Intracortical neural activity distal to seizure-onset-areas predicts human focal seizures

AbstractThe apparent unpredictability of epileptic seizures has a major impact in the quality of life of people with pharmacologically resistant seizures. Here, we present initial results and a proof-of-concept of how focal seizures can be predicted early in advance based on intracortical signals recorded from small neocortical patches away from identified seizure onset areas. We show that machine learning algorithms can discriminate between interictal and preictal periods based on multiunit activity (i.e. thresholded action potential counts) and multi-frequency band local field potentials recorded via 4 X 4 mm2 microelectrode arrays. Microelectrode arrays were implanted in 5 patients undergoing neuromonitoring for resective surgery. Post-implant analysis revealed arrays were outside the seizure onset areas. Preictal periods were defined as the 1-hour period leading to a seizure. A 5-minute gap between the preictal period and the putative seizure onset was enforced to account for potential errors in the determination of actual seizure onset times. We used extreme gradient boosting and long short-term memory networks for prediction. Prediction accuracy based on the area under the receiver operating characteristic curves reached 90% for at least one feature type in each patient. Importantly, successful prediction could be achieved based exclusively on multiunit activity. This result indicates that preictal activity in the recorded neocortical patches involved not only subthreshold postsynaptic potentials, perhaps driven by the distal seizure onset areas, but also neuronal spiking in distal recurrent neocortical networks. Beyond the commonly identified seizure onset areas, our findings point to the engagement of large-scale neuronal networks in the neural dynamics building up toward a seizure. Our initial results obtained on currently available human intracortical recordings warrant new studies on larger datasets, and open new perspectives for seizure prediction and control by emphasizing the contribution of multiscale neural signals in large-scale neuronal networks.

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Comparison of Machine-Learning Algorithms for Near-Surface Air-Temperature Estimation from FY-4A AGRI Data

Advances in Meteorology ◽

10.1155/2020/8887364 ◽

2020 ◽

Vol 2020 ◽

pp. 1-14

Author(s):

Ke Zhou ◽

Hailei Liu ◽

Xiaobo Deng ◽

Hao Wang ◽

Shenglan Zhang

Keyword(s):

Machine Learning ◽

Air Temperature ◽

Large Scale ◽

Weather Prediction ◽

Surface Air Temperature ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Temporal And Spatial Distribution ◽

Near Surface ◽

Extreme Gradient Boosting

Six machine-learning approaches, including multivariate linear regression (MLR), gradient boosting decision tree, k-nearest neighbors, random forest, extreme gradient boosting (XGB), and deep neural network (DNN), were compared for near-surface air-temperature (Tair) estimation from the new generation of Chinese geostationary meteorological satellite Fengyun-4A (FY-4A) observations. The brightness temperatures in split-window channels from the Advanced Geostationary Radiation Imager (AGRI) of FY-4A and numerical weather prediction data from the global forecast system were used as the predictor variables for Tair estimation. The performance of each model and the temporal and spatial distribution of the estimated Tair errors were analyzed. The results showed that the XGB model had better overall performance, with R2 of 0.902, bias of −0.087°C, and root-mean-square error of 1.946°C. The spatial variation characteristics of the Tair error of the XGB method were less obvious than those of the other methods. The XGB model can provide more stable and high-precision Tair for a large-scale Tair estimation over China and can serve as a reference for Tair estimation based on machine-learning models.

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Predicting Undesired Treatment Outcome in Mental Healthcare: Machine Learning Study (Preprint)

10.2196/preprints.17235 ◽

2019 ◽

Author(s):

Kasper Van Mens ◽

Joran Lokkerbol ◽

Richard Janssen ◽

Robert de Lange ◽

Bea Tiemens

Keyword(s):

Machine Learning ◽

Treatment Outcome ◽

Mental Health Treatment ◽

Mental Healthcare ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Trade Off ◽

