How is the limit_data used in exp.json ?

[abhik1368]

When we are training a million molecules should we keep the limit_data as 5000 or we change ? What are the parameters affecting in training a set of 1 million ?

[AustinApple]

Hello, According to the code in the train_vae.py

if 'limit_data' in params.keys():
        sample_idx = np.random.choice(np.arange(len(smiles)), params['limit_data'], replace=False)
        smiles=list(np.array(smiles)[sample_idx])
        if params['do_prop_pred'] and ('data_file' in params):
            if "reg_prop_tasks" in params:
                Y_reg =  Y_reg[sample_idx]
            if "logit_prop_tasks" in params:
                Y_logit =  Y_logit[sample_idx]

so when you want to train a million molecules data you have, you should remove the key "limit_data" in the file exp.json.

[jnwei-zz]

Yeah, you should remove "limit_data" in the exp.json

…

On Tue, Jun 4, 2019 at 6:17 PM AustinApple ***@***.***> wrote: Hello, According to the code in the train_vae.py if 'limit_data' in params.keys(): sample_idx = np.random.choice(np.arange(len(smiles)), params['limit_data'], replace=False) smiles=list(np.array(smiles)[sample_idx]) if params['do_prop_pred'] and ('data_file' in params): if "reg_prop_tasks" in params: Y_reg = Y_reg[sample_idx] if "logit_prop_tasks" in params: Y_logit = Y_logit[sample_idx] so when you want to train a million molecules data you have, you should remove the key "limit_data" in the file exp.json. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_aspuru-2Dguzik-2Dgroup_chemical-5Fvae_issues_21-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DADT3XUA54GMXFLERADWAASLPY3SWPA5CNFSM4HTC4RC2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW6A6SA-23issuecomment-2D498863944&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=UPzYrSHLXjnX3tYn90C8Ljjzb-yfrb1UtMOxOFh-tKk&m=DuM37F6EjV2dncnzpae3f9QfufndP8EGe89i2qLoqyo&s=Tyqck1YFU2YVHO5uca6dy497XxhXdyOniLRlQgODVMg&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADT3XUEUOSXV2ZDKKMXAKEDPY3SWPANCNFSM4HTC4RCQ&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=UPzYrSHLXjnX3tYn90C8Ljjzb-yfrb1UtMOxOFh-tKk&m=DuM37F6EjV2dncnzpae3f9QfufndP8EGe89i2qLoqyo&s=aki1UYtgTX-U9bfGge07i27SA0yIAHIGkp7cCbLorGM&e=> .