Add files using upload-large-folder tool
Browse files- training_checkpoints/checkpoint-10000/scheduler.pt +3 -0
- training_checkpoints/checkpoint-10000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-10000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-10000/vocab.json +78 -0
- training_checkpoints/checkpoint-15000/scheduler.pt +3 -0
- training_checkpoints/checkpoint-15000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-15000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-15000/vocab.json +78 -0
- training_checkpoints/checkpoint-20000/scheduler.pt +3 -0
- training_checkpoints/checkpoint-20000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-20000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-20000/vocab.json +78 -0
- training_checkpoints/checkpoint-25000/scheduler.pt +3 -0
- training_checkpoints/checkpoint-25000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-25000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-25000/vocab.json +78 -0
- training_checkpoints/checkpoint-30000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-30000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-30000/vocab.json +78 -0
- training_checkpoints/checkpoint-35000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-35000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-35000/vocab.json +78 -0
- training_checkpoints/checkpoint-40000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-40000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-40000/vocab.json +78 -0
- training_checkpoints/checkpoint-45000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-45000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-45000/vocab.json +78 -0
- training_checkpoints/checkpoint-5000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-5000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-5000/vocab.json +78 -0
- training_checkpoints/checkpoint-50000/optimizer.pt +3 -0
- training_checkpoints/checkpoint-50000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-50000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-50000/vocab.json +78 -0
- training_checkpoints/checkpoint-55000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-55000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-55000/vocab.json +78 -0
- training_checkpoints/checkpoint-60000/optimizer.pt +3 -0
- training_checkpoints/checkpoint-60000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-60000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-60000/vocab.json +78 -0
- training_checkpoints/checkpoint-65000/optimizer.pt +3 -0
- training_checkpoints/checkpoint-65000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-65000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-65000/vocab.json +78 -0
- training_checkpoints/checkpoint-70000/optimizer.pt +3 -0
- training_checkpoints/checkpoint-70000/trainer_config.json +17 -0
- training_checkpoints/checkpoint-70000/trainer_state.json +4 -0
- training_checkpoints/checkpoint-70000/vocab.json +78 -0
training_checkpoints/checkpoint-10000/scheduler.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c5823671ed3b2bc675facedd77f22ad8483ff92e91fd3c718219687507cdf4c0
|
| 3 |
+
size 1465
|
training_checkpoints/checkpoint-10000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-10000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 0,
|
| 3 |
+
"global_step": 10000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-10000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-15000/scheduler.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:0de62c70093d4935c1964c4ad211b0aebc926c8bd2f29cc09e917906ecba7f53
|
| 3 |
+
size 1465
|
training_checkpoints/checkpoint-15000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-15000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 0,
|
| 3 |
+
"global_step": 15000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-15000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-20000/scheduler.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:477c0b4b118e155de3b3e6948133bdde7b504978d0ea45ddea8c8b2bd9db684c
|
| 3 |
+
size 1465
|
training_checkpoints/checkpoint-20000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-20000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 0,
|
| 3 |
+
"global_step": 20000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-20000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-25000/scheduler.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b72fbb8e4f4f60881f28c8afc2275790fe5cc94af4898d509e453957929b4cce
|
| 3 |
+
size 1465
|
training_checkpoints/checkpoint-25000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-25000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 1,
|
| 3 |
+
"global_step": 25000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-25000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-30000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-30000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 1,
|
| 3 |
+
"global_step": 30000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-30000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-35000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-35000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 1,
|
| 3 |
+
