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Correct ALDEx rank tails and harden numerical boundaries after fuzz review - #14
The correctness rereview found failures at numerical boundaries and in the ALDEx2 directional rank calculation. Inclusive discrete upper tails cannot be complemented to obtain inclusive lower tails: the old calculation loses the observed atom and changes with group direction. This patch evaluates both tails directly, uses tie-adjusted normal rank tests when needed, and refuses degenerate Welch fits explicitly.
Count closure and multiplicative replacement now scale before summing so valid integer or finite floating-point libraries cannot overflow their normalization. Shared validation keeps signed-zero group memberships disjoint, canonically encodes equivalent mixed numeric labels for R, and checks high-precision parameter domains before and after Float64 conversion. The optional R adapters reject invalid inputs before entering the caller's R runner.
Validation is pinned to this branch's final source:
CI at 9119890: Julia 1.10 and 1.12.5, Aqua, Agda 2.6.4.3/stdlib 2.1, and R 4.5.0/Bioconductor 3.22.
20,341 Julia assertions: deterministic regressions, three seeded composition/BH fuzz campaigns, exhaustive rank allocations at group sizes two through four, ALDEx2 determinism/feature permutation/directional checks, and ANCOM-BC scaling/order/contrast/likelihood checks plus analytic scalar variance optima. Windows Julia 1.12.5 also passes the complete suite. Follow-ups retain generic ZeroPolicy validation, widen narrow floats including abstract Real matrices, handle exact near-cancellation, and multiply BH probabilities by m/rank to preserve q >= p at the last rank.
The safe Agda gate adds a finite-tail count identity and a false-complement rejection control. This proves the missing-atom arithmetic, not floating-point refinement or statistical calibration.
Pristine ALDEx2 1.42.0 first reproduces the rank-tail defect. The positive oracle explicitly loads the signed repair proposed in ALDEx_bioc#83. Independent R tests cover 670 assertions plus the two existing aldex.ttest comparisons. Native tests additionally compare tied and 49/50-sample branches to stats::wilcox.test/t.test. All eight output columns and identical-instance p/q results remain checked at the unchanged thresholds.
ANCOMBC retains the explicit pristine-2.12.0 defect control and the pinned positive comparison against ANCOMBC#344. No oracle failure is hidden by loosening a tolerance.
The specification records that this rereview inspected upstream GPL R sources to diagnose and repair them. The Julia change is independently derived from the discrete CDF identity and the existing native recurrence; it does not claim pristine ALDEx2 equivalence. The original clean-room implementation's historical provenance is preserved, and no R source was copied or translated into the MPL implementation.
AI assistance was used. These are additional source changes after the maintainer's confirmation that PRs 12/13 were manually reviewed. Registration must await human review and understanding of this new diff under General's policy. Passing tests and the conditional algebraic proofs do not establish unconditional calibration, FDR control, a global optimizer guarantee, or correctness for every possible input.
The subsequent launch pilot in draft PR #15 found adverse small-unbalanced ANCOM-BC null calibration in both native and repaired-R fits, plus one expanded-regime conformance counterexample. The three established fixture gates above still pass, but they must not be expanded into a universal conformance or calibration claim. Registration and release remain pending.
Add seeded core/statistical fuzz, exhaustive rank distributions, independent R checks and a finite-tail Agda identity with a rejection control. Keep pristine-reference defect controls explicit.
Name the Agda negative-control module by its actual path so the gate verifies the intended false equality; compare native tails at 49/50 samples and tied ranks against independent R stats.
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Reviewing files that changed from the base of the PR and between 6c906da and 9119890.
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src/Core/bh.jl
src/Core/composition.jl
src/Core/zeros.jl
test/fuzz_core.jl
Summary
Summary by CodeRabbit
Bug Fixes
Corrected Wilcoxon two-sided p-values to account for observed outcomes in both directional tails, including tied observations.
Improved handling of extreme count values and numerical inputs; invalid or unrepresentable values are now rejected more consistently.
Strengthened validation of group labels and structural-zero settings.
Documentation
Clarified the interpretation and limitations of directional-tail results.
Tests
Expanded checks for statistical results, input boundaries, repeatability and consistency when groups or samples are reordered.
The changes add numerical boundary checks across compositional analysis and ANCOM-BC. ALDEx2 now calculates inclusive directional tails for Welch and Wilcoxon tests. New tests, Agda proofs, specifications, reference-oracle checks, and CI steps cover these changes.
