Lal Claude Opus 4.6 commited on
Commit
886ffff
·
1 Parent(s): 9b86426

Add split distributions and fix loading code

Browse files

- Add human split distribution (train/valid/test counts)
- Add mouse split distribution (train/valid/test counts)
- Fix repo_type="dataset" missing from hf_hub_download

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Files changed (1) hide show
  1. README.md +28 -4
README.md CHANGED
@@ -13,7 +13,7 @@ size_categories:
13
  # enformer-data
14
 
15
  ## Dataset Summary
16
- This dataset contains the specific genomic intervals used for training, validating, and testing the Enformer model, a deep learning architecture for predicting functional genomic tracks from DNA sequence. The intervals are provided for both human and mouse genomes. As done in the publication, we modified the Basenji2 dataset by extending the input sequence to 196,608bp from the original 131,072bp using the hg38 reference genome.
17
 
18
  - **Source Publication:** [Avsec, Ž., et al. "Effective gene expression prediction from sequence by integrating long-range interactions." Nat Methods 18, 1196–1203 (2021).](https://www.nature.com/articles/s41592-021-01252-x)
19
  - **Genome Builds:**
@@ -47,15 +47,39 @@ Both files follow a standard genomic interval format:
47
  | `human_intervals.tsv` | 38,171 | hg38 |
48
  | `mouse_intervals.tsv` | 33,521 | mm10 |
49
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
50
  ## Usage
51
 
52
  ```python
53
  from huggingface_hub import hf_hub_download
54
  import pandas as pd
55
 
56
- file_path = hf_hub_download(repo_id="Genentech/enformer-data", filename="human_intervals.tsv")
 
 
 
 
57
  df_human = pd.read_csv(file_path, sep='\t')
58
 
59
- file_path = hf_hub_download(repo_id="Genentech/enformer-data", filename="mouse_intervals.tsv")
 
 
 
 
60
  df_mouse = pd.read_csv(file_path, sep='\t')
61
- ```
 
13
  # enformer-data
14
 
15
  ## Dataset Summary
16
+ This dataset contains the specific genomic intervals used for training, validating, and testing the Enformer model, a deep learning architecture for predicting functional genomic tracks from DNA sequence. The intervals are provided for both human and mouse genomes. As done in the publication, we modified the Basenji2 dataset by extending the input sequence to 196,608 bp from the original 131,072 bp using the hg38 reference genome.
17
 
18
  - **Source Publication:** [Avsec, Ž., et al. "Effective gene expression prediction from sequence by integrating long-range interactions." Nat Methods 18, 1196–1203 (2021).](https://www.nature.com/articles/s41592-021-01252-x)
19
  - **Genome Builds:**
 
47
  | `human_intervals.tsv` | 38,171 | hg38 |
48
  | `mouse_intervals.tsv` | 33,521 | mm10 |
49
 
50
+ ### Data Splits
51
+
52
+ **Human (hg38)**
53
+ | Split | Count |
54
+ |-------|-------|
55
+ | train | 34,021 |
56
+ | valid | 2,213 |
57
+ | test | 1,937 |
58
+
59
+ **Mouse (mm10)**
60
+ | Split | Count |
61
+ |-------|-------|
62
+ | train | 29,295 |
63
+ | valid | 2,209 |
64
+ | test | 2,017 |
65
+
66
  ## Usage
67
 
68
  ```python
69
  from huggingface_hub import hf_hub_download
70
  import pandas as pd
71
 
72
+ file_path = hf_hub_download(
73
+ repo_id="Genentech/enformer-data",
74
+ filename="human_intervals.tsv",
75
+ repo_type="dataset"
76
+ )
77
  df_human = pd.read_csv(file_path, sep='\t')
78
 
79
+ file_path = hf_hub_download(
80
+ repo_id="Genentech/enformer-data",
81
+ filename="mouse_intervals.tsv",
82
+ repo_type="dataset"
83
+ )
84
  df_mouse = pd.read_csv(file_path, sep='\t')
85
+ ```