Deduplicate causal and bidirectional configs

README.md

@@ -11,22 +11,14 @@ tags:
 - hg38
 - parquet
 configs:
-- config_name: canonical-causal
+- config_name: causal
   data_files:
   - split: all
     path: functional-random-gamba-causal.parquet
-- config_name: canonical-bidi
+- config_name: bidi
   data_files:
   - split: all
     path: functional-random-gamba-bidi.parquet
-- config_name: noncoding-added-causal
-  data_files:
-  - split: all
-    path: functional-random-gamba-noncoding-added-causal.parquet
-- config_name: noncoding-added-bidi
-  data_files:
-  - split: all
-    path: functional-random-gamba-noncoding-added-bidi.parquet
 ---
 
 # GAMBA Functional Regions: Feature vs Random
@@ -40,12 +32,11 @@ category.
 
 | Config | Train rows | Test rows | Total |
 |---|---:|---:|---:|
-| `canonical-causal`, `canonical-bidi` | 135,692 | 33,982 | 169,674 |
-| `noncoding-added-causal`, `noncoding-added-bidi` | 150,726 | 37,834 | 188,560 |
+| `causal`, `bidi` | 150,728 | 37,834 | 188,562 |
 
-The `noncoding-added-*` configs are an explicit extension from
-[Gamba-Processing](https://github.com/TaykhoomDalal/Gamba-Processing), not an
-additional category emitted by GAMBA's current `create_eval_data.py`.
+Each config includes the `noncoding_regions` extension. Filter
+`category != "noncoding_regions"` to recover the exact 169,674-row,
+ten-category GAMBA paper dataset without storing those rows twice.
 
 ## Choosing a context
 
@@ -62,13 +53,13 @@ context and is not the paper protocol.
 ```python
 from datasets import load_dataset
 
-canonical = load_dataset(
+dataset = load_dataset(
     "Taykhoom/functional-random-gamba",
-    "canonical-bidi",
+    "bidi",
     split="all",
 )
-train = canonical.filter(lambda row: row["split"] == "train")
-test = canonical.filter(lambda row: row["split"] == "test")
+paper = dataset.filter(lambda row: row["category"] != "noncoding_regions")
+test = paper.filter(lambda row: row["split"] == "test")
 ```
 
 Here, `split="all"` tells Hugging Face to load the single physical parquet

functional-random-gamba-bidi.parquet

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+size 130138195

functional-random-gamba-causal.parquet

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+size 122835184

functional-random-gamba-noncoding-added-bidi.parquet

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-size 130059181

functional-random-gamba-noncoding-added-causal.parquet

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functional-random-gamba-noncoding-added.parquet

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functional-random-gamba.parquet

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