Dataset Information

Predicting alcohol use disorder remission: a longitudinal multimodal multi-featured machine learning approach.

ABSTRACT: Predictive models for recovering from alcohol use disorder (AUD) and identifying related predisposition biomarkers can have a tremendous impact on addiction treatment outcomes and cost reduction. Our sample (N = 1376) included individuals of European (EA) and African (AA) ancestry from the Collaborative Study on the Genetics of Alcoholism (COGA) who were initially assessed as having AUD (DSM-5) and reassessed years later as either having AUD or in remission. To predict this difference in AUD recovery status, we analyzed the initial data using multimodal, multi-features machine learning applications including EEG source-level functional brain connectivity, Polygenic Risk Scores (PRS), medications, and demographic information. Sex and ancestry age-matched stratified analyses were performed with supervised linear Support Vector Machine application and were calculated twice, once when the ancestry was defined by self-report and once defined by genetic data. Multifeatured prediction models achieved higher accuracy scores than models based on a single domain and higher scores in male models when the ancestry was based on genetic data. The AA male group model with PRS, EEG functional connectivity, marital and employment status features achieved the highest accuracy of 86.04%. Several discriminative features were identified, including collections of PRS related to neuroticism, depression, aggression, years of education, and alcohol consumption phenotypes. Other discriminated features included being married, employed, medication, lower default mode network and fusiform connectivity, and higher insula connectivity. Results highlight the importance of increasing genetic homogeneity of analyzed groups, identifying sex, and ancestry-specific features to increase prediction scores revealing biomarkers related to AUD remission.

SUBMITTER: Kinreich S

PROVIDER: S-EPMC7960734 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Predicting alcohol use disorder remission: a longitudinal multimodal multi-featured machine learning approach.

Kinreich Sivan S McCutcheon Vivia V VV Aliev Fazil F Meyers Jacquelyn L JL Kamarajan Chella C Pandey Ashwini K AK Chorlian David B DB Zhang Jian J Kuang Weipeng W Pandey Gayathri G Viteri Stacey Subbie-Saenz de SS Francis Meredith W MW Chan Grace G Bourdon Jessica L JL Dick Danielle M DM Anokhin Andrey P AP Bauer Lance L Hesselbrock Victor V Schuckit Marc A MA Nurnberger John I JI Foroud Tatiana M TM Salvatore Jessica E JE Bucholz Kathleen K KK Porjesz Bernice B

Translational psychiatry 20210315 1

Predictive models for recovering from alcohol use disorder (AUD) and identifying related predisposition biomarkers can have a tremendous impact on addiction treatment outcomes and cost reduction. Our sample (N = 1376) included individuals of European (EA) and African (AA) ancestry from the Collaborative Study on the Genetics of Alcoholism (COGA) who were initially assessed as having AUD (DSM-5) and reassessed years later as either having AUD or in remission. To predict this difference in AUD rec ...[more]

PMID: 33723218

Similar Datasets

Project description:Predictive models have succeeded in distinguishing between individuals with Alcohol use Disorder (AUD) and controls. However, predictive models identifying who is prone to develop AUD and the biomarkers indicating a predisposition to AUD are still unclear. Our sample (n = 656) included offspring and non-offspring of European American (EA) and African American (AA) ancestry from the Collaborative Study of the Genetics of Alcoholism (COGA) who were recruited as early as age 12 and were unaffected at first assessment and reassessed years later as AUD (DSM-5) (n = 328) or unaffected (n = 328). Machine learning analysis was performed for 220 EEG measures, 149 alcohol-related single nucleotide polymorphisms (SNPs) from a recent large Genome-wide Association Study (GWAS) of alcohol use/misuse and two family history (mother DSM-5 AUD and father DSM-5 AUD) features using supervised, Linear Support Vector Machine (SVM) classifier to test which features assessed before developing AUD predict those who go on to develop AUD. Age, gender, and ancestry stratified analyses were performed. Results indicate significant and higher accuracy rates for the AA compared with the EA prediction models and a higher model accuracy trend among females compared with males for both ancestries. Combined EEG and SNP features model outperformed models based on only EEG features or only SNP features for both EA and AA samples. This multidimensional superiority was confirmed in a follow-up analysis in the AA age groups (12-15, 16-19, 20-30) and EA age group (16-19). In both ancestry samples, the youngest age group achieved higher accuracy score than the two other older age groups. Maternal AUD increased the model's accuracy in both ancestries' samples. Several discriminative EEG measures and SNPs features were identified, including lower posterior gamma, higher slow wave connectivity (delta, theta, alpha), higher frontal gamma ratio, higher beta correlation in the parietal area, and 5 SNPs: rs4780836, rs2605140, rs11690265, rs692854, and rs13380649. Results highlight the significance of sampling uniformity followed by stratified (e.g., ancestry, gender, developmental period) analysis, and wider selection of features, to generate better prediction scores allowing a more accurate estimation of AUD development.

