arXiv subjects

Marvin N. Wright

Publications and source records attributed to Marvin N. Wright.

32 records · Page 2Linked to original sources

arXiv2024

A Guide to Feature Importance Methods for Scientific Inference

While machine learning (ML) models are increasingly used due to their high predictive power, their use in understanding the data-generating process (DGP) is limited. Understanding the DGP requires insights into feature-target associations, which many ML models cannot directly provide due to their opaque internal mechanisms. Feature importance (FI) methods provide useful insights into the DGP under certain conditions. Since the results of different FI methods have different interpretations, selecting the correct FI method for a concrete use case is crucial and still requires expert knowledge. This paper serves as a comprehensive guide to help understand the different interpretations of global FI methods. Through an extensive review of FI methods and providing new proofs regarding their interpretation, we facilitate a thorough understanding of these methods and formulate concrete recommendations for scientific inference. We conclude by discussing options for FI uncertainty estimation and point to directions for future research aiming at full statistical inference from black-box ML models.

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arXiv2024

Toward Understanding the Disagreement Problem in Neural Network Feature Attribution

In recent years, neural networks have demonstrated their remarkable ability to discern intricate patterns and relationships from raw data. However, understanding the inner workings of these black box models remains challenging, yet crucial for high-stake decisions. Among the prominent approaches for explaining these black boxes are feature attribution methods, which assign relevance or contribution scores to each input variable for a model prediction. Despite the plethora of proposed techniques, ranging from gradient-based to backpropagation-based methods, a significant debate persists about which method to use. Various evaluation metrics have been proposed to assess the trustworthiness or robustness of their results. However, current research highlights disagreement among state-of-the-art methods in their explanations. Our work addresses this confusion by investigating the explanations' fundamental and distributional behavior. Additionally, through a comprehensive simulation study, we illustrate the impact of common scaling and encoding techniques on the explanation quality, assess their efficacy across different effect sizes, and demonstrate the origin of inconsistency in rank-based evaluation metrics.

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arXiv2024

Interpreting Deep Neural Networks with the Package innsight

The R package innsight offers a general toolbox for revealing variable-wise interpretations of deep neural networks' predictions with so-called feature attribution methods. Aside from the unified and user-friendly framework, the package stands out in three ways: It is generally the first R package implementing feature attribution methods for neural networks. Secondly, it operates independently of the deep learning library allowing the interpretation of models from any R package, including keras, torch, neuralnet, and even custom models. Despite its flexibility, innsight benefits internally from the torch package's fast and efficient array calculations, which builds on LibTorch $-$ PyTorch's C++ backend $-$ without a Python dependency. Finally, it offers a variety of visualization tools for tabular, signal, image data or a combination of these. Additionally, the plots can be rendered interactively using the plotly package.

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arXiv2023

survex: an R package for explaining machine learning survival models

Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to explain their internal operations and prediction rationales. To tackle this issue, we introduce the survex R package, which provides a cohesive framework for explaining any survival model by applying explainable artificial intelligence techniques. The capabilities of the proposed software encompass understanding and diagnosing survival models, which can lead to their improvement. By revealing insights into the decision-making process, such as variable effects and importances, survex enables the assessment of model reliability and the detection of biases. Thus, transparency and responsibility may be promoted in sensitive areas, such as biomedical research and healthcare applications.

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arXiv2023

arfpy: A python package for density estimation and generative modeling with adversarial random forests

This paper introduces $\textit{arfpy}$, a python implementation of Adversarial Random Forests (ARF) (Watson et al., 2023), which is a lightweight procedure for synthesizing new data that resembles some given data. The software $\textit{arfpy}$ equips practitioners with straightforward functionalities for both density estimation and generative modeling. The method is particularly useful for tabular data and its competitive performance is demonstrated in previous literature. As a major advantage over the mostly deep learning based alternatives, $\textit{arfpy}$ combines the method's reduced requirements in tuning efforts and computational resources with a user-friendly python interface. This supplies audiences across scientific fields with software to generate data effortlessly.

