Validation of a predictive model for obstructive sleep apnea in people with Down syndrome.

Detecting obstructive sleep apnea (OSA) is important to both prevent significant comorbidities in people with Down syndrome (DS) and untangle contributions to other behavioral and mental health diagnoses. However, laboratory-based polysomnograms are often poorly tolerated, unavailable, or not covered by health insurance for this population. In previous work, our team developed a prediction model that seemed to hold promise in identifying which people with DS might not have significant apnea and, consequently, might be able to forgo a diagnostic polysomnogram. In this study, we sought to validate these findings in a novel set of participants with DS. We recruited an additional 64 participants with DS, ages 3-35 years. Caregivers completed the same validated questionnaires, and our study team collected vital signs, physical exam findings, and medical histories that were previously shown to be predictive. Patients then had a laboratory-based polysomnogram. The best modeling had a validated negative predictive value of 50% for an apnea-hypopnea index (AHI) > 1/hTST and 73.7% for AHI >5/hTST. The positive predictive values were 60% and 39.1%, respectively. As such, a clinically reliable screening tool for OSA in people with DS was not achieved. Patients with DS should continue to be monitored for OSA according to current healthcare guidelines.

Machine learning in primary biliary cholangitis: A novel approach for risk stratification.

BACKGROUND & AIMS: Machine learning (ML) provides new approaches for prognostication through the identification of novel subgroups of patients. We explored whether ML could support disease sub-phenotyping and risk stratification in primary biliary cholangitis (PBC). METHODS: ML was applied to an international dataset of PBC patients. The dataset was split into a derivation cohort (training set) and a validation cohort (validation set), and key clinical features were analysed. The outcome was a composite of liver-related death or liver transplantation. ML and standard survival analysis were performed. RESULTS: The training set was composed of 11,819 subjects, while the validation set was composed of 1,069 subjects. ML identified four clusters of patients characterized by different phenotypes and long-term prognosis. Cluster 1 (n = 3566) included patients with excellent prognosis, whereas Cluster 2 (n = 3966) consisted of individuals at worse prognosis differing from Cluster 1 only for albumin levels around the limit of normal. Cluster 3 (n = 2379) included young patients with florid cholestasis and Cluster 4 (n = 1908) comprised advanced cases. Further sub-analyses on the dynamics of albumin within the normal range revealed that ursodeoxycholic acid-induced increase of albumin >1.2 x lower limit of normal (LLN) is associated with improved transplant-free survival. CONCLUSIONS: Unsupervised ML identified four novel groups of PBC patients with different phenotypes and prognosis and highlighted subtle variations of albumin within the normal range. Therapy-induced increase of albumin >1.2 x LLN should be considered a treatment goal.

Analyzing gene expression data for pediatric and adult cancer diagnosis using logic learning machine and standard supervised methods.

BACKGROUND: Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules. In this investigation the performance of LLM in classifying patients with cancer was evaluated using a set of eight publicly available gene expression databases for cancer diagnosis. LLM accuracy was assessed by summary ROC curve (sROC) analysis and estimated by the area under an sROC curve (sAUC). Its performance was compared in cross validation with that of standard supervised methods, namely: decision tree, artificial neural network, support vector machine (SVM) and k-nearest neighbor classifier. RESULTS: LLM showed an excellent accuracy (sAUC = 0.99, 95%CI: 0.98-1.0) and outperformed any other method except SVM. CONCLUSIONS: LLM is a new powerful tool for the analysis of gene expression data for cancer diagnosis. Simple rules generated by LLM could contribute to a better understanding of cancer biology, potentially addressing therapeutic approaches.

Uncovering Predictors of Lipid Goal Attainment in Type 2 Diabetes Outpatients Using Logic Learning Machine: Insights from the AMD Annals and AMD Artificial Intelligence Study Group.

