Brain Informatics最新文献

Random Survival Forests (RSF) has recently showed better performance than statistical survival methods as Cox proportional hazard (CPH) in predicting conversion risk from mild cognitive impairment (MCI) to Alzheimer's disease (AD). However, RSF application in real-world clinical setting is still limited due to its black-box nature.For this reason, we aimed at providing a comprehensive study of RSF explainability with SHapley Additive exPlanations (SHAP) on biomarkers of stable and progressive patients (sMCI and pMCI) from Alzheimer's Disease Neuroimaging Initiative. We evaluated three global explanations-RSF feature importance, permutation importance and SHAP importance-and we quantitatively compared them with Rank-Biased Overlap (RBO). Moreover, we assessed whether multicollinearity among variables may perturb SHAP outcome. Lastly, we stratified pMCI test patients in high, medium and low risk grade, to investigate individual SHAP explanation of one pMCI patient per risk group.We confirmed that RSF had higher accuracy (0.890) than CPH (0.819), and its stability and robustness was demonstrated by high overlap (RBO > 90%) between feature rankings within first eight features. SHAP local explanations with and without correlated variables had no substantial difference, showing that multicollinearity did not alter the model. FDG, ABETA42 and HCI were the first important features in global explanations, with the highest contribution also in local explanation. FAQ, mPACCdigit, mPACCtrailsB and RAVLT immediate had the highest influence among all clinical and neuropsychological assessments in increasing progression risk, as particularly evident in pMCI patients' individual explanation. In conclusion, our findings suggest that RSF represents a useful tool to support clinicians in estimating conversion-to-AD risk and that SHAP explainer boosts its clinical utility with intelligible and interpretable individual outcomes that highlights key features associated with AD prognosis.

In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology-Causal Activity Modelling, or GO-CAM). In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans [C. elegans Neural-Circuit Causal Activity Modelling (CeN-CAM)]. We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO₂) avoidance behaviors could be faithfully represented with CeN-CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate the C. elegans connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge.

In order to grasp and transport an object, grip and load forces must be scaled according to the object's properties (such as weight). To select the appropriate grip and load forces, the object weight is estimated based on experience or, in the case of robots, usually by use of image recognition. We propose a new approach that makes a robot's weight estimation less dependent on prior learning and, thereby, allows it to successfully grasp a wider variety of objects. This study evaluates whether it is feasible to predict an object's weight class in a replacement task based on the time series of upper body angles of the active arm or on object velocity profiles. Furthermore, we wanted to investigate how prediction accuracy is affected by (i) the length of the time series and (ii) different cross-validation (CV) procedures. To this end, we recorded and analyzed the movement kinematics of 12 participants during a replacement task. The participants' kinematics were recorded by an optical motion tracking system while transporting an object, 80 times in total from varying starting positions to a predefined end position on a table. The object's weight was modified (made lighter and heavier) without changing the object's visual appearance. Throughout the experiment, the object's weight (light/heavy) was randomly changed without the participant's knowledge. To predict the object's weight class, we used a discrete cosine transform to smooth and compress the time series and a support vector machine for supervised learning from the achieved discrete cosine transform parameters. Results showed good prediction accuracy (up to [Formula: see text], depending on the CV procedure and the length of the time series). Even at the beginning of a movement (after only 300 ms), we were able to predict the object weight reliably (within a classification rate of [Formula: see text]).

Background and objective: Postpartum Depression (PPD) is a frequently ignored birth-related consequence. Social network analysis can be used to address this issue because social media network serves as a platform for their users to communicate with their friends and share their opinions, photos, and videos, which reflect their moods, feelings, and sentiments. In this work, the depression of delivered mothers is identified using the PPD score and segregated into control and depressed groups. Recently, to detect depression, deep learning methods have played a vital role. However, these methods still do not clarify why some people have been identified as depressed.

Methods: We have developed Attribute Selection Hybrid Network (ASHN) to detect the postpartum depression diagnoses framework. Later analysis of the post of mothers who have been confirmed with the score calculated by the experts of the field using physiological questionnaire score. The model works on the analysis of the attributes of the negative Facebook posts for Depressed user Diagnosis, which is a large general forum. This framework explains the process of analyzing posts containing Sentiment, depressive symptoms, and reflective thinking and suggests psycho-linguistic and stylistic attributes of depression in posts.

Results: The experimental results show that ASHN works well and is easy to understand. Here, four attribute networks based on psychological studies were used to analyze the different parts of posts by depressed users. The results of the experiments show the extraction of psycho-linguistic markers-based attributes, the recording of assessment metrics including Precision, Recall and F1 score and visualization of those attributes were used title-wise as well as words wise and compared with daily life, depression and postpartum depressed people using Word cloud. Furthermore, a comparison to a reference with Baseline and ASHN model was carried out.

