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Not getting expected results for zero-shot molecule editing #23

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gihanpanapitiya opened this issue Mar 13, 2024 · 6 comments
Closed

Not getting expected results for zero-shot molecule editing #23

gihanpanapitiya opened this issue Mar 13, 2024 · 6 comments

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@gihanpanapitiya
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For zero-shot molecule editing, I am not getting the expected results as shown in the repository's notebook.
Do you have a suggestion to improve this result.

This is what I get.

===== for text prompt: This molecule is soluble in water. =====
===== for SMILES OC1C2C1CC2 =====
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
Use random noise for init
l2 lambda: 1.0
Use random noise for init
100%|██████████████████████████████████████████████████████████████████████████████████| 100/100 [00:06<00:00, 15.92it/s]
clip loss: -0.45563	L2 loss: 0.23571
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
SMILES_list: ['OC1C2C1CC2', '[73Se][O+][O+][O+][O+][O+][O+][O+][73Se][73Se][73Se][73Se][73Se][F-][32P][73Se][F-][32P][73Se][O+][O+][73Se][F-][73Se][F-][73Se][73Se][73Se][73Se][73Se][73Se][F-][32P][73Se][F-]1[SiH3-][73Se]', '[73Se]S[3H][Rb][85SrH2][SiH3-]LogD_change_(0.9, 1.1][SiH3-][C@H][3H][Rb][85SrH2][SiH3-][I-][123I][73Se][123I][73Se][123I][73Se]<UNUSED_166>[F-]<UNUSED_81>Clint_low->high[F-]<UNUSED_81>[C@H][3H][Rb][85SrH2][SiH3-][85SrH2][SiH3-][85SrH2][SiH3-][85SrH2][SiH3-][I-][123I][73Se]S[3H][Rb][85SrH2][SiH3-][SiH][SiH2]<UNUSED_0>Clint_low->high[F-]<UNUSED_81>Clint_low->high[KH][11CH]LogD_change_(0.9, 1.1]Br<UNUSED_0>Clint_low->highLogD_change_(0.9, 1.1]Br[Se][123I][85SrH2][C@H][3H][Rb][85SrH2][C@H][3H][Rb][85SrH2][C@H][3H][Rb][85SrH2][C@H][C@H][C@H][C@H][3H][Rb][85SrH2][O+][O+][O+][O+][O+][O+][O+][O+][O+][O+][O+][O+][O+][123I][73Se]S[3H]Clint_low->high<UNUSED_64><UNUSED_81>[C@H]<UNUSED_61><UNUSED_81>Clint_low->high[KH]<UNUSED_46><UNUSED_61>[C@H][3H][123I][O+][123I][O+][123I][P@@+]LogD_change_(1.1, 1.3][PH][C@H][3H][Rb][85SrH2][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][123I][73Se]S[3H]Clint_low->high[KH]Clint_low->high[KH][123I]/[Al]<UNUSED_182>[18OH][3H][123I]S[3H][123I]S[3H][123I][P@@+][KH]LogD_change_(2.1, 