Statistical and Machine Learning Models for Classification of Human Wear and Delivery Days in Accelerometry Data.
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ABSTRACT:
SUBMITTER: Moore R
PROVIDER: S-EPMC8069625 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Discerning behaviours of free-ranging animals allows for quantification of their activity budget, providing important insight into ecology. Over recent years, accelerometers have been used to unveil the cryptic lives of animals. The increased ability of accelerometers to store large quantities of high resolution data has prompted a need for automated behavioural classification. We assessed the performance of several machine learning (ML) classifiers to discern five behaviours performed by accelerometer-equipped juvenile lemon sharks (Negaprion brevirostris) at Bimini, Bahamas (25°44'N, 79°16'W). The sharks were observed to exhibit chafing, burst swimming, headshaking, resting and swimming in a semi-captive environment and these observations were used to ground-truth data for ML training and testing. ML methods included logistic regression, an artificial neural network, two random forest models, a gradient boosting model and a voting ensemble (VE) model, which combined the predictions of all other (base) models to improve classifier performance. The macro-averaged F-measure, an indicator of classifier performance, showed that the VE model improved overall classification (F-measure 0.88) above the strongest base learner model, gradient boosting (0.86). To test whether the VE model provided biologically meaningful results when applied to accelerometer data obtained from wild sharks, we investigated headshaking behaviour, as a proxy for prey capture, in relation to the variables: time of day, tidal phase and season. All variables were significant in predicting prey capture, with predations most likely to occur during early evening and less frequently during the dry season and high tides. These findings support previous hypotheses from sporadic visual observations.
| S-EPMC5842499 | biostudies-literature
Project description:BackgroundEarly onset preeclampsia (eoPE) is a hypertensive disorder of pregnancy with endothelial dysfunction manifested before 34 weeks where expectant management is usually attempted. However, the timing of hospitalization, corticosteroids, and delivery remain a challenge. We aim to develop a prediction model using machine-learning tools for the need for delivery within 7 days of diagnosis (model D) and the risk of developing hemolysis, elevated liver enzymes, and low platelets (HELLP) syndrome or abruptio placentae (model HA).Materials and methodsA retrospective cohort of singleton pregnancies with eoPE and attempted expectant management between 2014 and 2020. A Mono-objective Genetic Algorithm based on supervised classification models was implemented to develop D and HA models. Maternal basal characteristics and data gathered during eoPE diagnosis: gestational age, blood pressure, platelets, creatinine, transaminases, angiogenesis biomarkers (soluble fms-like tyrosine kinase-1, placental growth factor), and ultrasound data were pooled for analysis. The most relevant variables were selected by bio-inspired algorithms. We developed basal models that solely included demographic characteristics of the patient (D1, HA1), and advanced models adding information available at diagnosis of eoPE (D2, HA2).ResultsWe evaluated 215 eoPE cases and 47.9% required delivery within 7 days. The median time-to-delivery was 8 days. Basal models were better predicted by K-nearest-neighbor in D1, which had a diagnostic precision of 0.68 ± 0.09, with 63.6% sensitivity (Sn), 71.4% specificity (Sp), 70% positive predictive value (PPV), and 65.2% negative predictive value (NPV) using 13 variables and HA1 of 0.77 ± 0.09, 60.4% Sn, 80% Sp, 50% PPV, and 87.9% NPV. Models at diagnosis were better developed by support vector machine (SVM) using 18 variables, where D2's precision improved to 0.79 ± 0.05 with 77.3% Sn, 80.1% Sp, 81.5% PPV, and 76.2% NPV, and HA2 had a precision of 0.79 ± 0.08 with 66.7% Sn, 82.8% Sp, 51.6% PPV, and 90.3% NPV.ConclusionAt the time of diagnosis of eoPE, SVM with evolutionary feature selection process provides good predictive information of the need for delivery within 7 days and development of HELLP/abruptio placentae, using maternal characteristics and markers that can be obtained routinely. This information could be of value when assessing hospitalization and timing of antenatal corticosteroid administration.
