Add files using upload-large-folder tool

README.md

@@ -11,14 +11,22 @@ tags:
 - benchmark
 - parquet
 configs:
-- config_name: default
+- config_name: archive
   data_files:
   - split: train
-    path: train.parquet
+    path: archive/train.parquet
   - split: validation
-    path: validation.parquet
+    path: archive/validation.parquet
   - split: test
-    path: test.parquet
+    path: archive/test.parquet
+- config_name: corrected
+  data_files:
+  - split: train
+    path: corrected/train.parquet
+  - split: validation
+    path: corrected/validation.parquet
+  - split: test
+    path: corrected/test.parquet
 ---
 
 # GLM-Tang Task 5: INSERT-seq RNA Output
@@ -32,13 +40,13 @@ embryonic stem cells.
 ```python
 from datasets import load_dataset
 
-dataset = load_dataset("Taykhoom/insert-seq-glm-tang")
+dataset = load_dataset("Taykhoom/insert-seq-glm-tang", "corrected")
 train = dataset["train"]
 validation = dataset["validation"]
 test = dataset["test"]
 ```
 
-## Dataset size
+## Archive dataset size
 
 | Split | Rows |
 |---|---:|
@@ -78,10 +86,10 @@ HDF5 target columns:
 The released model does **not** train on raw total RNA. It uses:
 
 ```python
-label = log1p(totalRNA_average)
+label = np.log(totalRNA_average + np.float32(1))
 ```
 
-This transformed value is the model-facing `label`.
+This float32 expression is the bit-exact model-facing `label`.
 
 The raw and auxiliary assay values are retained as:
 
@@ -95,16 +103,17 @@ These are targets/measurements, not sequence features.
 
 | Column | Description |
 |---|---|
-| `split` | Released `train`, `val`, or `test` partition. |
+| `split` | Selected config's `train`, `val`, or `test` partition. |
+| `archive_split` | Original partition; present in `corrected` only. |
 | `sequence` | Exact 173 nt archived model input in transcribed orientation. |
-| `label` | `log1p(totalRNA_average)`, matching released training/evaluation code. |
+| `label` | Bit-exact float32 `np.log(totalRNA_average + np.float32(1))`. |
 | `example_id` | GEO FASTA sequence identifier. |
 | `source_index` | Zero-based row index in the 16,461-row GEO FASTA/table. |
 | `raw_total_rna` | Raw `totalRNA_average` assay value. |
 | `aux_target_run_on_rna` | `runonRNA_average`. |
 | `aux_target_sort_seq` | `sortseq_average`. |
 | `source_category`, `source_class`, `source_window`, `source_barcode` | Supplementary Table 2 design provenance. |
-| `locus_group_id`, `split_leakage` | Source `name` (unique-ID fallback for unnamed rows) and whether that group spans archived partitions. |
+| `locus_group_id`, `archive_locus_split_leakage` | Source `name` (unique-ID fallback for unnamed rows) and whether that group spans archive partitions. |
 | `chrom`, `start`, `end`, `strand`, `genome_build` | Nullable source-provided zero-based, half-open GRCm38/mm10 coordinates. |
 | `coordinates_available` | Whether all four source coordinate fields are present. |
 | `species` | Always `Mus musculus`. |
@@ -112,14 +121,22 @@ These are targets/measurements, not sequence features.
 | `is_synthetic` | True only for `randomized_control` rows. |
 
 The released code trains with mean-squared error and reports test Pearson
-correlation and MSE on `label`.
+correlation and MSE on `label`. The previous `log1p` implementation differed
+at the bit level for 4,302 rows and is not retained as a duplicate target.
 
 ## Reproduction boundary
 
 The public source has 16,461 rows, while Tang's archive retains 11,417. The
-source-row selection rule and split seed were not released. This dataset
-therefore preserves archived row membership/order exactly rather than claiming
-to recreate that unpublished selection from all GEO rows.
+archive split is deterministic: within each full Supplementary Table 2
+`class` in source order, the first `ceil(n/10)` rows are test, the next
+`ceil(n/10)` validation, and the remainder train; all `160-333` rows are then
+forced to train. Thus all 1,721 retained `160-333` rows are train-only.
+
+The `archive` config preserves those exact rows and splits. The `corrected`
+config assigns complete `locus_group_id` groups to a deterministic
+class/window-stratified 70/10/20 split. It contains 7,989 train, 1,144
+validation, and 2,284 test rows; every class/window stratum with at least three
+groups appears in all three splits, and no locus group crosses partitions.
 
 All archived assay values equal an explicit float32 conversion of the GEO
 table values.
@@ -131,8 +148,9 @@ the corresponding assay sequence is 173 nt; these values are preserved as
 source provenance rather than silently adjusted. No hg38 mapping is claimed.
 
 The archived split contains 424 `locus_group_id` values in multiple
-partitions, affecting 848 rows. Group-aware evaluation should use
-`locus_group_id` and inspect `split_leakage`.
+partitions, affecting 848 rows. Group-aware evaluation should use the
+`corrected` config; `archive_locus_split_leakage` documents the original
+contamination.
 
 ## Processing and verification
 

archive/test.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f6047accacb07aa3289974061233255b82de1bb7a673b8daed8b3eb5781a3a11
+size 122450

archive/train.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:de4e0391c08f334ce130869ff31b203c3aa53791513477d1c48fca8a6f754de2
+size 893945

archive/validation.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4329c5d2ee42b416fc5937d15c11f31d478a3155197547ce55c992adcdba9a37
+size 122579

corrected/test.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0f15813cd61e861b69acf040bd9b997250ff9e50f3ba39772562b4a38e94cd6d
+size 236359

corrected/train.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0d8738bbad7683a3ef5019f49816983e96515d81598ae0f607fdf72d6d124f12
+size 787785

corrected/validation.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f9a2f73f9c52a2c4606f83a18c0a5c358e4f06b8f1bd752cf5157e0950b6ca74
+size 125907