2.3]LogD_change_(2.1, 2.3]LogD_change_(2.1, 2.3]LogD_change_(2.1, 2.3]<UNUSED_161>[123I][73Se][123I][73Se][123I][73Se]S[3H][32P][PH][C@H][3H]Clint_low->high[KH][S@@+]S[3H]<UNUSED_0>S[3H]<UNUSED_0>S[3H]<UNUSED_0>S[3H]Clint_low->high[KH][S@@+]S[3H]<UNUSED_0>S[3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][85SrH2][SiH3-]S[3H][SiH][PH][3H][32P][PH][3H][Rb][C@H][3H][32P][PH][3H][32P][PH][3H][32P][PH][S@@][32P][PH][3H]<UNUSED_0>LogD_change_(2.1, 2.3]<UNUSED_81>[C@H][3H][Rb][C@H][3H]Clint_low->high<UNUSED_64>[C@H][3H][Rb][C@H][3H][Rb][85SrH2][C@H][3H][Rb][85SrH2][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][SiH][123I][P@@+]LogD_change_(0.3, 0.5][PH]S[3H][Rb][85SrH2][O+][O+][O+][123I][85SrH2][PH][3H][Rb][85SrH2][123I][85SrH2][123I][85SrH2][PH][3H][Rb][C@H][3H][Rb][85SrH2][PH][OH+][NH4+]<UNUSED_193>[PH]<UNUSED_193>[OH+][NH4+]<UNUSED_193>LogD_change_(0.9, 1.1][P@@+][As-][PH][3H][Rb][C@H][3H][Rb][C@H][3H]Clint_low->high[PH][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][85SrH2][PH][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][PH][AsH3][C@H][3H][Rb][C@H][3H][Rb][C@H][3H][Rb][C@H][SiH][PH][AsH3][C@H][3H][Rb][85SrH2]<UNUSED_64>[PH][85SrH2][PH][3H][Rb][85SrH2][PH][C@H][3H][Rb][C@H][3H][Rb][85SrH2][O+]LogD_change_(2.1, 2.3][F-]<UNUSED_81>[C@H][SiH][123I][As-][PH][C@H][SiH][PH][AsH3][C@H][SiH][PH][P@@+][As-][PH][C@H][3H][Rb][85SrH2][PH][3H][Rb][85SrH2][PH][3H][Rb][C@H][SiH][123I]<UNUSED_193><UNUSED_68><UNUSED_0>[As-][PH][S@@]<UNUSED_46>[PH]<UNUSED_193>LogD_change_(0.9, 1.1][TeH2][3H][NH4+]<UNUSED_193>[PH][3H][Rb][85SrH2][O+][123I][As-][PH][3H][Rb][85SrH2][PH][P@@+][As-][PH][P@@+][P@@+][P@@+][As-][PH][P@@+][As-][PH][3H][TeH2][3H][Rb][85SrH2][PH][3H][Rb][85SrH2][PH][3H][Rb][85SrH2][PH][P@@+][As-][PH][85SrH2][SiH3-][85SrH2][PH]<UNUSED_0>[TeH2][3H]<UNUSED_0>[TeH2][3H]<UNUSED_0>[TeH2][3H][Rb][85SrH2][PH]LogD_change_(3.5, 3.7][PH][85SrH2][PH][85SrH2][PH][85SrH2][PH][C@H][PH][C@H][PH][P@@+]LogD_change_(0.3, 0.5][PH][P@@+]LogD_change_(0.3, 0.5][PH][P@@+][PH][P@@+][PH][85SrH2][PH][85SrH2][PH]']
@chao1224
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chao1224 commented Mar 21, 2024 •
edited
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Hi @gihanpanapitiya,

