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marcopodda / fragment-based-dgm

Code for the paper "A Deep Generative Model for Fragment-Based Molecule Generation" (AISTATS 2020)
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FileNotFoundError: [Errno 2] No such file or directory: 'RUNS/2022-08-02@23:02:24-user-NF5468M6-ZINC/config/vocab.pkl' #3

Open renly0313 opened 2 years ago

renly0313 commented 2 years ago

hi, There is a bug when i run this line 'python manage.py train --dataset '. Training and clustering embeddings... Traceback (most recent call last): File "/home/zhyl_lbw/fragment-based-dgm-master/learner/dataset.py", line 77, in get_vocab self.vocab = Vocab.load(self.config) File "/home/zhyl_lbw/fragment-based-dgm-master/learner/skipgram.py", line 22, in load return load_pickle(path) File "/home/zhyl_lbw/fragment-based-dgm-master/utils/filesystem.py", line 8, in load_pickle return pkl.load(open(path, "rb")) FileNotFoundError: [Errno 2] No such file or directory: 'RUNS/2022-08-02@23:02:24-user-NF5468M6-ZINC/config/vocab.pkl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/zhyl_lbw/fragment-based-dgm-master/manage.py", line 63, in train_model(config) File "/home/zhyl_lbw/fragment-based-dgm-master/manage.py", line 18, in train_model vocab = dataset.get_vocab() File "/home/zhyl_lbw/fragment-based-dgm-master/learner/dataset.py", line 79, in get_vocab self.vocab = Vocab(self.config, self.data) File "/home/zhyl_lbw/fragment-based-dgm-master/learner/skipgram.py", line 34, in init train_embeddings(config, data) File "/home/zhyl_lbw/fragment-based-dgm-master/learner/skipgram.py", line 140, in train_embeddings sg=1) TypeError: init() got an unexpected keyword argument 'size'

This seems to be due to not creating 'vocab.pkl'. could you help me fix it? thank you!

marcopodda commented 2 years ago

Hi and thanks for bringing the issue up, it's probably because you are using an updated version of the gensim library with respect to the one used here. I have updated the code, pull the repo again, and let me know if it works now.

venkatadithya9 commented 2 years ago

Hi, I have the same issue. I have gensim 4.2.0 installed. Here is the error message encountered while training: Training and clustering embeddings... Traceback (most recent call last): File "/home/Desktop/DDDD/fragment-based-dgm/learner/dataset.py", line 77, in get_vocab self.vocab = Vocab.load(self.config) File "/home/Desktop/DDDD/fragment-based-dgm/learner/skipgram.py", line 22, in load return load_pickle(path) File "/home/Desktop/DDDD/fragment-based-dgm/utils/filesystem.py", line 8, in load_pickle return pkl.load(open(path, "rb")) FileNotFoundError: [Errno 2] No such file or directory: 'RUNS/2022-11-07@11:17:21-user-PCBA/config/vocab.pkl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/Desktop/DDDD/fragment-based-dgm/manage.py", line 59, in train_model(config) File "/home/Desktop/DDDD/fragment-based-dgm/manage.py", line 18, in train_model vocab = dataset.get_vocab() File "/home/Desktop/DDDD/fragment-based-dgm/learner/dataset.py", line 79, in get_vocab self.vocab = Vocab(self.config, self.data) File "/home/Desktop/DDDD/fragment-based-dgm/learner/skipgram.py", line 34, in init train_embeddings(config, data) File "/home/Desktop/DDDD/fragment-based-dgm/learner/skipgram.py", line 132, in train_embeddings w2v = Word2Vec( TypeError: Word2Vec.init() got an unexpected keyword argument 'iter'

marcopodda commented 2 years ago

It seems that many Word2Vec arguments have changed their name since the time I coded this. 'iter' is now changed to 'epochs'. It should work again, pull the repo and try again. Thanks for bringing this up!