Project description:IntroductionAlzheimer's disease (AD) is a progressive neurodegenerative disorder. Current core cerebrospinal fluid (CSF) AD biomarkers, widely employed for diagnosis, require a lumbar puncture to be performed, making them impractical as screening tools. Considering the role of sleep disturbances in AD, recent research suggests quantitative sleep electroencephalography features as potential non-invasive biomarkers of AD pathology. However, quantitative analysis of comprehensive polysomnography (PSG) signals remains relatively understudied. PSG is a non-invasive test enabling qualitative and quantitative analysis of a wide range of parameters, offering additional insights alongside other biomarkers. Machine Learning (ML) gained interest for its ability to discern intricate patterns within complex datasets, offering promise in AD neuropathology detection. Therefore, this study aims to evaluate the effectiveness of a multimodal ML approach in predicting core AD CSF biomarkers.MethodsMild-moderate AD patients were prospectively recruited for PSG, followed by testing of CSF and blood samples for biomarkers. PSG signals underwent preprocessing to extract non-linear, time domain and frequency domain statistics quantitative features. Multiple ML algorithms were trained using four subsets of input features: clinical variables (CLINVAR), conventional PSG parameters (SLEEPVAR), quantitative PSG signal features (PSGVAR) and a combination of all subsets (ALL). Cross-validation techniques were employed to evaluate model performance and ensure generalizability. Regression models were developed to determine the most effective variable combinations for explaining variance in the biomarkers.ResultsOn 49 subjects, Gradient Boosting Regressors achieved the best results in estimating biomarkers levels, using different loss functions for each biomarker: least absolute deviation (LAD) for the Aβ42, least squares (LS) for p-tau and Huber for t-tau. The ALL subset demonstrated the lowest training errors for all three biomarkers, albeit with varying test performance. Specifically, the SLEEPVAR subset yielded the best test performance in predicting Aβ42, while the ALL subset most accurately predicted p-tau and t-tau due to the lowest test errors.ConclusionsMultimodal ML can help predict the outcome of CSF biomarkers in early AD by utilizing non-invasive and economically feasible variables. The integration of computational models into medical practice offers a promising tool for the screening of patients at risk of AD, potentially guiding clinical decisions.

