Learning to Classify with Branching Tests: "A decision tree takes as input an object or situation described by a set of properties, and outputs a yes/no decision. Decision trees therefore represent Boolean functions. Functions with a larger range of outputs can also be represented...."
– Artificial Intelligence: A Modern Approach. By Stuart Russell & Peter Norvig. 2002. Section 18.3; page 531.
This post attempts to consolidate information on tree algorithms and their implementations in Scikit-learn and Spark. In particular, it was written to provide clarification on how feature importance is calculated. There are many great resources online discussing how decision trees and random forests are created and this post is not intended to be that. Although it includes short definitions for context, it assumes the reader has a grasp on these concepts and wishes to know how the algorithms are implemented in Scikit-learn and Spark. Decision trees learn how to best split the dataset into smaller and smaller subsets to predict the target value.
Gradient boosted decision trees (GBDTs) have seen widespread adoption in academia, industry and competitive data science due to their state-of-the-art performance in a wide variety of machine learning tasks. In this paper, we present an extensive empirical comparison of XGBoost, LightGBM and CatBoost, three popular GBDT algorithms, to aid the data science practitioner in the choice from the multitude of available implementations. Specifically, we evaluate their behavior on four large-scale datasets with varying shapes, sparsities and learning tasks, in order to evaluate the algorithms' generalization performance, training times (on both CPU and GPU) and their sensitivity to hyper-parameter tuning. In our analysis, we first make use of a distributed grid-search to benchmark the algorithms on fixed configurations, and then employ a state-of-the-art algorithm for Bayesian hyper-parameter optimization to fine-tune the models.
It does not require any statistical knowledge to read and interpret them. Its graphical representation is very intuitive and users can easily relate their hypothesis. Useful in Data exploration: Decision tree is one of the fastest way to identify most significant variables and relation between two or more variables. With the help of decision trees, we can identify features that have better power to predict target variable. For example, we are working on a problem where we have information available in hundreds of variables, there decision tree will help to identify most significant variable. Less data cleaning required: It requires less data cleaning compared to some other modeling techniques. It is not influenced by outliers and missing values to a fair degree. Data type is not a constraint: It can handle both numerical and categorical variables.
This paper examines the stability of learned explanations for black-box predictions via model distillation with decision trees. One approach to intelligibility in machine learning is to use an understandable `student' model to mimic the output of an accurate `teacher'. Here, we consider the use of regression trees as a student model, in which nodes of the tree can be used as `explanations' for particular predictions, and the whole structure of the tree can be used as a global representation of the resulting function. However, individual trees are sensitive to the particular data sets used to train them, and an interpretation of a student model may be suspect if small changes in the training data have a large effect on it. In this context, access to outcomes from a teacher helps to stabilize the greedy splitting strategy by generating a much larger corpus of training examples than was originally available. We develop tests to ensure that enough examples are generated at each split so that the same splitting rule would be chosen with high probability were the tree to be re trained. Further, we develop a stopping rule to indicate how deep the tree should be built based on recent results on the variability of Random Forests when these are used as the teacher. We provide concrete examples of these procedures on the CAD-MDD and COMPAS data sets.
Bagging (bootstrap aggregating) regression trees is a technique that can turn a single tree model with high variance and poor predictive power into a fairly accurate prediction function. Unfortunately, bagging regression trees typically suffers from tree correlation, which reduces the overall performance of the model. Random forests are a modification of bagging that builds a large collection of de-correlated trees and have become a very popular "out-of-the-box" learning algorithm that enjoys good predictive performance. This tutorial will cover the fundamentals of random forests. This tutorial serves as an introduction to the random forests.
With the increasing need of personalised decision making, such as personalised medicine and online recommendations, a growing attention has been paid to the discovery of the context and heterogeneity of causal relationships. Most existing methods, however, assume a known cause (e.g. a new drug) and focus on identifying from data the contexts of heterogeneous effects of the cause (e.g. patient groups with different responses to the new drug). There is no approach to efficiently detecting directly from observational data context specific causal relationships, i.e. discovering the causes and their contexts simultaneously. In this paper, by taking the advantages of highly efficient decision tree induction and the well established causal inference framework, we propose the Tree based Context Causal rule discovery (TCC) method, for efficient exploration of context specific causal relationships from data. Experiments with both synthetic and real world data sets show that TCC can effectively discover context specific causal rules from the data.
There are many parameters here that control the look and information displayed. Take a look at the documentation for specifics. This requires installation of graphviz which includes the dot utility. For the complete options for conversion, take a look at the documentation. With a random forest, every tree will be built differently.
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bias weight distribution. The bias weight distribution is obtained from the assignment of high weights to the drug targets and propagating the assigned weights over a protein-protein interaction network such as STRING. The propagation of weights, defines neighborhoods of influence around the drug targets and as such simulates the spread of perturbations within the cell, following drug administration. Using a synthetic dataset, we showcase how application of biased tree ensembles (BiTE) results in significant accuracy gains at a much lower computational cost compared to the unbiased random forests (RF) algorithm. We then apply NetBiTE to the Genomics of Drug Sensitivity in Cancer (GDSC) dataset and demonstrate that NetBiTE outperforms RF in predicting IC50 drug sensitivity, only for drugs that target membrane receptor pathways (MRPs): RTK, EGFR and IGFR signaling pathways. We propose based on the NetBiTE results, that for drugs that inhibit MRPs, the expression of target genes prior to drug administration is a biomarker for IC50 drug sensitivity following drug administration. We further verify and reinforce this proposition through control studies on, PI3K/MTOR signaling pathway inhibitors, a drug category that does not target MRPs, and through assignment of dummy targets to MRP inhibiting drugs and investigating the variation in NetBiTE accuracy.
Decision trees are one of my favorite models. They are simple, and they are powerful. In fact most high performing Kaggle entries are a combination of XGBoost, which is variant of decision tree, and some very clever feature engineering. The concept behind decision trees is refreshingly straightforward. Imagine creating a data set by recording the time you left your house, and noting whether you arrived at work on time.