I noticed that the losses are different, as in the notebook:

clip loss: -0.92124	L2 loss: 0.33059

This seems to be caused by the corrupted checkpoints. Can you help double-check them?

@gihanpanapitiya
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How can I double check?

These are are checkpoint related parameters I use,

########## for foundation ##########
parser.add_argument("--MoleculeSTM_model_dir", type=str, default="../data/demo/demo_checkpoints_SMILES")
parser.add_argument("--MoleculeSTM_molecule_type", type=str, default="SMILES", choices=["SMILES", "Graph"])
parser.add_argument("--vocab_path", type=str, default="../MoleculeSTM/bart_vocab.txt")

########## for generation ##########
parser.add_argument("--MegaMolBART_generation_model_dir", type=str, default="../data/pretrained_MegaMolBART/checkpoints")

########## for foundation and generation projection ##########
parser.add_argument("--language_edit_model_dir", type=str, default="../data/demo/demo_checkpoints_SMILES")

@HantingYang
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Hi, @chao1224 , thank you for your great work! I've been working with your notebook for molecule editing, but I'm running into some issues. Despite multiple attempts, the output doesn't seem to make sense. While the clip loss and L2 loss change, none of the results are valid.

I've directly downloaded the checkpoints from your Hugging Face project, and I'm experiencing the same problem even when using the optimal checkpoints in pretrained_MoleculeSTM_Raw/SciBERT-MegaMolBART-3e-5-1-1e-4-1-InfoNCE-0.1-32-32. Could you help me to get your output?

