Christina Theodoris commited on
Commit
7cf49a3
·
1 Parent(s): d319fef

add V2 models

Browse files
Files changed (27) hide show
  1. Geneformer-V1-10M/config.json +23 -0
  2. Geneformer-V1-10M/model.safetensors +3 -0
  3. Geneformer-V1-10M/pytorch_model.bin +3 -0
  4. Geneformer-V1-10M/training_args.bin +3 -0
  5. Geneformer-V2-104M/config.json +24 -0
  6. Geneformer-V2-104M/generation_config.json +5 -0
  7. Geneformer-V2-104M/model.safetensors +3 -0
  8. Geneformer-V2-104M/training_args.bin +3 -0
  9. Geneformer-V2-104M_CLcancer/config.json +25 -0
  10. Geneformer-V2-104M_CLcancer/generation_config.json +5 -0
  11. Geneformer-V2-104M_CLcancer/model.safetensors +3 -0
  12. Geneformer-V2-104M_CLcancer/training_args.bin +3 -0
  13. Geneformer-V2-316M/config.json +24 -0
  14. Geneformer-V2-316M/generation_config.json +5 -0
  15. Geneformer-V2-316M/model.safetensors +3 -0
  16. Geneformer-V2-316M/training_args.bin +3 -0
  17. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/config.json +35 -0
  18. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/optimizer.pt +3 -0
  19. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/pytorch_model.bin +3 -0
  20. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/rng_state.pth +3 -0
  21. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/scheduler.pt +3 -0
  22. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/trainer_state.json +150 -0
  23. fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/training_args.bin +3 -0
  24. geneformer/ensembl_mapping_dict_gc104M.pkl +3 -0
  25. geneformer/gene_median_dictionary_gc104M.pkl +3 -0
  26. geneformer/gene_name_id_dict_gc104M.pkl +3 -0
  27. geneformer/token_dictionary_gc104M.pkl +3 -0
Geneformer-V1-10M/config.json ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architectures": [
3
+ "BertForMaskedLM"
4
+ ],
5
+ "attention_probs_dropout_prob": 0.02,
6
+ "gradient_checkpointing": false,
7
+ "hidden_act": "relu",
8
+ "hidden_dropout_prob": 0.02,
9
+ "hidden_size": 256,
10
+ "initializer_range": 0.02,
11
+ "intermediate_size": 512,
12
+ "layer_norm_eps": 1e-12,
13
+ "max_position_embeddings": 2048,
14
+ "model_type": "bert",
15
+ "num_attention_heads": 4,
16
+ "num_hidden_layers": 6,
17
+ "pad_token_id": 0,
18
+ "position_embedding_type": "absolute",
19
+ "transformers_version": "4.6.0",
20
+ "type_vocab_size": 2,
21
+ "use_cache": true,
22
+ "vocab_size": 25426
23
+ }
Geneformer-V1-10M/model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a5e33a757431643b3697de7ef6127950cdc49e06e58d4266b3a3ab191b683f14
3
+ size 41183536
Geneformer-V1-10M/pytorch_model.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8d860e2125884475dd42bc2cd9a0e60c60808a7351241e08f2154931ffc142da
3
+ size 41216562
Geneformer-V1-10M/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f0ec3459454205174c9d2e4d6c6930f6b0fbf3364fc03a6f4d99c4d3add2012b
3
+ size 2607
Geneformer-V2-104M/config.json ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architectures": [
3
+ "BertForMaskedLM"
4
+ ],
5
+ "attention_probs_dropout_prob": 0.1,
6
+ "classifier_dropout": null,
7
+ "hidden_act": "relu",
8
+ "hidden_dropout_prob": 0.1,
9
+ "hidden_size": 768,
10
+ "initializer_range": 0.02,
11
+ "intermediate_size": 3072,
12
+ "layer_norm_eps": 1e-12,
13
+ "max_position_embeddings": 4096,
14
+ "model_type": "bert",
15
+ "num_attention_heads": 12,
16
+ "num_hidden_layers": 12,
17
