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Browse files- cafa5_cafa6_propagated_processed/artifacts/go_tokenizer.pkl +3 -0
- cafa5_cafa6_propagated_processed/artifacts/limited_vocabulary.json +0 -0
- cafa5_cafa6_propagated_processed/artifacts/organism_mapper.pkl +3 -0
- cafa5_cafa6_propagated_processed/artifacts/tokenizer_info.json +59 -0
- cafa5_cafa6_propagated_processed/dataset/dataset_dict.json +1 -0
- cafa5_cafa6_propagated_processed/dataset/train/data-00000-of-00004.arrow +3 -0
- cafa5_cafa6_propagated_processed/dataset/train/data-00001-of-00004.arrow +3 -0
- cafa5_cafa6_propagated_processed/dataset/train/data-00002-of-00004.arrow +3 -0
- cafa5_cafa6_propagated_processed/dataset/train/data-00003-of-00004.arrow +3 -0
- cafa5_cafa6_propagated_processed/dataset/train/dataset_info.json +83 -0
- cafa5_cafa6_propagated_processed/dataset/train/state.json +22 -0
- cafa5_cafa6_propagated_processed/dataset/validation/data-00000-of-00001.arrow +3 -0
- cafa5_cafa6_propagated_processed/dataset/validation/dataset_info.json +90 -0
- cafa5_cafa6_propagated_processed/dataset/validation/state.json +13 -0
- cafa5_cafa6_propagated_processed/preprocess_config.yaml +20 -0
cafa5_cafa6_propagated_processed/artifacts/go_tokenizer.pkl
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cafa5_cafa6_propagated_processed/artifacts/limited_vocabulary.json
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cafa5_cafa6_propagated_processed/artifacts/organism_mapper.pkl
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cafa5_cafa6_propagated_processed/artifacts/tokenizer_info.json
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cafa5_cafa6_propagated_processed/dataset/dataset_dict.json
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{"splits": ["train", "validation"]}
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cafa5_cafa6_propagated_processed/dataset/train/data-00000-of-00004.arrow
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cafa5_cafa6_propagated_processed/dataset/train/data-00001-of-00004.arrow
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cafa5_cafa6_propagated_processed/dataset/train/data-00002-of-00004.arrow
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cafa5_cafa6_propagated_processed/dataset/train/data-00003-of-00004.arrow
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cafa5_cafa6_propagated_processed/dataset/train/dataset_info.json
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cafa5_cafa6_propagated_processed/dataset/train/state.json
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cafa5_cafa6_propagated_processed/dataset/validation/data-00000-of-00001.arrow
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cafa5_cafa6_propagated_processed/dataset/validation/dataset_info.json
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| 46 |
+
"_type": "Value"
|
| 47 |
+
},
|
| 48 |
+
"_type": "List"
|
| 49 |
+
},
|
| 50 |
+
"protein_mask": {
|
| 51 |
+
"feature": {
|
| 52 |
+
"dtype": "int64",
|
| 53 |
+
"_type": "Value"
|
| 54 |
+
},
|
| 55 |
+
"_type": "List"
|
| 56 |
+
},
|
| 57 |
+
"go_input_tokens": {
|
| 58 |
+
"feature": {
|
| 59 |
+
"dtype": "int64",
|
| 60 |
+
"_type": "Value"
|
| 61 |
+
},
|
| 62 |
+
"_type": "List"
|
| 63 |
+
},
|
| 64 |
+
"go_targets": {
|
| 65 |
+
"feature": {
|
| 66 |
+
"dtype": "int64",
|
| 67 |
+
"_type": "Value"
|
| 68 |
+
},
|
| 69 |
+
"_type": "List"
|
| 70 |
+
},
|
| 71 |
+
"organism_id": {
|
| 72 |
+
"dtype": "int64",
|
| 73 |
+
"_type": "Value"
|
| 74 |
+
},
|
| 75 |
+
"organism_name": {
|
| 76 |
+
"dtype": "string",
|
| 77 |
+
"_type": "Value"
|
| 78 |
+
},
|
| 79 |
+
"num_go_terms": {
|
| 80 |
+
"dtype": "int64",
|
| 81 |
+
"_type": "Value"
|
| 82 |
+
},
|
| 83 |
+
"protein_length": {
|
| 84 |
+
"dtype": "int64",
|
| 85 |
+
"_type": "Value"
|
| 86 |
+
}
|
| 87 |
+
},
|
| 88 |
+
"homepage": "",
|
| 89 |
+
"license": ""
|
| 90 |
+
}
|
cafa5_cafa6_propagated_processed/dataset/validation/state.json
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"_data_files": [
|
| 3 |
+
{
|
| 4 |
+
"filename": "data-00000-of-00001.arrow"
|
| 5 |
+
}
|
| 6 |
+
],
|
| 7 |
+
"_fingerprint": "daa0b97ba07b488d",
|
| 8 |
+
"_format_columns": null,
|
| 9 |
+
"_format_kwargs": {},
|
| 10 |
+
"_format_type": null,
|
| 11 |
+
"_output_all_columns": false,
|
| 12 |
+
"_split": null
|
| 13 |
+
}
|
cafa5_cafa6_propagated_processed/preprocess_config.yaml
ADDED
|
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
seed: 42
|
| 2 |
+
hf_dataset_name: /home/guloglut/scratch/cafa5_cafa6_data/combined_propagated_deduped
|
| 3 |
+
hf_dataset_config: experiment_data_reasoning
|
| 4 |
+
embed_model_path: facebook/esm2_t33_650M_UR50D
|
| 5 |
+
embed_model_type: esm2
|
| 6 |
+
vocab_limits:
|
| 7 |
+
mf:
|
| 8 |
+
method: min_freq
|
| 9 |
+
value: 20
|
| 10 |
+
bp:
|
| 11 |
+
method: min_freq
|
| 12 |
+
value: 20
|
| 13 |
+
cc:
|
| 14 |
+
method: min_freq
|
| 15 |
+
value: 20
|
| 16 |
+
top_n_organisms: 200
|
| 17 |
+
max_go_terms: 500
|
| 18 |
+
num_proc: 32
|
| 19 |
+
output_dir: artifacts/preprocessed
|
| 20 |
+
dataset_name: cafa5_cafa6_processed
|