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arXiv2023

Conditional Feature Importance for Mixed Data

Despite the popularity of feature importance (FI) measures in interpretable machine learning, the statistical adequacy of these methods is rarely discussed. From a statistical perspective, a major distinction is between analyzing a variable's importance before and after adjusting for covariates - i.e., between $\textit{marginal}$ and $\textit{conditional}$ measures. Our work draws attention to this rarely acknowledged, yet crucial distinction and showcases its implications. Further, we reveal that for testing conditional FI, only few methods are available and practitioners have hitherto been severely restricted in method application due to mismatching data requirements. Most real-world data exhibits complex feature dependencies and incorporates both continuous and categorical data (mixed data). Both properties are oftentimes neglected by conditional FI measures. To fill this gap, we propose to combine the conditional predictive impact (CPI) framework with sequential knockoff sampling. The CPI enables conditional FI measurement that controls for any feature dependencies by sampling valid knockoffs - hence, generating synthetic data with similar statistical properties - for the data to be analyzed. Sequential knockoffs were deliberately designed to handle mixed data and thus allow us to extend the CPI approach to such datasets. We demonstrate through numerous simulations and a real-world example that our proposed workflow controls type I error, achieves high power and is in line with results given by other conditional FI measures, whereas marginal FI metrics result in misleading interpretations. Our findings highlight the necessity of developing statistically adequate, specialized methods for mixed data.

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arXiv2023

Adversarial random forests for density estimation and generative modeling

We propose methods for density estimation and data synthesis using a novel form of unsupervised random forests. Inspired by generative adversarial networks, we implement a recursive procedure in which trees gradually learn structural properties of the data through alternating rounds of generation and discrimination. The method is provably consistent under minimal assumptions. Unlike classic tree-based alternatives, our approach provides smooth (un)conditional densities and allows for fully synthetic data generation. We achieve comparable or superior performance to state-of-the-art probabilistic circuits and deep learning models on various tabular data benchmarks while executing about two orders of magnitude faster on average. An accompanying $\texttt{R}$ package, $\texttt{arf}$, is available on $\texttt{CRAN}$.

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arXiv2023

Unifying local and global model explanations by functional decomposition of low dimensional structures

We consider a global representation of a regression or classification function by decomposing it into the sum of main and interaction components of arbitrary order. We propose a new identification constraint that allows for the extraction of interventional SHAP values and partial dependence plots, thereby unifying local and global explanations. With our proposed identification, a feature's partial dependence plot corresponds to the main effect term plus the intercept. The interventional SHAP value of feature $k$ is a weighted sum of the main component and all interaction components that include $k$, with the weights given by the reciprocal of the component's dimension. This brings a new perspective to local explanations such as SHAP values which were previously motivated by game theory only. We show that the decomposition can be used to reduce direct and indirect bias by removing all components that include a protected feature. Lastly, we motivate a new measure of feature importance. In principle, our proposed functional decomposition can be applied to any machine learning model, but exact calculation is only feasible for low-dimensional structures or ensembles of those. We provide an algorithm and efficient implementation for gradient-boosted trees (xgboost) and random planted forest. Conducted experiments suggest that our method provides meaningful explanations and reveals interactions of higher orders. The proposed methods are implemented in an R package, available at \url{https://github.com/PlantedML/glex}.

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arXiv2021

Relating the Partial Dependence Plot and Permutation Feature Importance to the Data Generating Process

Scientists and practitioners increasingly rely on machine learning to model data and draw conclusions. Compared to statistical modeling approaches, machine learning makes fewer explicit assumptions about data structures, such as linearity. However, their model parameters usually cannot be easily related to the data generating process. To learn about the modeled relationships, partial dependence (PD) plots and permutation feature importance (PFI) are often used as interpretation methods. However, PD and PFI lack a theory that relates them to the data generating process. We formalize PD and PFI as statistical estimators of ground truth estimands rooted in the data generating process. We show that PD and PFI estimates deviate from this ground truth due to statistical biases, model variance and Monte Carlo approximation errors. To account for model variance in PD and PFI estimation, we propose the learner-PD and the learner-PFI based on model refits, and propose corrected variance and confidence interval estimators.

