Open sleeper2173 opened 5 years ago
Which model (network) you are using? Can you share your prediction code?
Please refer typical usage for predict
method.
https://github.com/pfnet-research/chainer-chemistry/blob/master/examples/qm9/predict_qm9.py#L146
train_qm9.py.txt predict_qm9.py.txt
Thank you for your quick reply. I attached the code files train_qm9.py (same as the original) and predict_qm9.py (just modified few lines). Our problem could be reproduced as follows: 1) training a qm9 model python train_qm9.py \ --method ggnn \ --label A \ --conv-layers 1 \ --gpu 0 \ --epoch 10 \ --unit-num 10 \ --num-data 100
2) predict the property of the first molecule python predict_qm9.py \ --method ggnn \ --label A \ --gpu -1 \ --num-data 1
3) predict the properties of the first 10 molecules python predict_qm9.py \ --method ggnn \ --label A \ --gpu -1 \ --num-data 10
I get the difference between predicted values of the first molecule at 2) and 3).
Thank you for the report.
What we know is actually current GGNN model is not input size invariant. When 0-vector is padded for the "virtual node", its output value changes. We are going to fix this by the following PR. https://github.com/pfnet-research/chainer-chemistry/pull/311
I am trying to predict molecular properties using a pre-traind model. Howeber, I find that the predicted values are changing with a different number of input molecules and a different batchsize parameter in the predict() function. How to get unique values?