HbA1c, triglycerides, low-density lipoprotein, high-density lipoprotein, and demographic variables.

Conclusions

It is recommended to select optimal algorithms by testing various techniques. Support vector machine and naive Bayesian might achieve better performance than other applications due to the type of variables and targets in diabetes-related outcomes classification.

Machine learning and blood pressure

Machine learning (ML) is a type of artificial intelligence (AI) based on pattern recognition. There are different forms of supervised and unsupervised learning algorithms that are being used to identify and predict blood pressure (BP) and other measures of cardiovascular risk. Since 1999, starting with neural network methods, ML has been used to gauge the relationship between BP and pulse wave forms. Since then, the scope of the research has expanded to using different cardiometabolic risk factors like BMI, waist circumference, waist-to-hip ratio in concert with BP and its various pharmaceutical agents to estimate biochemical measures (like HDL cholesterol, LDL and total cholesterol, fibrinogen, and uric acid) as well as effectiveness of anti-hypertensive regimens. Data from large clinical trials like the SPRINT are being re-analyzed by ML methods to unearth new findings and identify unique relationships between predictors and outcomes. In summary, AI and ML methods are gaining immense attention in the management of chronic disease. Elevated BP is a very important early metric for the risk of development of cardiovascular and renal injury; therefore, advances in AI and ML will aid in early disease prediction and intervention.

Bidirectional General Graphs for inference. Principles and implications for medicine

Probabilistic inference methods require a more general and realistic description of the world as a Bidirectional General Graph (BGG). While in its original form the Bayes Net (BN) has been promoted as a predictive tool, it is more immediately a way of testing a hypothesis or model about interactions in a system usually considered on a causal basis. Once established, the model can be used in a predictive way, but the problem here is that for a traditional BN the hypotheses or models that can be formed are limited to the Directed Acyclic Graph (DAG) by definition. Three interrelated features are highlighted that represent deficiencies of the DAG which are corrected by conversion to a method based on a BGG: (i) lack of intrinsic representation of coherence by Bayes' rule, (ii) relatedly the need to consider interdependence in parent nodes, and (iii) the need for management of a property called recurrence. These deficiencies can represent large errors in absolute estimates of probabilities, and while relative and renormalized probabilities ameliorate that, they can often make much of a net superfluous through cancelations by division. The Hyperbolic Dirac Net (HDN) based on Dirac's quantum mechanics is a solution that led naturally to avoiding these deficiencies. It encodes bidirectional probabilities in an h-complex value rediscovered by Dirac, i.e. with the imaginary number h such that hh = +1. Properties of the HDN described previously are reviewed (though emphasis is on descriptions in familiar probability terms), the issue of recurrence is introduced, methods of construction are simplified, and the severity of the quantitative differences between BNs and analogous HDNs are exemplified. There is also discussion of how results compare with other approaches in practice.

Identification of Traditional Chinese Medicine Constitutions and Physiological Indexes Risk Factors in Metabolic Syndrome: A Data Mining Approach

Objective

In order to find the predictive indexes for metabolic syndrome (MS), a data mining method was used to identify significant physiological indexes and traditional Chinese medicine (TCM) constitutions.

Methods

The annual health check-up data including physical examination data; biochemical tests and Constitution in Chinese Medicine Questionnaire (CCMQ) measurement data from 2014 to 2016 were screened according to the inclusion and exclusion criteria. A predictive matrix was established by the longitudinal data of three consecutive years. TreeNet machine learning algorithm was applied to build prediction model to uncover the dependence relationship between physiological indexes, TCM constitutions, and MS.

Results

By model testing, the overall accuracy rate for prediction model by TreeNet was 73.23%. Top 12.31% individuals in test group (n=325) that have higher probability of having MS covered 23.68% MS patients, showing 0.92 times more risk of having MS than the general population. Importance of ranked top 15 was listed in descending order . The top 5 variables of great importance in MS prediction were TBIL difference between 2014 and 2015 (D_TBIL), TBIL in 2014 (TBIL 2014), LDL-C difference between 2014 and 2015 (D_LDL-C), CCMQ scores for balanced constitution in 2015 (balanced constitution 2015), and TCH in 2015 (TCH 2015). When D_TBIL was between 0 and 2, TBIL 2014 was between 10 and 15, D_LDL-C was above 19, balanced constitution 2015 was below 60, or TCH 2015 was above 5.7, the incidence of MS was higher. Furthermore, there were interactions between balanced constitution 2015 score and TBIL 2014 or D_LDL-C in MS prediction.