Trade Offs ◽

Outcome Monitoring ◽

Extreme Gradient Boosting

BACKGROUND It remains a challenge to predict which treatment will work for which patient in mental healthcare. OBJECTIVE In this study we compare machine algorithms to predict during treatment which patients will not benefit from brief mental health treatment and present trade-offs that must be considered before an algorithm can be used in clinical practice. METHODS Using an anonymized dataset containing routine outcome monitoring data from a mental healthcare organization in the Netherlands (n = 2,655), we applied three machine learning algorithms to predict treatment outcome. The algorithms were internally validated with cross-validation on a training sample (n = 1,860) and externally validated on an unseen test sample (n = 795). RESULTS The performance of the three algorithms did not significantly differ on the test set. With a default classification cut-off at 0.5 predicted probability, the extreme gradient boosting algorithm showed the highest positive predictive value (ppv) of 0.71(0.61 – 0.77) with a sensitivity of 0.35 (0.29 – 0.41) and area under the curve of 0.78. A trade-off can be made between ppv and sensitivity by choosing different cut-off probabilities. With a cut-off at 0.63, the ppv increased to 0.87 and the sensitivity dropped to 0.17. With a cut-off of at 0.38, the ppv decreased to 0.61 and the sensitivity increased to 0.57. CONCLUSIONS Machine learning can be used to predict treatment outcomes based on routine monitoring data.This allows practitioners to choose their own trade-off between being selective and more certain versus inclusive and less certain.

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Techniques for Detecting Malware Traffic: A Comprehensive Approach to Feature Selection and Classification

International Journal for Research in Applied Science and Engineering Technology ◽

10.22214/ijraset.2021.39088 ◽

2021 ◽

Vol 9 (12) ◽

pp. 1-10

Author(s):

Harsha A K

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Random Forest ◽

Learning Algorithms ◽

Malware Detection ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Steady Increase ◽

Extreme Gradient Boosting

Abstract: Since the advent of encryption, there has been a steady increase in malware being transmitted over encrypted networks. Traditional approaches to detect malware like packet content analysis are inefficient in dealing with encrypted data. In the absence of actual packet contents, we can make use of other features like packet size, arrival time, source and destination addresses and other such metadata to detect malware. Such information can be used to train machine learning classifiers in order to classify malicious and benign packets. In this paper, we offer an efficient malware detection approach using classification algorithms in machine learning such as support vector machine, random forest and extreme gradient boosting. We employ an extensive feature selection process to reduce the dimensionality of the chosen dataset. The dataset is then split into training and testing sets. Machine learning algorithms are trained using the training set. These models are then evaluated against the testing set in order to assess their respective performances. We further attempt to tune the hyper parameters of the algorithms, in order to achieve better results. Random forest and extreme gradient boosting algorithms performed exceptionally well in our experiments, resulting in area under the curve values of 0.9928 and 0.9998 respectively. Our work demonstrates that malware traffic can be effectively classified using conventional machine learning algorithms and also shows the importance of dimensionality reduction in such classification problems. Keywords: Malware Detection, Extreme Gradient Boosting, Random Forest, Feature Selection.

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Machine learning algorithms for predicting undernutrition among under-five children in Ethiopia

Public Health Nutrition ◽

10.1017/s1368980021004262 ◽

2021 ◽

pp. 1-29

Author(s):

Fikrewold H. Bitew ◽

Corey S. Sparks ◽

Samuel H. Nyarko

Keyword(s):

Machine Learning ◽

Linear Models ◽

Learning Algorithms ◽

Public Health Problem ◽

Water Source ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Global Public Health ◽