start editing



===== for text prompt: This molecule is soluble in water. =====
===== for SMILES OC1C2C1CC2 =====
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
Use random noise for init
l2 lambda: 1.0
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 52.32it/s]
clip loss: -0.26693	L2 loss: 0.13136
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
SMILES_list: ['OC1C2C1CC2', '[S@@][Bi]<UNUSED_48>[Cl+3]LogD_change_(5.3, 5.5][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_158><UNUSED_17>[133Xe]<UNUSED_27>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_158><UNUSED_17><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17>[NaH][B]LogD_change_(2.5, 2.7][Cl+3]<UNUSED_108><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_40><UNUSED_7>LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94><UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_37><UNUSED_17><UNUSED_87>[B]<UNUSED_41>[Ag+][AsH][42K+]<UNUSED_41><UNUSED_7><UNUSED_41>[Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, -0.9]<UNUSED_48>Clint_low->high[Te]<UNUSED_167>[85Sr+2]<UNUSED_17>[85Sr+2]<UNUSED_17>[85Sr+2]<UNUSED_17><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1[Ag+]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][11C][Ag+]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_41><UNUSED_17>[11C][Ag+][Cl+3]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[Cl+3][S-2]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_43><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7>Clint_low->high[Te][B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B][B][B][B][B][B][B][B]<UNUSED_41><UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->highLogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_164>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high[Te]<UNUSED_167><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[S@@]Clint_low->high<UNUSED_87><UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_48><UNUSED_48><UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>Clint_low->high<UNUSED_94><UNUSED_12><UNUSED_12><UNUSED_12><UNUSED_12>[S@@][Bi]<UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>[B]<UNUSED_41><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_17><UNUSED_94>[Bi]<UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_12>[As]<UNUSED_17><UNUSED_48>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17><UNUSED_94>[Cl+3][S-2]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[Bi][Bi][Bi]LogD_change_(0.7, 0.9]<UNUSED_12><UNUSED_17><UNUSED_94><UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_48>[Cl+3][Cl+3][B]<UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high[Te]<UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->highLogD_change_(0.7, 0.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>LogD_change_(0.7, 0.9]<UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17><UNUSED_142><UNUSED_142>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Cl+3]<UNUSED_41><UNUSED_17>[11C]<UNUSED_48>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9][11C]<UNUSED_142>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[F-][Te]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>[F-][Te][Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_48>', '[S@@]<UNUSED_112>[42K+][AsH][42K+][AsH][42K+][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[BH2-]<UNUSED_18>[BH2-][125IH]<UNUSED_10>[Cs+]<UNUSED_82>[Cl+3][S-2]<UNUSED_10><UNUSED_112>[BH2-]<UNUSED_37><UNUSED_17><UNUSED_94>[Li][BH2-][Ag+][AsH][42K+][BH2-][Ag+][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_142><UNUSED_164>[AsH][42K+]<UNUSED_18>[BH2-]<UNUSED_37>[BH2-]<UNUSED_18>[AsH][42K+]<UNUSED_18><UNUSED_18>[BH2-][Ag+][AsH][42K+]<UNUSED_18>[BH2-]<UNUSED_18>[BH2-]