Hugging Face's logo

Datasets:
HarriziSaad
/
IDP-Pathogenicity-Model

Languages:
English
Tags:
mitochondrial-variants
pathogenicity-prediction
protein-language-model
ESM-2
machine-learning
bioinformatics
License:
Dataset card Files
xet
 Community
HarriziSaad commited on
Commit
0bb0bcb
·
1 Parent(s): f809f2d

upload dataset

Browse files
Files changed (37) hide show
  1. .gitattributes +2 -0
  2. data/frozen/FREEZE_METADATA.json +23 -0
  3. data/frozen/mutations_dataset_final_FROZEN.parquet +3 -0
  4. data/frozen/mutations_dataset_mito_strict_FROZEN.parquet +3 -0
  5. data/processed/dataset_stats.json +9 -0
  6. data/processed/mutation_dataset.parquet +3 -0
  7. data/processed/mutation_features.parquet +3 -0
  8. data/processed/mutation_features.pkl +3 -0
  9. data/processed/mutations_dataset_final.parquet +3 -0
  10. data/processed/mutations_dataset_final.tsv +0 -0
  11. data/processed/mutations_dataset_mito_strict.parquet +3 -0
  12. data/processed/mutations_dataset_mito_strict.tsv +0 -0
  13. data/raw/alphamissense_cox17_chchd4.tsv +0 -0
  14. data/raw/clinvar/clinvar_variants.parquet +3 -0
  15. data/raw/clinvar_mito_parsed.parquet +3 -0
  16. data/raw/disprot/disprot_data.parquet +3 -0
  17. data/raw/mobidb/mobidb_data.parquet +3 -0
  18. data/raw/uniprot/uniprot_mitochondrial.parquet +3 -0
  19. data/raw/uniprot_human_reviewed.parquet +3 -0
  20. embeddings/embeddings_by_protein.pkl +3 -0
  21. embeddings/embeddings_combined_full.npy +3 -0
  22. embeddings/embeddings_combined_strict.npy +3 -0
  23. embeddings/embeddings_global_full.npy +3 -0
  24. embeddings/embeddings_global_strict.npy +3 -0
  25. embeddings/embeddings_local_full.npy +3 -0
  26. embeddings/embeddings_local_strict.npy +3 -0
  27. features/features_classical_full.parquet +3 -0
  28. features/features_classical_mito_strict.parquet +3 -0
  29. models/checkpoints/pathogenicity_classifier.pkl +3 -0
  30. models/checkpoints/pathogenicity_classifier_v2.pkl +3 -0
  31. models/model_classical_baseline.pkl +3 -0
  32. models/model_classical_mito_strict.pkl +3 -0
  33. results/evaluations/lpocv_results.json +112 -0
  34. results/feature_importances_classical.csv +3 -0
  35. results/full_analysis_with_ensemble.parquet +3 -0
  36. results/hierarchical_validation_final.pkl +3 -0
  37. results/lpocv_predictions_final.parquet +3 -0
.gitattributes CHANGED
@@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
58
  # Video files - compressed
59
  *.mp4 filter=lfs diff=lfs merge=lfs -text
60
  *.webm filter=lfs diff=lfs merge=lfs -text
61
+ *.csv filter=lfs diff=lfs merge=lfs -text
62
+ *.sdf filter=lfs diff=lfs merge=lfs -text
data/frozen/FREEZE_METADATA.json ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "freeze_date": "2025-12-29T10:31:09.762908",
3
+ "freeze_version": "1.0",
4
+ "datasets": {
5
+ "full": {
6
+ "filename": "mutations_dataset_final_FROZEN.parquet",
7
+ "n_mutations": 11928,
8
+ "n_pathogenic": 6882,
9
+ "n_benign": 5046,
10
+ "n_genes": 648,
11
+ "hash": "af2cbcd7509c46d15984052bac4ff39b"
12
+ },
13
+ "mito_strict": {
14
+ "filename": "mutations_dataset_mito_strict_FROZEN.parquet",
15
+ "n_mutations": 2530,
16
+ "n_pathogenic": 1757,
17
+ "n_benign": 773,
18
+ "n_genes": 144,
19
+ "hash": "fdf629b8ef68861eeba4c90c9dd653f2"
20
+ }
21
+ },
22
+ "note": "FROZEN - DO NOT MODIFY LABELS AFTER THIS POINT"
23
+ }
data/frozen/mutations_dataset_final_FROZEN.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:73a72764baade47fb6a1f1100938ee0d45ab2773b95983cb7b97f8b53199a277
3
+ size 351970
data/frozen/mutations_dataset_mito_strict_FROZEN.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:69ce14f7e6a3b1a8b316ee4ef7357fd2f0dcfc964d24742775970a843ded0666
3
+ size 92749
data/processed/dataset_stats.json ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "total_mutations": 2154,
3
+ "pathogenic": 326,
4
+ "benign": 1828,
5
+ "unique_genes": 99,
6
+ "unique_proteins": 99,
7
+ "in_disorder_region": 20,
8
+ "annotated_for_disorder": 55
9
+ }
data/processed/mutation_dataset.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:85a99b33a219bb29ab544705cc8476e6fad23c25091035885fb89b3f94b3a300
3
+ size 78448
data/processed/mutation_features.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:83db7250f9711ebbe13f771919e3179a558219f70e6979405dae2bdf06f10407
3
+ size 238385
data/processed/mutation_features.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:202fc141d93308ce33156c6c4b8699157707815c6a48a7481a22582621cddfec
3
+ size 851028
data/processed/mutations_dataset_final.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:73a72764baade47fb6a1f1100938ee0d45ab2773b95983cb7b97f8b53199a277
3
+ size 351970
data/processed/mutations_dataset_final.tsv ADDED
The diff for this file is too large to render. See raw diff
 
