REVIEW 5 major objections 5 minor 1 cited by
Are machine learning interpretations reliable? A stability study on global interpretations
T0 review · 5 major / 5 minor · reviewed 2026-08-07 · deepseek-v4-flash
Pith's one-line read Popular machine learning interpretation methods are frequently less stable than the predictions they explain, and prediction accuracy does not predict interpretation stability.
desk verdict A broad, useful stability benchmark for global IML interpretations with a plausible core finding, but uncalibrated noise and post-hoc dataset selection weaken the generality. read the letter →
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
The reading
What carries the argument
The load-bearing machinery is a perturbation-and-resampling protocol paired with a family of stability metrics. Interpretations are recomputed across 100 random 70/30 train/test splits for supervised tasks and across subsampling plus additive Gaussian or Laplace noise (variance up to 5) for unsupervised tasks. Stability is scored with top-K rank metrics (Jaccard similarity, average overlap, and top-K Kendall's tau), clustering agreement metrics (adjusted Rand index, Fowlkes-Mallows index, mutual information, V-measure), and a new nearest-neighbor Jaccard area-under-the-curve score for dimension reduction. These scores quantify how much an interpretation changes under small perturbations, which is the paper's operational definition of reliability.
What would settle it
Run the same protocol on datasets using alternative perturbation types not covered in the paper, such as bootstrap resampling, feature permutation, time-based or grouped splits, and noise scaled to each feature's standard deviation, then check whether top-K Jaccard and average-overlap scores remain low and whether accuracy-stability regression slopes stay flat. If many methods show high stability under realistic perturbations, or if prediction accuracy strongly predicts interpretation stability, the paper's central claim would be contradicted.
Extended reading notes
Core claim
The paper's central empirical discovery is that stability and accuracy come apart: models with similar prediction accuracy can have very different interpretation stability, and more accurate models do not generally give more stable feature importance rankings. Within-method stability scores for feature importance are often low, while prediction stability is comparatively high; between-method agreement on interpretations is also weak, even when predictions agree strongly. In clustering and dimension reduction, stability is higher on average but still varies sharply by method and dataset, and methods that give stable clustering labels can still give unstable nearest-neighbor structure. The authors conclude that interpretation reliability must be assessed directly, not inferred from predictive performance, and they provide an open-source dashboard and Python package for doing so.
Load-bearing premise
The load-bearing premise is that random 70/30 train/test splits and additive Gaussian or Laplace noise with variance up to 5 constitute 'small random perturbations' that mimic realistic data variability; if real-world distribution shifts behave differently, the measured instability could be overstated or understated.
Editorial extensions
If this is right
- Practitioners who report a model's accuracy without reporting interpretation stability are missing a key axis of trustworthiness, since high accuracy can coexist with volatile explanations.
- The choice of an interpretation method should be justified empirically on the specific dataset, because no method is consistently most stable across datasets.
- Stable predictions do not guarantee stable interpretations, so stability analyses must target the interpretation itself rather than the model output.
- Unsupervised interpretations, such as cluster assignments or embeddings, should undergo the same stability checks as supervised feature importance before being used for scientific discovery.
- The released software enables researchers to run the same perturbation-and-metric protocol on their own data and IML methods, making stability assessment a routine step.
Reading between the lines
- An implication the authors leave implicit is that stability scores could be used to build more trustworthy interpretations by identifying which methods agree on a given dataset and focusing on their consensus, rather than trusting a single method's output.
- The observed instability may extend beyond tabular feature importance and clusterings to other explanation formats such as rules, textual explanations, and visual saliency maps, since the underlying sensitivity to data perturbations is a general phenomenon.
- A testable extension would be to check whether stability rankings change when perturbations are scaled to each feature's natural variability instead of using a global noise variance, which could reveal whether the reported instability is an artifact of noise levels that are large relative to signal.
- The accuracy-stability decoupling suggests that benchmarks for interpretable machine learning should treat interpretation stability as a reporting requirement rather than an optional diagnostic, especially in high-stakes applications.
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The paper reports a large-scale empirical study of the stability of global interpretable machine learning (IML) outputs for classification, regression, clustering, and dimensionality reduction on tabular benchmark data. Stability is operationalized as agreement under repeated 70/30 train/test splits and under additive Gaussian or Laplace noise, measured with Jaccard, average overlap, top-K Kendall's tau, ARI, Fowlkes-Mallows, mutual information, V-measure, and a proposed NN-Jaccard-AUC metric. Across roughly 50 IML method-dataset combinations, the authors report that interpretations are frequently unstable, are notably less stable than the predictions themselves, show no association with predictive accuracy, and that no single method is most stable across datasets. The paper also releases an interactive dashboard and a Python package for users to run similar reliability assessments.
