1. Introduction
The original KernelSHAP paper by Lundberg and Lee [
1] from 2017 was a landmark success for interpretable machine learning. Its primary achievement was making the Shapley value [
2]—a theoretically optimal but computationally intractable [
3,
4,
5] concept from cooperative game theory [
6]—practical for explaining machine learning models. Lundberg and Lee [
1] discovered that the exact Shapley values for a prediction could be recovered as the solution to a specially weighted least squares regression problem. By sampling a manageable number of coalitional inputs and solving this approximate regression, KernelSHAP provided a single, consistent metric for feature importance. The accompanying open-source library SHAP [
1] fueled its widespread use, making it a predominant standard for model interpretation, particularly in the model-agnostic setting.
The follow-up work on Unbiased KernelSHAP by Covert and Lee [
7] represents a success in strengthening methodological rigor. It addresses the problem that the original KernelSHAP algorithm has not been proven to be unbiased, does not provide uncertainty estimates, and offers no finite-sample error guarantees, making it difficult to assess the reliability of its explanations in practice. While not as publicly visible as the initial breakthrough, this refinement solidified SHAP’s foundation as a robust, statistically sound tool. Despite these advances, KernelSHAP (and to a lesser extent, its unbiased variant) still leaves several methodological questions open: the original algorithm lacks unbiasedness and uncertainty quantification, and neither variant provides explicit guidance on how to choose the number of samples to achieve a desired precision. These gaps motivate the search for alternative estimators with clearer theoretical properties.
According to Lundberg and Lee [
1], KernelSHAP was developed without knowledge of prior articles on cooperative game theory like Charnes et al. [
8] and Ruiz et al. [
9], who decades earlier had already derived the precise weighting scheme that makes a least squares regression yield the Shapley value when complete data is available. This outlines a fascinating case of parallel innovation across disciplines. Cooperative game theory, with the Shapley value [
2] as its most important solution concept, had long been a mature and applied field providing rigorous solutions to real-world problems of fair division and coalitional analysis, from allocating airport landing fees among airlines based on runway use [
10] to measuring the voting power of political blocs in a legislature [
11,
12,
13]. Yet, the field of machine learning, increasingly reliant on inscrutable black-box models, had not seen its own predictions as precisely such a system—where input features act as cooperating agents whose joint effort produces a model’s output. Lundberg and Lee’s pivotal contribution [
1] was to bridge this conceptual gap. They recognized that the abstract “game” defined by a model’s prediction function was a natural domain for Shapley’s theory. By doing so, they inadvertently reinvented a specific computational tool—the weighted least squares approximation—from the game theory literature, but with a transformative new purpose: not to analyze economic coalitions, but to explain the inner logic of artificial intelligence.
Whereas KernelSHAP [
1] and its unbiased variant [
7] are widely used, the methods from Benati et al. [
14]—which are equally based on the least squares formulation of the Shapley value—have received comparatively little attention. This article represents, to the best of our knowledge, their first application in explainable artificial intelligence. We adapt the ideas from Benati et al. [
14] as general TU game approximation algorithms, terming their weighted sampling strategy LSS (least squares sampling). Regarding their proposal for stratification, we differentiate S-LSS (no sample reuse across strata) from SRS-LSS (with sample reuse), while noting that both stratification schemes introduce theoretical complications that we specify in detail below. However, the framework by Benati et al. [
14] itself has received little critical examination. Its stratified estimators (S-LSS and SRS-LSS) are presented without formal variance analysis or finite-sample guarantees, and the practical implications of their overlapping strata and sample reuse remain unexplored. Thus, while these methods are theoretically elegant, their strengths and weaknesses relative to KernelSHAP and UKS are not well understood. Consequently, the following theoretical questions remain unresolved: (i) Under what conditions does stratification reduce variance, and does S-LSS guarantee such a reduction? (ii) How does sample reuse across strata affect the covariance structure of SRS-LSS? (iii) What is the exact relationship between LSS and UKS, and why do their theoretical Hoeffding bounds differ? (iv) How tight are these finite-sample bounds in practice? These questions are not merely academic: without answers, practitioners cannot predict which algorithm will perform well on a given problem, nor can they rely on finite-sample guarantees for the least squares-based methods. Moreover, the relationship between the approach by Benati et al. [
14] and the widely used KernelSHAP family remains opaque, hindering informed method selection.