| S-EPMC9283699 | biostudies-literature
Project description:BackgroundThe lack of nonparametric statistical tests for confounding bias significantly hampers the development of robust, valid, and generalizable predictive models in many fields of research. Here I propose the partial confounder test, which, for a given confounder variable, probes the null hypotheses of the model being unconfounded.ResultsThe test provides a strict control for type I errors and high statistical power, even for nonnormally and nonlinearly dependent predictions, often seen in machine learning. Applying the proposed test on models trained on large-scale functional brain connectivity data (N= 1,865) (i) reveals previously unreported confounders and (ii) shows that state-of-the-art confound mitigation approaches may fail preventing confounder bias in several cases.ConclusionsThe proposed test (implemented in the package mlconfound; https://mlconfound.readthedocs.io) can aid the assessment and improvement of the generalizability and validity of predictive models and, thereby, fosters the development of clinically useful machine learning biomarkers.
| S-EPMC9412867 | biostudies-literature
Project description:ObjectiveTo predict a woman's risk of postpartum hemorrhage at labor admission using machine learning and statistical models.MethodsPredictive models were constructed and compared using data from 10 of 12 sites in the U.S. Consortium for Safe Labor Study (2002-2008) that consistently reported estimated blood loss at delivery. The outcome was postpartum hemorrhage, defined as an estimated blood loss at least 1,000 mL. Fifty-five candidate risk factors routinely available on labor admission were considered. We used logistic regression with and without lasso regularization (lasso regression) as the two statistical models, and random forest and extreme gradient boosting as the two machine learning models to predict postpartum hemorrhage. Model performance was measured by C statistics (ie, concordance index), calibration, and decision curves. Models were constructed from the first phase (2002-2006) and externally validated (ie, temporally) in the second phase (2007-2008). Further validation was performed combining both temporal and site-specific validation.ResultsOf the 152,279 assessed births, 7,279 (4.8%, 95% CI 4.7-4.9) had postpartum hemorrhage. All models had good-to-excellent discrimination. The extreme gradient boosting model had the best discriminative ability to predict postpartum hemorrhage (C statistic: 0.93; 95% CI 0.92-0.93), followed by random forest (C statistic: 0.92; 95% CI 0.91-0.92). The lasso regression model (C statistic: 0.87; 95% CI 0.86-0.88) and logistic regression (C statistic: 0.87; 95% CI 0.86-0.87) had lower-but-good discriminative ability. The above results held with validation across both time and sites. Decision curve analysis demonstrated that, although all models provided superior net benefit when clinical decision thresholds were between 0% and 80% predicted risk, the extreme gradient boosting model provided the greatest net benefit.ConclusionPostpartum hemorrhage on labor admission can be predicted with excellent discriminative ability using machine learning and statistical models. Further clinical application is needed, which may assist health care providers to be prepared and triage at-risk women.
| S-EPMC7236480 | biostudies-literature
Project description:Incorporating brain-computer interfaces (BCIs) into daily life requires reducing the reliance of decoding algorithms on the calibration or enabling calibration with the minimal burden on the user. A potential solution could be a pre-trained decoder demonstrating a reasonable accuracy on the naive operators. Addressing this issue, we considered ambiguous stimuli classification tasks and trained an artificial neural network to classify brain responses to the stimuli of low and high ambiguity. We built a pre-trained classifier utilizing time-frequency features corresponding to the fundamental neurophysiological processes shared between subjects. To extract these features, we statistically contrasted electroencephalographic (EEG) spectral power between the classes in the representative group of subjects. As a result, the pre-trained classifier achieved 74% accuracy on the data of newly recruited subjects. Analysis of the literature suggested that a pre-trained classifier could help naive users to start using BCI bypassing training and further increased accuracy during the feedback session. Thus, our results contribute to using BCI during paralysis or limb amputation when there is no explicit user-generated kinematic output to properly train a decoder. In machine learning, our approach may facilitate the development of transfer learning (TL) methods for addressing the cross-subject problem. It allows extracting the interpretable feature subspace from the source data (the representative group of subjects) related to the target data (a naive user), preventing the negative transfer in the cross-subject tasks.
| S-EPMC8635058 | biostudies-literature
Project description:Hip-worn triaxial accelerometers are widely used to assess physical activity in terms of energy expenditure. Methods for classification in terms of different types of activity of relevance to the skeleton in populations at risk of osteoporosis are not currently available. This publication aims to assess the accuracy of four machine learning models on binary (standing and walking) and tertiary (standing, walking, and jogging) classification tasks in postmenopausal women. Eighty women performed a shuttle test on an indoor track, of which thirty performed the same test on an indoor treadmill. The raw accelerometer data were pre-processed, converted into eighteen different features and then combined into nine unique feature sets. The four machine learning models were evaluated using three different validation methods. Using the leave-one-out validation method, the highest average accuracy for the binary classification model, 99.61%, was produced by a k-NN Manhattan classifier using a basic statistical feature set. For the tertiary classification model, the highest average accuracy, 94.04%, was produced by a k-NN Manhattan classifier using a feature set that included all 18 features. The methods and classifiers within this study can be applied to accelerometer data to more accurately characterize weight-bearing activity which are important to skeletal health.