Count conversion, group validation, compositional transforms, zero replacement, and ANCOM-BC option checks now validate representability and numerical bounds. Fuzz tests cover edge cases and numerical properties across these operations.
ALDEx2 calculates both Welch and Wilcoxon tails. Wilcoxon uses inclusive exact tails when available and a tie-adjusted normal approximation for tied data. Two-sided values and BH adjustments use both directions. The specification, finite-count proofs, and tests document and check these rules.
Reference adapters and CI conformance ext/CompositionalDARCallExt.jl, test/oracle/*, .github/workflows/ci.yml
Reference adapters validate and convert inputs before invoking their runners. Oracle tests check adapter boundaries and compare directional tails with R. CI adds a pristine defect control and runs conformance using pinned repair files.
sequenceDiagram
participant ALDEx2Analysis
participant welch_tails
participant wilcoxon_tails
participant DirectionalAggregation
participant bh_adjust
ALDEx2Analysis->>welch_tails: Calculate both Welch tails when using Welch
ALDEx2Analysis->>wilcoxon_tails: Calculate both Wilcoxon tails when using Wilcoxon
welch_tails->>DirectionalAggregation: Return right and left tail probabilities
wilcoxon_tails->>DirectionalAggregation: Return right and left tail probabilities
DirectionalAggregation->>bh_adjust: Adjust values calculated separately by direction
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Merge Risk: Low · previous review 6c906
The changes retain narrow edge-case regressions: valid numerical inputs can be rejected or lose precision, and existing custom zero policies can accept invalid counts. These are bounded issues suitable for owner-aware follow-up, preferably corrected before merge.
Pre-merge checks: 5
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Explanation
Title check
The title names the main change: correcting ALDEx2 directional rank tails. It also names the numerical boundary hardening, which the changeset covers. The title is specific and maps to the ALDEx2 Meth…
Description check
The description explains the directional rank-tail defect, the tie-adjusted normal tests, the closure and replacement scaling, shared validation, the optional R adapters, and the proof and test scope.…
Docstring Coverage
No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
Linked Issues check
Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check
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Full details: Title check
Explanation
The title names the main change: correcting ALDEx2 directional rank tails. It also names the numerical boundary hardening, which the changeset covers. The title is specific and maps to the ALDEx2 Methods, Core validation, and proof changes.
Full details: Description check
Explanation
The description explains the directional rank-tail defect, the tie-adjusted normal tests, the closure and replacement scaling, shared validation, the optional R adapters, and the proof and test scope. All of this matches the changeset, so the description is on-topic and detailed.
Full details: Docstring Coverage
Explanation
No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 0 functions across 0 files. (20 skipped: 20 unsupported.)
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Inline comments:
Review comments at @src/Core/composition.jl:
- Line 120: Update the composition entry point around replace_zeros so counts
are validated before being passed to the zero policy, ensuring invalid negative
counts are rejected even when a custom policy changes them. Keep the existing
clr flow for validated results.
- Line 88: Update the scaling in closure so narrow floating-point inputs are
widened before division, preserving representable positive proportions without
underflow. Keep large-integer inputs supported by using a scaling approach that
does not overflow when converting their values; retain the existing closure
behaviour for other inputs.
Review comments at @src/Core/zeros.jl:
- Around line 88-91: The shrink calculation in the zero-replacement path can
round to zero when the replacement amount is near one. Update the calculation
after `r` is determined to preserve a positive shrink factor without losing the
existing overflow protection; add a regression test for
`MultiplicativeReplacement(prevfloat(1.0))` with `[3 2 0 0 0 0 0]`, confirming
it returns a positive composition rather than throwing `CompositionError`.
After applying the fix, consider running `coderabbit review --agent` for local
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Review info
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Run ID: 2b260011-d510-4a33-9642-086e2c389cdd
Commits
Reviewing files that changed from the base of the PR and between ca18716 and 6c906da.