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>[BH2-]<UNUSED_37><UNUSED_94>[BH2-]<UNUSED_37>[BH2-]<UNUSED_37>[BH2-][Ag+][AsH][42K+]<UNUSED_18>[BH2-][Ag+][AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>[AsH][85Sr+2][AsH][85Sr+2][BH2-][Ag+]<UNUSED_94>[Li][BH2-][Ag+]<UNUSED_94>[BH2-][Ag+][Cl+3]<UNUSED_112>[BH2-][Ag+][AsH][42K+][BH2-][Ag+][Cl+3][S-2][Ag+]<UNUSED_94>[BH2-][Ag+][AsH][42K+][BH2-][Ag+][Cl+3][S-2][BH2-][BH2-][BH2-][BH2-][BH2-][BH2-][Ag+][AsH][42K+][BH2-][Ag+][AsH][42K+][Ag+][AsH][42K+]<UNUSED_18>[BH2-][Ag+][AsH][42K+]<UNUSED_18>[BH2-]<UNUSED_18>[BH2-][Ag+][AsH][42K+]<SEP>[Ag+][AsH]LogD_change_(1.7, 1.9]<UNUSED_48>[SeH]LogD_change_(1.7, 1.9]<UNUSED_48>[SeH]LogD_change_(1.7, 1.9]<UNUSED_48><UNUSED_82>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94>[BH2-]<UNUSED_12>[SeH]LogD_change_(1.7, 1.9][BH2-]<UNUSED_12>[SeH][BH2-][BH2-][BH2-][S@@][SeH][BH2-][S@@]Clint_low->high<UNUSED_94>[BH2-]<UNUSED_37><UNUSED_94>[BH2-][BH2-]<UNUSED_37><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_112>[BH2-]<UNUSED_12><UNUSED_112>[BH2-][Ag+]<UNUSED_94>[BH2-][S@@][Bi][BH2-][Ag+][AsH][42K+]<UNUSED_164><UNUSED_92>[Cl+3][S-2][Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>[Cl+3][S-2][Ag+][Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>Clint_low->high[B-]<UNUSED_48>Clint_low->high[S-2]<UNUSED_48>Clint_low->high[B-][Ag+]<UNUSED_94>[Li][As]<UNUSED_82>[Cl+3][S-2]Clint_low->high[B-][Ag+][AsH][42K+]<SEP>[Ag+][AsH][42K+]<UNUSED_18>[BH2-]Clint_low->high[B-][P-3]<UNUSED_112>[BH2-]<UNUSED_18>[BH2-][S-2]<UNUSED_112>[BH2-][S@@]Clint_low->high[B-]<UNUSED_48>Clint_low->high[B-]<UNUSED_48>Clint_low->high[B-]<UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_18>[BH2-]<UNUSED_18>[BH2-]<UNUSED_18>[BH2-][S-2]<UNUSED_48><UNUSED_18>[BH2-]<UNUSED_94>[BH2-][S-2]<UNUSED_48>Clint_low->high<UNUSED_94>[BH2-]<UNUSED_94>[BH2-][S@@]Clint_low->high<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94><UNUSED_48><UNUSED_48>[Cl+3]<UNUSED_94>[BH2-]<UNUSED_12><UNUSED_112>[BH2-]<UNUSED_12><UNUSED_43><UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94><UNUSED_94><UNUSED_94><UNUSED_94><UNUSED_94>[BH2-]<UNUSED_37><UNUSED_94>[BH2-]<UNUSED_12>[As]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-][S-2][BH2-][S-2][Ag+]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[Cl+3]<UNUSED_94>[Se-]<UNUSED_112>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_12><UNUSED_112>[BH2-]<UNUSED_12><UNUSED_112>[BH2-][Ag+][Cl+3][S-2]<UNUSED_48>[Cl+3]<UNUSED_94>[BH2-]<UNUSED_37><UNUSED_94>[BH2-]<UNUSED_94>[Se-]<UNUSED_112>[BH2-]<UNUSED_37><UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_94>[BH2-]<UNUSED_37><UNUSED_94>[BH2-]<UNUSED_12><SEP><UNUSED_12>Clint_low->high<UNUSED_94>[BH2-][S@@]Clint_low->high<UNUSED_94><SEP>[Ag+]<UNUSED_94>[BH2-][S@@]Clint_low->high<UNUSED_94>[BH2-][S@@]Clint_low->high<UNUSED_94>[BH2-][S@@][P+]<UNUSED_94>[BH2-][BH2-]<UNUSED_12>[AsH][42K+]<SEP>[Ag+]<UNUSED_94>[BH2-]LogD_change_(-4.1, -3.9][BH2-]LogD_change_(-4.1, -3.9][BH2-]<UNUSED_94><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142>[Bi]<SEP>[Ag+]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[P+]<UNUSED_94>[BH2-][S@@]Clint_low->high[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[BH2-]LogD_change_(-4.1, -3.9][BH2-]LogD_change_(-4.1, -3.9][BH2-][Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3][S-2][Cl+3]<UNUSED_94>[BH2-]LogD_change_(-4.1, -3.9][BH2-][Te]<UNUSED_94>[Cl+3]<UNUSED_94>[Se-][Cl+3][S-2][Cl+3][S-2]<UNUSED_48>[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3][S-2]<UNUSED_48>Clint_low->high[Te]<UNUSED_94>[BH2-][Te]<UNUSED_94>[Bi][AsH][85Sr+2]']

@chao1224
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Hi @HantingYang,

Can you help check #16? You need to tune the hyper l2 lambda.

