Add closed DNA tags and mutation location text

README.md

@@ -97,7 +97,7 @@ Dataset-wide provenance summary:
 }
 ```
 
-Every prompt sequence is 8,192 bp long. The variant is placed at the final base of the sequence context: `variant_index_0based = 8191`, equivalent to `variant_position_1based = 8192`.
+Every prompt sequence is 8,192 bp long and is wrapped in closed DNA tags, for example `<dna>...</dna>`. The variant is placed at the final base of the sequence context: `variant_index_0based = 8191`, equivalent to `variant_position_1based = 8192`.
 
 The `all_tasks` config has 6,000 task rows but 4,000 unique variant keys. The `binary` and `clinvar_levels` configs are two views of the same 2,000 clinical-classification variants; `pathogenic_pairwise` contributes 2,000 additional pathogenic or likely pathogenic variants.
 
@@ -214,7 +214,7 @@ excluded_from_benchmark_eval: true
 
 ### `binary`
 
-The prompt shows the reference allele, alternate allele, and an 8,192 bp DNA sequence window containing the alternate allele at the final base of the context. The model is asked to answer with exactly one option:
+The prompt states the mutation location in natural language and shows an 8,192 bp DNA sequence window containing the alternate allele at the final base of the context. For example, it tells the model that the variant is at position 8,192 using 1-based indexing, and that the reference allele is changed to the alternate allele at that position. The model is asked to answer with exactly one option:
 
 ```text
 benign or likely benign
@@ -225,7 +225,7 @@ This config collapses ClinVar benign/likely-benign labels and pathogenic/likely-
 
 ### `clinvar_levels`
 
-This task uses the same sequence prompt style as `binary`, but preserves the retained raw ClinVar label. Allowed answers are:
+This task uses the same sequence prompt style as `binary`, including the natural-language mutation location sentence, but preserves the retained raw ClinVar label. Allowed answers are:
 
 ```text
 Benign

all_tasks/train-00000-of-00001.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e96535d15744930b81154e8d7c3ee96aff217f9c0a160070b7a9272739d3fe82
-size 210851553
+oid sha256:9995e04aa33b9163c8894faabc97ac226b60409d5a4b6e8dfd5003ca1b2f428d
+size 212099553

binary/train-00000-of-00001.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:0192484cf7a48e60291f8a53d0160f61a67f393bf45d2f957e4fb72078f4ba71
-size 54112557
+oid sha256:6630bdc1a94cc6a6769c73de779001a0cef6a6d86b3aa3ca05d596c96b254330
+size 54700557

clinvar_levels/train-00000-of-00001.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a311857606a5e035bb4edb650307f4c3f9a62c39196be2973f350a396dd7fab1
-size 54448553
+oid sha256:637a086379095a8ed0da6b9eada1f05dfcd1024629245e0e17f106bd77401a27
+size 55036553

pathogenic_pairwise/train-00000-of-00001.jsonl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ad6a2ea8543d0a52c3798fe311da9914373150285f450ae515028bfd4f3b4233
-size 102290443
+oid sha256:cea36c57277b45d08c9e5e822742cd8f19521613c345f9224282b6683c436d2f
+size 102362443