+ "pad_token_id": 0,
18
+ "position_embedding_type": "absolute",
19
+ "torch_dtype": "float32",
20
+ "transformers_version": "4.44.2",
21
+ "type_vocab_size": 2,
22
+ "use_cache": true,
23
+ "vocab_size": 20275
24
+ }
Geneformer-V2-104M/generation_config.json ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ {
2
+ "_from_model_config": true,
3
+ "pad_token_id": 0,
4
+ "transformers_version": "4.44.2"
5
+ }
Geneformer-V2-104M/model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:fff5cba29ddd8792991fa77b4872246fbe548a178cebda3775cdc72b67780e7f
3
+ size 417571156
Geneformer-V2-104M/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0d8ddd9e4f35b5fe23a3adaae03aa4480705ca82eed546a488f970adb3752d9d
3
+ size 5496
Geneformer-V2-104M_CLcancer/config.json ADDED
@@ -0,0 +1,25 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "_name_or_path": "/gladstone/theodoris/lab/ctheodoris/gf-104m/models/241127_143148_geneformer_94M_L12_emb768_SL4096_E3_B18_LR0.0002_LScosine_WR0.007_Oadamw_DS13/models",
3
+ "architectures": [
4
+ "BertForMaskedLM"
5
+ ],
6
+ "attention_probs_dropout_prob": 0.1,
7
+ "classifier_dropout": null,
8
+ "hidden_act": "relu",
9
+ "hidden_dropout_prob": 0.1,
10
+ "hidden_size": 768,
11
+ "initializer_range": 0.02,
12
+ "intermediate_size": 3072,
13
+ "layer_norm_eps": 1e-12,
14
+ "max_position_embeddings": 4096,
15
+ "model_type": "bert",
16
+ "num_attention_heads": 12,
17
+ "num_hidden_layers": 12,
18
+ "pad_token_id": 0,
19
+ "position_embedding_type": "absolute",
20
+ "torch_dtype": "float32",
21
+ "transformers_version": "4.37.1",
22
+ "type_vocab_size": 2,
23
+ "use_cache": true,
24
+ "vocab_size": 20275
25
+ }
Geneformer-V2-104M_CLcancer/generation_config.json ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ {
2
+ "_from_model_config": true,
3
+ "pad_token_id": 0,
4
+ "transformers_version": "4.37.1"
5
+ }
Geneformer-V2-104M_CLcancer/model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:827738139bfed4bafa9d1f3df7c6146da2e3b85f7225076adc32c6eda0ba4357
3
+ size 417571156
Geneformer-V2-104M_CLcancer/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8cf8ce52b498253adc6df53197a99821fa145c19b8ae5eeb8d15be76b8b7ddb3
3
+ size 4984
Geneformer-V2-316M/config.json ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "architectures": [
3
+ "BertForMaskedLM"
4
+ ],
5
+ "attention_probs_dropout_prob": 0.1,
6
+ "classifier_dropout": null,
7
+ "hidden_act": "relu",
8
+ "hidden_dropout_prob": 0.1,
9
+ "hidden_size": 1152,
10
+ "initializer_range": 0.02,
11
+ "intermediate_size": 4608,
12
+ "layer_norm_eps": 1e-12,
13
+ "max_position_embeddings": 4096,
14
+ "model_type": "bert",
15
+ "num_attention_heads": 18,
16
+ "num_hidden_layers": 18,
17
+ "pad_token_id": 0,
18
+ "position_embedding_type": "absolute",
19
+ "torch_dtype": "float32",
20
+ "transformers_version": "4.44.2",
21
+ "type_vocab_size": 2,
22
+ "use_cache": true,
23
+ "vocab_size": 20275
24
+ }
Geneformer-V2-316M/generation_config.json ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ {
2
+ "_from_model_config": true,
3
+ "pad_token_id": 0,
4
+ "transformers_version": "4.44.2"
5
+ }
Geneformer-V2-316M/model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:965ceccea81953d362081ef3843560a0e4fef88d396c28017881f1e94b1246f3
3
+ size 1265455076
Geneformer-V2-316M/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e45150f9a4ca34cb4e91ce79f65f3d99d9d66df9f66a37517a352d291008e0b8
