fix: issue #59 — ad-hoc 微小正定数の整理と論文外モデリング床の削除 - #62
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数値安定化定数を numerical_eps.py に集約し、encoder clamp(0.2) と legacy +1e-4 を削除。 sqrt(0) 勾配爆発を sqrt(dist_sq + NUMERICAL_EPS) で修正し、TopologicalLoss の全バッチ失敗を RuntimeError にする。 Closes uda-lab#59 Co-authored-by: Cursor <cursoragent@cursor.com>
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This was referenced Jun 18, 2026
Codex 指摘のドキュメント/実装不一致を解消。early_abort・診断を main に統合し REPRODUCIBILITY.md が案内する experiments/issue59_verify_mahalanobis.py を追加。 Co-authored-by: Cursor <cursoragent@cursor.com>
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レビュー指摘への対応（
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Summary
Closes #59.
PR #54–#58 マージ後の follow-up として、教師あり本線
tda_ml/の ad-hoc 微小正定数を棚卸しし、論文に無いモデリング床を削除しました。再検証で見つかったsqrt(0)勾配爆発（AMP 下で学習停止）も修正しています。clamp(base_axes, min=0.2)、legacyaxes + 1e-4、metric への軸長+1e-6tda_ml/numerical_eps.py（NUMERICAL_EPS,PCA_RIDGE_EPS,EIGENVALUE_FLOOR,INLIER_PROB_MIN）sqrt(dist_sq + NUMERICAL_EPS)（対角の勾配有限化；宣言的 L2 床）TopologicalLossがバッチ全件失敗時に黙って0を返さずRuntimeErrorVerification
mahalanobis 12ep（
configs/issue59_verify_mahalanobis.yaml, seed=42,reproduce_1week_tuned相当）:outputs/issue59_verify_mahalanobis_20260617_090007詳細は issue コメント を参照。
Test plan
pytest tests/test_topology.py tests/test_topology_gradients.pytest_legacy_axes_positive_without_modeling_floorOut of scope (follow-up)
rk_tanh/hybrid_rk_tanh等の軸パラメータ拡張reproduce_pd_animation.py等）の定数棚卸しMade with Cursor