The objective of this paper is to address these open questions by providing a detailed structural, theoretical, and algorithmic analysis of the methods LSS, S-LSS, and SRS-LSS from Benati et al. [
14]. In contrast to prior work, we do not propose a new estimator but rather clarify the properties of existing ones, resolving the ambiguities listed above. Specifically, our research question is as follows: What are the structural relationships between the least squares-based Shapley value approximation algorithms proposed by Benati et al. [
14] (LSS, S-LSS, SRS-LSS) and the widely used KernelSHAP and Unbiased KernelSHAP (UKS)? These strategies differ fundamentally: KernelSHAP estimates both the regression matrix and the target vector from samples, whereas UKS precomputes the exact matrix. LSS uses a single importance sampling distribution over all coalitions, while S-LSS and SRS-LSS introduce player- and size-dependent sampling schemes.
This article does the following:
Compares the variances of LSS and S-LSS in detail, showing that S-LSS is not a valid stratified estimator in the classical sense and that neither algorithm dominates the other.
Points out how sample reuse across strata may introduce non-zero covariance terms between strata for SRS-LSS, making its theoretical analysis difficult.
Proves that LSS and UKS approximate the same underlying problem, thereby only differing in their respective sampling strategies, which explains why their empirical performance is often similar despite different theoretical bounds.
Derives finite-sample bounds for LSS, UKS, and S-LSS and then critically assesses their tightness and practical relevance through numerical experiments in
Section 6.
Tests how the unbiased Shapley estimators LSS, S-LSS, and SRS-LSS compare with KernelSHAP and UKS for both classical cooperative games and real-world applications from interpretable machine learning.
The remainder of this article is structured as follows. In
Section 2, we summarize basic ideas from cooperative game theory, including linear solution concepts and the Shapley value, and introduce the BShap (Baseline Shapley) model for interpretable machine learning.
Section 3 briefly reviews Monte Carlo methods, along with stratified sampling and importance sampling for variance reduction. A summary of results on approximating linear solution concepts by means of importance sampling on the coalition space from our previous work [
15] is presented in
Section 4. The central developments of this paper are detailed in
Section 5, where we formally introduce the LSS, S-LSS, and SRS-LSS estimators and elaborate on the first three contributions outlined above: the variance comparison between LSS and S-LSS, the analysis of non-zero covariances in SRS-LSS, and the formal proof of structural equivalence between LSS and UKS. In addition, we derive finite-sample Hoeffding bounds for LSS, UKS, and S-LSS. The empirical performance of all algorithms—including a critical assessment of these bounds—is analyzed in
Section 6 using two types of cooperative games and three real-world explainability scenarios, thereby numerically substantiating our previous analytical claims. The paper concludes in
Section 7 with a summary and recommendations.
6. Empirical Results
We validate our results by applying the algorithms introduced in
Section 5.2 to approximate Shapley values for airport games, weighted voting games, and three real-world interpretable machine learning problems.
We consistently assume that all players’ Shapley values must be estimated. Although not universal, this is common in explainable machine learning, where one seeks to explain a prediction using all features.
Before proceeding, we note that each algorithm uses different parameters to determine the number of sampled coalitions and thus evaluations of the characteristic function v. For fair comparisons, we introduce a unified sample budget T, ensuring each algorithm performs T evaluations of v, up to negligible rounding errors.
The overall sample budget
T, introduced above, sets the total number of
v evaluations per algorithm. We now express the parameters of each algorithm from
Section 5.2 in terms of
T.
For LSS (Algorithm 1) and UKS (see the end of
Section 5.2), this is a one-to-one mapping, i.e.,
. Note that we ignore the single evaluation of
v needed for calculating the initial term
, since it is negligible compared with the rounding errors of other algorithms, especially for large
T.