@HantingYang
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Hi @HantingYang,

Can you help check #16? You need to tune the hyper l2 lambda.

Hi, thanks for getting back to me so quickly! I've been playing around with different l2 lambda values, but I'm still getting the same weird output. Are there any other settings I should be tweaking? Really appreciate your help on this!

start editing



===== for text prompt: This molecule is soluble in water. =====
===== for SMILES OC1C2C1CC2 =====
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
Use random noise for init
l2 lambda: 10
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 51.07it/s]
clip loss: -0.00805	L2 loss: 0.06729
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
SMILES_list: ['OC1C2C1CC2', '[S@@][Bi]<UNUSED_48>[Cl+3]LogD_change_(5.3, 5.5][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_158><UNUSED_17>[133Xe]<UNUSED_27>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_158><UNUSED_17><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17>[NaH][B]LogD_change_(2.5, 2.7][Cl+3]<UNUSED_108><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_40><UNUSED_7>LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94><UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_37><UNUSED_17><UNUSED_87>[B]<UNUSED_41>[Ag+][AsH][42K+]<UNUSED_41><UNUSED_7><UNUSED_41>[Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, -0.9]<UNUSED_48>Clint_low->high[Te]<UNUSED_167>[85Sr+2]<UNUSED_17>[85Sr+2]<UNUSED_17>[85Sr+2]<UNUSED_17><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1[Ag+]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][11C][Ag+]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_41><UNUSED_17>[11C][Ag+][Cl+3]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[Cl+3][S-2]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_43><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7>Clint_low->high[Te][B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B][B][B][B][B][B][B][B]<UNUSED_41><UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->highLogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_164>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high[Te]<UNUSED_167><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[S@@]Clint_low->high<UNUSED_87><UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_48><UNUSED_48><UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>Clint_low->high<UNUSED_94><UNUSED_12><UNUSED_12><UNUSED_12><UNUSED_12>[S@@][Bi]<UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>[B]<UNUSED_41><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_17><UNUSED_94>[Bi]<UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_12>[As]<UNUSED_17><UNUSED_48>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17><UNUSED_94>[Cl+3][S-2]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[Bi][Bi][Bi]LogD_change_(0.7, 0.9]<UNUSED_12><UNUSED_17><UNUSED_94><UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_48>[Cl+3][Cl+3][B]<UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high[Te]<UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->highLogD_change_(0.7, 0.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>LogD_change_(0.7, 0.9]<UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17><UNUSED_142><UNUSED_142>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Cl+3]<UNUSED_41><UNUSED_17>[11C]<UNUSED_48>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9][11C]<UNUSED_142>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[F-][Te]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>[F-][Te][Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_48>', '[S@@][Bi]<UNUSED_48>[Cl+3]LogD_change_(5.3, 5.5][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_158><UNUSED_17>[133Xe]<UNUSED_27>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_158><UNUSED_17><UNUSED_142>[Bi]<UNUSED_48>Clint_low->high1[Ag+][Cl+3][Ag+][Cl+3][Ag+][Cl+3][Ag+][Cl+3]<UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_142><UNUSED_164>[Ag+][AsH][85Sr+2][AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94><UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_12>[Ag+][AsH][Ag+][AsH][42K+]<UNUSED_41><UNUSED_7><UNUSED_41>[Ag+][Cl+3][Ag+][Cl+3][Ag+][AsH][85Sr+2]LogD_change_(-1.1, -0.9]<UNUSED_40>LogD_change_(-1.1, -0.9]<UNUSED_40><UNUSED_41>[Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9]<UNUSED_82>LogD_change_(1.7, 1.9]<UNUSED_48><UNUSED_82>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high[Te][BH2-][Ag+]LogD_change_(-1.1, -0.9]<UNUSED_82>[11C][Ag+]LogD_change_(-1.1, -0.9]<UNUSED_12>[Ag+]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+]LogD_change_(-1.1, -0.9][Ag+][Cl+3][Ag+][Cl+3]<UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48><SEP>[Ag+]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_43><UNUSED_142>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_43><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B]<UNUSED_41><UNUSED_7>LogD_change_(0.7, 0.9]<UNUSED_7>Clint_low->high[Te][B]<UNUSED_41><UNUSED_7>[Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>[B][B][B][B][B][B]<UNUSED_41><UNUSED_17><UNUSED_94>[B][B][B][B][B]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->highLogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_164>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high[Te]<UNUSED_167><UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[S@@]Clint_low->highLogD_change_(-3.3, -3.1]<UNUSED_17><UNUSED_94><UNUSED_41><UNUSED_7><UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_167><UNUSED_17><UNUSED_94><UNUSED_48><UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>Clint_low->high<UNUSED_94><UNUSED_12><UNUSED_43><UNUSED_142><UNUSED_12>[S@@][Bi]<UNUSED_48>[Cl+3]<UNUSED_94><UNUSED_12>[B]<UNUSED_41><UNUSED_12>[B]<UNUSED_41><UNUSED_7><UNUSED_12>Clint_low->high<UNUSED_94>[Bi]<UNUSED_48>Clint_low->high<UNUSED_94><UNUSED_12>[As]<UNUSED_17><UNUSED_48>Clint_low->high<UNUSED_106>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12><UNUSED_17><UNUSED_94>[BH2-]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_94><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_92><UNUSED_41><UNUSED_17><UNUSED_94>[Bi]LogD_change_(0.7, 0.9]<UNUSED_12>[S@@]Clint_low->high[Te]<UNUSED_17><UNUSED_94>LogD_change_(0.7, 0.9][Cl+3][Cl+3][B]<UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high[Te]<UNUSED_94>[Bi]<UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high<UNUSED_106>[Bi]<UNUSED_48><UNUSED_48>Clint_low->highLogD_change_(0.7, 0.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_94><SEP><UNUSED_12><SEP><UNUSED_12>[S@@]Clint_low->high[Te]<UNUSED_94>LogD_change_(0.7, 0.9]<UNUSED_82><UNUSED_193><UNUSED_112><SEP><UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142>[B]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[B]<UNUSED_41><UNUSED_7><UNUSED_41>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9][CH]LogD_change_(-4.1, -3.9]<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_48>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9][Cl+3]<UNUSED_41>[Cl+3]<UNUSED_41>[F-][Te][Cl+3]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>[F-][Te]<UNUSED_41>LogD_change_(-4.1, -3.9]LogD_change_(-1.5, -1.3]Clint_low->high[Te]<UNUSED_167>LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>[Bi]LogD_change_(-1.1, -0.9]']

l2 lambda: 1.0
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 51.04it/s]
clip loss: -0.29620	L2 loss: 0.15633
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
SMILES_list: ['OC1C2C1CC2', '[S@@][Bi]<UNUSED_48>[Cl+3]LogD_change_(5.3, 5.5][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_158><UNUSED_17>[133Xe]<UNUSED_27>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_158><UNUSED_17><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17>[NaH][B]LogD_change_(2.5, 2.7][Cl+3]<UNUSED_108><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_40><UNUSED_7>LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94><UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_37><UNUSED_17><UNUSED_87>[B]<UNUSED_41>[Ag+][AsH][42K+]<UNUSED_41><UNUSED_7><UNUSED_41>[Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, 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0.9]<UNUSED_12><UNUSED_17><UNUSED_94><UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_48>[Cl+3][Cl+3][B]<UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high[Te]<UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->highLogD_change_(0.7, 0.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>LogD_change_(0.7, 0.9]<UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17><UNUSED_142><UNUSED_142>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Cl+3]<UNUSED_41><UNUSED_17>[11C]<UNUSED_48>[Cl+3]<UNUSED_41>LogD_change_(-4.1, 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1.9][Cl+3][S-2][Cl+3][S-2][Cl+3][S-2][Cl+3][S-2]<UNUSED_48>[Cl+3][S-2][Ag+][Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>Clint_low->high[S-2]<UNUSED_48>Clint_low->high[S-2]<UNUSED_48>Clint_low->high[B-]LogD_change_(-1.1, -0.9]<UNUSED_82>[B]<UNUSED_7>6Clint_low->high[B-][Ag+][Cl+3][S-2]<UNUSED_48>Clint_low->high[B-][P-3]<UNUSED_82>[13C][BH2-][Bi][BH2-]Clint_low->high[B-][P-3][BH2-]<UNUSED_18>[BH2-][S-2]<UNUSED_112>[BH2-][S@@][Bi]LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high[B-][P-3][BH2-]<UNUSED_12><UNUSED_43><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, 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-1.9]<UNUSED_94>[BH2-]LogD_change_(-4.1, -3.9][BH2-]<UNUSED_94>[BH2-]<UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142><UNUSED_142>[Bi]6<UNUSED_145>[BH2-]<UNUSED_12><SEP><UNUSED_12><SEP>[Ag+][Cl+3][S-2]<UNUSED_142>[Cl+3][S-2][Cl+3]<UNUSED_94>[Cl+3]<UNUSED_94>[BH2-]LogD_change_(-4.1, -3.9][BH2-][Cl+3][S-2][Cl+3]<UNUSED_94>[Cl+3][S-2][Cl+3][S-2][Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>[Cl+3][S-2]<UNUSED_48>[Cl+3][S-2][Cl+3][S-2][Cl+3][S-2]<UNUSED_48>Clint_low->highBr[Cl+3][S-2]<UNUSED_48>Clint_low->high[B-]<UNUSED_48>Clint_low->high[Te][BH2-]LogD_change_(-4.1, -3.9]LogD_change_(-1.5, -1.3]Clint_low->high[AsH]']