Project description:Abstract Background Diagnosis of schizophrenia is based on a collection of symptoms which are heterogeneous from one patient to the other. Therefore, improving the reliability of this diagnosis is a currently unmet need. Schizophrenia risk is associated with genetic variation and with environmental factors potentially affecting neurodevelopment. Moreover, among the symptoms, cognitive abnormalities are heritable and predate its clinical onset. Multivariate techniques can leverage the high dimensionality of data in order to study the combined effect of multiple risk factors and symptoms on clinical predictions. The aim of the current study is therefore to assess the predictability of schizophrenia diagnosis applying machine learning techniques to an ensemble of genetic, early environmental and cognitive deficits variables. Methods 442 subjects (339 healthy controls – HC – and 103 patients with schizophrenia – SCZ) were recruited for the study. Participants underwent a full neuropsychological evaluation (Modality 1, assessment of working memory, verbal fluency, intelligence quotient, attention, speed of processing and cognitive control), a broad environmental assessment (Modality 2, investigation of urbanicity, obstetric complications, developmental anomalies, socio-economic parental status and age of parents at birth) and genome-wide genotyping (Modality 3). Following published procedures, we computed individual risk scores for each of the single nucleotide polymorphisms (SNPs) associated with risk for schizophrenia in the Psychiatric Genomics Consortium (PGC) study. Data from Modalities 1, 2 and 3 entered NeuroMiner v0.998 and underwent preprocessing procedures through scaling, pruning of non-informative variables and imputation of missing values through Euclidean distance-based nearest-neighbor search. Then, these three modalities were included in a Support Vector Machine HC vs. SCZ classification algorithm, which applied decision-based data fusion strategies to integrate the individual predictions of the three modalities in a nested cross-validation framework. Results Our cross-validated results revealed that Modality 1 (cognition) predicted schizophrenia diagnosis with the highest Balanced Accuracy (BAC, 87.3%) and that the most selected cognitive indices were intelligence quotient scores and attentional abilities. Modality 2 (environment) classified HC and SCZ with a BAC of 67.2%, and the most predictive environmental features were the parental socio-economic status, the presence of developmental anomalies during the first year of life and the age of father at birth. On the other hand, Modality 3 (genetics) predicted schizophrenia diagnosis with BAC=54,1%. The most informative SNPs were FUT9 rs117074560, TCF4 rs72934570 and STAG1 rs7432375. Decision-based fusion combining individual cognitive, environmental and genetic decision scores predicted the classification of SCZ from HC with a 78.9% BAC. Discussion Our results using a novel machine learning approach suggest that an ensemble of cognitive, early environmental and genetic features can predict schizophrenia with significant accuracy. Our results also give key information on cognitive and environmental factors that can be targeted in early identification programs and offer novel insights about genetic loci that may be prioritized in future investigations of the pathophysiology of the disease. However, the near chance-level predictive ability of the genetic modality alone calls for the implementation and testing of more complex models of interaction between multiple risk factors.

Project description:Although emerging evidence has implicated structural/functional abnormalities of patients with Autism Spectrum Disorder(ASD), definitive neuroimaging markers remain obscured due to inconsistent or incompatible findings, especially for structural imaging. Furthermore, brain differences defined by statistical analysis are difficult to implement individual prediction. The present study has employed the machine learning techniques under the unified framework in neuroimaging to identify the neuroimaging markers of patients with ASD and distinguish them from typically developing controls(TDC). To enhance the interpretability of the machine learning model, the study has processed three levels of assessments including model-level assessment, feature-level assessment, and biology-level assessment. According to these three levels assessment, the study has identified neuroimaging markers of ASD including the opercular part of bilateral inferior frontal gyrus, the orbital part of right inferior frontal gyrus, right rolandic operculum, right olfactory cortex, right gyrus rectus, right insula, left inferior parietal gyrus, bilateral supramarginal gyrus, bilateral angular gyrus, bilateral superior temporal gyrus, bilateral middle temporal gyrus, and left inferior temporal gyrus. In addition, negative correlations between the communication skill score in the Autism Diagnostic Observation Schedule (ADOS_G) and regional gray matter (GM) volume in the gyrus rectus, left middle temporal gyrus, and inferior temporal gyrus have been detected. A significant negative correlation has been found between the communication skill score in ADOS_G and the orbital part of the left inferior frontal gyrus. A negative correlation between verbal skill score and right angular gyrus and a significant negative correlation between non-verbal communication skill and right angular gyrus have been found. These findings in the study have suggested the GM alteration of ASD and correlated with the clinical severity of ASD disease symptoms. The interpretable machine learning framework gives sight to the pathophysiological mechanism of ASD but can also be extended to other diseases.

Dataset Information

Predicting alcohol use disorder remission: a longitudinal multimodal multi-featured machine learning approach.

Publications

Predicting alcohol use disorder remission: a longitudinal multimodal multi-featured machine learning approach.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets