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Browse files- .gitattributes +2 -0
- .gitignore +1 -0
- emb_cache/molecule_knn_tanimoto_k256.pt +3 -0
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- repro_ft_v1_e5_freezemol_20260105_100642/loss.json +1 -0
- repro_ft_v1_e5_freezemol_20260105_100642/projection.pt +3 -0
- repro_ft_v1_e5_freezemol_20260105_100642/protein_model/config.json +29 -0
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- repro_ft_v1_e5_freezemol_20260105_100642/protein_model/tokenizer_config.json +53 -0
- repro_ft_v1_e5_freezemol_20260105_100642/protein_model/vocab.txt +446 -0
- repro_ft_v1_e5_freezemol_20260105_100642/train_args.json +45 -0
- repro_ft_v2_e5cont_freezemol_20260105_100642/loss.json +1 -0
- repro_ft_v2_e5cont_freezemol_20260105_100642/projection.pt +3 -0
- repro_ft_v2_e5cont_freezemol_20260105_100642/protein_model/config.json +29 -0
- repro_ft_v2_e5cont_freezemol_20260105_100642/protein_model/model.safetensors +3 -0
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- repro_ft_v2_e5cont_freezemol_20260105_100642/train_args.json +45 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/loss.json +1 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/projection.pt +3 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/config.json +29 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/model.safetensors +3 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/special_tokens_map.json +37 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/tokenizer_config.json +53 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/vocab.txt +446 -0
- repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/train_args.json +45 -0
- repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/loss.json +0 -0
- repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/projection.pt +3 -0
- repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/projection_last.pt +3 -0
- repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/train_args.json +54 -0
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repro_ft_v1_e5_freezemol_20260105_100642/projection.pt
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repro_ft_v1_e5_freezemol_20260105_100642/protein_model/config.json
ADDED
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repro_ft_v1_e5_freezemol_20260105_100642/protein_model/model.safetensors
ADDED
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repro_ft_v1_e5_freezemol_20260105_100642/protein_model/special_tokens_map.json
ADDED
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repro_ft_v1_e5_freezemol_20260105_100642/protein_model/tokenizer_config.json
ADDED
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repro_ft_v1_e5_freezemol_20260105_100642/protein_model/vocab.txt
ADDED
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|
| 1 |
+
<cls>
|
| 2 |
+
<pad>
|
| 3 |
+
<eos>
|
| 4 |
+
<unk>
|
| 5 |
+
<mask>
|
| 6 |
+
Ap
|
| 7 |
+
Ay
|
| 8 |
+
An
|
| 9 |
+
Aw
|
| 10 |
+
Ar
|
| 11 |
+
Aq
|
| 12 |
+
Ah
|
| 13 |
+
Ag
|
| 14 |
+
Ad
|
| 15 |
+
Al
|
| 16 |
+
Av
|
| 17 |
+
At
|
| 18 |
+
Am
|
| 19 |
+
Af
|
| 20 |
+
As
|
| 21 |
+
Aa
|
| 22 |
+
Ae
|
| 23 |
+
Ai
|
| 24 |
+
Ak
|
| 25 |
+
Ac
|
| 26 |
+
A#
|
| 27 |
+
Cp
|
| 28 |
+
Cy
|
| 29 |
+
Cn
|
| 30 |
+
Cw
|
| 31 |
+
Cr
|
| 32 |
+
Cq
|
| 33 |
+
Ch
|
| 34 |
+
Cg
|
| 35 |
+
Cd
|
| 36 |
+
Cl
|
| 37 |
+
Cv
|
| 38 |
+
Ct
|
| 39 |
+
Cm
|
| 40 |
+
Cf
|
| 41 |
+
Cs
|
| 42 |
+
Ca
|
| 43 |
+
Ce
|
| 44 |
+
Ci
|
| 45 |
+
Ck
|
| 46 |
+
Cc
|
| 47 |
+
C#
|
| 48 |
+
Dp
|
| 49 |
+
Dy
|
| 50 |
+
Dn
|
| 51 |
+
Dw
|
| 52 |
+
Dr
|
| 53 |
+
Dq
|
| 54 |
+
Dh
|
| 55 |
+
Dg
|
| 56 |
+
Dd
|
| 57 |
+
Dl
|
| 58 |
+
Dv
|
| 59 |
+
Dt
|
| 60 |
+
Dm
|
| 61 |
+
Df
|
| 62 |
+
Ds
|
| 63 |
+
Da
|
| 64 |
+
De
|
| 65 |
+
Di
|
| 66 |
+
Dk
|
| 67 |
+
Dc
|
| 68 |
+
D#
|
| 69 |
+
Ep
|
| 70 |
+
Ey
|
| 71 |
+
En
|
| 72 |
+
Ew
|
| 73 |
+
Er
|
| 74 |
+
Eq
|
| 75 |
+
Eh
|
| 76 |
+
Eg
|
| 77 |
+
Ed
|
| 78 |
+
El
|
| 79 |
+
Ev
|
| 80 |
+
Et
|
| 81 |
+
Em
|
| 82 |
+
Ef
|
| 83 |
+
Es
|
| 84 |
+
Ea
|
| 85 |
+
Ee
|
| 86 |
+
Ei
|
| 87 |
+
Ek
|
| 88 |
+
Ec
|
| 89 |
+
E#
|
| 90 |
+
Fp
|
| 91 |
+
Fy
|
| 92 |
+
Fn
|
| 93 |
+
Fw
|
| 94 |
+
Fr
|
| 95 |
+
Fq
|
| 96 |
+
Fh
|
| 97 |
+
Fg
|
| 98 |
+
Fd
|
| 99 |
+
Fl
|
| 100 |
+
Fv
|
| 101 |
+
Ft
|
| 102 |
+
Fm
|
| 103 |
+
Ff
|
| 104 |
+
Fs
|
| 105 |
+
Fa
|
| 106 |
+
Fe
|
| 107 |
+
Fi
|
| 108 |
+
Fk
|
| 109 |
+
Fc
|
| 110 |
+
F#
|
| 111 |
+
Gp
|
| 112 |
+
Gy
|
| 113 |
+
Gn
|
| 114 |
+
Gw
|
| 115 |
+
Gr
|
| 116 |
+
Gq
|
| 117 |
+
Gh
|
| 118 |
+
Gg
|
| 119 |
+
Gd
|
| 120 |
+
Gl
|
| 121 |
+
Gv
|
| 122 |
+
Gt
|
| 123 |
+
Gm
|
| 124 |
+
Gf
|
| 125 |
+
Gs
|
| 126 |
+
Ga
|
| 127 |
+
Ge
|
| 128 |
+
Gi
|
| 129 |
+
Gk
|
| 130 |
+
Gc
|
| 131 |
+
G#
|
| 132 |
+
Hp
|
| 133 |
+
Hy
|
| 134 |
+
Hn
|
| 135 |
+
Hw
|
| 136 |
+
Hr
|
| 137 |
+
Hq
|
| 138 |
+
Hh
|
| 139 |
+
Hg
|
| 140 |
+
Hd
|
| 141 |
+
Hl
|
| 142 |
+
Hv
|
| 143 |
+
Ht
|
| 144 |
+
Hm
|
| 145 |
+
Hf
|
| 146 |
+
Hs
|
| 147 |
+
Ha
|
| 148 |
+
He
|
| 149 |
+
Hi
|
| 150 |
+
Hk
|
| 151 |
+
Hc
|
| 152 |
+
H#
|
| 153 |
+
Ip
|
| 154 |
+
Iy
|
| 155 |
+
In
|
| 156 |
+
Iw
|
| 157 |
+
Ir
|
| 158 |
+
Iq
|
| 159 |
+
Ih
|
| 160 |
+
Ig
|
| 161 |
+
Id
|
| 162 |
+
Il
|
| 163 |
+
Iv
|
| 164 |
+
It
|
| 165 |
+
Im
|
| 166 |
+
If
|
| 167 |
+
Is
|
| 168 |
+
Ia
|
| 169 |
+
Ie
|
| 170 |
+
Ii
|
| 171 |
+
Ik
|
| 172 |
+
Ic
|
| 173 |
+
I#
|
| 174 |
+
Kp
|
| 175 |
+
Ky
|
| 176 |
+
Kn
|
| 177 |
+
Kw
|
| 178 |
+
Kr
|
| 179 |
+
Kq
|
| 180 |
+
Kh
|
| 181 |
+
Kg
|
| 182 |
+
Kd
|
| 183 |
+
Kl
|
| 184 |
+
Kv
|
| 185 |
+
Kt
|
| 186 |
+
Km
|
| 187 |
+
Kf
|
| 188 |
+
Ks
|
| 189 |
+
Ka
|
| 190 |
+
Ke
|
| 191 |
+
Ki
|
| 192 |
+
Kk
|
| 193 |
+
Kc
|
| 194 |
+
K#
|
| 195 |
+
Lp
|
| 196 |
+
Ly
|
| 197 |
+
Ln
|
| 198 |
+
Lw
|
| 199 |
+
Lr
|
| 200 |
+
Lq
|
| 201 |
+
Lh
|
| 202 |
+
Lg
|
| 203 |
+
Ld
|
| 204 |
+
Ll
|
| 205 |
+
Lv
|
| 206 |
+
Lt
|
| 207 |
+
Lm
|
| 208 |
+
Lf
|
| 209 |
+
Ls
|
| 210 |
+
La
|
| 211 |
+
Le
|
| 212 |
+
Li
|
| 213 |
+
Lk
|
| 214 |
+
Lc
|
| 215 |
+
L#
|
| 216 |
+
Mp
|
| 217 |
+
My
|
| 218 |
+
Mn
|
| 219 |
+
Mw
|
| 220 |
+
Mr
|
| 221 |
+
Mq
|
| 222 |
+
Mh
|
| 223 |
+
Mg
|
| 224 |
+
Md
|
| 225 |
+
Ml
|
| 226 |
+
Mv
|
| 227 |
+
Mt
|
| 228 |
+
Mm
|
| 229 |
+
Mf
|
| 230 |
+
Ms
|
| 231 |
+
Ma
|
| 232 |
+
Me
|
| 233 |
+
Mi
|
| 234 |
+
Mk
|
| 235 |
+
Mc
|
| 236 |
+
M#
|
| 237 |
+
Np
|
| 238 |
+
Ny
|
| 239 |
+
Nn
|
| 240 |
+
Nw
|
| 241 |
+
Nr
|
| 242 |
+
Nq
|
| 243 |
+
Nh
|
| 244 |
+
Ng
|
| 245 |
+
Nd
|
| 246 |
+
Nl
|
| 247 |
+
Nv
|
| 248 |
+
Nt
|
| 249 |
+
Nm
|
| 250 |
+
Nf
|
| 251 |
+
Ns
|
| 252 |
+
Na
|
| 253 |
+
Ne
|
| 254 |
+
Ni
|
| 255 |
+
Nk
|
| 256 |
+
Nc
|
| 257 |
+
N#
|
| 258 |
+
Pp
|
| 259 |
+
Py
|
| 260 |
+
Pn
|
| 261 |
+
Pw
|
| 262 |
+
Pr
|
| 263 |
+
Pq
|
| 264 |
+
Ph
|
| 265 |
+
Pg
|
| 266 |
+
Pd
|
| 267 |
+
Pl
|
| 268 |
+
Pv
|
| 269 |
+
Pt
|
| 270 |
+
Pm
|
| 271 |
+
Pf
|
| 272 |
+
Ps
|
| 273 |
+
Pa
|
| 274 |
+
Pe
|
| 275 |
+
Pi
|
| 276 |
+
Pk
|
| 277 |
+
Pc
|
| 278 |
+
P#
|
| 279 |
+
Qp
|
| 280 |
+
Qy
|
| 281 |
+
Qn
|
| 282 |
+
Qw
|
| 283 |
+
Qr
|
| 284 |
+
Qq
|
| 285 |
+
Qh
|
| 286 |
+
Qg
|
| 287 |
+
Qd
|
| 288 |
+
Ql
|
| 289 |
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|
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|
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#c
|
| 446 |
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##
|
repro_ft_v1_e5_freezemol_20260105_100642/train_args.json
ADDED
|
@@ -0,0 +1,45 @@
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|
|
|
|
| 1 |
+
{
|
| 2 |
+
"interactions": "dataset/drug-target-activity/processed/interactions.parquet",
|
| 3 |
+
"protein_cache": "dataset/protein_sequences/saprot_combined_sequences_esmfold_nomask_cache.jsonl",
|
| 4 |
+
"split": "cold_drug",
|
| 5 |
+
"seed": 42,
|
| 6 |
+
"test_ratio": 0.2,
|
| 7 |
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"val_ratio": 0.1,
|
| 8 |
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"epochs": 5,
|
| 9 |
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"protein_per_step": 1,
|
| 10 |
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"lr_proj": 0.0001,
|
| 11 |
+
"lr_protein": 1e-06,
|
| 12 |
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"weight_decay": 0.001,
|
| 13 |
+
"warmup_steps": 50,
|
| 14 |
+
"log_interval": 50,
|
| 15 |
+
"temperature": 0.07,
|
| 16 |
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"max_logit_scale": 100.0,
|
| 17 |
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"projection_dim": 512,
|
| 18 |
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"protein_proj_hidden_dim": 0,
|
| 19 |
+
"molecule_proj_hidden_dim": 0,
|
| 20 |
+
"dropout": 0.2,
|
| 21 |
+
"hardneg_source": "none",
|
| 22 |
+
"hardneg_knn": "models/emb_cache/molecule_knn_tanimoto_k256.pt",
|
| 23 |
+
"hardneg_k": 0,
|
| 24 |
+
"hardneg_weight": 0.0,
|
| 25 |
+
"pos_weighting": "confidence",
|
| 26 |
+
"pxc50_threshold": 6.0,
|
| 27 |
+
"pxc50_std_threshold": 1.0,
|
| 28 |
+
"obs_threshold": 10.0,
|
| 29 |
+
"obs_std_threshold": 20.0,
|
| 30 |
+
"conflict_penalty": 0.5,
|
| 31 |
+
"severe_conflict_penalty": 0.2,
|
| 32 |
+
"weight_min": 0.2,
|
| 33 |
+
"weight_max": 1.0,
|
| 34 |
+
"protein_model": "westlake-repl/SaProt_1.3B_AF2",
|
| 35 |
+
"molecule_raw_cache": "models/emb_cache/raw_embeddings_saprot1p3b_struct_nomask_smiles20.pt",
|
| 36 |
+
"freeze_molecule_proj": true,
|
| 37 |
+
"init_projection": "models/repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/projection.pt",
|
| 38 |
+
"mixed_precision": "bf16",
|
| 39 |
+
"load_dtype": "bf16",
|
| 40 |
+
"gradient_checkpointing": true,
|
| 41 |
+
"max_grad_norm": 1.0,
|
| 42 |
+
"protein_max_length": 1024,
|
| 43 |
+
"device": "cuda",
|
| 44 |
+
"output_dir": "models/repro_ft_v1_e5_freezemol_20260105_100642"
|
| 45 |
+
}
|
repro_ft_v2_e5cont_freezemol_20260105_100642/loss.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
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| 26 |
+
"normalized": false,
|
| 27 |
+
"rstrip": false,
|
| 28 |
+
"single_word": false
|
| 29 |
+
},
|
| 30 |
+
"unk_token": {
|
| 31 |
+
"content": "<unk>",
|
| 32 |
+
"lstrip": false,
|
| 33 |
+
"normalized": false,
|
| 34 |
+
"rstrip": false,
|
| 35 |
+
"single_word": false
|
| 36 |
+
}
|
| 37 |
+
}
|
repro_ft_v2_e5cont_freezemol_20260105_100642/protein_model/tokenizer_config.json
ADDED
|
@@ -0,0 +1,53 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"added_tokens_decoder": {
|
| 3 |
+
"0": {
|
| 4 |
+
"content": "<cls>",
|
| 5 |
+
"lstrip": false,
|
| 6 |
+
"normalized": false,
|
| 7 |
+
"rstrip": false,
|
| 8 |
+
"single_word": false,
|
| 9 |
+
"special": true
|
| 10 |
+
},
|
| 11 |
+
"1": {
|
| 12 |
+
"content": "<pad>",
|
| 13 |
+
"lstrip": false,
|
| 14 |
+
"normalized": false,
|
| 15 |
+
"rstrip": false,
|
| 16 |
+
"single_word": false,
|
| 17 |
+
"special": true
|
| 18 |
+
},
|
| 19 |
+
"2": {
|
| 20 |
+
"content": "<eos>",
|
| 21 |
+
"lstrip": false,
|
| 22 |
+
"normalized": false,
|
| 23 |
+
"rstrip": false,
|
| 24 |
+
"single_word": false,
|
| 25 |
+
"special": true
|
| 26 |
+
},
|
| 27 |
+
"3": {
|
| 28 |
+
"content": "<unk>",
|
| 29 |
+
"lstrip": false,
|
| 30 |
+
"normalized": false,
|
| 31 |
+
"rstrip": false,
|
| 32 |
+
"single_word": false,
|
| 33 |
+
"special": true
|
| 34 |
+
},
|
| 35 |
+
"4": {
|
| 36 |
+
"content": "<mask>",
|
| 37 |
+
"lstrip": false,
|
| 38 |
+
"normalized": false,
|
| 39 |
+
"rstrip": false,
|
| 40 |
+
"single_word": false,
|
| 41 |
+
"special": true
|
| 42 |
+
}
|
| 43 |
+
},
|
| 44 |
+
"clean_up_tokenization_spaces": true,
|
| 45 |
+
"cls_token": "<cls>",
|
| 46 |
+
"eos_token": "<eos>",
|
| 47 |
+
"extra_special_tokens": {},
|
| 48 |
+
"mask_token": "<mask>",
|
| 49 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 50 |
+
"pad_token": "<pad>",
|
| 51 |
+
"tokenizer_class": "EsmTokenizer",
|
| 52 |
+
"unk_token": "<unk>"
|
| 53 |
+
}
|
repro_ft_v2_e5cont_freezemol_20260105_100642/protein_model/vocab.txt
ADDED
|
@@ -0,0 +1,446 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
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|
|
|
|
|
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|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
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|
|
|
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|
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|
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|
|
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|
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|
|
|
|
|
|
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|
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|
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|
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|
|
|
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|
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|
|
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|
|
|
|
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|
|
|
|
|
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|
|
|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
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|
|
|
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|
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|
|
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|
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|
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|
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|
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|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
<cls>
|
| 2 |
+
<pad>
|
| 3 |
+
<eos>
|
| 4 |
+
<unk>
|
| 5 |
+
<mask>
|
| 6 |
+
Ap
|
| 7 |
+
Ay
|
| 8 |
+
An
|
| 9 |
+
Aw
|
| 10 |
+
Ar
|
| 11 |
+
Aq
|
| 12 |
+
Ah
|
| 13 |
+
Ag
|
| 14 |
+
Ad
|
| 15 |
+
Al
|
| 16 |
+
Av
|
| 17 |
+
At
|
| 18 |
+
Am
|
| 19 |
+
Af
|
| 20 |
+
As
|
| 21 |
+
Aa
|
| 22 |
+
Ae
|
| 23 |
+
Ai
|
| 24 |
+
Ak
|
| 25 |
+
Ac
|
| 26 |
+
A#
|
| 27 |
+
Cp
|
| 28 |
+
Cy
|
| 29 |
+
Cn
|
| 30 |
+
Cw
|
| 31 |
+
Cr
|
| 32 |
+
Cq
|
| 33 |
+
Ch
|
| 34 |
+
Cg
|
| 35 |
+
Cd
|
| 36 |
+
Cl
|
| 37 |
+
Cv
|
| 38 |
+
Ct
|
| 39 |
+
Cm
|
| 40 |
+
Cf
|
| 41 |
+
Cs
|
| 42 |
+
Ca
|
| 43 |
+
Ce
|
| 44 |
+
Ci
|
| 45 |
+
Ck
|
| 46 |
+
Cc
|
| 47 |
+
C#
|
| 48 |
+
Dp
|
| 49 |
+
Dy
|
| 50 |
+
Dn
|
| 51 |
+
Dw
|
| 52 |
+
Dr
|
| 53 |
+
Dq
|
| 54 |
+
Dh
|
| 55 |
+
Dg
|
| 56 |
+
Dd
|
| 57 |
+
Dl
|
| 58 |
+
Dv
|
| 59 |
+
Dt
|
| 60 |
+
Dm
|
| 61 |
+
Df
|
| 62 |
+
Ds
|
| 63 |
+
Da
|
| 64 |
+
De
|
| 65 |
+
Di
|
| 66 |
+
Dk
|
| 67 |
+
Dc
|
| 68 |
+
D#
|
| 69 |
+
Ep
|
| 70 |
+
Ey
|
| 71 |
+
En
|
| 72 |
+
Ew
|
| 73 |
+
Er
|
| 74 |
+
Eq
|
| 75 |
+
Eh
|
| 76 |
+
Eg
|
| 77 |
+
Ed
|
| 78 |
+
El
|
| 79 |
+
Ev
|
| 80 |
+
Et
|
| 81 |
+
Em
|
| 82 |
+
Ef
|
| 83 |
+
Es
|
| 84 |
+
Ea
|
| 85 |
+
Ee
|
| 86 |
+
Ei
|
| 87 |
+
Ek
|
| 88 |
+
Ec
|
| 89 |
+
E#
|
| 90 |
+
Fp
|
| 91 |
+
Fy
|
| 92 |
+
Fn
|
| 93 |
+
Fw
|
| 94 |
+
Fr
|
| 95 |
+
Fq
|
| 96 |
+
Fh
|
| 97 |
+
Fg
|
| 98 |
+
Fd
|
| 99 |
+
Fl
|
| 100 |
+
Fv
|
| 101 |
+
Ft
|
| 102 |
+
Fm
|
| 103 |
+
Ff
|
| 104 |
+
Fs
|
| 105 |
+
Fa
|
| 106 |
+
Fe
|
| 107 |
+
Fi
|
| 108 |
+
Fk
|
| 109 |
+
Fc
|
| 110 |
+
F#
|
| 111 |
+
Gp
|
| 112 |
+
Gy
|
| 113 |
+
Gn
|
| 114 |
+
Gw
|
| 115 |
+
Gr
|
| 116 |
+
Gq
|
| 117 |
+
Gh
|
| 118 |
+
Gg
|
| 119 |
+
Gd
|
| 120 |
+
Gl
|
| 121 |
+
Gv
|
| 122 |
+
Gt
|
| 123 |
+
Gm
|
| 124 |
+
Gf
|
| 125 |
+
Gs
|
| 126 |
+
Ga
|
| 127 |
+
Ge
|
| 128 |
+
Gi
|
| 129 |
+
Gk
|
| 130 |
+
Gc
|
| 131 |
+
G#
|
| 132 |
+
Hp
|
| 133 |
+
Hy
|
| 134 |
+
Hn
|
| 135 |
+
Hw
|
| 136 |
+
Hr
|
| 137 |
+
Hq
|
| 138 |
+
Hh
|
| 139 |
+
Hg
|
| 140 |
+
Hd
|
| 141 |
+
Hl
|
| 142 |
+
Hv
|
| 143 |
+
Ht
|
| 144 |
+
Hm
|
| 145 |
+
Hf
|
| 146 |
+
Hs
|
| 147 |
+
Ha
|
| 148 |
+
He
|
| 149 |
+
Hi
|
| 150 |
+
Hk
|
| 151 |
+
Hc
|
| 152 |
+
H#
|
| 153 |
+
Ip
|
| 154 |
+
Iy
|
| 155 |
+
In
|
| 156 |
+
Iw
|
| 157 |
+
Ir
|
| 158 |
+
Iq
|
| 159 |
+
Ih
|
| 160 |
+
Ig
|
| 161 |
+
Id
|
| 162 |
+
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|
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|
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|
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|
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|
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Pd
|
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|
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|
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|
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|
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|
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|
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|
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Sy
|
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|
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Sl
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|
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|
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Se
|
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|
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|
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|
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S#
|
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|
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Ty
|
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|
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Tw
|
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|
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Tq
|
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|
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Tg
|
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|
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|
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|
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|
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Tf
|
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|
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Ta
|
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Te
|
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Ti
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Tk
|
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Tc
|
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T#
|
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Vp
|
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Vy
|
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Vn
|
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Vw
|
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|
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|
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|
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|
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|
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Vl
|
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|
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|
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|
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|
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Vi
|
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Vk
|
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|
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|
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Wp
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Wy
|
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|
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|
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|
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|
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Wh
|
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|
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|
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|
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|
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|
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|
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|
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|
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We
|
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|
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|
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Yp
|
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Yy
|
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Yn
|
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Yw
|
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Yr
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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#n
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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#a
|
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#e
|
| 443 |
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#i
|
| 444 |
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#k
|
| 445 |
+
#c
|
| 446 |
+
##
|
repro_ft_v2_e5cont_freezemol_20260105_100642/train_args.json
ADDED
|
@@ -0,0 +1,45 @@
|
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|
|
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|
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|
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|
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|
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|
|
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|
|
|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"interactions": "dataset/drug-target-activity/processed/interactions.parquet",
|
| 3 |
+
"protein_cache": "dataset/protein_sequences/saprot_combined_sequences_esmfold_nomask_cache.jsonl",
|
| 4 |
+
"split": "cold_drug",
|
| 5 |
+
"seed": 42,
|
| 6 |
+
"test_ratio": 0.2,
|
| 7 |
+
"val_ratio": 0.1,
|
| 8 |
+
"epochs": 5,
|
| 9 |
+
"protein_per_step": 1,
|
| 10 |
+
"lr_proj": 0.0001,
|
| 11 |
+
"lr_protein": 1e-06,
|
| 12 |
+
"weight_decay": 0.001,
|
| 13 |
+
"warmup_steps": 50,
|
| 14 |
+
"log_interval": 50,
|
| 15 |
+
"temperature": 0.07,
|
| 16 |
+
"max_logit_scale": 100.0,
|
| 17 |
+
"projection_dim": 512,
|
| 18 |
+
"protein_proj_hidden_dim": 0,
|
| 19 |
+
"molecule_proj_hidden_dim": 0,
|
| 20 |
+
"dropout": 0.2,
|
| 21 |
+
"hardneg_source": "none",
|
| 22 |
+
"hardneg_knn": "models/emb_cache/molecule_knn_tanimoto_k256.pt",
|
| 23 |
+
"hardneg_k": 0,
|
| 24 |
+
"hardneg_weight": 0.0,
|
| 25 |
+
"pos_weighting": "confidence",
|
| 26 |
+
"pxc50_threshold": 6.0,
|
| 27 |
+
"pxc50_std_threshold": 1.0,
|
| 28 |
+
"obs_threshold": 10.0,
|
| 29 |
+
"obs_std_threshold": 20.0,
|
| 30 |
+
"conflict_penalty": 0.5,
|
| 31 |
+
"severe_conflict_penalty": 0.2,
|
| 32 |
+
"weight_min": 0.2,
|
| 33 |
+
"weight_max": 1.0,
|
| 34 |
+
"protein_model": "models/repro_ft_v1_e5_freezemol_20260105_100642/protein_model",
|
| 35 |
+
"molecule_raw_cache": "models/emb_cache/raw_embeddings_saprot1p3b_struct_nomask_smiles20.pt",
|
| 36 |
+
"freeze_molecule_proj": true,
|
| 37 |
+
"init_projection": "models/repro_ft_v1_e5_freezemol_20260105_100642/projection.pt",
|
| 38 |
+
"mixed_precision": "bf16",
|
| 39 |
+
"load_dtype": "bf16",
|
| 40 |
+
"gradient_checkpointing": true,
|
| 41 |
+
"max_grad_norm": 1.0,
|
| 42 |
+
"protein_max_length": 1024,
|
| 43 |
+
"device": "cuda",
|
| 44 |
+
"output_dir": "models/repro_ft_v2_e5cont_freezemol_20260105_100642"
|
| 45 |
+
}
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/loss.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
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repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/projection.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:048ec6704793783de8880dbffb26de36ed91ea9883bf812a6e5eed1b6a5db7a4
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| 3 |
+
size 13141301
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/config.json
ADDED
|
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architectures": [
|
| 3 |
+
"EsmModel"
|
| 4 |
+
],
|
| 5 |
+
"attention_probs_dropout_prob": 0.1,
|
| 6 |
+
"classifier_dropout": null,
|
| 7 |
+
"dtype": "bfloat16",
|
| 8 |
+
"emb_layer_norm_before": false,
|
| 9 |
+
"esmfold_config": null,
|
| 10 |
+
"hidden_act": "gelu",
|
| 11 |
+
"hidden_dropout_prob": 0.1,
|
| 12 |
+
"hidden_size": 1280,
|
| 13 |
+
"initializer_range": 0.02,
|
| 14 |
+
"intermediate_size": 5120,
|
| 15 |
+
"is_folding_model": false,
|
| 16 |
+
"layer_norm_eps": 1e-05,
|
| 17 |
+
"mask_token_id": 4,
|
| 18 |
+
"max_position_embeddings": 1026,
|
| 19 |
+
"model_type": "esm",
|
| 20 |
+
"num_attention_heads": 20,
|
| 21 |
+
"num_hidden_layers": 66,
|
| 22 |
+
"pad_token_id": 1,
|
| 23 |
+
"position_embedding_type": "rotary",
|
| 24 |
+
"token_dropout": true,
|
| 25 |
+
"transformers_version": "4.57.3",
|
| 26 |
+
"use_cache": true,
|
| 27 |
+
"vocab_list": null,
|
| 28 |
+
"vocab_size": 446
|
| 29 |
+
}
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/model.safetensors
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4d2190bb21e80d7e946978ad85c548ca4d5ed7c49f276986e0920dcfb5333421
|
| 3 |
+
size 2601989354
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/special_tokens_map.json
ADDED
|
@@ -0,0 +1,37 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"cls_token": {
|
| 3 |
+
"content": "<cls>",
|
| 4 |
+
"lstrip": false,
|
| 5 |
+
"normalized": false,
|
| 6 |
+
"rstrip": false,
|
| 7 |
+
"single_word": false
|
| 8 |
+
},
|
| 9 |
+
"eos_token": {
|
| 10 |
+
"content": "<eos>",
|
| 11 |
+
"lstrip": false,
|
| 12 |
+
"normalized": false,
|
| 13 |
+
"rstrip": false,
|
| 14 |
+
"single_word": false
|
| 15 |
+
},
|
| 16 |
+
"mask_token": {
|
| 17 |
+
"content": "<mask>",
|
| 18 |
+
"lstrip": false,
|
| 19 |
+
"normalized": false,
|
| 20 |
+
"rstrip": false,
|
| 21 |
+
"single_word": false
|
| 22 |
+
},
|
| 23 |
+
"pad_token": {
|
| 24 |
+
"content": "<pad>",
|
| 25 |
+
"lstrip": false,
|
| 26 |
+
"normalized": false,
|
| 27 |
+
"rstrip": false,
|
| 28 |
+
"single_word": false
|
| 29 |
+
},
|
| 30 |
+
"unk_token": {
|
| 31 |
+
"content": "<unk>",
|
| 32 |
+
"lstrip": false,
|
| 33 |
+
"normalized": false,
|
| 34 |
+
"rstrip": false,
|
| 35 |
+
"single_word": false
|
| 36 |
+
}
|
| 37 |
+
}
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/tokenizer_config.json
ADDED
|
@@ -0,0 +1,53 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
|
|
|
|
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|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"added_tokens_decoder": {
|
| 3 |
+
"0": {
|
| 4 |
+
"content": "<cls>",
|
| 5 |
+
"lstrip": false,
|
| 6 |
+
"normalized": false,
|
| 7 |
+
"rstrip": false,
|
| 8 |
+
"single_word": false,
|
| 9 |
+
"special": true
|
| 10 |
+
},
|
| 11 |
+
"1": {
|
| 12 |
+
"content": "<pad>",
|
| 13 |
+
"lstrip": false,
|
| 14 |
+
"normalized": false,
|
| 15 |
+
"rstrip": false,
|
| 16 |
+
"single_word": false,
|
| 17 |
+
"special": true
|
| 18 |
+
},
|
| 19 |
+
"2": {
|
| 20 |
+
"content": "<eos>",
|
| 21 |
+
"lstrip": false,
|
| 22 |
+
"normalized": false,
|
| 23 |
+
"rstrip": false,
|
| 24 |
+
"single_word": false,
|
| 25 |
+
"special": true
|
| 26 |
+
},
|
| 27 |
+
"3": {
|
| 28 |
+
"content": "<unk>",
|
| 29 |
+
"lstrip": false,
|
| 30 |
+
"normalized": false,
|
| 31 |
+
"rstrip": false,
|
| 32 |
+
"single_word": false,
|
| 33 |
+
"special": true
|
| 34 |
+
},
|
| 35 |
+
"4": {
|
| 36 |
+
"content": "<mask>",
|
| 37 |
+
"lstrip": false,
|
| 38 |
+
"normalized": false,
|
| 39 |
+
"rstrip": false,
|
| 40 |
+
"single_word": false,
|
| 41 |
+
"special": true
|
| 42 |
+
}
|
| 43 |
+
},
|
| 44 |
+
"clean_up_tokenization_spaces": true,
|
| 45 |
+
"cls_token": "<cls>",
|
| 46 |
+
"eos_token": "<eos>",
|
| 47 |
+
"extra_special_tokens": {},
|
| 48 |
+
"mask_token": "<mask>",
|
| 49 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 50 |
+
"pad_token": "<pad>",
|
| 51 |
+
"tokenizer_class": "EsmTokenizer",
|
| 52 |
+
"unk_token": "<unk>"
|
| 53 |
+
}
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/protein_model/vocab.txt
ADDED
|
@@ -0,0 +1,446 @@
|
|
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|
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|
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|
|
| 1 |
+
<cls>
|
| 2 |
+
<pad>
|
| 3 |
+
<eos>
|
| 4 |
+
<unk>
|
| 5 |
+
<mask>
|
| 6 |
+
Ap
|
| 7 |
+
Ay
|
| 8 |
+
An
|
| 9 |
+
Aw
|
| 10 |
+
Ar
|
| 11 |
+
Aq
|
| 12 |
+
Ah
|
| 13 |
+
Ag
|
| 14 |
+
Ad
|
| 15 |
+
Al
|
| 16 |
+
Av
|
| 17 |
+
At
|
| 18 |
+
Am
|
| 19 |
+
Af
|
| 20 |
+
As
|
| 21 |
+
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|
| 22 |
+
Ae
|
| 23 |
+
Ai
|
| 24 |
+
Ak
|
| 25 |
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Ac
|
| 26 |
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A#
|
| 27 |
+
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|
| 28 |
+
Cy
|
| 29 |
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Cn
|
| 30 |
+
Cw
|
| 31 |
+
Cr
|
| 32 |
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Cq
|
| 33 |
+
Ch
|
| 34 |
+
Cg
|
| 35 |
+
Cd
|
| 36 |
+
Cl
|
| 37 |
+
Cv
|
| 38 |
+
Ct
|
| 39 |
+
Cm
|
| 40 |
+
Cf
|
| 41 |
+
Cs
|
| 42 |
+
Ca
|
| 43 |
+
Ce
|
| 44 |
+
Ci
|
| 45 |
+
Ck
|
| 46 |
+
Cc
|
| 47 |
+
C#
|
| 48 |
+
Dp
|
| 49 |
+
Dy
|
| 50 |
+
Dn
|
| 51 |
+
Dw
|
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+
Dr
|
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+
Dq
|
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+
Dh
|
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+
Dg
|
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|
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|
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|
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Dt
|
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|
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|
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Da
|
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De
|
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Di
|
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|
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|
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D#
|
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Ep
|
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+
Ey
|
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+
En
|
| 72 |
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Ew
|
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Er
|
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Eq
|
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Eh
|
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Eg
|
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Ed
|
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El
|
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Ev
|
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Et
|
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|
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|
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Es
|
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Ea
|
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+
Ee
|
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+
Ei
|
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+
Ek
|
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Ec
|
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+
E#
|
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+
Fp
|
| 91 |
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Fy
|
| 92 |
+
Fn
|
| 93 |
+
Fw
|
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+
Fr
|
| 95 |
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Fq
|
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+
Fh
|
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|
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Fd
|
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Fl
|
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Fv
|
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Ft
|
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Fm
|
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Ff
|
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|
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|
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Fe
|
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+
Fi
|
| 108 |
+
Fk
|
| 109 |
+
Fc
|
| 110 |
+
F#
|
| 111 |
+
Gp
|
| 112 |
+
Gy
|
| 113 |
+
Gn
|
| 114 |
+
Gw
|
| 115 |
+
Gr
|
| 116 |
+
Gq
|
| 117 |
+
Gh
|
| 118 |
+
Gg
|
| 119 |
+
Gd
|
| 120 |
+
Gl
|
| 121 |
+
Gv
|
| 122 |
+
Gt
|
| 123 |
+
Gm
|
| 124 |
+
Gf
|
| 125 |
+
Gs
|
| 126 |
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Ga
|
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+
Ge
|
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Gi
|
| 129 |
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Gk
|
| 130 |
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|
| 131 |
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G#
|
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Hp
|
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Hy
|
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+
Hn
|
| 135 |
+
Hw
|
| 136 |
+
Hr
|
| 137 |
+
Hq
|
| 138 |
+
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|
| 139 |
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Hg
|
| 140 |
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Hd
|
| 141 |
+
Hl
|
| 142 |
+
Hv
|
| 143 |
+
Ht
|
| 144 |
+
Hm
|
| 145 |
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Hf
|
| 146 |
+
Hs
|
| 147 |
+
Ha
|
| 148 |
+
He
|
| 149 |
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Hi
|
| 150 |
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Hk
|
| 151 |
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Hc
|
| 152 |
+
H#
|
| 153 |
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Ip
|
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Iy
|
| 155 |
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In
|
| 156 |
+
Iw
|
| 157 |
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Ir
|
| 158 |
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Iq
|
| 159 |
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Ih
|
| 160 |
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Ig
|
| 161 |
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Id
|
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Il
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|
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It
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Im
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|
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|
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|
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|
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|
| 172 |
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Ic
|
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I#
|
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Kp
|
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Ky
|
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Kn
|
| 177 |
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Kw
|
| 178 |
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|
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|
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|
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|
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|
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Kl
|
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|
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|
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|
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|
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|
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Ka
|
| 190 |
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Ke
|
| 191 |
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Ki
|
| 192 |
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Kk
|
| 193 |
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Kc
|
| 194 |
+
K#
|
| 195 |
+
Lp
|
| 196 |
+
Ly
|
| 197 |
+
Ln
|
| 198 |
+
Lw
|
| 199 |
+
Lr
|
| 200 |
+
Lq
|
| 201 |
+
Lh
|
| 202 |
+
Lg
|
| 203 |
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Ld
|
| 204 |
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Ll
|
| 205 |
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Lv
|
| 206 |
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Lt
|
| 207 |
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Lm
|
| 208 |
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|
| 209 |
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Ls
|
| 210 |
+
La
|
| 211 |
+
Le
|
| 212 |
+
Li
|
| 213 |
+
Lk
|
| 214 |
+
Lc
|
| 215 |
+
L#
|
| 216 |
+
Mp
|
| 217 |
+
My
|
| 218 |
+
Mn
|
| 219 |
+
Mw
|
| 220 |
+
Mr
|
| 221 |
+
Mq
|
| 222 |
+
Mh
|
| 223 |
+
Mg
|
| 224 |
+
Md
|
| 225 |
+
Ml
|
| 226 |
+
Mv
|
| 227 |
+
Mt
|
| 228 |
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Mm
|
| 229 |
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Mf
|
| 230 |
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Ms
|
| 231 |
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Ma
|
| 232 |
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Me
|
| 233 |
+
Mi
|
| 234 |
+
Mk
|
| 235 |
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Mc
|
| 236 |
+
M#
|
| 237 |
+
Np
|
| 238 |
+
Ny
|
| 239 |
+
Nn
|
| 240 |
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Nw
|
| 241 |
+
Nr
|
| 242 |
+
Nq
|
| 243 |
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Nh
|
| 244 |
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Ng
|
| 245 |
+
Nd
|
| 246 |
+
Nl
|
| 247 |
+
Nv
|
| 248 |
+
Nt
|
| 249 |
+
Nm
|
| 250 |
+
Nf
|
| 251 |
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Ns
|
| 252 |
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Na
|
| 253 |
+
Ne
|
| 254 |
+
Ni
|
| 255 |
+
Nk
|
| 256 |
+
Nc
|
| 257 |
+
N#
|
| 258 |
+
Pp
|
| 259 |
+
Py
|
| 260 |
+
Pn
|
| 261 |
+
Pw
|
| 262 |
+
Pr
|
| 263 |
+
Pq
|
| 264 |
+
Ph
|
| 265 |
+
Pg
|
| 266 |
+
Pd
|
| 267 |
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Pl
|
| 268 |
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Pv
|
| 269 |
+
Pt
|
| 270 |
+
Pm
|
| 271 |
+
Pf
|
| 272 |
+
Ps
|
| 273 |
+
Pa
|
| 274 |
+
Pe
|
| 275 |
+
Pi
|
| 276 |
+
Pk
|
| 277 |
+
Pc
|
| 278 |
+
P#
|
| 279 |
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Qp
|
| 280 |
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Qy
|
| 281 |
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Qn
|
| 282 |
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Qw
|
| 283 |
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Qr
|
| 284 |
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Qq
|
| 285 |
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Qh
|
| 286 |
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Qg
|
| 287 |
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Qd
|
| 288 |
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Ql
|
| 289 |
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Qv
|
| 290 |
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Qt
|
| 291 |
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Qm
|
| 292 |
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Qf
|
| 293 |
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Qs
|
| 294 |
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Qa
|
| 295 |
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Qe
|
| 296 |
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Qi
|
| 297 |
+
Qk
|
| 298 |
+
Qc
|
| 299 |
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Q#
|
| 300 |
+
Rp
|
| 301 |
+
Ry
|
| 302 |
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Rn
|
| 303 |
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Rw