l2 lambda: 0.1
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 50.98it/s]
clip loss: -0.96769	L2 loss: 0.11409
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
SMILES_list: ['OC1C2C1CC2', '[S@@][Bi]<UNUSED_48>[Cl+3]LogD_change_(5.3, 5.5][AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164>[AsH][42K+]<UNUSED_164><UNUSED_158><UNUSED_17>[133Xe]<UNUSED_27>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_158><UNUSED_17><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17><UNUSED_17>[NaH][B]LogD_change_(2.5, 2.7][Cl+3]<UNUSED_108><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[B]LogD_change_(2.5, 2.7]<UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_40><UNUSED_7>LogD_change_(2.5, 2.7]<UNUSED_37><UNUSED_17><UNUSED_87>[AsH][42K+]<UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18><UNUSED_18>LogD_change_(1.7, 1.9]<UNUSED_48>Clint_low->high1<UNUSED_94><UNUSED_37>LogD_change_(-1.1, -0.9]<UNUSED_37><UNUSED_17><UNUSED_87>[B]<UNUSED_41>[Ag+][AsH][42K+]<UNUSED_41><UNUSED_7><UNUSED_41>[Ag+][Cl+3][Ag+][Cl+3][Ag+]LogD_change_(-1.1, 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1.9]<UNUSED_48>[B]<UNUSED_41><UNUSED_7><UNUSED_12><UNUSED_43><UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, -0.9]LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9]<UNUSED_12>LogD_change_(-1.1, -0.9][Bi]LogD_change_(-1.1, 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0.9]<UNUSED_12><UNUSED_17><UNUSED_94><UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_48>[Cl+3][Cl+3][B]<UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->high[Te]<UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_94><UNUSED_37><UNUSED_94><UNUSED_37><UNUSED_17><UNUSED_48><UNUSED_48><UNUSED_48>Clint_low->highLogD_change_(0.7, 0.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_94>[Cl+3]<UNUSED_94>[Cl+3]LogD_change_(-4.1, -3.9]<UNUSED_12>Clint_low->high[Te]<UNUSED_17><UNUSED_94>LogD_change_(0.7, 0.9]<UNUSED_12>[B]<UNUSED_17><UNUSED_94>[Cl+3]<UNUSED_41><UNUSED_17><UNUSED_94>[Bi]<SEP><UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41>LogD_change_(-4.1, -3.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17><UNUSED_142><UNUSED_142>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Bi]LogD_change_(-1.1, -0.9]<UNUSED_12>[B]<UNUSED_41><UNUSED_17>[11C]<UNUSED_142>[Cl+3]<UNUSED_41><UNUSED_17>[11C]<UNUSED_48>[Cl+3]<UNUSED_41>LogD_change_(-4.1, 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1.9]Br[BH2-][S-2][BH2-][SH-]Br[BH2-][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra]<UNUSED_2><UNUSED_179>[Br+2]BrBr[223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra]BrBrBrBrBrBrBrBrBrBrBrBrBr[BH2-]<UNUSED_179><UNUSED_179>[Br+2][se][BH2-]<UNUSED_2>6<UNUSED_179>[Br+2]Br[BH2-]<UNUSED_2>[BH2-][S@@]<UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_2>[BH2-]<UNUSED_2>[BH2-]<UNUSED_2>[BH2-]<UNUSED_2><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179>[Br+2]Br[BH2-]<UNUSED_2>[BH2-]<UNUSED_2>[BH2-]<UNUSED_2>BrBr<UNUSED_12><UNUSED_134><UNUSED_134><UNUSED_134><UNUSED_134><UNUSED_156>Br[BH2-]<UNUSED_2><UNUSED_134><UNUSED_164>[S@@]LogD_change_(4.7, 4.9]<UNUSED_2>6<UNUSED_134><UNUSED_164>[S@@][Si]LogD_change_(1.7, 1.9]<UNUSED_156>Br[P@@+][BH2-][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][SeH]LogD_change_(1.7, 1.9]<UNUSED_134><UNUSED_164>[BH2-][S@@][SeH][BH2-][S@@]LogD_change_(4.7, 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1.9]<UNUSED_156>Br<UNUSED_12>[Si][BH2-]<UNUSED_12>[IH2]<UNUSED_12>[IH2]<UNUSED_12>[IH2]<UNUSED_12>[S@@][Si]LogD_change_(1.7, 1.9]<UNUSED_156>Br<UNUSED_12><UNUSED_12>[S@@][Si]LogD_change_(1.7, 1.9]<UNUSED_156>Br<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_156>Br<UNUSED_12>LogD_change_(1.7, 1.9]<UNUSED_156>[BH2-]<UNUSED_12><UNUSED_194><UNUSED_94>[Si]LogD_change_(1.7, 1.9]<UNUSED_156>Br<UNUSED_12>[S@@]LogD_change_(4.7, 4.9]<UNUSED_12><UNUSED_12>[Si]LogD_change_(1.7, 1.9]<UNUSED_156>[BH2-]<UNUSED_156>[BH2-]<UNUSED_156>[BH2-][S-2]<UNUSED_134><UNUSED_1><UNUSED_88>[S@@]LogD_change_(1.7, 1.9]<UNUSED_156>[Se-][BH2-]<UNUSED_2>[BH2-]<UNUSED_2><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179>[IH2]<UNUSED_12>[Si]LogD_change_(1.7, 1.9]<UNUSED_156>Br<UNUSED_12>[IH2]<UNUSED_12>[IH2]<UNUSED_12>[Si][BH2-][223Ra]<UNUSED_48><UNUSED_48><UNUSED_48><UNUSED_48>[se]<UNUSED_94>[Se-]<UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179><UNUSED_179>[Br+2]<UNUSED_12>[IH2]<UNUSED_12>[IH2]<UNUSED_12>[IH2]<UNUSED_12>[S@@][Si][BH2-][S@@][Si][Si][Si][Si][Si][BH2-][S@@][Si][BH2-]<UNUSED_2>6[223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra][223Ra]']

l2 lambda: 0.01
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 50.82it/s]
clip loss: -0.94331	L2 loss: 0.03802
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
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l2 lambda: 0.001
Use random noise for init
100%|██████████| 100/100 [00:01<00:00, 52.22it/s]
clip loss: -0.92840	L2 loss: 0.00467
WARNING: MOLECULE VALIDATION AND SANITIZATION CURRENTLY DISABLED
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@HantingYang
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Sorry I make a stupid mistake. I forgot to download the pretrained MegaMolBART models. It's working fine now. Thanks for your help!

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@chao1224 @gihanpanapitiya @HantingYang