Targeted Maximum Likelihood Estimation for Integral Projection Models in Population Ecology

Integral projection models (IPMs) are widely used to study population growth and the dynamics of demographic structure (e.g. age and size distributions) within a population.These models use data on individuals' growth, survival, and reproduction to predict changes in the population from one time point to the next and use these in turn to ask about long-term growth rates, the sensitivity of that growth rate to environmental factors, and aspects of the long term population such as how much reproduction concentrates in a few individuals; these quantities are not directly measurable from data and must be inferred from the model. Building IPMs requires us to develop models for individual fates over the next time step -- Did they survive? How much did they grow or shrink? Did they Reproduce? -- conditional on their initial state as well as on environmental covariates in a manner that accounts for the unobservable quantities that are are ultimately interested in estimating.Targeted maximum likelihood estimation (TMLE) methods are particularly well-suited to a framework in which we are largely interested in the consequences of models. These build machine learning-based models that estimate the probability distribution of the data we observe and define a target of inference as a function of these. The initial estimate for the distribution is then modified by tilting in the direction of the efficient influence function to both de-bias the parameter estimate and provide more accurate inference. In this paper, we employ TMLE to develop robust and efficient estimators for properties derived from a fitted IPM. Mathematically, we derive the efficient influence function and formulate the paths for the least favorable sub-models. Empirically, we conduct extensive simulations using real data from both long term studies of Idaho steppe plant communities and experimental Rotifer populations.

Targeted Learning for Variable Importance

Variable importance is one of the most widely used measures for interpreting machine learning with significant interest from both statistics and machine learning communities. Recently, increasing attention has been directed toward uncertainty quantification in these metrics. Current approaches largely rely on one-step procedures, which, while asymptotically efficient, can present higher sensitivity and instability in finite sample settings. To address these limitations, we propose a novel method by employing the targeted learning (TL) framework, designed to enhance robustness in inference for variable importance metrics. Our approach is particularly suited for conditional permutation variable importance. We show that it (i) retains the asymptotic efficiency of traditional methods, (ii) maintains comparable computational complexity, and (iii) delivers improved accuracy, especially in finite sample contexts. We further support these findings with numerical experiments that illustrate the practical advantages of our method and validate the theoretical results.

Accelerated Inference for Partially Observed Markov Processes using Automatic Differentiation

Automatic differentiation (AD) has driven recent advances in machine learning, including deep neural networks and Hamiltonian Markov Chain Monte Carlo methods. Partially observed nonlinear stochastic dynamical systems have proved resistant to AD techniques because widely used particle filter algorithms yield an estimated likelihood function that is discontinuous as a function of the model parameters. We show how to embed two existing AD particle filter methods in a theoretical framework that provides an extension to a new class of algorithms. This new class permits a bias/variance tradeoff and hence a mean squared error substantially lower than the existing algorithms. We develop likelihood maximization algorithms suited to the Monte Carlo properties of the AD gradient estimate. Our algorithms require only a differentiable simulator for the latent dynamic system; by contrast, most previous approaches to AD likelihood maximization for particle filters require access to the system's transition probabilities. Numerical results indicate that a hybrid algorithm that uses AD to refine a coarse solution from an iterated filtering algorithm show substantial improvement on current state-of-the-art methods for a challenging scientific benchmark problem.

Differentiable Programming for Differential Equations: A Review

The differentiable programming paradigm is a cornerstone of modern scientific computing. It refers to numerical methods for computing the gradient of a numerical model's output. Many scientific models are based on differential equations, where differentiable programming plays a crucial role in calculating model sensitivities, inverting model parameters, and training hybrid models that combine differential equations with data-driven approaches. Furthermore, recognizing the strong synergies between inverse methods and machine learning offers the opportunity to establish a coherent framework applicable to both fields. Differentiating functions based on the numerical solution of differential equations is non-trivial. Numerous methods based on a wide variety of paradigms have been proposed in the literature, each with pros and cons specific to the type of problem investigated. Here, we provide a comprehensive review of existing techniques to compute derivatives of numerical solutions of differential equations. We first discuss the importance of gradients of solutions of differential equations in a variety of scientific domains. Second, we lay out the mathematical foundations of the various approaches and compare them with each other. Third, we cover the computational considerations and explore the solutions available in modern scientific software. Last but not least, we provide best-practices and recommendations for practitioners. We hope that this work accelerates the fusion of scientific models and data, and fosters a modern approach to scientific modelling.

