Update README.md

README.md

@@ -275,7 +275,7 @@ dataset_info:
   dataset_size: 334784354
 ---
 
-# Carbon Perturbation Bench
+# Perturbation Bench
 
 A benchmark of **sequence-level perturbation tasks** for evaluating DNA foundation models.
 Each task presents pairs of genomic sequences — one real (unperturbed) and one structurally
@@ -304,16 +304,20 @@ optimised variant.
 
 ### `motif_human` — CAG repeat insertion (20,000 pairs)
 
-A 30 bp region starting 60 bp downstream of the CDS start is replaced with 10 consecutive
-CAG triplets (`CAGCAGCAGCAGCAGCAGCAGCAGCAGCAG`),
-mimicking the pathological trinucleotide repeat expansions underlying polyglutamine
-disorders (Huntington's disease, SCAs, DRPLA). The substitution is length-preserving
-(30 bp in, 30 bp out), so the total window remains 8,192 bp. All sequence outside the
-patch is identical between original and perturbed.
-
-- Annotations: GENCODE v45 / GRCh38; 9,705 unique genes.
-- Window layout: 8,102 bp upstream flank, CDS start at position 8,102, patch at positions 8,162–8,192.
+A 30 bp codon-aligned region beginning 60 bp downstream of the first complete codon of the
+CDS exon is replaced with 10 consecutive CAG triplets
+(`CAGCAGCAGCAGCAGCAGCAGCAGCAGCAG`), mimicking the pathological trinucleotide repeat
+expansions underlying polyglutamine disorders (Huntington's disease, SCAs, DRPLA).
+The substitution is length- and reading-frame-preserving (30 bp in, 30 bp out), so the
+total window remains 8,192 bp. All sequence outside the patch is identical between
+original and perturbed.
 
+- Annotations: GENCODE v45 / GRCh38; all CDS exons (all ranks); 9,705 unique genes.
+- Window layout: first complete CDS codon always at position 8,102;
+  patch always at positions 8,162–8,192 (`patch_start_in_seq`–`patch_end_in_seq`).
+  For exons with phase 1 or 2, the 1–2 split-codon bases from the preceding exon are
+  placed immediately before position 8,102, so the upstream genomic context is
+  8,102 bp (phase 0), 8,101 bp (phase 1), or 8,100 bp (phase 2).
 ---
 
 ## Schema
@@ -341,17 +345,17 @@ from datasets import load_dataset
 
 # Synonymous codon substitution — human
 syn_human = load_dataset(
-    "HuggingFaceBio/carbon-perturbation-bench", "syn_human", split="test"
+    "HuggingFaceBio/perturbation-bench", "syn_human", split="test"
 )
 
 # Synonymous codon substitution — mouse
 syn_mouse = load_dataset(
-    "HuggingFaceBio/carbon-perturbation-bench", "syn_mouse", split="test"
+    "HuggingFaceBio/perturbation-bench", "syn_mouse", split="test"
 )
 
 # CAG motif insertion
 motif = load_dataset(
-    "HuggingFaceBio/carbon-perturbation-bench", "motif_human", split="test"
+    "HuggingFaceBio/perturbation-bench", "motif_human", split="test"
 )
 ```