Significance. If the findings hold, this is a useful systematic benchmark for the IML community: it goes beyond single-method studies, covers supervised and unsupervised tasks, uses multiple stability metrics, and ships open-source tooling for practitioners. The scale of the experiment (hundreds of thousands of repeats) and the public dashboard are concrete strengths. However, the abstract-level claims currently outrun the methodological rigor of the study: the perturbation scale is uncalibrated, the dataset inventory is internally inconsistent, some dataset and hyperparameter choices are made after looking at performance, and the headline comparisons with prediction stability are not formalized with uncertainty quantification. These issues do not invalidate the empirical enterprise, but they must be fixed before the broad claims can be accepted as stated.
major comments (5)
- [Appendix A.1 and Figure 8] The noise perturbation is not calibrated to feature scale and the parameterization is ambiguous. Appendix A.1 defines noise as Normal(0, sigma^2) or Laplace(0, sigma^2) with variance sigma^2 in [0, 5], while Figure 8 and Section B.2 use 'normal noise with a standard deviation of 0.15' and 'sigma = 0.15'. If sigma is a standard deviation there, the variance is 0.0225, which is not clearly connected to the grid in A.1; if sigma is read as variance, then the 'standard deviation' statement in B.2 is wrong. More importantly, no standardization is described before adding noise, so a fixed magnitude is applied to datasets with very different feature scales (e.g., PANCAN RNA-seq counts versus Iris physical measurements). A fixed noise level can be negligible for high-variance features and overwhelming for low-variance features, which directly affects the NN-Jaccard-AUC stability results in Figure 8 and the claim that dimension-reduction interpretations are 'frequently unstable'. Please state one convention, standardize features or calibrate noise to per-feature variance, and report a sensitivity sweep over noise levels.
- [Section 2.4 and Table 5] The dataset inventory is internally inconsistent. Table 5 lists 25 datasets, but Section 2.4 and the results refer to datasets that do not appear in the table, including DNase, Madelon, Amphibians, Theorem, Digit MNIST, and Darmanis. Appendix C states that the study covers 'over 50 IML methodologies, 33 data sets' and that the classification/regression pages use 13 datasets, neither of which matches Table 5. This mismatch prevents the reader from reconstructing the actual experimental scope and undermines the reproducibility of the paper's central claims. Please provide a complete dataset table and reconcile the counts throughout the text and appendix.
- [Section 2.4] The dataset inclusion rules appear to be applied after seeing the methods' performance. The text says 'We select classification data sets whose ARIs are all above 0.2' and, for dimension reduction, excludes datasets whose clustering accuracy on the first two reduced dimensions falls below an ARI cutoff of 0.2, with additional cutoffs P>15 and N<2000. It is unclear what 'ARIs' means for classification datasets, since ARI is defined as a clustering similarity metric and not a classification accuracy measure. If these thresholds were fixed after inspecting results, the benchmark is restricted to datasets on which the studied methods achieve a minimum level of accuracy, which can only weaken the accuracy-stability association and bias the 'no single method' conclusion. Please state when and why the thresholds were chosen, justify them independently of the methods' performance, and report results before and after the exclusions.
- [Section 2.2.3 and Table 3] The hierarchical clustering distance metric is selected per dataset by the highest clustering accuracy on the true labels. This means the HC stability rankings in Figure 4 are not the stability of a fixed, pre-specified method; the selection itself uses label information on the same datasets whose stability is later compared. The choice among distance metrics is a hyperparameter and should be made by a procedure that does not leak the test labels, or results for all distances should be reported so the reader can assess the sensitivity of the stability rankings.
- [Section 3.2 and abstract] The claim that interpretations are 'notably less stable than the predictions themselves' is supported only by visual comparison of heatmaps (A) and (E) in Figures 2 and 3, without a paired statistical test or an effect-size summary across datasets and methods. Similarly, the 'no single method consistently provides the most stable interpretations' claim rests on bump plots (Figures 2B-5B) that rank methods without error bars or confidence intervals; with 50-100 repeats per setting, the rank differences may be within sampling variation. Please add uncertainty quantification for the stability scores and a formal comparison of interpretation stability versus prediction stability, or temper the abstract-level wording accordingly.
minor comments (5)
- [Equation (2)] The definition of top-K Kendall's tau in Eq. (2) uses the term \bar{K}^{(p)}_{i,j} without giving its piecewise definition; please include the missing definition from the cited Fagin et al. reference.
