Evaluation of predictive models of aneurysm focal growth and bleb development using machine learning techniques.

BACKGROUND: The presence of blebs increases the rupture risk of intracranial aneurysms (IAs). OBJECTIVE: To evaluate whether cross-sectional bleb formation models can identify aneurysms with focalized enlargement in longitudinal series. METHODS: Hemodynamic, geometric, and anatomical variables derived from computational fluid dynamics models of 2265 IAs from a cross-sectional dataset were used to train machine learning (ML) models for bleb development. ML algorithms, including logistic regression, random forest, bagging method, support vector machine, and K-nearest neighbors, were validated using an independent cross-sectional dataset of 266 IAs. The models' ability to identify aneurysms with focalized enlargement was evaluated using a separate longitudinal dataset of 174 IAs. Model performance was quantified by the area under the receiving operating characteristic curve (AUC), the sensitivity and specificity, positive predictive value, negative predictive value, F1 score, balanced accuracy, and misclassification error. RESULTS: The final model, with three hemodynamic and four geometrical variables, along with aneurysm location and morphology, identified strong inflow jets, non-uniform wall shear stress with high peaks, larger sizes, and elongated shapes as indicators of a higher risk of focal growth over time. The logistic regression model demonstrated the best performance on the longitudinal series, achieving an AUC of 0.9, sensitivity of 85%, specificity of 75%, balanced accuracy of 80%, and a misclassification error of 21%. CONCLUSIONS: Models trained with cross-sectional data can identify aneurysms prone to future focalized growth with good accuracy. These models could potentially be used as early indicators of future risk in clinical practice.

Exploring county-level spatio-temporal patterns in opioid overdose related emergency department visits.

Opioid overdoses within the United States continue to rise and have been negatively impacting the social and economic status of the country. In order to effectively allocate resources and identify policy solutions to reduce the number of overdoses, it is important to understand the geographical differences in opioid overdose rates and their causes. In this study, we utilized data on emergency department opioid overdose (EDOOD) visits to explore the county-level spatio-temporal distribution of opioid overdose rates within the state of Virginia and their association with aggregate socio-ecological factors. The analyses were performed using a combination of techniques including Moran's I and multilevel modeling. Using data from 2016-2021, we found that Virginia counties had notable differences in their EDOOD visit rates with significant neighborhood-level associations: many counties in the southwestern region were consistently identified as the hotspots (areas with a higher concentration of EDOOD visits) whereas many counties in the northern region were consistently identified as the coldspots (areas with a lower concentration of EDOOD visits). In most Virginia counties, EDOOD visit rates declined from 2017 to 2018. In more recent years (since 2019), the visit rates showed an increasing trend. The multilevel modeling revealed that the change in clinical care factors (i.e., access to care and quality of care) and socio-economic factors (i.e., levels of education, employment, income, family and social support, and community safety) were significantly associated with the change in the EDOOD visit rates. The findings from this study have the potential to assist policymakers in proper resource planning thereby improving health outcomes.

Prediction of bleb formation in intracranial aneurysms using machine learning models based on aneurysm hemodynamics, geometry, location, and patient population.

BACKGROUND: Bleb presence in intracranial aneurysms (IAs) is a known indication of instability and vulnerability. OBJECTIVE: To develop and evaluate predictive models of bleb development in IAs based on hemodynamics, geometry, anatomical location, and patient population. METHODS: Cross-sectional data (one time point) of 2395 IAs were used for training bleb formation models using machine learning (random forest, support vector machine, logistic regression, k-nearest neighbor, and bagging). Aneurysm hemodynamics and geometry were characterized using image-based computational fluid dynamics. A separate dataset with 266 aneurysms was used for model evaluation. Model performance was quantified by the area under the receiving operating characteristic curve (AUC), true positive rate (TPR), false positive rate (FPR), precision, and balanced accuracy. RESULTS: The final model retained 18 variables, including hemodynamic, geometrical, location, multiplicity, and morphology parameters, and patient population. Generally, strong and concentrated inflow jets, high speed, complex and unstable flow patterns, and concentrated, oscillatory, and heterogeneous wall shear stress patterns together with larger, more elongated, and more distorted shapes were associated with bleb formation. The best performance on the validation set was achieved by the random forest model (AUC=0.82, TPR=91%, FPR=36%, misclassification error=27%). CONCLUSIONS: Based on the premise that aneurysm characteristics prior to bleb formation resemble those derived from vascular reconstructions with their blebs virtually removed, machine learning models can identify aneurysms prone to bleb development with good accuracy. Pending further validation with longitudinal data, these models may prove valuable for assessing the propensity of IAs to progress to vulnerable states and potentially rupturing.

Incorporating variability of patient inflow conditions into statistical models for aneurysm rupture assessment.