Conclusion

Balanced constitution, TBIL, LDL-C, and TCH level can act as predictors for MS. The combination of TCM constitution and physiological indexes can give early warning to MS.

Proteomic and bioinformatic discovery of biomarkers for diabetic nephropathy

Diabetes is associated with numerous metabolic and vascular risk factors that contribute to a high rate of micro-vascular and macro-vascular disorders leading to mortality and morbidity from diabetic complications. In this case, the major cause of death in overall diabetic patients results from diabetic nephropathy (DN) or renal failure. The risk factors and mechanisms that correspond to the development of DN are not fully understood and so far, no specific and sufficient diagnostic biomarkers are currently available other than micro- or macroalbuminuria. Therefore, this review describes current and novel protein biomarkers in the context of DN as well as probable proteins biomarkers associated with pathological processes for the early stage of DN via proteomics data together with bioinformatics. In addition, the mechanisms involved in early development of diabetic vascular disorders and complications resulting from glucose induced oxidative stress will also be explored.

Machine Learning and Data Mining Methods in Diabetes Research

The remarkable advances in biotechnology and health sciences have led to a significant production of data, such as high throughput genetic data and clinical information, generated from large Electronic Health Records (EHRs). To this end, application of machine learning and data mining methods in biosciences is presently, more than ever before, vital and indispensable in efforts to transform intelligently all available information into valuable knowledge. Diabetes mellitus (DM) is defined as a group of metabolic disorders exerting significant pressure on human health worldwide. Extensive research in all aspects of diabetes (diagnosis, etiopathophysiology, therapy, etc.) has led to the generation of huge amounts of data. The aim of the present study is to conduct a systematic review of the applications of machine learning, data mining techniques and tools in the field of diabetes research with respect to a) Prediction and Diagnosis, b) Diabetic Complications, c) Genetic Background and Environment, and e) Health Care and Management with the first category appearing to be the most popular. A wide range of machine learning algorithms were employed. In general, 85% of those used were characterized by supervised learning approaches and 15% by unsupervised ones, and more specifically, association rules. Support vector machines (SVM) arise as the most successful and widely used algorithm. Concerning the type of data, clinical datasets were mainly used. The title applications in the selected articles project the usefulness of extracting valuable knowledge leading to new hypotheses targeting deeper understanding and further investigation in DM.

Applying Naive Bayesian Networks to Disease Prediction: a Systematic Review

INTRODUCTION

Naive Bayesian networks (NBNs) are one of the most effective and simplest Bayesian networks for prediction.

OBJECTIVE

This paper aims to review published evidence about the application of NBNs in predicting disease and it tries to show NBNs as the fundamental algorithm for the best performance in comparison with other algorithms.

METHODS

PubMed was electronically checked for articles published between 2005 and 2015. For characterizing eligible articles, a comprehensive electronic searching method was conducted. Inclusion criteria were determined based on NBN and its effects on disease prediction. A total of 99 articles were found. After excluding the duplicates (n= 5), the titles and abstracts of 94 articles were skimmed according to the inclusion criteria. Finally, 38 articles remained. They were reviewed in full text and 15 articles were excluded. Eventually, 23 articles were selected which met our eligibility criteria and were included in this study.

RESULT

In this article, the use of NBN in predicting diseases was described. Finally, the results were reported in terms of Accuracy, Sensitivity, Specificity and Area under ROC curve (AUC). The last column in Table 2 shows the differences between NBNs and other algorithms.

DISCUSSION

This systematic review (23 studies, 53,725 patients) indicates that predicting diseases based on a NBN had the best performance in most diseases in comparison with the other algorithms. Finally in most cases NBN works better than other algorithms based on the reported accuracy.

CONCLUSION

The method, termed NBNs is proposed and can efficiently construct a prediction model for disease.

A New Data Analysis System to Quantify Associations between Biochemical Parameters of Chronic Kidney Disease-Mineral Bone Disease

BACKGROUND

In hemodialysis patients, deviations from KDIGO recommended values of individual parameters, phosphate, calcium or parathyroid hormone (PTH), are associated with increased mortality. However, it is widely accepted that these parameters are not regulated independently of each other and that therapy aimed to correct one parameter often modifies the others. The aim of the present study is to quantify the degree of association between parameters of chronic kidney disease and mineral bone disease (CKD-MBD).

