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README.md

@@ -52,10 +52,10 @@ paper_test = causal.filter(
 
 | Scope | Rows | Held-out `test` rows |
 |---|---:|---:|
-| Complete release | 186,370 | 37,240 |
-| Corrected paper categories | 167,234 | 33,450 |
+| Complete release | 184,978 | 36,808 |
+| Corrected paper categories | 165,972 | 33,012 |
 
-Labels are balanced: 93,185 `feature` and 93,185 `random-noannot` rows.
+Labels are balanced: 92,489 `feature` and 92,489 `random-noannot` rows.
 Every pair shares `pair_id`.
 
 The row-level `split` uses held-out chromosomes `chr2`, `chr3`, `chr16`, and
@@ -74,7 +74,7 @@ For each control, the sampler avoids the union of retained annotation
 intervals and previously selected annotation-free controls. The control has
 the same chromosome and length as its feature. Independent verification
 repeats this check without using the sampler and finds zero overlaps across
-all 93,185 controls. It also confirms every causal and bidirectional control
+all 92,489 controls. It also confirms every causal and bidirectional control
 context contains only uppercase `A/C/G/T`.
 
 Exclude `noncoding_regions` for the corrected ten-category paper view.
@@ -86,8 +86,8 @@ Use:
 - `causal` for left-to-right models;
 - `bidi` for bidirectional/masked models.
 
-All `bidi` contexts are 2,048 bp. In `causal`, 165,782 rows are 2,048 bp and
-20,590 long-feature rows are 1,000 bp. For paper evaluation:
+All 184,978 `bidi` contexts are 2,048 bp. In `causal`, 165,012 rows are
+2,048 bp and 19,966 long-feature rows are 1,000 bp. For paper evaluation:
 
 1. filter held-out `test` rows;
 2. exclude `noncoding_regions`;
@@ -116,8 +116,10 @@ repeat-derived features/controls with correct orientation. `repeat_class`
 remains available as metadata. Unknown `source_strand` stays `.`, while
 `sequence_orientation` is always explicit `+` or `-`.
 
-Release `hg38-exact-input-v5` retains only VISTA rows explicitly annotated as
-hg38 (2,889 retained; 1,750 excluded without liftover). It removes every
+Release `hg38-positive-exact-input-v5.2` retains only VISTA rows explicitly
+annotated as hg38 with normalized positive expression (1,367 raw records,
+1,240 unique elements). It excludes 1,522 non-positive hg38 and 1,750
+non-hg38 rows without liftover and removes every
 ambiguous feature/control group and every conflicting-label exact-input group.
 Same-label duplicates remaining within a config share `context_group_id`;
 independent checks find zero exact inputs crossing train/test and zero

functional-random-noannot-gamba-bidi.parquet

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functional-random-noannot-gamba-causal.parquet

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