S-LSS (Algorithm 2) divides the sample space based on
distinct values of
s, for each
. We use the heuristically motivated proportional sample allocation from (
58) to obtain
Lastly, we examine SRS-LSS (Algorithm 3), including the warm-up phase (Algorithm 4). The latter needs
samples and is employed as a safeguard to ensure that SRS-LSS executes without failure across all trials (compare Proposition 4). While our theoretical analysis omits this step for brevity, its empirical impact is minimal. For all
strata, we adopt the straightforward allocation scheme:
acknowledging that more sophisticated distributions may provide better results.
We conclude that the deviation from the true total sample budget T is 1 for LSS and UKS, while the upper bounds of their deviations are given by for S-LSS and for SRS-LSS. We consider these deviations to be negligible in our subsequent analysis, in particular for large T.
With these definitions established, we proceed with our experiments.
Figure 5 confirms the theoretical variances of LSS and S-LSS presented in Propositions 2 and 3, respectively. Moreover, it underscores our results from Theorem 2, where we demonstrated that one or the other algorithm might achieve a smaller variance, depending on the underlying cooperative game. Furthermore, we validate that LSS and UKS perform as expected with respect to the theoretical variances presented in Propositions 2 and 11. As
Figure 5 clearly illustrates, the derived theoretical variances are accurate, and, depending on the specific problem, either LSS or UKS may slightly outperform the other; one sampling strategy might be better suited to the given task than the other (see Theorem 4).
As for mean squared error comparisons, we first look at an airport game with 100 players specified in Castro et al. [
35] and compare the approximation methods from
Section 5.2 in
Figure 6. In this test game, the maximum possible value of a coalition is
.
Figure 9 uses the standard
diabetes dataset (442 patients, 10 baseline features) where the target is disease progression after one year. We train a Gradient Boosting Regressor and evaluate the approximation methods from
Section 5.2 by their mean squared error against exact reference Shapley values. In this problem, the maximum possible value of a coalition is
(rounded to 4 decimal places).
In
Figure 10, the
California housing dataset (20,640 entries, 8 features) predicts median house value in hundreds of thousands of dollars. Using an MLP regressor, we compare approximation methods by their mean squared error on Shapley value estimation against exact references. In this problem, the maximum possible value of a coalition is
(rounded to 4 decimal places).
Figure 11 uses the classic
wine dataset (178 instances, 13 features, 3 wine classes). We train a Random Forest Classifier and evaluate the approximation methods from
Section 5.2 via mean squared error in estimating Shapley values for predicting the probability of class 0 only. In this problem, the maximum possible value of a coalition is
.
Let us succinctly summarize the comparisons of mean squared errors of all algorithms for approximating the Shapley value from
Section 5.2 in
Figure 6,
Figure 7,
Figure 8,
Figure 9,
Figure 10 and
Figure 11. As expected, LSS and UKS perform more or less equally for all six test problems. SRS-LSS outperforms the other three provably unbiased algorithms, LSS, S-LSS, and UKS, for all test problems. This observation is consistent with the results shown in
Figure 1 in Benati et al. [
14], where only LSS and SRS-LSS were compared. Therefore, we conclude that the covariance terms established in Theorem 3 do not significantly affect the overall variances of individual players’ Shapley value estimators negatively. S-LSS performs worst for four out of six test problems, with the two notable exceptions of the 50-player voting game in
Figure 7, where S-LSS outperforms LSS and UKS, and the airport game with 100 players in
Figure 6, where S-LSS is even faster than KS in the sense of achieving lower MSE for a fixed number of evaluations
T. Not surprisingly, KS is consistently faster than UKS and LSS. For the three large cooperative games in
Figure 6,
Figure 7 and
Figure 8 SRS-LSS converges faster than KS, whereas that comparison reverses for the machine learning tasks in
Figure 9,
Figure 10 and
Figure 11.
