xplainfi 1.0.0 - Initial CRAN release

The major version bump is largely to mark the occasion that the package is now considered “released”.

Minor changes

• Removed the fippy comparison article since a more comprehensive comparison is now available in xplainfi-benchmark.
• Clean up various documentation issues and other metadata.
• Adjusted the min_permutations default in SAGE methods to 10 rather than 3, since the previous value was found to lead to spurious early stopping.
• Fix sim_dgp_ewald lading to erroneous variances when compared to their settings.
• Reduce runtime of tests (mostly by using less ARF and mor Gaussian sampling)
• Remove KnockoffSequentialSampler as the seqknockoff package is not available on CRAN or R-universe. KnockoffSampler with the corresponding knockoff_fun = seqknockoff::knockoffs_seq still works.

xplainfi 0.2.1

• Simplify sim_dgp_confounded, removing x2 which doesn’t add anything interesting over x1.
• Ensure integers are preserved in Gaussian samplers
• Fix compatibility with mlr3 >= 1.3.0 due to the change in the way obs_loss() is computed (see https://github.com/mlr-org/mlr3/pull/1411).
• Methods not allowing measure to be unspecified and falling back to a task_type-specific default measure

xplainfi 0.2.0

User-facing API improvements

Importance aggregation and confidence intervals

• $importance() gains ci_method parameter for variance estimation (#40):
  • "none" (default): Simple aggregation without confidence intervals
  • "raw": Uncorrected variance estimates (informative only, CIs too narrow)
  • "nadeau_bengio": Variance correction by Nadeau & Bengio (2003) as recommended by Molnar et al. (2023)
  • "quantile": Empirical quantile-based confidence intervals
  • "cpi": Conditional Predictive Impact for perturbation methods (PFI/CFI/RFI), supporting t-, Wilcoxon-, Fisher-, and binomial tests
• CPI is now properly scoped to PerturbationImportance methods only (not available for WVIM/LOCO or SAGE)
• $importance() gains standardize parameter to normalize scores to [-1, 1] range
• $importance() and $scores() gain relation parameter (default: "difference") to compute importances as difference or ratio of baseline and post-modification loss
  • Moved from $compute() to avoid recomputing predictions/refits when changing aggregation method

Data simulation helpers

• Add focused simulation DGPs for testing importance methods:
  • sim_dgp_independent(): Baseline with additive independent effects
  • sim_dgp_correlated(): Highly correlated features (PFI fails, CFI succeeds)
  • sim_dgp_mediated(): Mediation structure (total vs direct effects)
  • sim_dgp_confounded(): Confounding structure
  • sim_dgp_interactions(): Interaction effects between features
• Each DGP illustrates specific methodological challenges for importance methods

Observation-wise losses and predictions

• $obs_loss() computes observation-wise importance scores when measure has a Measure$obs_loss() method
• $predictions field stores prediction objects for further analysis

Grouped feature importance

• PerturbationImportance and WVIM methods support groups parameter for grouped feature importance:
  • Example: groups = list(effects = c("x1", "x2", "x3"), noise = c("noise1", "noise2"))
  • In output, feature column contains group names instead of individual features
  • Allows measuring importance of feature sets rather than individual features

Method-specific improvements

WVIM (Williamson’s Variable Importance Measure)

• Generalizes LOCO (Leave-One-Covariate-Out) and LOCI (Leave-One-Covariate-In)
• Implemented using mlr3fselect for cleaner internals
• Parameter renamed: iters_refit → n_repeats for consistency

PerturbationImportance (PFI, CFI, RFI)

• Performance improvements:
  • Uses learner$predict_newdata_fast() for faster predictions (requires mlr3 >= 1.1.0)
  • Batches permutation iterations internally to reduce sampler$sample() calls
  • New batch_size parameter to control memory usage with large datasets
• Parallelization support:
  • Parallel execution via mirai or future backends
  • Set up with mirai::daemons() or future::plan()
  • Parallelizes across features within each resampling iteration
• Parameter renamed: iters_perm → n_repeats for consistency

Feature Samplers

• Breaking changes:
  • Refactored API separates task-based vs external data sampling (#49):
    • $sample(feature, row_ids): Samples from stored task using row IDs
    • $sample_newdata(feature, newdata): Samples from external data
  • Renamed sampler classes for hierarchical consistency:
    • PermutationSampler → MarginalPermutationSampler
    • ARFSampler → ConditionalARFSampler
    • GaussianConditionalSampler → ConditionalGaussianSampler
    • KNNConditionalSampler → ConditionalKNNSampler
    • CtreeConditionalSampler → ConditionalCtreeSampler
  • Standardized parameter name: conditioning_set for features to condition on
• New samplers:
  • MarginalSampler: Base class for marginal sampling methods
  • MarginalReferenceSampler: Samples complete rows from reference data (for SAGE)
  • KnockoffSampler: Knockoff-based sampling (#16 via @mnwright)
    • Convenience wrappers: KnockoffGaussianSampler, KnockoffSequentialSampler
    • Supports row_ids-based sampling
    • iters parameter for multiple knockoff iterations
    • Compatible with CFI (not RFI/SAGE)

SAGE (Shapley Additive Global Importance)

• Bug fix: ConditionalSAGE now properly uses conditional sampling (was accidentally using marginal sampling)

• Performance improvements:

  • Uses learner$predict_newdata_fast() for faster predictions
  • batch_size parameter controls memory usage for large coalitions

• Convergence tracking (#29, #33):

  • Enable with early_stopping = TRUE
  • Stops when relative standard error falls below se_threshold (default: 0.01)
  • Requires at least min_permutations (default: 3)
  • Checks convergence every check_interval permutations (default: 1)
  • New fields:
    • $converged: Boolean indicating if convergence was reached
    • $n_permutations_used: Actual permutations used (may be less than requested)
    • $convergence_history: Per-feature importance and SE over permutations
  • $plot_convergence(): Visualize convergence curves
  • Convergence tracked for first resampling iteration only

xplainfi 0.1.0

• Initial prototype with
  • PFI
  • CFI and RFI (via arf-powered conditional sampling)
  • SAGE (marginal and conditional, the latter via arf)
  • LOCO and LOCI
• Includes comparison to reference implementation in Python via fippy

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