Deep learning example with DeepExplainer (TensorFlow/Keras models) Deep SHAP is a high-speed approximation algorithm for SHAP values in deep learning models that builds on a connection with DeepLIFT described in the SHAP NIPS paper. The implementation here differs from the original DeepLIFT by using...
We build risk classes according to each region’s risk of exposure to COVID-19 cases by performing a 1-dimensional k-means38 unsupervised clustering algorithm on the number of cases for each wave, with a varying number of clusters: we found that two clusters is an optimal choice, in terms...
"Purifying Interaction Effects with the Functional ANOVA: An Efficient Algorithm for Recovering Identifiable Additive Models" (B. Lengerich, S. Tan, C. Chang, G. Hooker, R. Caruana 2019) @article{lengerich2019purifying, title={Purifying Interaction Effects with the Functional ANOVA: An Efficient Al...
We used a random forest algorithm in combination with phylogenetic trait imputation to fill gaps in the trait data and not omit missing data (Penone et al. 2014). To strengthen the predictive power of the model, we used the missForest::misForest() function (Stekhoven 2022) and phylogenetic ...
TreeSHAP is an algorithm to compute SHAP values for tree ensemble models such as decision trees, random forests, and gradient boosted trees in a polynomial-time proposed by Lundberg et. al (2018)¹. The algorithm allows us to reduce the complexity from O(TL2^M)to O(TLD^2) (T = numb...
On the basis of homocline matching (Booth et al., 1987), the BIOCLIM algorithm then compares the climatic characteristics of each grid cell in a geographic layer with the percentile distributions of variables inferred from species occurrences. The program, run with the BIOCLIM 'classic' option ...
In this study, we used the CCDC algorithm with the Landsat images as input data, thus the algorithm could not fully distinguish the different land cover types within the 30 m Landsat pixel. For example, the greening trends occurred in impervious land cover (Fig. 3a) due to the size of ...
For example, if we created one decision tree, the third one, it would predict 0. But if we relied on the mode of all 4 decision trees, then the predicted value would be 1. This is the power of random forests. AdaBoost AdaBoost is a boosted algorithm that is similar to Random Fores...
community 999 times, with the observed abundances randomly shifted across all the OTUs of the site × OTU table (note that this randomization does not preserve the row sum or column sum). The null model was calculated using the PF algorithm (proportional taxa occurrence frequency, fixed ...
Deep learning example with DeepExplainer (TensorFlow/Keras models) Deep SHAP is a high-speed approximation algorithm for SHAP values in deep learning models that builds on a connection with DeepLIFT described in the SHAP NIPS paper. The implementation here differs from the original DeepLIFT by using...