BACKGROUND: Hemodynamic patterns have been associated with cerebral aneurysm instability. For patient-specific computational fluid dynamics (CFD) simulations, the inflow rates of a patient are typically not known. The aim of this study was to analyze the influence of inter- and intra-patient variations of cerebral blood flow on the computed hemodynamics through CFD simulations and to incorporate these variations into statistical models for aneurysm rupture prediction. METHODS: Image data of 1820 aneurysms were used for patient-specific steady CFD simulations with nine different inflow rates per case, capturing inter- and intra-patient flow variations. Based on the computed flow fields, 17 hemodynamic parameters were calculated and compared for the different flow conditions. Next, statistical models for aneurysm rupture were trained in 1571 of the aneurysms including hemodynamic parameters capturing the flow variations either by defining hemodynamic "response variables" (model A) or repeatedly randomly selecting flow conditions by patients (model B) as well as morphological and patient-specific variables. Both models were evaluated in the remaining 249 cases. RESULTS: All hemodynamic parameters were significantly different for the varying flow conditions (p < 0.001). Both the flow-independent "response" model A and the flow-dependent model B performed well with areas under the receiver operating characteristic curve of 0.8182 and 0.8174 ± 0.0045, respectively. CONCLUSIONS: The influence of inter- and intra-patient flow variations on computed hemodynamics can be taken into account in multivariate aneurysm rupture prediction models achieving a good predictive performance. Such models can be applied to CFD data independent of the specific inflow boundary conditions.

Comparison of statistical learning approaches for cerebral aneurysm rupture assessment.

PURPOSE: Incidental aneurysms pose a challenge to physicians who need to decide whether or not to treat them. A statistical model could potentially support such treatment decisions. The aim of this study was to compare a previously developed aneurysm rupture logistic regression probability model (LRM) to other machine learning (ML) classifiers for discrimination of aneurysm rupture status. METHODS: Hemodynamic, morphological, and patient-related information of 1631 cerebral aneurysms characterized by computational fluid dynamics simulations were used to train support vector machines (SVMs) with linear and RBF kernel (RBF-SVM), k-nearest neighbors (kNN), decision tree, random forest, and multilayer perceptron (MLP) neural network classifiers for predicting the aneurysm rupture status. The classifiers' accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) were evaluated and compared to the LRM using 249 test cases obtained from two external cohorts. Additionally, important variables were determined based on the random forest and weights of the linear SVM. RESULTS: The AUCs of the MLP, LRM, linear SVM, RBF-SVM, kNN, decision tree, and random forest were 0.83, 0.82, 0.80, 0.81, 0.76, 0.70, and 0.79, respectively. The accuracy ranged between 0.76 (decision tree,) and 0.79 (linear SVM, RBF-SVM, and MLP). Important variables for predicting the aneurysm rupture status included aneurysm location, the mean surface curvature, and maximum flow velocity. CONCLUSION: The performance of the LRM was overall comparable to that of the other ML classifiers, confirming its potential for aneurysm rupture assessment. To further improve the predictions, additional information, e.g., related to the aneurysm wall, might be needed.

Extending statistical learning for aneurysm rupture assessment to Finnish and Japanese populations using morphology, hemodynamics, and patient characteristics.

OBJECTIVE: Incidental aneurysms pose a challenge for physicians, who need to weigh the rupture risk against the risks associated with treatment and its complications. A statistical model could potentially support such treatment decisions. A recently developed aneurysm rupture probability model performed well in the US data used for model training and in data from two European cohorts for external validation. Because Japanese and Finnish patients are known to have a higher aneurysm rupture risk, the authors' goals in the present study were to evaluate this model using data from Japanese and Finnish patients and to compare it with new models trained with Finnish and Japanese data. METHODS: Patient and image data on 2129 aneurysms in 1472 patients were used. Of these aneurysm cases, 1631 had been collected mainly from US hospitals, 249 from European (other than Finnish) hospitals, 147 from Japanese hospitals, and 102 from Finnish hospitals. Computational fluid dynamics simulations and shape analyses were conducted to quantitatively characterize each aneurysm's shape and hemodynamics. Next, the previously developed model's discrimination was evaluated using the Finnish and Japanese data in terms of the area under the receiver operating characteristic curve (AUC). Models with and without interaction terms between patient population and aneurysm characteristics were trained and evaluated including data from all four cohorts obtained by repeatedly randomly splitting the data into training and test data. RESULTS: The US model's AUC was reduced to 0.70 and 0.72, respectively, in the Finnish and Japanese data compared to 0.82 and 0.86 in the European and US data. When training the model with Japanese and Finnish data, the average AUC increased only slightly for the Finnish sample (to 0.76 ± 0.16) and Finnish and Japanese cases combined (from 0.74 to 0.75 ± 0.14) and decreased for the Japanese data (to 0.66 ± 0.33). In models including interaction terms, the AUC in the Finnish and Japanese data combined increased significantly to 0.83 ± 0.10. CONCLUSIONS: Developing an aneurysm rupture prediction model that applies to Japanese and Finnish aneurysms requires including data from these two cohorts for model training, as well as interaction terms between patient population and the other variables in the model. When including this information, the performance of such a model with Japanese and Finnish data is close to its performance with US or European data. These results suggest that population-specific differences determine how hemodynamics and shape associate with rupture risk in intracranial aneurysms.