To assess the practical relevance of the probabilistic error bounds introduced in
Section 5.6, we conducted two sets of experiments for UKS, LSS, and S-LSS for two test games. The first experiment uses the weighted voting game with
players and characteristic function values bounded by
(since
), which was previously studied in
Figure 7. The second experiment uses the airport game with
players and cost values such that
, which was already investigated in
Figure 6. In both settings, we fixed a sampling budget of
50,000 coalition evaluations per algorithm and repeated each experiment 1000 times with independent random seeds to obtain stable error statistics. The full results can be found on the GitHub page of the first author via
https://github.com/tim-pollmann/shapley-least-squares/tree/main/data (accessed on 25 April 2026).
For each algorithm and each run, we recorded the maximum absolute deviation
and the mean squared error
.
Table 3 and
Table 4 report the theoretical Hoeffding bounds for
(which can be obtained from (
84), (
85), (
90), (
91), (
99) and (
100), respectively), the mean of the respective error metrics over the 1000 runs, and the overall maximum error observed across all runs.
From
Table 3 and
Table 4, we observe that the Hoeffding bounds for UKS, LSS, and S-LSS are extremely loose compared with the empirical errors. For the weighted voting game in
Table 3, the Hoeffding bound for UKS predicts a maximum deviation less than or equal to
with
confidence, yet the empirical mean of the maximal errors is only
, i.e., about 13 times smaller. Similarly, the MSE bound of
is about 1100 times larger than the empirical average MSE of
.
Second, despite the theory predicting UKS to be vastly superior to LSS, the empirical performance of UKS and LSS is virtually identical in both games. Their empirical means for the maximal errors and average MSEs are nearly indistinguishable. This confirms our claim that neither algorithm is universally superior; the theoretical advantage of UKS only manifests in adversarial or specially constructed games, not in these realistic benchmarks.
Third, S-LSS shows slightly smaller empirical errors than both UKS and LSS in both tables, despite having by far the largest Hoeffding bounds. This again demonstrates that worst-case bounds can be misleading; S-LSS can perform well in practice because its stratification effectively reduces variance, even though its theoretical guarantees are poor due to the many strata and the union bound penalty.
Fourth, comparing the two games, the airport game with and shows larger absolute errors, because M is 10 times larger and n is doubled, increasing the scale and complexity. Yet the pattern remains: UKS and LSS perform nearly identically, S-LSS performs slightly better for these two games, and all Hoeffding bounds are orders of magnitude too conservative.
Finally,
Table 3 and
Table 4 underscore a key lesson, though not a new one: When approximating Shapley values and Hoeffding bounds provide safe but extremely loose guarantees. We refer to the work by Saavedra-Nieves [
34] for a detailed and illuminating study on probabilistic error bounds in the context of cooperative games. For practical algorithm comparison, empirical evaluation on representative problems is far more informative than worst-case theoretical bounds. Our conclusion that no single sampling strategy dominates all problems is strongly supported by the experiments in
Table 3 and
Table 4.
While the previous analysis focused on validating theoretical Hoeffding bounds against empirical means and extremes, we now turn to the stability of the estimators across repeated runs.
Table 5 and
Table 6 report standard deviation (SD), coefficient of variation (CV), and the 2.5% and 97.5% percentiles for both maximum deviation and MSE, based on the same 1000 runs. These metrics quantify run-to-run variability and help assess the reproducibility of the estimates.
Table 7 complements this by providing classical 95% confidence intervals for the mean errors, which reflect the precision of the reported averages.
Table 5 presents the stability metrics for the weighted voting game, whereas
Table 6 presents the corresponding results for the airport game.
Table 5 reveals several important patterns. First, the coefficients of variation (CV) for both maximum deviation and MSE range between
and
across all methods. This indicates low to moderate run-to-run variability; the typical deviation from the mean is about 17–21% of the mean itself. Given that the absolute errors are very small (mean max deviation ≈ 0.02 for UKS and LSS), the corresponding standard deviations are on the order of
–
, indicating that the estimates are stable relative to their magnitude.