3
+ size 5432
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/config.json ADDED
@@ -0,0 +1,35 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "_name_or_path": "/n/home01/ctheodoris/models/210602_111318_geneformer_27M_L6_emb256_SL2048_E3_B12_LR0.001_LSlinear_WU10000_Oadamw_DS12/models/",
3
+ "architectures": [
4
+ "BertForSequenceClassification"
5
+ ],
6
+ "attention_probs_dropout_prob": 0.02,
7
+ "gradient_checkpointing": false,
8
+ "hidden_act": "relu",
9
+ "hidden_dropout_prob": 0.02,
10
+ "hidden_size": 256,
11
+ "id2label": {
12
+ "0": "LABEL_0",
13
+ "1": "LABEL_1",
14
+ "2": "LABEL_2"
15
+ },
16
+ "initializer_range": 0.02,
17
+ "intermediate_size": 512,
18
+ "label2id": {
19
+ "LABEL_0": 0,
20
+ "LABEL_1": 1,
21
+ "LABEL_2": 2
22
+ },
23
+ "layer_norm_eps": 1e-12,
24
+ "max_position_embeddings": 2048,
25
+ "model_type": "bert",
26
+ "num_attention_heads": 4,
27
+ "num_hidden_layers": 6,
28
+ "pad_token_id": 0,
29
+ "position_embedding_type": "absolute",
30
+ "problem_type": "single_label_classification",
31
+ "transformers_version": "4.6.0",
32
+ "type_vocab_size": 2,
33
+ "use_cache": true,
34
+ "vocab_size": 25426
35
+ }
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/optimizer.pt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3ced328122d57a847fc3914732337674500e259a82e64437c67b4954ac2f4e07
3
+ size 73720721
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/pytorch_model.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:12ead3bad8cf4b853bac87eadeb79c9308ae492e9d29f32da1a2c85e8586108d
3
+ size 41115113
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/rng_state.pth ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:dd8c0a739c2fe6a9ab4bb8f4a62ad8d7b879efcdceb5376b128a2040ff1bbe62
3
+ size 14657
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/scheduler.pt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3d0797845afdae765a74ddab7966e0e1837617fd8171af8ee6aef9dedce248f2
3
+ size 623
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/trainer_state.json ADDED
@@ -0,0 +1,150 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "best_metric": 0.39658036828041077,
3
+ "best_model_checkpoint": "/n/holyscratch01/xiaoleliu_lab/Users/ctheodoris/models/220224_geneformer_27M_SequenceClassifier_tuning_hCMdCM_L2048_B12_LR1e-05_LScosine_WU500_E1_Oadamw_F2/run-8429a330/checkpoint-7020",
4
+ "epoch": 0.9,
5
+ "global_step": 7020,
6
+ "is_hyper_param_search": true,
7
+ "is_local_process_zero": true,
8
+ "is_world_process_zero": true,
9
+ "log_history": [
10
+ {
11
+ "epoch": 0.1,
12
+ "learning_rate": 0.00034606438343856935,
13
+ "loss": 0.911,
14
+ "step": 780
15
+ },
16
+ {
17
+ "epoch": 0.1,
18
+ "eval_accuracy": 0.4531576503366612,
19
+ "eval_loss": 1.4550466537475586,
20
+ "eval_runtime": 66.5164,
21
+ "eval_samples_per_second": 259.004,
22
+ "step": 780
23
+ },
24
+ {
25
+ "epoch": 0.2,
26
+ "learning_rate": 0.0006921287668771387,
27
+ "loss": 0.6273,
28
+ "step": 1560
29
+ },
30
+ {
31
+ "epoch": 0.2,
32
+ "eval_accuracy": 0.5953680055723242,
33
+ "eval_loss": 0.846651554107666,
34
+ "eval_runtime": 66.1267,
35
+ "eval_samples_per_second": 260.53,
36
+ "step": 1560
37
+ },
38
+ {
39
+ "epoch": 0.3,
40
+ "learning_rate": 0.0007330550166223805,
41
+ "loss": 0.5592,
42
+ "step": 2340
43
+ },
44
+ {
45
+ "epoch": 0.3,
46
+ "eval_accuracy": 0.5935105641978176,
47
+ "eval_loss": 1.0599186420440674,