"global_step": 35000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-35000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-40000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-40000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 1,
|
| 3 |
+
"global_step": 40000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-40000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-45000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-45000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 1,
|
| 3 |
+
"global_step": 45000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-45000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-5000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-5000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 0,
|
| 3 |
+
"global_step": 5000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-5000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-50000/optimizer.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4713f6f2b96b5c1835d83677851797d82a59fe15b7654bd70b106e73c105e3bb
|
| 3 |
+
size 1237115851
|
training_checkpoints/checkpoint-50000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-50000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 2,
|
| 3 |
+
"global_step": 50000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-50000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-55000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-55000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 2,
|
| 3 |
+
"global_step": 55000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-55000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-60000/optimizer.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:255c4293630a42d81f4921a32d3c042ba93b1f54afa52b942acfe9f988c8ff1c
|
| 3 |
+
size 1237115851
|
training_checkpoints/checkpoint-60000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-60000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 2,
|
| 3 |
+
"global_step": 60000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-60000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-65000/optimizer.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b2049a6b4d0270b1d72cce3973bd6940697cc3e95ef3e0dc922eeaae2e36cbcc
|
| 3 |
+
size 1237115851
|
training_checkpoints/checkpoint-65000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-65000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 2,
|
| 3 |
+
"global_step": 65000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-65000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|
training_checkpoints/checkpoint-70000/optimizer.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e0c4d54ea41cabec318a0452f21880c6e655b814aaccaa5fd7d4a5e756012c71
|
| 3 |
+
size 1237115851
|
training_checkpoints/checkpoint-70000/trainer_config.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"max_length": 2048,
|
| 3 |
+
"max_species_prefix": 0,
|
| 4 |
+
"max_protein_prefix": 1024,
|
| 5 |
+
"hidden_size": 750,
|
| 6 |
+
"num_hidden_layers": 20,
|
| 7 |
+
"num_attention_heads": 15,
|
| 8 |
+
"mlp_ratio": 3.2,
|
| 9 |
+
"prepend_species": true,
|
| 10 |
+
"prepend_protein": true,
|
| 11 |
+
"species_embedding_dim": 1024,
|
| 12 |
+
"esm_model_name": "esmc_300m",
|
| 13 |
+
"esm_device": "cuda:0",
|
| 14 |
+
"esm_dtype": "bf16",
|
| 15 |
+
"attn_impl": "mha",
|
| 16 |
+
"num_kv_groups": 5
|
| 17 |
+
}
|
training_checkpoints/checkpoint-70000/trainer_state.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"epoch": 2,
|
| 3 |
+
"global_step": 70000
|
| 4 |
+
}
|
training_checkpoints/checkpoint-70000/vocab.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"special_token_str": {
|
| 3 |
+
"bos": "<bos>",
|
| 4 |
+
"eos": "<stop>",
|
| 5 |
+
"pad": "<pad>",
|
| 6 |
+
"unk": "<unk>"
|
| 7 |
+
},
|
| 8 |
+
"vocab": {
|
| 9 |
+
"<bos>": 2,
|
| 10 |
+
"<pad>": 0,
|
| 11 |
+
"<stop>": 3,
|
| 12 |
+
"<unk>": 1,
|
| 13 |
+
"AAA": 4,
|
| 14 |
+
"AAC": 5,
|
| 15 |
+
"AAG": 6,
|
| 16 |
+
"AAT": 7,
|
| 17 |
+
"ACA": 8,
|
| 18 |
+
"ACC": 9,
|
| 19 |
+
"ACG": 10,
|
| 20 |
+
"ACT": 11,
|
| 21 |
+
"AGA": 12,
|
| 22 |
+
"AGC": 13,
|
| 23 |
+
"AGG": 14,
|
| 24 |
+
"AGT": 15,
|
| 25 |
+
"ATA": 16,
|
| 26 |
+
"ATC": 17,
|
| 27 |
+
"ATG": 18,
|
| 28 |
+
"ATT": 19,
|
| 29 |
+
"CAA": 20,
|
| 30 |
+
"CAC": 21,
|
| 31 |
+
"CAG": 22,
|
| 32 |
+
"CAT": 23,
|
| 33 |
+
"CCA": 24,
|
| 34 |
+
"CCC": 25,
|
| 35 |
+
"CCG": 26,
|
| 36 |
+
"CCT": 27,
|
| 37 |
+
"CGA": 28,
|
| 38 |
+
"CGC": 29,
|
| 39 |
+
"CGG": 30,
|
| 40 |
+
"CGT": 31,
|
| 41 |
+
"CTA": 32,
|
| 42 |
+
"CTC": 33,
|
| 43 |
+
"CTG": 34,
|
| 44 |
+
"CTT": 35,
|
| 45 |
+
"GAA": 36,
|
| 46 |
+
"GAC": 37,
|
| 47 |
+
"GAG": 38,
|
| 48 |
+
"GAT": 39,
|
| 49 |
+
"GCA": 40,
|
| 50 |
+
"GCC": 41,
|
| 51 |
+
"GCG": 42,
|
| 52 |
+
"GCT": 43,
|
| 53 |
+
"GGA": 44,
|
| 54 |
+
"GGC": 45,
|
| 55 |
+
"GGG": 46,
|
| 56 |
+
"GGT": 47,
|
| 57 |
+
"GTA": 48,
|
| 58 |
+
"GTC": 49,
|
| 59 |
+
"GTG": 50,
|
| 60 |
+
"GTT": 51,
|
| 61 |
+
"TAA": 52,
|
| 62 |
+
"TAC": 53,
|
| 63 |
+
"TAG": 54,
|
| 64 |
+
"TAT": 55,
|
| 65 |
+
"TCA": 56,
|
| 66 |
+
"TCC": 57,
|
| 67 |
+
"TCG": 58,
|
| 68 |
+
"TCT": 59,
|
| 69 |
+
"TGA": 60,
|
| 70 |
+
"TGC": 61,
|
| 71 |
+
"TGG": 62,
|
| 72 |
+
"TGT": 63,
|
| 73 |
+
"TTA": 64,
|
| 74 |
+
"TTC": 65,
|
| 75 |
+
"TTG": 66,
|
| 76 |
+
"TTT": 67
|
| 77 |
+
}
|
| 78 |
+
}
|