METHODS

Data was extracted from a cohort of 1758 adult HD patients between January 2000 and June 2013 obtaining a total of 46.141 records (10 year follow-up). We used an advanced data analysis system called Random Forest (RF) which is based on self-learning procedure with similar axioms to those utilized for the development of artificial intelligence. This new approach is particularly useful when the variables analyzed are closely dependent to each other.

RESULTS

The analysis revealed a strong association between PTH and phosphate that was superior to that of PTH and Calcium. The classical linear regression analysis between PTH and phosphate shows a correlation coefficient is 0.27, p<0.001, the possibility to predict PTH changes from phosphate modification is marginal. Alternatively, RF assumes that changes in phosphate will cause modifications in other associated variables (calcium and others) that may also affect PTH values. Using RF the correlation coefficient between changes in serum PTH and phosphate is 0.77, p<0.001; thus, the power of prediction is markedly increased. The effect of therapy on biochemical variables was also analyzed using this RF.

CONCLUSION

Our results suggest that the analysis of the complex interactions between mineral metabolism parameters in CKD-MBD may demand a more advanced data analysis system such as RF.

An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients

Background

The prevalence of type 2 diabetes is increasing at an alarming rate. Various complications are associated with type 2 diabetes, with diabetic nephropathy being the leading cause of renal failure among diabetics. Often, when patients are diagnosed with diabetic nephropathy, their renal functions have already been significantly damaged. Therefore, a risk prediction tool may be beneficial for the implementation of early treatment and prevention.

Results

In the present study, we developed a decision tree-based model integrating genetic and clinical features in a gender-specific classification for the identification of diabetic nephropathy among type 2 diabetic patients. Clinical and genotyping data were obtained from a previous genetic association study involving 345 type 2 diabetic patients (185 with diabetic nephropathy and 160 without diabetic nephropathy). Using a five-fold cross-validation approach, the performance of using clinical or genetic features alone in various classifiers (decision tree, random forest, Naïve Bayes, and support vector machine) was compared with that of utilizing a combination of attributes. The inclusion of genetic features and the implementation of an additional gender-based rule yielded better classification results.

Conclusions

The current model supports the notion that genes and gender are contributing factors of diabetic nephropathy. Further refinement of the proposed approach has the potential to facilitate the early identification of diabetic nephropathy and the development of more efficient treatment in a clinical setting.

Attenuation of hyperlipidemia- and diabetes-induced early-stage apoptosis and late-stage renal dysfunction via administration of fibroblast growth factor-21 is associated with suppression of renal inflammation

Background

Lipotoxicity is a key feature of the pathogenesis of diabetic kidney disease, and is attributed to excessive lipid accumulation (hyperlipidemia). Increasing evidence suggests that fibroblast growth factor (FGF)21 has a crucial role in lipid metabolism under diabetic conditions.

Objective

The present study investigated whether FGF21 can prevent hyperlipidemia- or diabetes-induced renal damage, and if so, the possible mechanism.

Methods

Mice were injected with free fatty acids (FFAs, 10 mg/10 g body weight) or streptozotocin (150 mg/kg) to establish a lipotoxic model or type 1 diabetic model, respectively. Simultaneously the mice were treated with FGF21 (100 µg/kg) for 10 or 80 days. The kidney weight-to-tibia length ratio and renal function were assessed. Systematic and renal lipid levels were detected by ELISA and Oil Red O staining. Renal apoptosis was examined by TUNEL assay. Inflammation, oxidative stress, and fibrosis were assessed by Western blot.

Results

Acute FFA administration and chronic diabetes were associated with lower kidney-to-tibia length ratio, higher lipid levels, severe renal apoptosis and renal dysfunction. Obvious inflammation, oxidative stress and fibrosis also observed in the kidney of both mice models. Deletion of the fgf21 gene further enhanced the above pathological changes, which were significantly prevented by administration of exogenous FGF21.

Conclusion

These results suggest that FFA administration and diabetes induced renal damage, which was further enhanced in FGF21 knock-out mice. Administration of FGF21 significantly prevented both FFA- and diabetes-induced renal damage partially by decreasing renal lipid accumulation and suppressing inflammation, oxidative stress, and fibrosis.