Bayesian Network as a Decision Tool for Predicting ALS Disease

Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank

Background and Objectives

Amyotrophic lateral sclerosis (ALS) causes profound impairments in neurological function and a cure for this devastating disease remains elusive. Early detection and risk stratification are crucial for timely intervention and improving patient outcomes. This study aimed to identify predisposing genetic, phenotypic, and exposure-related factors for Amyotrophic lateral sclerosis using multi-modal data and assess their joint predictive potential.

Methods

Utilizing data from the UK Biobank, we analyzed an unrelated set of 292 ALS cases and 408,831 controls of European descent. Two polygenic risk scores (PRS) are constructed: "GWAS Hits PRS" and "PRS-CS," reflecting oligogenic and polygenic ALS risk profiles, respectively. Time-restricted phenome-wide association studies (PheWAS) were performed to identify pre-existing conditions increasing ALS risk, integrated into phenotypic risk scores (PheRS). A poly-exposure score ("PXS") captures the influence of environmental exposures measured through survey questionnaires. We evaluate the performance of these scores for predicting ALS incidence and stratifying risk, adjusting for baseline demographic covariates.

Results

Both PRSs modestly predicted ALS diagnosis, but with increased predictive power when combined (covariate-adjusted receiver operating characteristic [AAUC] = 0.584 [0.525, 0.639]). PheRS incorporated diagnoses 1 year before ALS onset (PheRS1) modestly discriminated cases from controls (AAUC = 0.515 [0.472, 0.564]). The "PXS" did not significantly predict ALS. However, a model incorporating PRSs and PheRS1 improved prediction of ALS (AAUC = 0.604 [0.547, 0.667]), outperforming a model combining all risk scores. This combined risk score identified the top 10% of risk score distribution with a 4-fold higher ALS risk (95% CI: [2.04, 7.73]) versus those in the 40%-60% range.

Discussions

By leveraging UK Biobank data, our study uncovers predisposing ALS factors, highlighting the improved effectiveness of multi-factorial prediction models to identify individuals at highest risk for ALS.

Quantitative association between lead exposure and amyotrophic lateral sclerosis: a Bayesian network-based predictive study

BACKGROUND

Environmental lead (Pb) exposure have been suggested as a causative factor for amyotrophic lateral sclerosis (ALS). However, the role of Pb content of human body in ALS outcomes has not been quantified clearly. The purpose of this study was to apply Bayesian networks to forecast the risk of Pb exposure on the disease occurrence.

METHODS

We retrospectively collected medical records of ALS inpatients who underwent blood Pb testing, while matched controlled inpatients on age, gender, hospital ward and admission time according to the radio of 1:9. Tree Augmented Naïve Bayes (TAN), a semi-naïve Bayes classifier, was established to predict probability of ALS or controls with risk factors.

RESULTS

A total of 140 inpatients were included in this study. The whole blood Pb levels of ALS patients (57.00 μg/L) were more than twice as high as the controls (27.71 μg/L). Using the blood Pb concentrations to calculate probability of ALS, TAN produced the total coincidence rate of 90.00%. The specificity, sensitivity of Pb for ALS prediction was 0.79, or 0.74, respectively.

CONCLUSION

Therefore, these results provided quantitative evidence that Pb exposure may contribute to the development of ALS. Bayesian networks may be used to predict the ALS early onset with blood Pb levels.

A Bayesian network perspective on neonatal pneumonia in pregnant women with diabetes mellitus

OBJECTIVE

To predict the influencing factors of neonatal pneumonia in pregnant women with diabetes mellitus using a Bayesian network model. By examining the intricate network connections between the numerous variables given by Bayesian networks (BN), this study aims to compare the prediction effect of the Bayesian network model and to analyze the influencing factors directly associated to neonatal pneumonia.

METHOD

Through the structure learning algorithms of BN, Naive Bayesian (NB), Tree Augmented Naive Bayes (TAN), and k-Dependence Bayesian Classifier (KDB), complex networks connecting variables were presented and their predictive abilities were tested. The BN model and three machine learning models computed using the R bnlean package were also compared in the data set.

RESULTS

In constraint-based algorithms, three algorithms had different presentation DAGs. KDB had a better prediction effect than NB and TAN, and it achieved higher AUC compared with TAN. Among three machine learning modes, Support Vector Machine showed a accuracy rate of 91.04% and 67.88% of precision, which was lower than TAN (92.70%; 72.10%).

CONCLUSION

KDB was applicable, and it can detect the dependencies between variables, identify more potential associations and track changes between variables and outcome.

Bayesian Techniques in Predicting Frailty among Community-Dwelling Older Adults in the Netherlands