Second, the 2.5% and 97.5% percentiles show that in 95% of runs, the maximum deviation lies between and for UKS, and between and for LSS. The intervals for S-LSS are slightly narrower (), reflecting its smaller mean error. Notably, SRS-LSS exhibits the smallest spread (), indicating exceptionally stable estimates, while KS lies in between (). For MSE, the percentiles follow the same ordering.
Third, the standard deviations across methods are consistent with the mean errors: SRS-LSS has the smallest SD ( for max deviation), followed by KS (), then UKS/LSS (), and finally S-LSS (). Importantly, all CVs are similar (≈0.17–), suggesting that the relative variability is comparable across algorithms despite large differences in absolute error magnitude.
Table 6 shows the same stability metrics for the airport game, where both
n and
M are larger. The absolute errors are substantially larger (e.g., mean max deviation for UKS is
), yet the CVs remain in the same range (
–
). This indicates that the relative variability is consistent across games and algorithms.
Examining the 95% ranges for maximum deviation, we see that SRS-LSS again has the narrowest spread and the smallest absolute errors, followed by S-LSS and then KS. UKS and LSS exhibit wider spreads, which is expected given their larger means. The standard deviations follow the same pattern: SRS-LSS () < S-LSS () < KS () < LSS () < UKS (). The CVs are remarkably similar across all methods (≈0.14–), confirming that relative stability is largely independent of the algorithm and the game.
For MSE, the pattern is analogous: SRS-LSS has the smallest mean () and the smallest SD (), while UKS and LSS have larger means (≈0.019 and ) and proportionally larger SDs. The CVs again cluster around –.
Finally,
Table 7 provides 95% confidence intervals for the mean errors in the airport game, calculated using classical statistical methods. These confidence intervals quantify the precision of the reported averages. Because we have 1000 runs, the standard errors are very small, resulting in extremely narrow intervals.
For maximum deviation, the CI for UKS is (width ), for LSS (width ), for S-LSS (width ), for SRS-LSS (width ), and for KS (width ). All intervals are narrow, indicating that the sample means are highly precise estimates of the true expected errors.
The MSE intervals are even narrower relative to the scale: UKS: (width ), LSS: (width ), S-LSS: (width ), SRS-LSS: (width ), KS: (width ).
These narrow intervals confirm that the differences in mean errors across algorithms are statistically significant and not due to sampling variability. They also demonstrate that with 1000 runs, the reported means are reliable to at least three decimal places for max deviation and four decimal places for MSE.
Taken together,
Table 5,
Table 6 and
Table 7 paint a consistent picture. All algorithms produce estimates with low to moderate relative variability (CV ≈0.15–
), meaning that the typical run-to-run fluctuation is about 15–20% of the mean error. The narrow confidence intervals in
Table 7 confirm that the means are estimated with high precision. SRS-LSS stands out with the smallest absolute errors and the tightest percentiles, while UKS and LSS show similar stability to each other. Importantly, no algorithm exhibits problematic instability (e.g., CV
), and the relative variability is comparable across all methods. These findings support the practical use of any of these algorithms, with the choice depending primarily on the desired trade-off between bias (for KernelSHAP), theoretical guarantees (for UKS), and empirical accuracy (for SRS-LSS in the two games we studied).
7. Summary, Conclusions, and Outlook
The celebrated KernelSHAP approach introduced by Lundberg and Lee [
1], along with its later refinement, Unbiased KernelSHAP (UKS), proposed by Covert and Lee [
7], computes the Shapley value as a least squares optimization problem. While these two algorithms are extremely well established in the machine learning community, the methods proposed by Benati et al. [
14]—which are also based on the least squares formula for the Shapley value—have received fairly little attention. To our knowledge, we are the first to apply these methods in the context of explainable artificial intelligence. Moreover, this paper is also the first to derive finite-sample Hoeffding bounds for UKS, LSS, and S-LSS, providing explicit probabilistic guarantees for these estimators. We formulate the ideas from Benati et al. [
14] as approximation algorithms for general TU games. We refer to their weighted sampling strategy as LSS (least squares sampling). For their approach to stratification, we distinguish S-LSS without reuse of samples across strata and SRS-LSS with sample reuse across strata, as proposed by Benati et al. [
14].
