fix dataset_info: add script_version to all three configs

README.md

@@ -25,6 +25,8 @@ dataset_info:
   features:
   - name: benchmark_id
     dtype: string
+  - name: script_version
+    dtype: string
   - name: annotation_source
     dtype: string
   - name: genome_assembly
@@ -109,6 +111,8 @@ dataset_info:
   features:
   - name: benchmark_id
     dtype: string
+  - name: script_version
+    dtype: string
   - name: annotation_source
     dtype: string
   - name: genome_assembly
@@ -193,6 +197,8 @@ dataset_info:
   features:
   - name: benchmark_id
     dtype: string
+  - name: script_version
+    dtype: string
   - name: annotation_source
     dtype: string
   - name: genome_assembly
@@ -269,7 +275,7 @@ dataset_info:
   dataset_size: 334784354
 ---
 
-# Perturbation Bench
+# Carbon 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
@@ -284,7 +290,7 @@ altered — and asks whether the model assigns higher log-likelihood to the orig
 ### `syn_human` · `syn_mouse` — Synonymous codon substitution (20,000 pairs each)
 
 Codons within a real CDS are replaced with the highest-frequency synonym for the target
-species, while the upstream and
+species (`recoding_mode = "optimize"`, `optimization_rate = 1.0`), while the upstream and
 downstream flanking sequence is left unchanged. Amino acid identity is preserved by
 construction. The model should prefer the natural codon usage over the artificially
 optimised variant.
@@ -298,20 +304,15 @@ optimised variant.
 
 ### `motif_human` — CAG repeat insertion (20,000 pairs)
 
-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.
+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; 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).
+- 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.
 
 ---
 
@@ -340,17 +341,17 @@ from datasets import load_dataset
 
 # Synonymous codon substitution — human
 syn_human = load_dataset(
-    "HuggingFaceBio/perturbation-bench", "syn_human", split="test"
+    "HuggingFaceBio/carbon-perturbation-bench", "syn_human", split="test"
 )
 
 # Synonymous codon substitution — mouse
 syn_mouse = load_dataset(
-    "HuggingFaceBio/perturbation-bench", "syn_mouse", split="test"
+    "HuggingFaceBio/carbon-perturbation-bench", "syn_mouse", split="test"
 )
 
 # CAG motif insertion
 motif = load_dataset(
-    "HuggingFaceBio/perturbation-bench", "motif_human", split="test"
+    "HuggingFaceBio/carbon-perturbation-bench", "motif_human", split="test"
 )
 ```