|
| 304 |
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Rr
|
| 305 |
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Rq
|
| 306 |
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Rh
|
| 307 |
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Rg
|
| 308 |
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Rd
|
| 309 |
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Rl
|
| 310 |
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Rv
|
| 311 |
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Rt
|
| 312 |
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Rm
|
| 313 |
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Rf
|
| 314 |
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Rs
|
| 315 |
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Ra
|
| 316 |
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Re
|
| 317 |
+
Ri
|
| 318 |
+
Rk
|
| 319 |
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Rc
|
| 320 |
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R#
|
| 321 |
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Sp
|
| 322 |
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Sy
|
| 323 |
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Sn
|
| 324 |
+
Sw
|
| 325 |
+
Sr
|
| 326 |
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Sq
|
| 327 |
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Sh
|
| 328 |
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Sg
|
| 329 |
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Sd
|
| 330 |
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Sl
|
| 331 |
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Sv
|
| 332 |
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St
|
| 333 |
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Sm
|
| 334 |
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Sf
|
| 335 |
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Ss
|
| 336 |
+
Sa
|
| 337 |
+
Se
|
| 338 |
+
Si
|
| 339 |
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Sk
|
| 340 |
+
Sc
|
| 341 |
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S#
|
| 342 |
+
Tp
|
| 343 |
+
Ty
|
| 344 |
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Tn
|
| 345 |
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Tw
|
| 346 |
+
Tr
|
| 347 |
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Tq
|
| 348 |
+
Th
|
| 349 |
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Tg
|
| 350 |
+
Td
|
| 351 |
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Tl
|
| 352 |
+
Tv
|
| 353 |
+
Tt
|
| 354 |
+
Tm
|
| 355 |
+
Tf
|
| 356 |
+
Ts
|
| 357 |
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Ta
|
| 358 |
+
Te
|
| 359 |
+
Ti
|
| 360 |
+
Tk
|
| 361 |
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Tc
|
| 362 |
+
T#
|
| 363 |
+
Vp
|
| 364 |
+
Vy
|
| 365 |
+
Vn
|
| 366 |
+
Vw
|
| 367 |
+
Vr
|
| 368 |
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Vq
|
| 369 |
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Vh
|
| 370 |
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Vg
|
| 371 |
+
Vd
|
| 372 |
+
Vl
|
| 373 |
+
Vv
|
| 374 |
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Vt
|
| 375 |
+
Vm
|
| 376 |
+
Vf
|
| 377 |
+
Vs
|
| 378 |
+
Va
|
| 379 |
+
Ve
|
| 380 |
+
Vi
|
| 381 |
+
Vk
|
| 382 |
+
Vc
|
| 383 |
+
V#
|
| 384 |
+
Wp
|
| 385 |
+
Wy
|
| 386 |
+
Wn
|
| 387 |
+
Ww
|
| 388 |
+
Wr
|
| 389 |
+
Wq
|
| 390 |
+
Wh
|
| 391 |
+
Wg
|
| 392 |
+
Wd
|
| 393 |
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Wl
|
| 394 |
+
Wv
|
| 395 |
+
Wt
|
| 396 |
+
Wm
|
| 397 |
+
Wf
|
| 398 |
+
Ws
|
| 399 |
+
Wa
|
| 400 |
+
We
|
| 401 |
+
Wi
|
| 402 |
+
Wk
|
| 403 |
+
Wc
|
| 404 |
+
W#
|
| 405 |
+
Yp
|
| 406 |
+
Yy
|
| 407 |
+
Yn
|
| 408 |
+
Yw
|
| 409 |
+
Yr
|
| 410 |
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Yq
|
| 411 |
+
Yh
|
| 412 |
+
Yg
|
| 413 |
+
Yd
|
| 414 |
+
Yl
|
| 415 |
+
Yv
|
| 416 |
+
Yt
|
| 417 |
+
Ym
|
| 418 |
+
Yf
|
| 419 |
+
Ys
|
| 420 |
+
Ya
|
| 421 |
+
Ye
|
| 422 |
+
Yi
|
| 423 |
+
Yk
|
| 424 |
+
Yc
|
| 425 |
+
Y#
|
| 426 |
+
#p
|
| 427 |
+
#y
|
| 428 |
+
#n
|
| 429 |
+
#w
|
| 430 |
+
#r
|
| 431 |
+
#q
|
| 432 |
+
#h
|
| 433 |
+
#g
|
| 434 |
+
#d
|
| 435 |
+
#l
|
| 436 |
+
#v
|
| 437 |
+
#t
|
| 438 |
+
#m
|
| 439 |
+
#f
|
| 440 |
+
#s
|
| 441 |
+
#a
|
| 442 |
+
#e
|
| 443 |
+
#i
|
| 444 |
+
#k
|
| 445 |
+
#c
|
| 446 |
+
##
|
repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642/train_args.json
ADDED
|
@@ -0,0 +1,45 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"interactions": "dataset/drug-target-activity/processed/interactions.parquet",
|
| 3 |
+
"protein_cache": "dataset/protein_sequences/saprot_combined_sequences_esmfold_nomask_cache.jsonl",
|
| 4 |
+
"split": "cold_drug",
|
| 5 |
+
"seed": 42,
|
| 6 |
+
"test_ratio": 0.2,
|
| 7 |
+
"val_ratio": 0.1,
|
| 8 |
+
"epochs": 5,
|
| 9 |
+
"protein_per_step": 1,
|
| 10 |
+
"lr_proj": 0.0001,
|
| 11 |
+
"lr_protein": 1e-06,
|
| 12 |
+
"weight_decay": 0.001,
|
| 13 |
+
"warmup_steps": 50,
|
| 14 |
+
"log_interval": 50,
|
| 15 |
+
"temperature": 0.07,
|
| 16 |
+
"max_logit_scale": 100.0,
|
| 17 |
+
"projection_dim": 512,
|
| 18 |
+
"protein_proj_hidden_dim": 0,
|
| 19 |
+
"molecule_proj_hidden_dim": 0,
|
| 20 |
+
"dropout": 0.2,
|
| 21 |
+
"hardneg_source": "inactive_only",
|
| 22 |
+
"hardneg_knn": "models/emb_cache/molecule_knn_tanimoto_k256.pt",
|
| 23 |
+
"hardneg_k": 8,
|
| 24 |
+
"hardneg_weight": 0.1,
|
| 25 |
+
"pos_weighting": "confidence",
|
| 26 |
+
"pxc50_threshold": 6.0,
|
| 27 |
+
"pxc50_std_threshold": 1.0,
|
| 28 |
+
"obs_threshold": 10.0,
|
| 29 |
+
"obs_std_threshold": 20.0,
|
| 30 |
+
"conflict_penalty": 0.5,
|
| 31 |
+
"severe_conflict_penalty": 0.2,
|
| 32 |
+
"weight_min": 0.2,
|
| 33 |
+
"weight_max": 1.0,
|
| 34 |
+
"protein_model": "models/repro_ft_v2_e5cont_freezemol_20260105_100642/protein_model",
|
| 35 |
+
"molecule_raw_cache": "models/emb_cache/raw_embeddings_saprot1p3b_struct_nomask_smiles20.pt",
|
| 36 |
+
"freeze_molecule_proj": true,
|
| 37 |
+
"init_projection": "models/repro_ft_v2_e5cont_freezemol_20260105_100642/projection.pt",
|
| 38 |
+
"mixed_precision": "bf16",
|
| 39 |
+
"load_dtype": "bf16",
|
| 40 |
+
"gradient_checkpointing": true,
|
| 41 |
+
"max_grad_norm": 1.0,
|
| 42 |
+
"protein_max_length": 1024,
|
| 43 |
+
"device": "cuda",
|
| 44 |
+
"output_dir": "models/repro_ft_v5_hardneg_inactive_k8_w0p1_e5_20260105_100642"
|
| 45 |
+
}
|
repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/loss.json
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/projection.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:1fae4e97195da98edaa27270ed274278ed2680835ba74f11a4ee94a511d0c54d