data/processed/mutations_dataset_mito_strict.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:69ce14f7e6a3b1a8b316ee4ef7357fd2f0dcfc964d24742775970a843ded0666
3
+ size 92749
data/processed/mutations_dataset_mito_strict.tsv ADDED
The diff for this file is too large to render. See raw diff
 
data/raw/alphamissense_cox17_chchd4.tsv ADDED
The diff for this file is too large to render. See raw diff
 
data/raw/clinvar/clinvar_variants.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:61482076f5d09ff267efaf79a6ff149aff9b325d583d82a9079c41a7d34d023c
3
+ size 113260
data/raw/clinvar_mito_parsed.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5c9d8264f513249518ab4d0c9ae756eb5b6ceb71670fb2fa730944d7acfd366d
3
+ size 287985
data/raw/disprot/disprot_data.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:22c67d975096e666f1692caf651776ae898ab126442ee9d0aabedc82527f7ba7
3
+ size 2388595
data/raw/mobidb/mobidb_data.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5d8a97a4d53cd7e72502fc7cf6e26d6e92b51cb91799825500e103e7792028c0
3
+ size 6406
data/raw/uniprot/uniprot_mitochondrial.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:fc89e3760653a090a7ffa5ea66807a45b50a36546d3dd8e1c2b1dc2fccec73a8
3
+ size 250724
data/raw/uniprot_human_reviewed.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:34b22aa3a2e23966ece28d16417906414c56a58eefac43022985da773192cb10
3
+ size 12779272
embeddings/embeddings_by_protein.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:037902bdf9a4abdfc9a00c5bb64c5ce3f9de8f3f6d17eb6b5ce70e6be9f4f10d
3
+ size 3299720
embeddings/embeddings_combined_full.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:07018cfb1c63d8695d22f1883326ad81ed123ae5880eaf6cbda58c31f801c92f
3
+ size 244285568
embeddings/embeddings_combined_strict.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:96c2f92b6a50673aed9632314dff8aca4f5e85d91f54aaae10e4555090def8aa
3
+ size 51814528
embeddings/embeddings_global_full.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:c3d79ec985b86f631ebca5287f7824fba15166b0ca43ab5a1ad78538b0093fb8
3
+ size 122142848
embeddings/embeddings_global_strict.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5e3e8caeb1397c562e00601beb67c875be8dbc4967aae4034f04af65ee43e6ac
3
+ size 25907328
embeddings/embeddings_local_full.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:89ffd1b8a3d4dadcba5b1da97691f7c966a4b3924462d6ce330052057ccc3de7
3
+ size 122142848
embeddings/embeddings_local_strict.npy ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:00fa3b1f078bdc944b16cce080ab81d066c0bf4064698fecf55842a798e67d0c
3
+ size 25907328
features/features_classical_full.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d803d653db3929db3d1afe6cba43027ffd63ece6a5382230b15826230d8924da
3
+ size 752576
features/features_classical_mito_strict.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:cd3aebae4bc3842d13395760045931bc01df4249499fdb40529bad710abe404a
3
+ size 196181
models/checkpoints/pathogenicity_classifier.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9d1f5decfbf027bc23aaf656d7f00b78be2300b216e47a094f0c0ab62c23a347
3
+ size 738933
models/checkpoints/pathogenicity_classifier_v2.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:414667ae63e1aecf42e275e4e440b0d088b4151209fe87c93852790d5d1090ec
3
+ size 1333100
models/model_classical_baseline.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:39e9533d2771bc05392fd65d7cfcd1eb28b2123fc818c9aef004130aa8dfebd6
3
+ size 1173824
models/model_classical_mito_strict.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e0615ac8b1caa5b86df0db948a8a9399f298fa8a6b7d4bad67e7459262fe2d4f
3
+ size 1126365
results/evaluations/lpocv_results.json ADDED