Prediction Ability ◽

Extreme Gradient Boosting

Abstract Objective: Child undernutrition is a global public health problem with serious implications. In this study, estimate predictive algorithms for the determinants of childhood stunting by using various machine learning (ML) algorithms. Design: This study draws on data from the Ethiopian Demographic and Health Survey of 2016. Five machine learning algorithms including eXtreme gradient boosting (xgbTree), k-nearest neighbors (K-NN), random forest (RF), neural network (NNet), and the generalized linear models (GLM) were considered to predict the socio-demographic risk factors for undernutrition in Ethiopia. Setting: Households in Ethiopia. Participants: A total of 9,471 children below five years of age. Results: The descriptive results show substantial regional variations in child stunting, wasting, and underweight in Ethiopia. Also, among the five ML algorithms, xgbTree algorithm shows a better prediction ability than the generalized linear mixed algorithm. The best predicting algorithm (xgbTree) shows diverse important predictors of undernutrition across the three outcomes which include time to water source, anemia history, child age greater than 30 months, small birth size, and maternal underweight, among others. Conclusions: The xgbTree algorithm was a reasonably superior ML algorithm for predicting childhood undernutrition in Ethiopia compared to other ML algorithms considered in this study. The findings support improvement in access to water supply, food security, and fertility regulation among others in the quest to considerably improve childhood nutrition in Ethiopia.

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Evaluating Variable Selection and Machine Learning Algorithms for Estimating Forest Heights by Combining Lidar and Hyperspectral Data

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi9090507 ◽

2020 ◽

Vol 9 (9) ◽

pp. 507

Author(s):

Sanjiwana Arjasakusuma ◽

Sandiaga Swahyu Kusuma ◽

Stuart Phinn

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Learning Algorithms ◽

Principal Component ◽

Hyperspectral Data ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Forest Height ◽

Extreme Gradient Boosting

Machine learning has been employed for various mapping and modeling tasks using input variables from different sources of remote sensing data. For feature selection involving high- spatial and spectral dimensionality data, various methods have been developed and incorporated into the machine learning framework to ensure an efficient and optimal computational process. This research aims to assess the accuracy of various feature selection and machine learning methods for estimating forest height using AISA (airborne imaging spectrometer for applications) hyperspectral bands (479 bands) and airborne light detection and ranging (lidar) height metrics (36 metrics), alone and combined. Feature selection and dimensionality reduction using Boruta (BO), principal component analysis (PCA), simulated annealing (SA), and genetic algorithm (GA) in combination with machine learning algorithms such as multivariate adaptive regression spline (MARS), extra trees (ET), support vector regression (SVR) with radial basis function, and extreme gradient boosting (XGB) with trees (XGbtree and XGBdart) and linear (XGBlin) classifiers were evaluated. The results demonstrated that the combinations of BO-XGBdart and BO-SVR delivered the best model performance for estimating tropical forest height by combining lidar and hyperspectral data, with R2 = 0.53 and RMSE = 1.7 m (18.4% of nRMSE and 0.046 m of bias) for BO-XGBdart and R2 = 0.51 and RMSE = 1.8 m (15.8% of nRMSE and −0.244 m of bias) for BO-SVR. Our study also demonstrated the effectiveness of BO for variables selection; it could reduce 95% of the data to select the 29 most important variables from the initial 516 variables from lidar metrics and hyperspectral data.

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High-Resolution Vegetation Mapping Using eXtreme Gradient Boosting Based on Extensive Features

Remote Sensing ◽

10.3390/rs11121505 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1505 ◽

Cited By ~ 7

Author(s):

Heng Zhang ◽

Anwar Eziz ◽

Jian Xiao ◽

Shengli Tao ◽

Shaopeng Wang ◽

...

Keyword(s):

New Zealand ◽

High Resolution ◽

Large Scale ◽

Field Survey ◽

Terrestrial Ecosystems ◽

Google Earth ◽

Gradient Boosting ◽

Global Changes ◽

Vegetation Map ◽

Extreme Gradient Boosting

Accurate mapping of vegetation is a premise for conserving, managing, and sustainably using vegetation resources, especially in conditions of intensive human activities and accelerating global changes. However, it is still challenging to produce high-resolution multiclass vegetation map in high accuracy, due to the incapacity of traditional mapping techniques in distinguishing mosaic vegetation classes with subtle differences and the paucity of fieldwork data. This study created a workflow by adopting a promising classifier, extreme gradient boosting (XGBoost), to produce accurate vegetation maps of two strikingly different cases (the Dzungarian Basin in China and New Zealand) based on extensive features and abundant vegetation data. For the Dzungarian Basin, a vegetation map with seven vegetation types, 17 subtypes, and 43 associations was produced with an overall accuracy of 0.907, 0.801, and 0.748, respectively. For New Zealand, a map of 10 habitats and a map of 41 vegetation classes were produced with 0.946, and 0.703 overall accuracy, respectively. The workflow incorporating simplified field survey procedures outperformed conventional field survey and remote sensing based methods in terms of accuracy and efficiency. In addition, it opens a possibility of building large-scale, high-resolution, and timely vegetation monitoring platforms for most terrestrial ecosystems worldwide with the aid of Google Earth Engine and citizen science programs.