48
+ "eval_runtime": 66.2608,
49
+ "eval_samples_per_second": 260.003,
50
+ "step": 2340
51
+ },
52
+ {
53
+ "epoch": 0.4,
54
+ "learning_rate": 0.0006283471571048975,
55
+ "loss": 0.3714,
56
+ "step": 3120
57
+ },
58
+ {
59
+ "epoch": 0.4,
60
+ "eval_accuracy": 0.686324587880195,
61
+ "eval_loss": 1.184874415397644,
62
+ "eval_runtime": 66.1411,
63
+ "eval_samples_per_second": 260.473,
64
+ "step": 3120
65
+ },
66
+ {
67
+ "epoch": 0.5,
68
+ "learning_rate": 0.0005236392975874146,
69
+ "loss": 0.2976,
70
+ "step": 3900
71
+ },
72
+ {
73
+ "epoch": 0.5,
74
+ "eval_accuracy": 0.7681100534014396,
75
+ "eval_loss": 0.6318939328193665,
76
+ "eval_runtime": 66.3309,
77
+ "eval_samples_per_second": 259.728,
78
+ "step": 3900
79
+ },
80
+ {
81
+ "epoch": 0.6,
82
+ "learning_rate": 0.0004189314380699318,
83
+ "loss": 0.2564,
84
+ "step": 4680
85
+ },
86
+ {
87
+ "epoch": 0.6,
88
+ "eval_accuracy": 0.7807058277223126,
89
+ "eval_loss": 0.7283642888069153,
90
+ "eval_runtime": 66.3416,
91
+ "eval_samples_per_second": 259.686,
92
+ "step": 4680
93
+ },
94
+ {
95
+ "epoch": 0.7,
96
+ "learning_rate": 0.0003142235785524487,
97
+ "loss": 0.2336,
98
+ "step": 5460
99
+ },
100
+ {
101
+ "epoch": 0.7,
102
+ "eval_accuracy": 0.8563965637334572,
103
+ "eval_loss": 0.5184123516082764,
104
+ "eval_runtime": 66.3416,
105
+ "eval_samples_per_second": 259.686,
106
+ "step": 5460
107
+ },
108
+ {
109
+ "epoch": 0.8,
110
+ "learning_rate": 0.0002095157190349659,
111
+ "loss": 0.1731,
112
+ "step": 6240
113
+ },
114
+ {
115
+ "epoch": 0.8,
116
+ "eval_accuracy": 0.8288832133735778,
117
+ "eval_loss": 0.5823884010314941,
118
+ "eval_runtime": 66.1535,
119
+ "eval_samples_per_second": 260.425,
120
+ "step": 6240
121
+ },
122
+ {
123
+ "epoch": 0.9,
124
+ "learning_rate": 0.00010480785951748295,
125
+ "loss": 0.1451,
126
+ "step": 7020
127
+ },
128
+ {
129
+ "epoch": 0.9,
130
+ "eval_accuracy": 0.886812166241003,
131
+ "eval_loss": 0.39658036828041077,
132
+ "eval_runtime": 66.3555,
133
+ "eval_samples_per_second": 259.632,
134
+ "step": 7020
135
+ }
136
+ ],
137
+ "max_steps": 7800,
138
+ "num_train_epochs": 1,
139
+ "total_flos": 0,
140
+ "trial_name": null,
141
+ "trial_params": {
142
+ "learning_rate": 0.0008039341830649843,
143
+ "lr_scheduler_type": "polynomial",
144
+ "num_train_epochs": 1,
145
+ "per_device_train_batch_size": 12,
146
+ "seed": 73.15243080311434,
147
+ "warmup_steps": 1812.6785581609881,
148
+ "weight_decay": 0.2588277764570262
149
+ }
150
+ }
fine_tuned_models/Geneformer-V1-10M_CellClassifier_cardiomyopathies_220224/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4ffee119596c99b50a422b2f80103f4c44f7e25c2ea0e457fe224bad59f1f955
3
+ size 2607
geneformer/ensembl_mapping_dict_gc104M.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0819bcbd869cfa14279449b037eb9ed1d09a91310e77bd1a19d927465030e95c
3
+ size 3957652
geneformer/gene_median_dictionary_gc104M.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a51c53f6a771d64508dfaf61529df70e394c53bd20856926117ae5d641a24bf5
3
+ size 1512661
geneformer/gene_name_id_dict_gc104M.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:fabfa0c2f49c598c59ae432a32c3499a5908c033756c663b5e0cddf58deea8e1
3
+ size 1660882
geneformer/token_dictionary_gc104M.pkl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:67c445f4385127adfc48dcc072320cd65d6822829bf27dd38070e6e787bc597f
3
+ size 425590