Identifying and treating lipid abnormalities is crucial for preventing cardiovascular disease in diabetic patients, yet only two-thirds of patients reach recommended cholesterol levels. Elucidating the factors associated with lipid goal attainment represents an unmet clinical need. To address this knowledge gap, we conducted a real-world analysis of the lipid profiles of 11.252 patients from the Annals of the Italian Association of Medical Diabetologists (AMD) database from 2005 to 2019. We used a Logic Learning Machine (LLM) to extract and classify the most relevant variables predicting the achievement of a low-density lipoprotein cholesterol (LDL-C) value lower than 100 mg/dL (2.60 mmol/L) within two years of the start of lipid-lowering therapy. Our analysis showed that 61.4% of the patients achieved the treatment goal. The LLM model demonstrated good predictive performance, with a precision of 0.78, accuracy of 0.69, recall of 0.70, F1 Score of 0.74, and ROC-AUC of 0.79. The most significant predictors of achieving the treatment goal were LDL-C values at the start of lipid-lowering therapy and their reduction after six months. Other predictors of a greater likelihood of reaching the target included high-density lipoprotein cholesterol, albuminuria, and body mass index at baseline, as well as younger age, male sex, more follow-up visits, no therapy discontinuation, higher Q-score, lower blood glucose and HbA1c levels, and the use of anti-hypertensive medication. At baseline, for each LDL-C range analysed, the LLM model also provided the minimum reduction that needs to be achieved by the next six-month visit to increase the likelihood of reaching the therapeutic goal within two years. These findings could serve as a useful tool to inform therapeutic decisions and to encourage further in-depth analysis and testing.

Achieving Good Metabolic Control Without Weight Gain with the Systematic Use of GLP-1-RAs and SGLT-2 Inhibitors in Type 2 Diabetes: A Machine-learning Projection Using Data from Clinical Practice.

PURPOSE: Recently, the 2022 American Diabetes Association and European Association for the Study of Diabetes (ADA-EASD) consensus report stressed the importance of weight control in the management of patients with type 2 diabetes; weight control should be a primary target of therapy. This retrospective analysis evaluated, through an artificial-intelligence (AI) projection of data from the AMD Annals database-a huge collection of most Italian diabetology medical records covering 15 years (2005-2019)-the potential effects of the extended use of sodium-glucose co-transporter 2 inhibitors (SGLT-2is) and of glucose-like peptide 1 receptor antagonists (GLP-1-RAs) on HbA1c and weight. METHODS: Data from 4,927,548 visits in 558,097 patients were retrospectively extracted using these exclusion criteria: type 1 diabetes, pregnancy, age >75 years, dialysis, and lack of data on HbA1c or weight. The analysis revealed late prescribing of SGLT-2is and GLP-1-RAs (innovative drugs), and considering a time frame of 4 years (2014-2017), a paradoxic greater percentage of combined-goal (HbA1c <7% and weight gain <2%) achievement was found with older drugs than with innovative drugs, demonstrating aspects of therapeutic inertia. Through a machine-learning AI technique, a "what-if" analysis was performed, using query models of two outcomes: (1) achievement of the combined goal at the visit subsequent to a hypothetical initial prescribing of an SGLT-2i or a GLP-1-RA, with and without insulin, selected according to the 2018 ADA-EASD diabetes recommendations; and (2) persistence of the combined goal for 18 months. The precision values of the two models were, respectively, sensitivity, 71.1 % and 69.8%, and specificity, 67% and 76%. FINDINGS: The first query of the AI analysis showed a great improvement in achievement of the combined goal: 38.8% with prescribing in clinical practice versus 66.5% with prescribing in the "what-if" simulation. Addressing persistence at 18 months after the initial achievement of the combined goal, the simulation showed a potential better performance of SGLT-2is and GLP-1-RAs with respect to each antidiabetic pharmacologic class or combination considered. IMPLICATIONS: AI appears potentially useful in the analysis of a great amount of data, such as that derived from the AMD Annals. In the present study, an LLM analysis revealed a great potential improvement in achieving metabolic targets with SGLT-2i and GLP-1-RA utilization. These results underscore the importance of early, timely, and extended use of these new drugs.

The clinical meaning of the area under a receiver operating characteristic curve for the evaluation of the performance of disease markers.