As a result of our thorough and detailed analysis of LSS, S-LSS, and SRS-LSS, we presented three key findings.
First, in Proposition 5, we showed that S-LSS, as proposed in [
14], is not a valid stratified variant of LSS under the definition provided in
Section 3.2; i.e., for S-LSS, the strata overlap. Therefore, we demonstrated that S-LSS can reduce the variance of the obtained estimator, but it can also lead to an increase compared with LSS; see Theorem 2.
Second, in Theorem 3, we showed that the SRS-LSS approach proposed by Benati et al. [
14] introduces covariance terms among stratum estimators, making its theoretical variance difficult to analyze. Although empirical results suggest that the variance is significantly reduced compared with LSS and S-LSS, a theoretical analysis remains an open research question.
Third, in Theorem 4, we established that LSS and UKS are importance sampling estimators in the sense of Theorem 1, addressing the same underlying problem but differing in their respective sampling strategies. Therefore, neither LSS nor UKS is superior to the other. Which algorithm’s variance is smaller depends on the underlying problem and whether the respective sampling strategy is suitable for this problem or not. The variance differences we derive have direct practical implications: an estimator with twice the variance requires twice as many samples to achieve the same mean squared error, directly impacting computational cost. For instance, in our experiments, the performance of LSS and UKS is often similar, meaning that neither consistently outperforms the other; however, in problems where one algorithm does have lower variance (e.g., UKS for large n in theory, LSS in some weighted voting games), the difference can translate into substantial savings in computation time. Moreover, lower variance implies more stable explanations across repeated runs, which is crucial for trust and reproducibility in high-stakes domains like medicine or finance. Thus, while no single algorithm dominates universally, identifying the variance structure of a given problem can guide algorithm selection and yield gains in efficiency and reliability.
Based on our theoretical and empirical analysis, we offer the following practical guidance. When within-stratum variance is low (e.g., in the airport game studied in
Figure 6), stratified methods (S-LSS, SRS-LSS) are advantageous, with SRS-LSS performing best. When within-stratum variance is high (e.g., weighted voting games, problems from interpretable machine learning), SRS-LSS still outperforms UKS and LSS, making it the preferred choice across all tested problems. UKS and LSS remain viable alternatives, particularly when simplicity of implementation (LSS) or theoretical worst-case guarantees (UKS) are desired. For very small sample budgets, KernelSHAP may be attractive despite its lack of unbiasedness. In all cases, we recommend that practitioners consider SRS-LSS as a strong default due to its consistent empirical superiority.
Regarding sampling constraints, when the sample budget is very small (e.g., ), KernelSHAP may be attractive due to its faster initial convergence (in the sense of achieving lower MSE for a fixed number of evaluations), despite its lack of unbiasedness. For larger , unbiased methods (UKS, LSS, SRS-LSS) become preferable. Regarding problem dimensionality, UKS and LSS scale better to very large n (e.g., ) because S-LSS and SRS-LSS require estimating strata, which demands a proportionally larger sample budget.
Table 8 summarizes the main theoretical claims and their empirical validation from
Section 6.
As noted in the introduction, this paper’s aim is neither to propose a new Shapley value estimator nor to compare numerous approximation algorithms. Rather, the focus is on providing structural, theoretical, and algorithmic insight into the methods from Benati et al. [
14]. While antithetic sampling—as discussed, for instance, in [
36]—could be integrated into the SRS-LSS algorithm, this would have vastly exceeded the scope of this study. In the future, it could be worthwhile to investigate whether there are algorithmic approaches comparable to sophisticated stratification strategies [
28,
37,
38] which could be successfully incorporated to enhance the performance of SRS-LSS. Clearly, our theoretical and numerical results suggest that the SRS-LSS estimator—which is unbiased—justifies more attention. Another (perhaps even more pressing) question is why SRS-LSS outperforms KernelSHAP for weighted voting games and airport games, while KernelSHAP exhibits superior performance for our test problems from interpretable machine learning. We have yet to identify the properties of the characteristic function responsible for this phenomenon.