Background Frailty is a syndrome that is defined as an accumulation of deficits in physical, psychological, and social domains. On a global scale, there is an urgent need to create frailty-ready healthcare systems due to the healthcare burden that frailty confers on systems and the increased risk of falls, healthcare utilization, disability, and premature mortality. Several studies have been conducted to develop prediction models for predicting frailty. Most studies used logistic regression as a technique to develop a prediction model. One area that has experienced significant growth is the application of Bayesian techniques, partly due to an increasing number of practitioners valuing the Bayesian paradigm as matching that of scientific discovery. Objective We compared ten different Bayesian networks as proposed by ten experts in the field of frail elderly people to predict frailty with a choice from ten dichotomized determinants for frailty. Methods We used the opinion of ten experts who could indicate, using an empty Bayesian network graph, the important predictors for frailty and the interactions between the different predictors. The candidate predictors were age, sex, marital status, ethnicity, education, income, lifestyle, multimorbidity, life events, and home living environment. The ten Bayesian network models were evaluated in terms of their ability to predict frailty. For the evaluation, we used the data of 479 participants that filled in the Tilburg Frailty indicator (TFI) questionnaire for assessing frailty among community-dwelling older people. The data set contained the aforementioned variables and the outcome "frail". The model fit of each model was measured using the Akaike information criterion (AIC) and the predictive performance of the models was measured using the area under the curve (AUC) of the receiver operator characteristic (ROC). The AUCs of the models were validated using bootstrapping with 100 repetitions. The relative importance of the predictors in the models was calculated using the permutation feature importance algorithm (PFI). Results The ten Bayesian networks of the ten experts differed considerably regarding the predictors and the connections between the predictors and the outcome. However, all ten networks had corrected AUCs >0.700. Evaluating the importance of the predictors in each model, "diseases or chronic disorders" was the most important predictor in all models (10 times). The predictors "lifestyle" and "monthly income" were also often present in the models (both 6 times). One or more diseases or chronic disorders, an unhealthy lifestyle, and a monthly income below 1800 euro increased the likelihood of frailty. Conclusions Although the ten experts all made different graphs, the predictive performance was always satisfying (AUCs >0.700). While it is true that the predictor importance varied all the time, the top three of the predictor importance consisted of "diseases or chronic disorders", "lifestyle" and "monthly income". All in all, asking for the opinion of experts in the field of frail elderly to predict frailty with Bayesian networks may be more rewarding than a data-driven forecast with Bayesian networks because they have expert knowledge regarding interactions between the different predictors.

The feasibility of a Bayesian network model to assess the probability of simultaneous symptoms in patients with advanced cancer

Although patients with advanced cancer often experience multiple symptoms simultaneously, clinicians usually focus on symptoms that are volunteered by patients during regular history-taking. We aimed to evaluate the feasibility of a Bayesian network (BN) model to predict the presence of simultaneous symptoms, based on the presence of other symptoms. Our goal is to help clinicians prioritize which symptoms to assess. Patient-reported severity of 11 symptoms (scale 0-10) was measured using an adapted Edmonton Symptom Assessment Scale (ESAS) in a national cross-sectional survey among advanced cancer patients. Scores were dichotomized (< 4 and ≥ 4). Using fourfold cross validation, the prediction error of 9 BN algorithms was estimated (Akaike information criterion (AIC). The model with the highest AIC was evaluated. Model predictive performance was assessed per symptom; an area under curve (AUC) of ≥ 0.65 was considered satisfactory. Model calibration compared predicted and observed probabilities; > 10% difference was considered inaccurate. Symptom scores of 532 patients were collected. A symptom score ≥ 4 was most prevalent for fatigue (64.7%). AUCs varied between 0.60 and 0.78, with satisfactory AUCs for 8/11 symptoms. Calibration was accurate for 101/110 predicted conditional probabilities. Whether a patient experienced fatigue was directly associated with experiencing 7 other symptoms. For example, in the absence or presence of fatigue, the model predicted a 8.6% and 33.1% probability of experiencing anxiety, respectively. It is feasible to use BN development for prioritizing symptom assessment. Fatigue seems most eligble to serve as a starting symptom for predicting the probability of experiencing simultaneous symptoms.

Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review

BACKGROUND

Network medicine is an emerging area of research that focuses on delving into the molecular complexity of the disease, leading to the discovery of network biomarkers and therapeutic target discovery. Amyotrophic lateral sclerosis (ALS) is a complicated rare disease with unknown pathogenesis and no available treatment. In ALS, network properties appear to be potential biomarkers that can be beneficial in disease-related applications when explored independently or in tandem with machine learning (ML) techniques.

OBJECTIVE

This systematic literature review explores recent trends in network medicine and implementations of network-based ML algorithms in ALS. We aim to provide an overview of the identified primary studies and gather details on identifying the potential biomarkers and delineated pathways.

METHODS

The current study consists of searching for and investigating primary studies from PubMed and Dimensions.ai, published between 2018 and 2022 that reported network medicine perspectives and the coupling of ML techniques. Each abstract and full-text study was individually evaluated, and the relevant studies were finally included in the review for discussion once they met the inclusion and exclusion criteria.

RESULTS

We identified 109 eligible publications from primary studies representing this systematic review. The data coalesced into two themes: application of network science to identify disease modules and promising biomarkers in ALS, along with network-based ML approaches. Conclusion This systematic review gives an overview of the network medicine approaches and implementations of network-based ML algorithms in ALS to determine new disease genes, and identify critical pathways and therapeutic target discovery for personalized treatment.

Applied Bayesian Approaches for Research in Motor Neuron Disease

Statistical evaluation of empirical data is the basis of the modern scientific method. Available tools include various hypothesis tests for specific data structures, as well as methods that are used to quantify the uncertainty of an obtained result. Statistics are pivotal, but many misconceptions arise due to their complexity and difficult-to-acquire mathematical background. Even though most studies rely on a frequentist interpretation of statistical readouts, the application of Bayesian statistics has increased due to the availability of easy-to-use software suites and an increased outreach favouring this topic in the scientific community. Bayesian statistics take our prior knowledge together with the obtained data to express a degree of belief how likely a certain event is. Bayes factor hypothesis testing (BFHT) provides a straightforward method to evaluate multiple hypotheses at the same time and provides evidence that favors the null hypothesis or alternative hypothesis. In the present perspective, we show the merits of BFHT for three different use cases, including a clinical trial, basic research as well as a single case study. Here we show that Bayesian statistics is a viable addition of a scientist's statistical toolset, which can help to interpret data.