OBJECTIVES: The area under a receiver operating characteristic (ROC) curve (AUC) is a popular measure of pure diagnostic accuracy that is independent from the proportion of diseased subjects in the analysed sample. However, its actual usefulness in the clinical context has been questioned, because it does not seem to be directly related to the actual performance of a diagnostic marker in identifying diseased and non-diseased subjects in real clinical settings. This study evaluates the relationship between the AUC and the proportion of correct classifications (global diagnostic accuracy, GDA) in relation to the shape of the corresponding ROC curves. METHODS: We demonstrate that AUC represents an upward-biased measure of GDA at an optimal accuracy cut-off for balanced groups. The magnitude of bias depends on the shape of the ROC plot and on the proportion of diseased and non-diseased subjects. In proper curves, the bias is independent from the diseased/non-diseased ratio and can be easily estimated and removed. Moreover, a comparison between 2 partial AUCs can be replaced by a more powerful test for the corresponding whole AUCs. RESULTS: Applications to 3 real datasets are provided: a marker for a hormone deficit in children, 2 tumour markers for malignant mesothelioma, and 2 gene expression profiles in ovarian cancer patients. CONCLUSIONS: The AUC is a measure of accuracy with potential clinical relevance for the evaluation of disease markers. The clinical meaning of ROC parameters should always be evaluated with an analysis of the shape of the corresponding ROC curve.

LLM-PBC: Logic Learning Machine-Based Explainable Rules Accurately Stratify the Genetic Risk of Primary Biliary Cholangitis.

BACKGROUND: The application of Machine Learning (ML) to genetic individual-level data represents a foreseeable advancement for the field, which is still in its infancy. Here, we aimed to evaluate the feasibility and accuracy of an ML-based model for disease risk prediction applied to Primary Biliary Cholangitis (PBC). METHODS: Genome-wide significant variants identified in subjects of European ancestry in the recently released second international meta-analysis of GWAS in PBC were used as input data. Quality-checked, individual genomic data from two Italian cohorts were used. The ML included the following steps: import of genotype and phenotype data, genetic variant selection, supervised classification of PBC by genotype, generation of "if-then" rules for disease prediction by logic learning machine (LLM), and model validation in a different cohort. RESULTS: The training cohort included 1345 individuals: 444 were PBC cases and 901 were healthy controls. After pre-processing, 41,899 variants entered the analysis. Several configurations of parameters related to feature selection were simulated. The best LLM model reached an Accuracy of 71.7%, a Matthews correlation coefficient of 0.29, a Youden's value of 0.21, a Sensitivity of 0.28, a Specificity of 0.93, a Positive Predictive Value of 0.66, and a Negative Predictive Value of 0.72. Thirty-eight rules were generated. The rule with the highest covering (19.14) included the following genes: RIN3, KANSL1, TIMMDC1, TNPO3. The validation cohort included 834 individuals: 255 cases and 579 controls. By applying the ruleset derived in the training cohort, the Area under the Curve of the model was 0.73. CONCLUSIONS: This study represents the first illustration of an ML model applied to common variants associated with PBC. Our approach is computationally feasible, leverages individual-level data to generate intelligible rules, and can be used for disease prediction in at-risk individuals.

Artificial intelligence for precision medicine in autoimmune liver disease.

Autoimmune liver diseases (AiLDs) are rare autoimmune conditions of the liver and the biliary tree with unknown etiology and limited treatment options. AiLDs are inherently characterized by a high degree of complexity, which poses great challenges in understanding their etiopathogenesis, developing novel biomarkers and risk-stratification tools, and, eventually, generating new drugs. Artificial intelligence (AI) is considered one of the best candidates to support researchers and clinicians in making sense of biological complexity. In this review, we offer a primer on AI and machine learning for clinicians, and discuss recent available literature on its applications in medicine and more specifically how it can help to tackle major unmet needs in AiLDs.

Logic Learning Machine and standard supervised methods for Hodgkin's lymphoma prognosis using gene expression data and clinical variables.

This study evaluates the performance of a set of machine learning techniques in predicting the prognosis of Hodgkin's lymphoma using clinical factors and gene expression data. Analysed samples from 130 Hodgkin's lymphoma patients included a small set of clinical variables and more than 54,000 gene features. Machine learning classifiers included three black-box algorithms ( k-nearest neighbour, Artificial Neural Network, and Support Vector Machine) and two methods based on intelligible rules (Decision Tree and the innovative Logic Learning Machine method). Support Vector Machine clearly outperformed any of the other methods. Among the two rule-based algorithms, Logic Learning Machine performed better and identified a set of simple intelligible rules based on a combination of clinical variables and gene expressions. Decision Tree identified a non-coding gene ( XIST) involved in the early phases of X chromosome inactivation that was overexpressed in females and in non-relapsed patients. XIST expression might be responsible for the better prognosis of female Hodgkin's lymphoma patients.