@@ -0,0 +1,112 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "model_A_mechanistic": {
3
+ "features": [
4
+ "delta_hydrophobicity",
5
+ "delta_charge",
6
+ "delta_volume",
7
+ "delta_disorder_propensity",
8
+ "delta_aromatic",
9
+ "local_charge_density",
10
+ "local_disorder_mean",
11
+ "local_disorder_variance",
12
+ "local_hydrophobicity",
13
+ "local_aromatic_density",
14
+ "local_proline_density",
15
+ "local_glycine_density",
16
+ "local_cysteine_density",
17
+ "predicted_delta_disorder_mean",
18
+ "predicted_delta_disorder_std",
19
+ "propagation_extent",
20
+ "max_effective_delta",
21
+ "delta_cpr",
22
+ "delta_ncpr",
23
+ "delta_kappa",
24
+ "ros_sensitivity",
25
+ "import_efficiency_change",
26
+ "cysteine_gained",
27
+ "cysteine_lost",
28
+ "disulfide_disruption_risk",
29
+ "oxidation_sensitivity_change",
30
+ "region_matrix",
31
+ "region_ims",
32
+ "region_presequence",
33
+ "region_membrane",
34
+ "disorder_x_charge",
35
+ "disorder_x_hydro",
36
+ "ros_x_cysteine",
37
+ "propagation_x_disorder",
38
+ "disorder_confidence_ratio",
39
+ "abs_delta_disorder",
40
+ "abs_delta_charge",
41
+ "abs_delta_hydro",
42
+ "is_n_terminal",
43
+ "is_charge_changing",
44
+ "is_disorder_increasing",
45
+ "is_high_ros"
46
+ ],
47
+ "auc_roc": 0.5896924111269854,
48
+ "auc_pr": 0.2004002656019795,
49
+ "threshold": 0.08934491262314229,
50
+ "recall": 0.588957055214724,
51
+ "precision": 0.1979381443298969
52
+ },
53
+ "model_B_integrated": {
54
+ "features": [
55
+ "delta_hydrophobicity",
56
+ "delta_charge",
57
+ "delta_volume",
58
+ "delta_disorder_propensity",
59
+ "delta_aromatic",
60
+ "local_charge_density",
61
+ "local_disorder_mean",
62
+ "local_disorder_variance",
63
+ "local_hydrophobicity",
64
+ "local_aromatic_density",
65
+ "local_proline_density",
66
+ "local_glycine_density",
67
+ "local_cysteine_density",
68
+ "predicted_delta_disorder_mean",
69
+ "predicted_delta_disorder_std",
70
+ "propagation_extent",
71
+ "max_effective_delta",
72
+ "delta_cpr",
73
+ "delta_ncpr",
74
+ "delta_kappa",
75
+ "ros_sensitivity",
76
+ "import_efficiency_change",
77
+ "cysteine_gained",
78
+ "cysteine_lost",
79
+ "disulfide_disruption_risk",
80
+ "oxidation_sensitivity_change",
81
+ "region_matrix",
82
+ "region_ims",
83
+ "region_presequence",
84
+ "region_membrane",
85
+ "disorder_x_charge",
86
+ "disorder_x_hydro",
87
+ "ros_x_cysteine",
88
+ "propagation_x_disorder",
89
+ "disorder_confidence_ratio",
90
+ "abs_delta_disorder",
91
+ "abs_delta_charge",
92
+ "abs_delta_hydro",
93
+ "is_n_terminal",
94
+ "is_charge_changing",
95
+ "is_disorder_increasing",
96
+ "is_high_ros",
97
+ "bayesian_confidence",
98
+ "n_thresholds_exceeded",
99
+ "pathogenicity_score",
100
+ "confidence_score"
101
+ ],
102
+ "auc_roc": 0.5845734935708884,
103
+ "auc_pr": 0.20449918815641716,
104
+ "threshold": 0.09127901130149482,
105
+ "recall": 0.5705521472392638,
106
+ "precision": 0.19850586979722518
107
+ },
108
+ "comparison": {
109
+ "delta_auc_roc": -0.005118917556097058,
110
+ "delta_auc_pr": 0.004098922554437667
111
+ }
112
+ }
results/feature_importances_classical.csv ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f06d55a3f6b4a414e751b2d2ed691d59cbdc1d1019a016575ee421fdb4adc613
3
+ size 1819
results/full_analysis_with_ensemble.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:81120881bc2295e4007721b31a60bfa65702581e9d419c92b58f36c3f91b125c
3
+ size 1149086
results/hierarchical_validation_final.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3c8d7360c5b64909157391be16c739bfcfe9bb717e60ac21f3e9a75b591af5c0
3
+ size 1736
results/lpocv_predictions_final.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a034f0b13736f36efe7c2b1fd7b3875f0787a8cbdad5bd483d8da5e0e2b98159
3
+ size 94169