Dataset Information

O9.4. PREDICTING SCHIZOPHRENIA: IDENTIFICATION OF MULTIMODAL MARKERS OF DISEASE THROUGH A MACHINE LEARNING APPROACH

ABSTRACT: 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.

SUBMITTER: Antonucci L

PROVIDER: S-EPMC5887307 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Project description:BackgroundWith millisecond-level resolution, electroencephalographic (EEG) recording provides a sensitive tool to assay neural dynamics of human cognition. However, selection of EEG features used to answer experimental questions is typically determined a priori. The utility of machine learning was investigated as a computational framework for extracting the most relevant features from EEG data empirically.MethodsSchizophrenia (SZ; n = 40) and healthy community (HC; n = 12) subjects completed a Sternberg Working Memory Task (SWMT) during EEG recording. EEG was analyzed to extract 5 frequency components (theta1, theta2, alpha, beta, gamma) at 4 processing stages (baseline, encoding, retention, retrieval) and 3 scalp sites (frontal-Fz, central-Cz, occipital-Oz) separately for correctly and incorrectly answered trials. The 1-norm support vector machine (SVM) method was used to build EEG classifiers of SWMT trial accuracy (correct vs. incorrect; Model 1) and diagnosis (HC vs. SZ; Model 2). External validity of SVM models was examined in relation to neuropsychological test performance and diagnostic classification using conventional regression-based analyses.ResultsSWMT performance was significantly reduced in SZ (p < .001). Model 1 correctly classified trial accuracy at 84 % in HC, and at 74 % when cross-validated in SZ data. Frontal gamma at encoding and central theta at retention provided highest weightings, accounting for 76 % of variance in SWMT scores and 42 % variance in neuropsychological test performance across samples. Model 2 identified frontal theta at baseline and frontal alpha during retrieval as primary classifiers of diagnosis, providing 87 % classification accuracy as a discriminant function.ConclusionsEEG features derived by SVM are consistent with literature reports of gamma's role in memory encoding, engagement of theta during memory retention, and elevated resting low-frequency activity in schizophrenia. Tests of model performance and cross-validation support the stability and generalizability of results, and utility of SVM as an analytic approach for EEG feature selection.

Project description:BackgroundMental health disorders affect multiple aspects of patients' lives, including mood, cognition, and behavior. eHealth and mobile health (mHealth) technologies enable rich sets of information to be collected noninvasively, representing a promising opportunity to construct behavioral markers of mental health. Combining such data with self-reported information about psychological symptoms may provide a more comprehensive and contextualized view of a patient's mental state than questionnaire data alone. However, mobile sensed data are usually noisy and incomplete, with significant amounts of missing observations. Therefore, recognizing the clinical potential of mHealth tools depends critically on developing methods to cope with such data issues.ObjectiveThis study aims to present a machine learning-based approach for emotional state prediction that uses passively collected data from mobile phones and wearable devices and self-reported emotions. The proposed methods must cope with high-dimensional and heterogeneous time-series data with a large percentage of missing observations.MethodsPassively sensed behavior and self-reported emotional state data from a cohort of 943 individuals (outpatients recruited from community clinics) were available for analysis. All patients had at least 30 days' worth of naturally occurring behavior observations, including information about physical activity, geolocation, sleep, and smartphone app use. These regularly sampled but frequently missing and heterogeneous time series were analyzed with the following probabilistic latent variable models for data averaging and feature extraction: mixture model (MM) and hidden Markov model (HMM). The extracted features were then combined with a classifier to predict emotional state. A variety of classical machine learning methods and recurrent neural networks were compared. Finally, a personalized Bayesian model was proposed to improve performance by considering the individual differences in the data and applying a different classifier bias term for each patient.ResultsProbabilistic generative models proved to be good preprocessing and feature extractor tools for data with large percentages of missing observations. Models that took into account the posterior probabilities of the MM and HMM latent states outperformed those that did not by more than 20%, suggesting that the underlying behavioral patterns identified were meaningful for individuals' overall emotional state. The best performing generalized models achieved a 0.81 area under the curve of the receiver operating characteristic and 0.71 area under the precision-recall curve when predicting self-reported emotional valence from behavior in held-out test data. Moreover, the proposed personalized models demonstrated that accounting for individual differences through a simple hierarchical model can substantially improve emotional state prediction performance without relying on previous days' data.ConclusionsThese findings demonstrate the feasibility of designing machine learning models for predicting emotional states from mobile sensing data capable of dealing with heterogeneous data with large numbers of missing observations. Such models may represent valuable tools for clinicians to monitor patients' mood states.

Dataset Information

O9.4. PREDICTING SCHIZOPHRENIA: IDENTIFICATION OF MULTIMODAL MARKERS OF DISEASE THROUGH A MACHINE LEARNING APPROACH

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