Development and internal validation of an aneurysm rupture probability model based on patient characteristics and aneurysm location, morphology, and hemodynamics.

PURPOSE: Unruptured cerebral aneurysms pose a dilemma for physicians who need to weigh the risk of a devastating subarachnoid hemorrhage against the risk of surgery or endovascular treatment and their complications when deciding on a treatment strategy. A prediction model could potentially support such treatment decisions. The aim of this study was to develop and internally validate a model for aneurysm rupture based on hemodynamic and geometric parameters, aneurysm location, and patient gender and age. METHODS: Cross-sectional data from 1061 patients were used for image-based computational fluid dynamics and shape characterization of 1631 aneurysms for training an aneurysm rupture probability model using logistic group Lasso regression. The model's discrimination and calibration were internally validated based on the area under the curve (AUC) of the receiver operating characteristic and calibration plots. RESULTS: The final model retained 11 hemodynamic and 12 morphological variables, aneurysm location, as well as patient age and gender. An adverse hemodynamic environment characterized by a higher maximum oscillatory shear index, higher kinetic energy and smaller low shear area as well as a more complex aneurysm shape, male gender and younger age were associated with an increased rupture risk. The corresponding AUC of the model was 0.86 (95% CI [0.85, 0.86], after correction for optimism 0.84). CONCLUSION: The model combining variables from various domains was able to discriminate between ruptured and unruptured aneurysms with an AUC of 86%. Internal validation indicated potential for the application of this model in clinical practice after evaluation with longitudinal data.

Development of a statistical model for discrimination of rupture status in posterior communicating artery aneurysms.

BACKGROUND: Intracranial aneurysms at the posterior communicating artery (PCOM) are known to have high rupture rates compared to other locations. We developed and internally validated a statistical model discriminating between ruptured and unruptured PCOM aneurysms based on hemodynamic and geometric parameters, angio-architectures, and patient age with the objective of its future use for aneurysm risk assessment. METHODS: A total of 289 PCOM aneurysms in 272 patients modeled with image-based computational fluid dynamics (CFD) were used to construct statistical models using logistic group lasso regression. These models were evaluated with respect to discrimination power and goodness of fit using tenfold nested cross-validation and a split-sample approach to mimic external validation. RESULTS: The final model retained maximum and minimum wall shear stress (WSS), mean parent artery WSS, maximum and minimum oscillatory shear index, shear concentration index, and aneurysm peak flow velocity, along with aneurysm height and width, bulge location, non-sphericity index, mean Gaussian curvature, angio-architecture type, and patient age. The corresponding area under the curve (AUC) was 0.8359. When omitting data from each of the three largest contributing hospitals in turn, and applying the corresponding model on the left-out data, the AUCs were 0.7507, 0.7081, and 0.5842, respectively. CONCLUSIONS: Statistical models based on a combination of patient age, angio-architecture, hemodynamics, and geometric characteristics can discriminate between ruptured and unruptured PCOM aneurysms with an AUC of 84%. It is important to include data from different hospitals to create models of aneurysm rupture that are valid across hospital populations.

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.

It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.

BACKGROUND: The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlapping patterns arising e.g. from post-translational modifications. As the classification of the recorded data points into either 'noise' or 'signal' lies at the very root of essentially every proteomic application, the quality of the automated processing of mass spectra can significantly influence the way the data might be interpreted within a given biological context. RESULTS: We propose non-negative least squares/non-negative least absolute deviation regression to fit a raw spectrum by templates imitating isotope patterns. In a carefully designed validation scheme, we show that the method exhibits excellent performance in pattern picking. It is demonstrated that the method is able to disentangle complicated overlaps of patterns. CONCLUSIONS: We find that regularization is not necessary to prevent overfitting and that thresholding is an effective and user-friendly way to perform feature selection. The proposed method avoids problems inherent in regularization-based approaches, comes with a set of well-interpretable parameters whose default configuration is shown to generalize well without the need for fine-tuning, and is applicable to spectra of different platforms. The R package IPPD implements the method and is available from the Bioconductor platform (http://bioconductor.fhcrc.org/help/bioc-views/devel/bioc/html/IPPD.html).

Stability and aggregation of ranked gene lists.

Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature, but they have grown to a hot topic in the last few years, perhaps as a consequence of the increasing skepticism on the reproducibility and clinical applicability of molecular research findings. In this article, we review existing approaches for the assessment of stability of ranked gene lists and the related problem of aggregation, give some practical recommendations, and warn against potential misuse of these methods. This overview is illustrated through an application to a recent leukemia data set using the freely available Bioconductor package GeneSelector.