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arXiv2021

Generalization of the Change of Variables Formula with Applications to Residual Flows

Normalizing flows leverage the Change of Variables Formula (CVF) to define flexible density models. Yet, the requirement of smooth transformations (diffeomorphisms) in the CVF poses a significant challenge in the construction of these models. To enlarge the design space of flows, we introduce $\mathcal{L}$-diffeomorphisms as generalized transformations which may violate these requirements on zero Lebesgue-measure sets. This relaxation allows e.g. the use of non-smooth activation functions such as ReLU. Finally, we apply the obtained results to planar, radial, and contractive residual flows.

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arXiv2021

Testing Conditional Independence in Supervised Learning Algorithms

We propose the conditional predictive impact (CPI), a consistent and unbiased estimator of the association between one or several features and a given outcome, conditional on a reduced feature set. Building on the knockoff framework of Candès et al. (2018), we develop a novel testing procedure that works in conjunction with any valid knockoff sampler, supervised learning algorithm, and loss function. The CPI can be efficiently computed for high-dimensional data without any sparsity constraints. We demonstrate convergence criteria for the CPI and develop statistical inference procedures for evaluating its magnitude, significance, and precision. These tests aid in feature and model selection, extending traditional frequentist and Bayesian techniques to general supervised learning tasks. The CPI may also be applied in causal discovery to identify underlying multivariate graph structures. We test our method using various algorithms, including linear regression, neural networks, random forests, and support vector machines. Empirical results show that the CPI compares favorably to alternative variable importance measures and other nonparametric tests of conditional independence on a diverse array of real and simulated datasets. Simulations confirm that our inference procedures successfully control Type I error and achieve nominal coverage probability. Our method has been implemented in an R package, cpi, which can be downloaded from https://github.com/dswatson/cpi.

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arXiv2019

A Random Forest Approach for Modeling Bounded Outcomes

Random forests have become an established tool for classification and regression, in particular in high-dimensional settings and in the presence of complex predictor-response relationships. For bounded outcome variables restricted to the unit interval, however, classical random forest approaches may severely suffer as they do not account for the heteroscedasticity in the data. A random forest approach is proposed for relating beta distributed outcomes to explanatory variables. The approach explicitly makes use of the likelihood function of the beta distribution for the selection of splits during the tree-building procedure. In each iteration of the tree-building algorithm one chooses the combination of explanatory variable and splitting rule that maximizes the log-likelihood function of the beta distribution with the parameter estimates derived from the nodes of the currently built tree. Several simulation studies demonstrate the properties of the method and compare its performance to classical random forest approaches as well as to parametric regression models.

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arXiv2018

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the implementation, provide examples, validate the package with a reference implementation, and compare runtime and memory usage with other implementations. The new software proves to scale best with the number of features, samples, trees, and features tried for splitting. Finally, we show that ranger is the fastest and most memory efficient implementation of random forests to analyze data on the scale of a genome-wide association study.

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arXiv2018

Unbiased split variable selection for random survival forests using maximally selected rank statistics

The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistics, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables. An alternative is to use maximally selected rank statistics for the split point selection. As in conditional inference forests, splitting variables are compared on the p-value scale. However, instead of the conditional Monte-Carlo approach used in conditional inference forests, p-value approximations are employed. We describe several p-value approximations and the implementation of the proposed random forest approach. A simulation study demonstrates that unbiased split variable selection is possible. However, there is a trade-off between unbiased split variable selection and runtime. In benchmark studies of prediction performance on simulated and real datasets the new method performs better than random survival forests if informative dichotomous variables are combined with uninformative variables with more categories and better than conditional inference forests if non-linear covariate effects are included. In a runtime comparison the method proves to be computationally faster than both alternatives, if a simple p-value approximation is used.

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