Dataset Information

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

ABSTRACT: Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/ .

SUBMITTER: Stein D

PROVIDER: S-EPMC10688473 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

Stein David D Kars Meltem Ece ME Wu Yiming Y Bayrak Çiğdem Sevim ÇS Stenson Peter D PD Cooper David N DN Schlessinger Avner A Itan Yuval Y

Genome medicine 20231130 1

Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad ra ...[more]

PMID: 38037155

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Project description:Landslides pose significant threats to ecosystems, lives, and economies, particularly in the geologically fragile Sub-Himalayan region of West Bengal, India. This study enhances landslide susceptibility prediction by developing an ensemble framework integrating Recursive Feature Elimination (RFE) with meta-learning techniques. Seven advanced machine learning models- Logistic Regression (LR), Support Vector Machine (SVM), Random Forest (RF), Extremely Randomized Trees (ET), Gradient Boosting (GB), Extreme Gradient Boosting (XGBoost), and a Meta Classifier (MC) were applied using Remote Sensing and GIS tools to identify key landslide-conditioning factors and classify susceptibility zones. Model performance was assessed through metrics such as accuracy, precision, recall, F1 score, and AUC of the ROC curve. Among the models, the Meta Classifier (MC) achieved the highest accuracy (0.956) and AUC (0.987), demonstrating superior predictive ability. Gradient Boosting (GB), XGBoost, and RF also performed well, with accuracies of 0.943 and AUC values of 0.987 (GB and XGBoost) and 0.983 (RF). Extremely Randomized Trees (ET) exhibited the highest accuracy (0.946) among individual models and an AUC of 0.985. SVM and LR, while slightly less accurate (0.941 and 0.860, respectively), provided valuable insights, with SVM achieving an AUC of 0.972 and LR achieving 0.935. The models effectively delineated landslide susceptibility into five zones (very low, low, moderate, high, and very high), with high and very high susceptibility zones concentrated in Darjeeling and Kalimpong subdivisions. These zones are influenced by intense rainfall, unstable geological structures, and anthropogenic activities like deforestation and urbanization. Notably, ET, RF, GB, and XGBoost demonstrated efficiency in feature selection, requiring fewer input variables while maintaining high performance. This study establishes a benchmark for landslide susceptibility mapping, providing a scalable and adaptable framework for geospatial hazard prediction. The findings hold significant implications for land-use planning, disaster management, and environmental conservation in vulnerable regions worldwide.

Dataset Information

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

Publications

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

Similar Datasets

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