Why You Should Not Trust Interpretations in Machine Learning: Adversarial Attacks on Partial Dependence Plots

The adoption of artificial intelligence (AI) across industries has led to the widespread use of complex black-box models and interpretation tools for decision making. This paper proposes an adversarial framework to uncover the vulnerability of permutation-based interpretation methods for machine learning tasks, with a particular focus on partial dependence (PD) plots. This adversarial framework modifies the original black box model to manipulate its predictions for instances in the extrapolation domain. As a result, it produces deceptive PD plots that can conceal discriminatory behaviors while preserving most of the original model's predictions. This framework can produce multiple fooled PD plots via a single model. By using real-world datasets including an auto insurance claims dataset and COMPAS (Correctional Offender Management Profiling for Alternative Sanctions) dataset, our results show that it is possible to intentionally hide the discriminatory behavior of a predictor and make the black-box model appear neutral through interpretation tools like PD plots while retaining almost all the predictions of the original black-box model. Managerial insights for regulators and practitioners are provided based on the findings.

Longitudinal Counterfactuals: Constraints and Opportunities

Counterfactual explanations are a common approach to providing recourse to data subjects. However, current methodology can produce counterfactuals that cannot be achieved by the subject, making the use of counterfactuals for recourse difficult to justify in practice. Though there is agreement that plausibility is an important quality when using counterfactuals for algorithmic recourse, ground truth plausibility continues to be difficult to quantify. In this paper, we propose using longitudinal data to assess and improve plausibility in counterfactuals. In particular, we develop a metric that compares longitudinal differences to counterfactual differences, allowing us to evaluate how similar a counterfactual is to prior observed changes. Furthermore, we use this metric to generate plausible counterfactuals. Finally, we discuss some of the inherent difficulties of using counterfactuals for recourse.

Provably Stable Feature Rankings with SHAP and LIME

Feature attributions are ubiquitous tools for understanding the predictions of machine learning models. However, popular methods for scoring input variables such as SHAP and LIME suffer from high instability due to random sampling. Leveraging ideas from multiple hypothesis testing, we devise attribution methods that correctly rank the most important features with high probability. Our algorithm RankSHAP guarantees that the $K$ highest Shapley values have the proper ordering with probability exceeding $1-\alpha$. Empirical results demonstrate its validity and impressive computational efficiency. We also build on previous work to yield similar results for LIME, ensuring the most important features are selected in the right order.

Stabilizing Estimates of Shapley Values with Control Variates

Shapley values are among the most popular tools for explaining predictions of blackbox machine learning models. However, their high computational cost motivates the use of sampling approximations, inducing a considerable degree of uncertainty. To stabilize these model explanations, we propose ControlSHAP, an approach based on the Monte Carlo technique of control variates. Our methodology is applicable to any machine learning model and requires virtually no extra computation or modeling effort. On several high-dimensional datasets, we find it can produce dramatic reductions in the Monte Carlo variability of Shapley estimates.

A Generic Approach for Reproducible Model Distillation

Model distillation has been a popular method for producing interpretable machine learning. It uses an interpretable "student" model to mimic the predictions made by the black box "teacher" model. However, when the student model is sensitive to the variability of the data sets used for training, the corresponded interpretation is not reliable. Existing strategies stabilize model distillation by checking whether a large enough corpus of pseudo-data is generated to reliably reproduce student models, but methods to do so have so far been developed for a specific student model. In this paper, we develop a generic approach for stable model distillation based on central limit theorem for the average loss. We start with a collection of candidate student models and search for candidates that reasonably agree with the teacher. Then we construct a multiple testing framework to select a corpus size such that the consistent student model would be selected under different pseudo sample. We demonstrate the application of our proposed approach on three commonly used intelligible models: decision trees, falling rule lists and symbolic regression. Finally, we conduct simulation experiments on Mammographic Mass and Breast Cancer datasets and illustrate the testing procedure throughout a theoretical analysis with Markov process.

S-LIME: Stabilized-LIME for Model Explanation

An increasing number of machine learning models have been deployed in domains with high stakes such as finance and healthcare. Despite their superior performances, many models are black boxes in nature which are hard to explain. There are growing efforts for researchers to develop methods to interpret these black-box models. Post hoc explanations based on perturbations, such as LIME, are widely used approaches to interpret a machine learning model after it has been built. This class of methods has been shown to exhibit large instability, posing serious challenges to the effectiveness of the method itself and harming user trust. In this paper, we propose S-LIME, which utilizes a hypothesis testing framework based on central limit theorem for determining the number of perturbation points needed to guarantee stability of the resulting explanation. Experiments on both simulated and real world data sets are provided to demonstrate the effectiveness of our method.