| S-EPMC9740741 | biostudies-literature
Project description:Early detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of IDC. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying IDC progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.
| S-EPMC7057992 | biostudies-literature
Project description:In this review, we outline the current trends in the field of machine learning-driven classification studies related to ADME (absorption, distribution, metabolism and excretion) and toxicity endpoints from the past six years (2015-2021). The study focuses only on classification models with large datasets (i.e. more than a thousand compounds). A comprehensive literature search and meta-analysis was carried out for nine different targets: hERG-mediated cardiotoxicity, blood-brain barrier penetration, permeability glycoprotein (P-gp) substrate/inhibitor, cytochrome P450 enzyme family, acute oral toxicity, mutagenicity, carcinogenicity, respiratory toxicity and irritation/corrosion. The comparison of the best classification models was targeted to reveal the differences between machine learning algorithms and modeling types, endpoint-specific performances, dataset sizes and the different validation protocols. Based on the evaluation of the data, we can say that tree-based algorithms are (still) dominating the field, with consensus modeling being an increasing trend in drug safety predictions. Although one can already find classification models with great performances to hERG-mediated cardiotoxicity and the isoenzymes of the cytochrome P450 enzyme family, these targets are still central to ADMET-related research efforts.
| S-EPMC8342376 | biostudies-literature
Project description:The nested data structure is prevalent for cognitive measure experiments due to repeatedly taken observations from different brain locations within subjects. The analysis methods used for this data type should consider the dependency structure among the repeated measurements. However, the dependency assumption is mainly ignored in the cognitive neuroscience data analysis literature. We consider both statistical, and machine learning methods extended to repeated data analysis and compare distinct algorithms in terms of their advantage and disadvantages. Unlike basic algorithm comparison studies, this article analyzes novel neuroscience data considering the dependency structure for the first time with several statistical and machine learning methods and their hybrid forms. In addition, the fitting performances of different algorithms are compared using contaminated data sets, and the cross-validation approach. One of our findings suggests that the GLMM tree, including random term indices indicating the location of functional near-infrared spectroscopy optodes nested within experimental units, shows the best predictive performance with the lowest MSE, RMSE, and MAE model performance metrics. However, there is a trade-off between accuracy and speed since this algorithm is required the highest computational time.
| S-EPMC11018039 | biostudies-literature
Project description:Sufficient physical activity (PA) reduces the risk of a myriad of diseases and preserves physical capabilities in later life. While there have been significant achievements in mapping accelerations to real-life movements using machine learning (ML), errors continue to be common, particularly for wrist-worn devices. It remains unknown whether ML models are robust for estimating age-related loss of physical function. In this study, we evaluated the performance of ML models (XGBoost and LASSO) to estimate the hallmark measures of PA in low physical performance (LPP) and high physical performance (HPP) groups. Our models were built to recognize PA types and intensities, identify each individual activity, and estimate energy expenditure (EE) using wrist-worn accelerometer data (33 activities per participant) from a large sample of participants (n = 247, 57% females, aged 60+ years). Results indicated that the ML models were accurate in recognizing PA by type and intensity while also estimating EE accurately. However, the models built to recognize individual activities were less robust. Across all tasks, XGBoost outperformed LASSO. XGBoost obtained F1-Scores for sedentary (0.932 ± 0.005), locomotion (0.946 ± 0.003), lifestyle (0.927 ± 0.006), and strength flexibility exercise (0.915 ± 0.017) activity type recognition tasks. The F1-Scores for recognizing low, light, and moderate activity intensity were (0.932 ± 0.005), (0.840 ± 0.004), and (0.869 ± 0.005), respectively. The root mean square error for EE estimation was 0.836 ± 0.059 METs. There was no evidence showing that splitting the participants into the LPP and HPP groups improved the models' performance on estimating the hallmark measures of physical activities. In conclusion, using features derived from wrist-worn accelerometer data, machine learning models can accurately recognize PA types and intensities and estimate EE for older adults with high and low physical function.
| S-EPMC9032589 | biostudies-literature