forked from mims-harvard/decagon
-
Notifications
You must be signed in to change notification settings - Fork 0
/
configuration.json
47 lines (47 loc) · 1.89 KB
/
configuration.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
{
"DataSetType": "DecagonPublicData",
"TrainableType": "DecagonTrainable",
"ActiveLearnerType": "RandomMaskingActiveLearner",
"TrainerType": "DecagonTrainer",
"NumProteins": 200,
"NumDrugs": 250,
"NumDrugDrugRelationTypes": 3,
"TrainWithTransposedAdjacencyMatrices": true,
"DecagonDrugDrugRelationsFilename": "/Users/jarridr/repos/decagon/data/bio-decagon-combo-server.csv",
"DecagonProteinProteinRelationsFilename": "/Users/jarridr/repos/decagon/data/bio-decagon-ppi-server.csv",
"DecagonDrugProteinRelationsFilename": "/Users/jarridr/repos/decagon/data/bio-decagon-targets-server.csv",
"DecagonNodeFeaturesFilename": "/Users/jarridr/repos/decagon/data/bio-decagon-mono.csv",
"PPIEdgeDecoder": "bilinear",
"ProteinToDrugEdgeDecoder": "bilinear",
"DrugProteinEdgeDecoder": "bilinear",
"DrugDrugEdgeDecoder": "dedicom",
"neg_sample_size": 1.0,
"learning_rate": 0.001,
"epochs": 50,
"hidden1": 64,
"hidden2": 32,
"weight_decay": 0,
"dropout": 0.1,
"max_margin": 0.1,
"batch_size": 512,
"bias": true,
"TestSetProportion": 0.8,
"InitTrainSetProportion": 1.0,
"NumIterationsPerLog": 1,
"NumIterationsPerCheckpoint": 1,
"CheckpointDirectory": "/Users/jarridr/repos/decagon/ckpts/",
"TrainIterationResultDir": "/Users/jarridr/repos/decagon/results/",
"MaxCheckpointsToKeep": 3,
"CustomCheckpointName": "public_data",
"NumEpochs": 30,
"ApkRank": 50,
"InitialUnmaskedProportion": 0.5,
"ProportionUnmaskedPerIteration": 0.05,
"UseGpu": false,
"ShouldCheckpoint": true,
"TestEdgeFilename": "/Users/jarridr/repos/decagon/test-edges-all.csv",
"WriteNdarrays": true,
"NdarrayWriteDir": "/Users/jarridr/repos/decagon/ndarray-dump/",
"NpSaveDir": "/Users/jarridr/repos/decagon/all-ndarray-from-ckpts/",
"EdgeFileToRepair": "/Users/jarridr/repos/decagon/test-edges-all.csv"
}