task string | train_rows int64 | test_rows int64 | train_unique_sequences int64 | test_unique_sequences int64 | train_unique_loci int64 | test_unique_loci int64 | coord_rows_train int64 | coord_rows_test int64 | coord_coverage_test float64 | chromosomes_train_n int64 | chromosomes_test_n int64 | chromosome_intersection float64 | chromosome_intersection_n int64 | union_any_tier_test_rows int64 | match_rows int64 | test_rows_exact_row int64 | pairs_exact_row int64 | test_rows_exact_sequence int64 | pairs_exact_sequence int64 | test_rows_reverse_complement int64 | pairs_reverse_complement int64 | test_rows_exact_locus int64 | pairs_exact_locus int64 | test_rows_interval_overlap_any int64 | pairs_interval_overlap_any int64 | test_rows_interval_overlap_50 int64 | pairs_interval_overlap_50 int64 | test_rows_interval_overlap_90 int64 | pairs_interval_overlap_90 int64 | test_rows_near_sequence_98 int64 | pairs_near_sequence_98 int64 | test_rows_near_sequence_95 int64 | pairs_near_sequence_95 int64 | test_rows_label_conflict int64 | pairs_label_conflict int64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H2AFZ | 30,000 | 3,000 | 29,853 | 2,960 | 29,853 | 2,960 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 10 | 0 | 0 |
H3K27ac | 30,000 | 1,616 | 29,885 | 1,605 | 29,885 | 1,605 | 30,000 | 1,616 | 1 | 21 | 2 | null | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 6 | 0 | 0 |
H3K27me3 | 30,000 | 3,000 | 29,871 | 2,947 | 29,871 | 2,947 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 7 | 0 | 0 |
H3K36me3 | 30,000 | 3,000 | 29,885 | 2,960 | 29,885 | 2,960 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 10 | 0 | 0 |
H3K4me1 | 30,000 | 3,000 | 29,877 | 2,967 | 29,877 | 2,967 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 16 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 12 | 16 | 0 | 0 |
H3K4me2 | 30,000 | 2,138 | 29,898 | 2,114 | 29,898 | 2,114 | 30,000 | 2,138 | 1 | 21 | 2 | null | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 4 | 0 | 0 |
H3K4me3 | 17,468 | 776 | 17,423 | 773 | 17,423 | 773 | 17,468 | 776 | 1 | 21 | 2 | null | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
H3K9ac | 23,274 | 1,004 | 23,203 | 1,000 | 23,203 | 1,000 | 23,274 | 1,004 | 1 | 21 | 2 | null | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 6 | 0 | 0 |
H3K9me3 | 27,438 | 850 | 27,332 | 845 | 27,333 | 845 | 27,438 | 850 | 1 | 21 | 2 | null | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 7 | 0 | 0 |
H4K20me1 | 30,000 | 2,270 | 29,862 | 2,242 | 29,862 | 2,242 | 30,000 | 2,270 | 1 | 21 | 2 | null | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 6 | 0 | 0 |
enhancers | 30,000 | 3,000 | 29,803 | 2,943 | 29,803 | 2,944 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13 | 18 | 0 | 0 |
enhancers_types | 30,000 | 3,000 | 29,803 | 2,943 | 29,803 | 2,944 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13 | 18 | 0 | 0 |
promoter_all | 30,000 | 1,584 | 29,872 | 1,571 | 29,874 | 1,571 | 30,000 | 1,584 | 1 | 21 | 2 | null | 0 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 3 | 2 | 0 | 0 |
promoter_no_tata | 30,000 | 1,372 | 29,872 | 1,363 | 29,875 | 1,363 | 30,000 | 1,372 | 1 | 21 | 2 | null | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
promoter_tata | 5,062 | 212 | 5,059 | 212 | 5,059 | 212 | 5,062 | 212 | 1 | 21 | 2 | null | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
splice_sites_acceptors | 30,000 | 3,000 | 29,858 | 2,964 | 29,862 | 2,964 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 7 | 0 | 0 |
splice_sites_all | 30,000 | 3,000 | 29,937 | 2,976 | 29,939 | 2,979 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 7 | 0 | 0 |
splice_sites_donors | 30,000 | 3,000 | 29,840 | 2,957 | 29,848 | 2,958 | 30,000 | 3,000 | 1 | 21 | 2 | null | 0 | 0 | 17 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 | 17 | 0 | 0 |
NUCLEOTIDE TRANSFORMER REVISED // INTEGRITY AUDIT
ANTIMEME SYSTEMWORKS // RESEARCH DIVISION // DOC: AM-DA-2026 // V1.0
All 18 tasks hold chr20/21 out of train, and 0 of 38,822 test rows reuse a train sequence, reverse complement, locus or interval within their task. One near pair reaches 0.98 identity. The README's H3K4me3 train count is 12,532 rows high.
Interactive version: b4ph/nt-revised-audit Space · Discussion: #6
01 // RESULT
Pinned revision 851f9946252e90c665cdb3cc3eedb78f1f26197c, all 18 task folders, both splits.
| CHECK | VALUE |
|---|---|
| Rows, train / test | 493,242 / 38,822 |
| Rows, total | 532,064 |
| Coordinates parsed | 532,064 / 532,064 |
| Chromosome intersections, train vs test | 0 of 18 tasks |
| Exact, reverse-complement, locus, interval reuse | 0 of 38,822 |
| Union of reporting tiers | 1 of 38,822 |
| Near identity >= 0.98 | 1 of 38,822 |
| Near identity >= 0.95 | 113 of 38,822 |
| Label conflicts | 0 |
.fna/Parquet pairs multiset-equal |
34 of 34 |
02 // FINDING
THE CHR20/21 HOLDOUT HOLDS ON THE PINNED REVISION. README LISTS 30,000 H3K4ME3 TRAIN ROWS; THE FILE HAS 17,468. THAT 12,532 GAP IS THE ENTIRE 544,596 VS 532,064 DIFFERENCE.
FINDING // VERIFIED // REVISION-PINNED
The one 0.98-identity pair sits on chr21 and chr13, 5 substitutions plus a 1 bp insertion over 299 aligned bases. No shared locus; repeat homology is plausible, and no RepeatMasker or Dfam annotation was run.
03 // METHOD
Strict grammar parse of name, SHA-256 sequence identity, interval trees for loci, edlib infix alignment for the near tier, DuckDB recomputation of exact and coordinate counters (90 of 90 checks match), 28 fixture tests. Evidence tables are Parquet so every test row and every matched pair is individually addressable.
04 // REPRODUCTION
The verified archive nt_revised_audit_research_only_v4.zip is at the repository root and unpacks into evaluation/. Package documentation: evaluation/README.md. Source lock, per-task tables, test_status.parquet and matches.parquet are inside.
05 // LIMITS
The assembly is not stated in the source files. Near-tier candidate recall is 0.88-0.95 at a 0.05 substitution rate. Cross-task sequence sharing is expected and not counted as leakage. No model evaluation was performed.
Source dataset: InstaDeepAI/nucleotide_transformer_downstream_tasks_revised. Its card declares no license; this repository republishes audit outputs and row references only, not source sequences.
ANTIMEME SYSTEMWORKS // RESEARCH DIVISION // AM-DA-2026 // V1.0 // P.01
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