- [Throughout] There are repeated typos and grammatical slips, including 'spannining' (Section 2), 'are have' (Section 3.2), 'logiaclly' (Section 3.3), 'underlyign' (Discussion), 'paramter' (Appendix A.3.1), 'featuers' (Appendix C.2.1), 'Tetragonla' (Appendix B.1), and 'Figure 4 P-values' in the Appendix B.3 caption; these should be corrected.
- [Section 2.2.2 and Table 2] The Deep Autoencoder row in Table 2 uses em-dashes for both the Global/Local and Linear/Non-linear columns; please specify the intended categorization or explain why it does not apply.
- [Appendix A.2.1] The NN-Jaccard-AUC metric is defined in prose but the formula in Table 4 is a compact notation; please state explicitly that it is an average over samples and over the 50 selected values of K, as described in the appendix, so the table is self-contained.
- [References] Several references are incomplete or garbled, notably the author string in reference [3]; please verify all references against the publisher records.
Circularity Check
No significant circularity: the stability measurements are empirical and self-contained; the reliability-stability link is an explicit definitional stance, not a hidden derivation.
full rationale
The paper's central claims—that popular interpretation methods are frequently unstable, that interpretation stability is lower than prediction stability, that accuracy is not associated with stability, and that no method is consistently most stable—are empirical results obtained by applying defined stability metrics (Jaccard, AO, Kendall's Tau, ARI, NN-Jaccard-AUC) to interpretations across repeated train/test splits and noise perturbations. Nothing in these measurements is fitted to the conclusions, and no fitted parameter is renamed as a prediction. The one terminological loop is explicit: Section 1 defines stability as findings that are 'consistent or reliable under small random perturbations,' and Appendix A.1 states 'We define an interpretation to be reliable if the same or similar interpretations can be derived from new data of the same distribution. Therefore, the reliability of a machine learning model can be measured by the stability of its derived interpretations.' The conclusion that unstable interpretations are unreliable follows from that definitional stance rather than from a hidden equivalence; the empirical content lies in the measured instability itself, which is not derived from the conclusion. Self-citations (Allen, Gan, Zheng 2023; Gan, Zheng, Allen 2022; Zikry and Allen 2025) appear only as background references and are not load-bearing for the stability measurements. The choice of perturbation scale (e.g., sigma^2 in [0,5]) and the mixing of variance versus standard deviation parameterizations are legitimate correctness concerns, but they are not circularity. The paper is self-contained against external benchmarks, so the score is 0.
Assumptions & free parameters
free parameters (4)
- Top-K features (K=10) =
10
- Noise level for dimension reduction (sigma) =
0.15
- Dataset inclusion cutoffs =
ARI>0.2, P>15, N<2000
- Per-dataset distance metric for hierarchical clustering =
varies (Table 3)
assumptions (3)
- domain assumption Stability is a prerequisite for reliability
- domain assumption Random train/test splits and additive noise represent small perturbations
- domain assumption Standard implementations of ML methods are unbiased representations
invented entities (1)
-
NN-Jaccard-AUC metric
Cite this review
Pith. "Pith review of Are machine learning interpretations reliable? A stability study on global interpretations." pith.science (2026). https://pith.science/paper/JOYBISVH
@misc{pith2026250515728,
author = {Pith},
title = {Pith review of: Are machine learning interpretations reliable? A stability study on global interpretations},
year = {2026},
howpublished = {\url{https://pith.science/paper/JOYBISVH}},
note = {Machine review of arXiv:2505.15728}
}
read the original abstract
As machine learning systems are increasingly used in high-stakes domains, there is a growing emphasis placed on making them interpretable to improve trust in these systems. In response, a range of interpretable machine learning (IML) methods have been developed to generate human-understandable insights into otherwise black box models. With these methods, a fundamental question arises: Are these interpretations reliable? Unlike with prediction accuracy or other evaluation metrics for supervised models, the proximity to the true interpretation is difficult to define. Instead, we ask a closely related question that we argue is a prerequisite for reliability: Are these interpretations stable? We define stability as findings that are consistent or reliable under small random perturbations to the data or algorithms. In this study, we conduct the first systematic, large-scale empirical stability study on popular machine learning global interpretations for both supervised and unsupervised tasks on tabular data. Our findings reveal that popular interpretation methods are frequently unstable, notably less stable than the predictions themselves, and that there is no association between the accuracy of machine learning predictions and the stability of their associated interpretations. Moreover, we show that no single method consistently provides the most stable interpretations across a range of benchmark datasets. Overall, these results suggest that interpretability alone does not warrant trust, and underscores the need for rigorous evaluation of interpretation stability in future work. To support these principles, we have developed and released an open source IML dashboard and Python package to enable researchers to assess the stability and reliability of their own data-driven interpretations and discoveries.
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Reference graph
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