Conclusions: Attribute Selection Hybrid Network (ASHN) mimics the importance of attributes in social media posts to predict depressed mothers. Those mothers were anticipated to be depressed by answering a questionnaire designed by domain experts with prior knowledge of depression. This work will help researchers look at social media posts to find useful evidence for other depressive symptoms.

Mental wellbeing of university students is a growing concern that has been worsening during the COVID-19 pandemic. Numerous studies have gathered empirical data to explore the mental health impact of the pandemic on university students and investigate factors associated with higher levels of distress. While the online questionnaire survey has been a prevalent means to collect data, regression analysis has been observed a dominating approach to interpret and understand the impact of independent factors on a mental wellbeing state of interest. Drawbacks such as sensitivity to outliers, ineffectiveness in case of multiple predictors highly correlated may limit the use of regression in complex scenarios. These observations motivate the underlying research to propose alternative computational methods to investigate the questionnaire data. Inspired by recent machine learning advances, this research aims to construct a framework through feature permutation importance to empower the application of a variety of machine learning algorithms that originate from different computational frameworks and learning theories, including algorithms that cannot directly provide exact numerical contributions of individual factors. This would enable to explore quantitative impact of predictors in influencing student mental wellbeing from multiple perspectives as a result of using different algorithms, thus complementing the single view due to the dominant use of regression. Applying the proposed approach over an online survey in a UK university, the analysis suggests the past medical record and wellbeing history and the experience of adversity contribute significantly to mental wellbeing states; and the frequent communication with families and friends to keep good relationship as well as regular exercise are generally contributing to improved mental wellbeing.

Objective: Clinical and surgical decisions for glioblastoma patients depend on a tumor imaging-based evaluation. Artificial Intelligence (AI) can be applied to magnetic resonance imaging (MRI) assessment to support clinical practice, surgery planning and prognostic predictions. In a real-world context, the current obstacles for AI are low-quality imaging and postoperative reliability. The aim of this study is to train an automatic algorithm for glioblastoma segmentation on a clinical MRI dataset and to obtain reliable results both pre- and post-operatively.

Methods: The dataset used for this study comprises 237 (71 preoperative and 166 postoperative) MRIs from 71 patients affected by a histologically confirmed Grade IV Glioma. The implemented U-Net architecture was trained by transfer learning to perform the segmentation task on postoperative MRIs. The training was carried out first on BraTS2021 dataset for preoperative segmentation. Performance is evaluated using DICE score (DS) and Hausdorff 95% (H95).

Results: In preoperative scenario, overall DS is 91.09 (± 0.60) and H95 is 8.35 (± 1.12), considering tumor core, enhancing tumor and whole tumor (ET and edema). In postoperative context, overall DS is 72.31 (± 2.88) and H95 is 23.43 (± 7.24), considering resection cavity (RC), gross tumor volume (GTV) and whole tumor (WT). Remarkably, the RC segmentation obtained a mean DS of 63.52 (± 8.90) in postoperative MRIs.

Conclusions: The performances achieved by the algorithm are consistent with previous literature for both pre-operative and post-operative glioblastoma's MRI evaluation. Through the proposed algorithm, it is possible to reduce the impact of low-quality images and missing sequences.

While a very few studies have been conducted on classifying loving kindness meditation (LKM) and non-meditation electroencephalography (EEG) data for a single session, there are no such studies conducted for multiple session EEG data. Thus, this study aims at classifying existing raw EEG meditation data on single and multiple sessions to come up with meaningful inferences which will be highly beneficial when developing algorithms that can support meditation practices. In this analysis, data have been collected on Pre-Resting (before-meditation), Post-Resting (after-meditation), LKM-Self and LKM-Others for 32 participants and hence allowing us to conduct six pairwise comparisons for the four mind tasks. Common Spatial Patterns (CSP) is a feature extraction method widely used in motor imaginary brain computer interface (BCI), but not in meditation EEG data. Therefore, using CSP in extracting features from meditation EEG data and classifying meditation/non-meditation instances, particularly for multiple sessions will create a new path in future meditation EEG research. The classification was done using Linear Discriminant Analysis (LDA) where both meditation techniques (LKM-Self and LKM-Others) were compared with Pre-Resting and Post-Resting instances. The results show that for a single session of 32 participants, around 99.5% accuracy was obtained for classifying meditation/Pre-Resting instances. For the 15 participants when using five sessions of EEG data, around 83.6% accuracy was obtained for classifying meditation/Pre-Resting instances. The results demonstrate the ability to classify meditation/Pre-Resting data. Most importantly, this classification is possible for multiple session data as well. In addition to this, when comparing the classification accuracies of the six mind task pairs; LKM-Self, LKM-Others and Post-Resting produced relatively lower accuracies among them than the accuracies obtained for classifying Pre-Resting with the other three. This indicates that Pre-Resting has some features giving a better classification indicating that it is different from the other three mind tasks.