|
| 3 |
+
size 13141301
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repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/projection_last.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:455bc8cbacef400197f8c9a644074f5c75ed6fccaf0e17f7ffdf57c7c3676c86
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size 13141396
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repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642/train_args.json
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{
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| 2 |
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"interactions": "dataset/drug-target-activity/processed/interactions.parquet",
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| 3 |
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"protein_cache": "dataset/protein_sequences/uniprot_sequences.jsonl",
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| 4 |
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"split": "cold_drug",
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| 5 |
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"seed": 42,
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| 6 |
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"test_ratio": 0.2,
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| 7 |
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"val_ratio": 0.1,
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| 8 |
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"epochs": 500,
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| 9 |
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"batch_size": 512,
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"lr": 0.001,
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| 11 |
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"weight_decay": 0.001,
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| 12 |
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"warmup_steps": 200,
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| 13 |
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"log_interval": 50,
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| 14 |
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"temperature": 0.07,
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| 15 |
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"max_logit_scale": 100.0,
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| 16 |
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"p2m_weight": 1.0,
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| 17 |
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"m2p_weight": 1.0,
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| 18 |
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"projection_dim": 512,
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| 19 |
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"protein_proj_hidden_dim": 0,
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| 20 |
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"molecule_proj_hidden_dim": 0,
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| 21 |
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"label_smoothing": 0.1,
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| 22 |
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"dropout": 0.2,
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| 23 |
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"pos_weighting": "pxc50_confidence",
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| 24 |
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"pxc50_threshold": 6.0,
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| 25 |
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"pxc50_std_threshold": 1.0,
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| 26 |
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"obs_threshold": 10.0,
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| 27 |
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"obs_std_threshold": 20.0,
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| 28 |
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"conflict_penalty": 0.5,
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| 29 |
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"severe_conflict_penalty": 0.2,
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| 30 |
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"weight_min": 0.2,
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| 31 |
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"weight_max": 1.0,
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| 32 |
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"raw_cache": "models/emb_cache/raw_embeddings_saprot1p3b_struct_nomask_smiles20.pt",
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| 33 |
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"protein_token_cache": null,
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| 34 |
+
"rebuild_raw_cache": false,
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| 35 |
+
"protein_batch_size": 8,
|
| 36 |
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"molecule_batch_size": 64,
|
| 37 |
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"device": "cuda",
|
| 38 |
+
"hardneg_source": "none",
|
| 39 |
+
"hardneg_k": 4,
|
| 40 |
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"hardneg_min_sim": 0.5,
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| 41 |
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"hardneg_topn": 256,
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| 42 |
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"hardneg_loss": "bpr",
|
| 43 |
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"hardneg_margin": 1.0,
|
| 44 |
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"hardneg_weight": 0.2,
|
| 45 |
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"eval_interval": 0,
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| 46 |
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"early_stop_patience": 0,
|
| 47 |
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"select_metric": "p2m_mrr",
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| 48 |
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"eval_k": [
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| 49 |
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1,
|
| 50 |
+
5,
|
| 51 |
+
10
|
| 52 |
+
],
|
| 53 |
+
"output_dir": "models/repro_proj_softmax_saprot1p3b_confobs_smiles20_20260105_100642"
|
| 54 |
+
}
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