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Prediction of hot spots in protein–DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting

BMC Bioinformatics ◽

10.1186/s12859-020-03683-3 ◽

2020 ◽

Vol 21 (S13) ◽

Cited By ~ 2

Author(s):

Ke Li ◽

Sijia Zhang ◽

Di Yan ◽

Yannan Bin ◽

Junfeng Xia

Keyword(s):

Feature Selection ◽

Manifold Learning ◽

Hot Spots ◽

Large Scale ◽

Computational Method ◽

Gradient Boosting ◽

Feature Mapping ◽

Accessible Information ◽

Extreme Gradient Boosting ◽

Isometric Feature Mapping

Abstract Background Identification of hot spots in protein-DNA interfaces provides crucial information for the research on protein-DNA interaction and drug design. As experimental methods for determining hot spots are time-consuming, labor-intensive and expensive, there is a need for developing reliable computational method to predict hot spots on a large scale. Results Here, we proposed a new method named sxPDH based on supervised isometric feature mapping (S-ISOMAP) and extreme gradient boosting (XGBoost) to predict hot spots in protein-DNA complexes. We obtained 114 features from a combination of the protein sequence, structure, network and solvent accessible information, and systematically assessed various feature selection methods and feature dimensionality reduction methods based on manifold learning. The results show that the S-ISOMAP method is superior to other feature selection or manifold learning methods. XGBoost was then used to develop hot spots prediction model sxPDH based on the three dimensionality-reduced features obtained from S-ISOMAP. Conclusion Our method sxPDH boosts prediction performance using S-ISOMAP and XGBoost. The AUC of the model is 0.773, and the F1 score is 0.713. Experimental results on benchmark dataset indicate that sxPDH can achieve generally better performance in predicting hot spots compared to the state-of-the-art methods.

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DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

Briefings in Bioinformatics ◽

10.1093/bib/bbaa125 ◽

2020 ◽

Cited By ~ 2

Author(s):

Ruopeng Xie ◽

Jiahui Li ◽

Jiawei Wang ◽

Wei Dai ◽

André Leier ◽

...

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Virulence Factors ◽

Bacterial Genome ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Wide Range ◽

Extreme Gradient Boosting ◽

Hybrid Framework

Abstract Virulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety of VFs, and the growing mass of bacterial genome sequence data provides an opportunity for computational methods aimed at predicting VFs. Despite their attractive advantages and performance improvements, the existing methods have some limitations and drawbacks. Firstly, as the characteristics and mechanisms of VFs are continually evolving with the emergence of antibiotic resistance, it is more and more difficult to identify novel VFs using existing tools that were previously developed based on the outdated data sets; secondly, few systematic feature engineering efforts have been made to examine the utility of different types of features for model performances, as the majority of tools only focused on extracting very few types of features. By addressing the aforementioned issues, the accuracy of VF predictors can likely be significantly improved. This, in turn, would be particularly useful in the context of genome wide predictions of VFs. In this work, we present a deep learning (DL)-based hybrid framework (termed DeepVF) that is utilizing the stacking strategy to achieve more accurate identification of VFs. Using an enlarged, up-to-date dataset, DeepVF comprehensively explores a wide range of heterogeneous features with popular machine learning algorithms. Specifically, four classical algorithms, including random forest, support vector machines, extreme gradient boosting and multilayer perceptron, and three DL algorithms, including convolutional neural networks, long short-term memory networks and deep neural networks are employed to train 62 baseline models using these features. In order to integrate their individual strengths, DeepVF effectively combines these baseline models to construct the final meta model using the stacking strategy. Extensive benchmarking experiments demonstrate the effectiveness of DeepVF: it achieves a more accurate and stable performance compared with baseline models on the benchmark dataset and clearly outperforms state-of-the-art VF predictors on the independent test. Using the proposed hybrid ensemble model, a user-friendly online predictor of DeepVF (http://deepvf.erc.monash.edu/) is implemented. Furthermore, its utility, from the user’s viewpoint, is compared with that of existing toolkits. We believe that DeepVF will be exploited as a useful tool for screening and identifying potential VFs from protein-coding gene sequences in bacterial genomes.

