An Interpretable Machine Learning Method for the Detection of Schizophrenia Using EEG Signals.
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ABSTRACT:
SUBMITTER: Vazquez MA
PROVIDER: S-EPMC8194273 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Parkinson's disease (PD) is a very common brain abnormality that affects people all over the world. Early detection of such abnormality is critical in clinical diagnosis in order to prevent disease progression. Electroencephalography (EEG) is one of the most important PD diagnostic tools since this disease is linked to the brain. In this study, novel efficient common spatial pattern-based approaches for detecting Parkinson's disease in two cases, off-medication and on-medication, are proposed. First, the EEG signals are preprocessed to remove major artifacts before spatial filtering using a common spatial pattern. Several features are extracted from spatially filtered signals using different metrics, namely, variance, band power, energy, and several types of entropy. Machine learning techniques, namely, random forest, linear/quadratic discriminant analysis, support vector machine, and k-nearest neighbor, are investigated to classify the extracted features. The impacts of frequency bands, segment length, and reduction number on the results are also investigated in this work. The proposed methods are tested using two EEG datasets: the SanDiego dataset (31 participants, 93 min) and the UNM dataset (54 participants, 54 min). The results show that the proposed methods, particularly the combination of common spatial patterns and log energy entropy, provide competitive results when compared to methods in the literature. The achieved results in terms of classification accuracy, sensitivity, and specificity in the case of off-medication PD detection are around 99%. In the case of on-medication PD, the results range from 95% to 98%. The results also reveal that features extracted from the alpha and beta bands have the highest classification accuracy.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2024-01-27 | GSE230012 | GEO
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2024-01-28 | GSE230011 | GEO
Project description:Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
2024-01-28 | GSE230010 | GEO
Project description:Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
2024-01-28 | GSE230007 | GEO
Project description:Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.
2024-01-28 | GSE230006 | GEO
Project description:Schizophrenia is a severe mental disorder that ranks among the leading causes of disability worldwide. However, many cases of schizophrenia remain untreated due to failure to diagnose, self-denial, and social stigma. With the advent of social media, individuals suffering from schizophrenia share their mental health problems and seek support and treatment options. Machine learning approaches are increasingly used for detecting schizophrenia from social media posts. This study aims to determine whether machine learning could be effectively used to detect signs of schizophrenia in social media users by analyzing their social media texts. To this end, we collected posts from the social media platform Reddit focusing on schizophrenia, along with non-mental health related posts (fitness, jokes, meditation, parenting, relationships, and teaching) for the control group. We extracted linguistic features and content topics from the posts. Using supervised machine learning, we classified posts belonging to schizophrenia and interpreted important features to identify linguistic markers of schizophrenia. We applied unsupervised clustering to the features to uncover a coherent semantic representation of words in schizophrenia. We identified significant differences in linguistic features and topics including increased use of third person plural pronouns and negative emotion words and symptom-related topics. We distinguished schizophrenic from control posts with an accuracy of 96%. Finally, we found that coherent semantic groups of words were the key to detecting schizophrenia. Our findings suggest that machine learning approaches could help us understand the linguistic characteristics of schizophrenia and identify schizophrenia or otherwise at-risk individuals using social media texts.
| S-EPMC8434514 | biostudies-literature
Project description:Objective: The brain age gap estimate (BrainAGE) is the difference between the estimated age and the individual chronological age. BrainAGE was studied primarily using MRI techniques. EEG signals in combination with machine learning (ML) approaches were not commonly used for the human age prediction, and BrainAGE. We investigated whether age-related changes are affecting brain EEG signals, and whether we can predict the chronological age and obtain BrainAGE estimates using a rigorous ML framework with a novel and extensive EEG features extraction. Methods: EEG data were obtained from 468 healthy, mood/anxiety, eating and substance use disorder participants (297 females) from the Tulsa-1000, a naturalistic longitudinal study based on Research Domain Criteria framework. Five sets of preprocessed EEG features across channels and frequency bands were used with different ML methods to predict age. Using a nested-cross-validation (NCV) approach and stack-ensemble learning from EEG features, the predicted age was estimated. The important features and their spatial distributions were deduced. Results: The stack-ensemble age prediction model achieved R2 = 0.37 (0.06), Mean Absolute Error (MAE) = 6.87(0.69) and RMSE = 8.46(0.59) in years. The age and predicted age correlation was r = 0.6. The feature importance revealed that age predictors are spread out across different feature types. The NCV approach produced a reliable age estimation, with features consistent behavior across different folds. Conclusion: Our rigorous ML framework and extensive EEG signal features allow a reliable estimation of chronological age, and BrainAGE. This general framework can be extended to test EEG association with and to predict/study other physiological relevant responses.
| S-EPMC6036180 | biostudies-literature
Project description:Background and purposeMachine learning models have been used to diagnose schizophrenia. The main purpose of this research is to introduce an effective schizophrenia hand-modeled classification method.MethodA public electroencephalogram (EEG) signal data set was used in this work, and an automated schizophrenia detection model is presented using a cyclic group of prime order with a modulo 17 operator. Therefore, the presented feature extractor was named as the cyclic group of prime order pattern, CGP17Pat. Using the proposed CGP17Pat, a new multilevel feature extraction model is presented. To choose a highly distinctive feature, iterative neighborhood component analysis (INCA) was used, and these features were classified using k-nearest neighbors (kNN) with the 10-fold cross-validation and leave-one-subject-out (LOSO) validation techniques. Finally, iterative hard majority voting was employed in the last phase to obtain channel-wise results, and the general results were calculated.ResultsThe presented CGP17Pat-based EEG classification model attained 99.91% accuracy employing 10-fold cross-validation and 84.33% accuracy using the LOSO strategy.ConclusionsThe findings and results depicted the high classification ability of the presented cryptologic pattern for the data set used.
| S-EPMC9027158 | biostudies-literature
Project description:PurposeTo develop a multimodal model to automate glaucoma detection DESIGN: Development of a machine-learning glaucoma detection model METHODS: We selected a study cohort from the UK Biobank data set with 1193 eyes of 863 healthy subjects and 1283 eyes of 771 subjects with glaucoma. We trained a multimodal model that combines multiple deep neural nets, trained on macular optical coherence tomography volumes and color fundus photographs, with demographic and clinical data. We performed an interpretability analysis to identify features the model relied on to detect glaucoma. We determined the importance of different features in detecting glaucoma using interpretable machine learning methods. We also evaluated the model on subjects who did not have a diagnosis of glaucoma on the day of imaging but were later diagnosed (progress-to-glaucoma [PTG]).ResultsResults show that a multimodal model that combines imaging with demographic and clinical features is highly accurate (area under the curve 0.97). Interpretation of this model highlights biological features known to be related to the disease, such as age, intraocular pressure, and optic disc morphology. Our model also points to previously unknown or disputed features, such as pulmonary function and retinal outer layers. Accurate prediction in PTG highlights variables that change with progression to glaucoma-age and pulmonary function.ConclusionsThe accuracy of our model suggests distinct sources of information in each imaging modality and in the different clinical and demographic variables. Interpretable machine learning methods elucidate subject-level prediction and help uncover the factors that lead to accurate predictions, pointing to potential disease mechanisms or variables related to the disease.
| S-EPMC8560651 | biostudies-literature