Early identification of mental disorders, based on subjective interviews, is extremely challenging in the clinical setting. There is a growing interest in developing automated screening tools for potential mental health problems based on biological markers. Here, we demonstrate the feasibility of an AI-powered diagnosis of different mental disorders using EEG data. Specifically, this work aims to classify different mental disorders in the following ecological context accurately: (1) using raw EEG data, (2) collected during rest, (3) during both eye open, and eye closed conditions, (4) at short 2-min duration, (5) on participants with different psychiatric conditions, (6) with some overlapping symptoms, and (7) with strongly imbalanced classes. To tackle this challenge, we designed and optimized a transformer-based architecture, where class imbalance is addressed through focal loss and class weight balancing. Using the recently released TDBRAIN dataset (n= 1274 participants), our method classifies each participant as either a neurotypical or suffering from major depressive disorder (MDD), attention deficit hyperactivity disorder (ADHD), subjective memory complaints (SMC), or obsessive-compulsive disorder (OCD). We evaluate the performance of the proposed architecture on both the window-level and the patient-level. The classification of the 2-min raw EEG data into five classes achieved a window-level accuracy of 63.2% and 65.8% for open and closed eye conditions, respectively. When the classification is limited to three main classes (MDD, ADHD, SMC), window level accuracy improved to 75.1% and 69.9% for eye open and eye closed conditions, respectively. Our work paves the way for developing novel AI-based methods for accurately diagnosing mental disorders using raw resting-state EEG data.

The increasing number of peer-reviewed publications constitutes a challenge for biocuration. For example, NeuroMorpho.Org, a sharing platform for digital reconstructions of neural morphology, must evaluate more than 6000 potentially relevant articles per year to identify data of interest. Here, we describe a tool that uses natural language processing and deep learning to assess the likelihood of a publication to be relevant for the project. The tool automatically identifies articles describing digitally reconstructed neural morphologies with high accuracy. Its processing rate of 900 publications per hour is not only amply sufficient to autonomously track new research, but also allowed the successful evaluation of older publications backlogged due to limited human resources. The number of bio-entities found since launching the tool almost doubled while greatly reducing manual labor. The classification tool is open source, configurable, and simple to use, making it extensible to other biocuration projects.

Background: Abstracting cerebrovascular disease (CeVD) from inpatient electronic medical records (EMRs) through natural language processing (NLP) is pivotal for automated disease surveillance and improving patient outcomes. Existing methods rely on coders' abstraction, which has time delays and under-coding issues. This study sought to develop an NLP-based method to detect CeVD using EMR clinical notes.

Methods: CeVD status was confirmed through a chart review on randomly selected hospitalized patients who were 18 years or older and discharged from 3 hospitals in Calgary, Alberta, Canada, between January 1 and June 30, 2015. These patients' chart data were linked to administrative discharge abstract database (DAD) and Sunrise^™ Clinical Manager (SCM) EMR database records by Personal Health Number (a unique lifetime identifier) and admission date. We trained multiple natural language processing (NLP) predictive models by combining two clinical concept extraction methods and two supervised machine learning (ML) methods: random forest and XGBoost. Using chart review as the reference standard, we compared the model performances with those of the commonly applied International Classification of Diseases (ICD-10-CA) codes, on the metrics of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

Result: Of the study sample (n = 3036), the prevalence of CeVD was 11.8% (n = 360); the median patient age was 63; and females accounted for 50.3% (n = 1528) based on chart data. Among 49 extracted clinical documents from the EMR, four document types were identified as the most influential text sources for identifying CeVD disease ("nursing transfer report," "discharge summary," "nursing notes," and "inpatient consultation."). The best performing NLP model was XGBoost, combining the Unified Medical Language System concepts extracted by cTAKES (e.g., top-ranked concepts, "Cerebrovascular accident" and "Transient ischemic attack"), and the term frequency-inverse document frequency vectorizer. Compared with ICD codes, the model achieved higher validity overall, such as sensitivity (25.0% vs 70.0%), specificity (99.3% vs 99.1%), PPV (82.6 vs. 87.8%), and NPV (90.8% vs 97.1%).

Conclusion: The NLP algorithm developed in this study performed better than the ICD code algorithm in detecting CeVD. The NLP models could result in an automated EMR tool for identifying CeVD cases and be applied for future studies such as surveillance, and longitudinal studies.