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Identification of Potential Type II Diabetes in a Large-Scale Chinese Population Using a Systematic Machine Learning Framework

Journal of Diabetes Research ◽

10.1155/2020/6873891 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Mingyue Xue ◽

Yinxia Su ◽

Chen Li ◽

Shuxia Wang ◽

Hua Yao

Keyword(s):

Machine Learning ◽

Risk Factors ◽

Decision Tree ◽

Type Ii Diabetes ◽

Large Scale ◽

Systolic Pressure ◽

Gradient Boosting ◽

Significant Feature ◽

Type Ii ◽

Extreme Gradient Boosting

Background. An estimated 425 million people globally have diabetes, accounting for 12% of the world’s health expenditures, and the number continues to grow, placing a huge burden on the healthcare system, especially in those remote, underserved areas. Methods. A total of 584,168 adult subjects who have participated in the national physical examination were enrolled in this study. The risk factors for type II diabetes mellitus (T2DM) were identified by p values and odds ratio, using logistic regression (LR) based on variables of physical measurement and a questionnaire. Combined with the risk factors selected by LR, we used a decision tree, a random forest, AdaBoost with a decision tree (AdaBoost), and an extreme gradient boosting decision tree (XGBoost) to identify individuals with T2DM, compared the performance of the four machine learning classifiers, and used the best-performing classifier to output the degree of variables’ importance scores of T2DM. Results. The results indicated that XGBoost had the best performance (accuracy=0.906, precision=0.910, recall=0.902, F‐1=0.906, and AUC=0.968). The degree of variables’ importance scores in XGBoost showed that BMI was the most significant feature, followed by age, waist circumference, systolic pressure, ethnicity, smoking amount, fatty liver, hypertension, physical activity, drinking status, dietary ratio (meat to vegetables), drink amount, smoking status, and diet habit (oil loving). Conclusions. We proposed a classifier based on LR-XGBoost which used fourteen variables of patients which are easily obtained and noninvasive as predictor variables to identify potential incidents of T2DM. The classifier can accurately screen the risk of diabetes in the early phrase, and the degree of variables’ importance scores gives a clue to prevent diabetes occurrence.

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Using Machine Learning to Predict National Hockey League Average Home Game Attendance

The Journal of Prediction Markets ◽

10.5750/jpm.v12i2.1608 ◽

2018 ◽

Vol 12 (2) ◽

pp. 85-98 ◽

Cited By ~ 1

Author(s):

Barry E King ◽

Jennifer L Rice ◽

Julie Vaughan

Keyword(s):

Machine Learning ◽

Machine Learning Algorithms ◽

National Hockey League ◽

Gradient Boosting ◽

Mean Square ◽

Sample Average ◽

Extreme Gradient Boosting ◽

Out Of Sample ◽

Game Attendance ◽

Home Game

Research predicting National Hockey League average attendance is presented. The seasons examined are the 2013 hockey season through the beginning of the 2017 hockey season. Multiple linear regression and three machine learning algorithms – random forest, M5 prime, and extreme gradient boosting – are employed to predict out-of-sample average home game attendance. Extreme gradient boosting generated the lowest out-of-sample root mean square error. The team identifier (team name), the number of Twitter followers (a surrogate for team popularity), median ticket price, and arena capacity have appeared as the top four predictor variables.

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