Files selected for processing: 20
.github/workflows/ci.yml
docs/ALDEx2-SPEC.md
ext/CompositionalDARCallExt.jl
proofs/PROOF-STATUS.md
proofs/agda/CompositionalDA/All.agda
proofs/agda/CompositionalDA/DiscreteTails.agda
proofs/agda/reject/LostAtom.agda
src/Core/bh.jl
src/Core/composition.jl
src/Core/zeros.jl
src/Methods/ALDEx2.jl
src/Methods/ANCOMBC.jl
test/fuzz_ancombc.jl
test/fuzz_core.jl
test/fuzz_statistics.jl
test/oracle/adapter_boundaries.jl
test/oracle/aldex2_tail_control.jl
test/oracle/ancombc_oracle.jl
test/oracle/runoracle.jl
test/runtests.jl
Included review availability: This review used your included allowance. Your plan provides up to 1 included review per hour; 0 remain after this review.
A predeclared calibration pilot exposed multiply/divide cancellation that could round a BH result below its input. Form the scale first and test continuous random probabilities. Independently audit the narrow-float repair on Matrix{Real}, preserving arbitrary-precision inputs. Complete Windows Julia suite: 20,341 assertions passed.
…eriments (#15)
The launch audit found that passing numerical conformance tests is
insufficient for a general calibration claim: in a prespecified
small-unbalanced complete-null pilot, original ANCOM-BC made false
discoveries in 19 of 29 successful fits at q <= 0.05, with three
additional refusals. This draft records that blocker and adds
reproducible calibration, benchmark and repaired-R-reference
investigation scripts.
The README, EXPLAINME, security policy and launch ledger separate proven
algebra, numerical comparison, empirical calibration and human approval.
They map actual fleet roles to remaining work without claiming the bots
have executed it or that RSR/CRG/TRG compliance is complete.
Registration remains explicitly on hold pending human review; this PR
does not authorise registration or release.
This follows PR #14, which was merged externally during the audit. That
merge is not interpreted as the human approval required to lift the
registration hold. The fixed protocol preceded the 384-fit pilot (365
returned, 19 refused); raw results and uncertainty remain in the review
packet. The CI experiment compares the problematic regime against
ANCOMBC 2.12.0 with the explicitly pinned variance-estimator repair,
requiring recorded convergence. Job success means the investigation ran,
not that calibration passed. Benchmark output is exploratory and
contains no speedup claim.
Validation: numerical source 9119890 has passing Julia 1.10/1.12.5, safe
Agda and both pinned R oracle jobs. [The new experiment passed its
execution
job](https://github.com/hyperpolymath/CompositionalDA.jl/actions/runs/42411431729):
all 32 repaired-R fits converged, and 19 made false discoveries. Of 29
paired native successes, 28 had q-value gaps below 8.5e-6; replicate 27
differed by about 0.5041 and changed the discovery decision. Both the
adverse calibration and the expanded conformance gap remain blockers,
now documented. These checks do not replace independent scientific
review, applicable estate release gates or a maintainer's review by
hand.
---------
Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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The correctness rereview found failures at numerical boundaries and in the ALDEx2 directional rank calculation. Inclusive discrete upper tails cannot be complemented to obtain inclusive lower tails: the old calculation loses the observed atom and changes with group direction. This patch evaluates both tails directly, uses tie-adjusted normal rank tests when needed, and refuses degenerate Welch fits explicitly.
Count closure and multiplicative replacement now scale before summing so valid integer or finite floating-point libraries cannot overflow their normalization. Shared validation keeps signed-zero group memberships disjoint, canonically encodes equivalent mixed numeric labels for R, and checks high-precision parameter domains before and after Float64 conversion. The optional R adapters reject invalid inputs before entering the caller's R runner.
Validation is pinned to this branch's final source:
The specification records that this rereview inspected upstream GPL R sources to diagnose and repair them. The Julia change is independently derived from the discrete CDF identity and the existing native recurrence; it does not claim pristine ALDEx2 equivalence. The original clean-room implementation's historical provenance is preserved, and no R source was copied or translated into the MPL implementation.
AI assistance was used. These are additional source changes after the maintainer's confirmation that PRs 12/13 were manually reviewed. Registration must await human review and understanding of this new diff under General's policy. Passing tests and the conditional algebraic proofs do not establish unconditional calibration, FDR control, a global optimizer guarantee, or correctness for every possible input.
The subsequent launch pilot in draft PR #15 found adverse small-unbalanced ANCOM-BC null calibration in both native and repaired-R fits, plus one expanded-regime conformance counterexample. The three established fixture gates above still pass, but they must not be expanded into a universal conformance or calibration claim. Registration and release remain pending.