babappai 2.2.1

BABAPPAi: diagnostic framework for identifiability of episodic branch-site structure

BABAPPAi (babappai)

BABAPPAi is the software framework built around the canonical frozen BABAPPAΩ model.

• BABAPPAΩ: fixed neural inference artifact (weights are immutable in this project).
• BABAPPAi: operational package around that model (raw EII, matched-neutral significance, applicability/abstention, optional cEII calibration, reporting, and packaging).

0) Final Submission Folder

For manuscript submission handoff, use the consolidated folder:

• final/

It contains the cleaned main manuscript files, supplementary files, cover letter, reviewer/metadata files, and packaged zip assembled for NAR Genomics and Bioinformatics submission.

1) Scope

BABAPPAi reports:

• raw dispersion diagnostics: eii_z_raw, eii_01_raw
• empirically calibrated identifiability probabilities (conditional): ceii_gene, ceii_site
• empirical matched-neutral significance: p_emp, q_emp, significant_bool

Important interpretation contract:

• raw EII and matched-neutral significance are universally reportable outputs
• cEII is an auxiliary post-inference calibration layer and may be withheld (null) under inapplicable/unstable regimes
• calibration updates do not imply model-weight changes

BABAPPAi does not perform classical dN/dS likelihood-ratio testing, and significance does not prove adaptive substitution.

2) Installation

pip install babappai

3) Quickstart

babappai model fetch
babappai example write --outdir demo
babappai run --alignment demo/aln.fasta --tree demo/tree.nwk --outdir demo_out

4) Statistical outputs

For each gene-level run:

• D_obs: observed dispersion statistic : sample variance (ddof=1) of site-level site_logit_mean across codon sites
• mu0: matched neutral mean
• sigma0_raw: raw neutral SD
• sigma0_final: SD after floor application
• eii_z_raw = (D_obs - mu0) / sigma0_final
• eii_01_raw = sigmoid(eii_z_raw) (diagnostic magnitude scale)
• ceii_gene: calibrated P(I_gene=1 | data)
• ceii_site: calibrated P(I_site=1 | data)
• ceii_gene_class, ceii_site_class: calibration-derived decision bands
• ceii_ci: bootstrap calibration interval (if calibration asset provides it)
• calibration_version, domain_shift_or_applicability
• p_emp = (1 + count(D0 >= D_obs)) / (M + 1) from matched neutral replicates
• q_emp: BH-adjusted p_emp across tested genes in an analysis set
• significant_bool = (q_emp <= alpha) (default alpha=0.05)
• significance_label ∈ {not_significant, significant}

ceii_* and q_emp are intentionally distinct layers:

• ceii_*: recoverability/identifiability probability calibration
• q_emp: excess-dispersion significance under matched-neutral calibration

ceii_* is conditional and abstention-aware:

• if applicability/null checks fail, ceii_gene and ceii_site are withheld (null)
• this does not invalidate raw EII or matched-neutral significance

5) Core CLI

babappai run --alignment aln.fasta --tree tree.nwk --outdir results
babappai run --alignment aln.fasta --tree tree.nwk --outdir results --alpha 0.05 --pvalue-mode empirical_monte_carlo --neutral-reps 200 --sigma-floor 0.05
babappai model fetch
babappai model status
babappai model verify
babappai doctor
babappai version
babappai version --ceii-asset babappai/data/ceii_calibration_v3_2.json

Significance-related options

• --alpha (default 0.05)
• --pvalue-mode (empirical_monte_carlo default; frozen_reference static reference-table mode)
• --neutral-reps (Monte Carlo neutral replicates)
• --min-neutral-group-size
• --sigma-floor
• --retain-eii-bands / --no-retain-eii-bands
• --report-threshold-bands / --no-report-threshold-bands
• --ceii-enabled / --no-ceii-enabled
• --ceii-asset

6) Validation workflows

babappai validate orthogroups select --input ORTHOGROUP_DIR --outdir selection_out
babappai validate orthogroups run --input selection_out --outdir empirical_out --alpha 0.05 --pvalue-mode empirical_monte_carlo

babappai validate synthetic run \
  --simulator scripts/simulator.py \
  --outdir synthetic_out \
  --alpha 0.05 \
  --pvalue-mode empirical_monte_carlo

babappai validate report --input validation_root --outdir report_out

Full-pipeline manuscript validation helper:

python scripts/run_full_pipeline_validation.py \
  --outdir results/validation/full_pipeline_v2 \
  --n_per_regime 100 \
  --n_replicates_per_scenario 5 \
  --bootstrap_reps 1000 \
  --alpha 0.05 \
  --pvalue_mode empirical_monte_carlo \
  --neutral_reps 200 \
  --sigma_floor 0.05 \
  --seed 123

cEII benchmark + calibration helper:

python scripts/run_ceii_calibration_benchmark.py \
  --outdir results/validation/ceii_benchmark_v1 \
  --n-per-regime 12 \
  --n-replicates-per-scenario 2 \
  --pvalue-mode frozen_reference \
  --bootstrap-reps 150 \
  --write-package-asset

7) Output files

babappai run writes:

• results.json
• branch_summary.tsv
• site_summary.tsv
• neutral_calibration_replicates.tsv
• interpretation.txt
• run_metadata.json

Validation runs add calibration/significance tables, bootstrap summaries, figures, and manuscript-facing markdown blocks.

8) Reproducibility and provenance

• neutral replicate distributions used for p_emp are written to disk
• run metadata includes software version, model DOI/SHA, calibration settings, and command provenance
• model provenance identifies BABAPPAΩ as the canonical frozen inference backbone used by BABAPPAi

9) Citation and interpretation guardrails

• cite BABAPPAi software version
• cite the BABAPPAΩ model DOI as the canonical frozen model artifact
• interpret significance as excess dispersion relative to matched neutral calibration, not as proof of adaptation

10) Development

pip install -e .[test]
pip install ruff build twine
ruff check .
pytest
python -m build --sdist --wheel
python -m twine check dist/*

11) Reproducibility and project policy

• large generated outputs policy: docs/reproducibility_artifacts.md
• citation metadata: CITATION.cff
• contribution guidelines: CONTRIBUTING.md
• code of conduct: CODE_OF_CONDUCT.md
• security reporting: SECURITY.md
• maintainer release process: RELEASE_CHECKLIST.md