Wengong Jin

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icon company CSAIL, Massachusetts Institute of Technology icon location Boston, MA

Results 21 comments of Wengong Jin

ValueError: Tried to convert 'indices' to a tensor and failed. Error: Argument must be a dense tensor: range(0, 3) - got shape [3], but wanted [].

This is very surprising. Which tensorflow version are you using? I know there's discrepancy between tf.0.12.0 and tf 1.0+. We only tested our code on v0.12.0.

missing functions

Hi, Suppose you downloaded our code at $BASEDIR/graph_knn, please run the following command to add all modules in the pythonpath. ``` export PYTHONPATH=$BASEDIR/graph_knn ``` Then python will not complain about...

pretrain molopt or molvae not working

Hi, I apologize for my late reply. I tested my code on ubuntu 14.04 / python 2.7 / cuda 8.0 / pytorch 0.3.1 / rdkit 2017_09 with NVIDIA TITAN X...

I know, I know. Thank you for responding to my question. What I want to ask is why you sort them like this, for example ('B', 0), ('B', -1) and ('Br', 0), ('Br', -1), ('Br', 2), etc. all start with 0 charge, then why 'I' starts with -1 charge，such as ('I', -1), ('I', 0), ('I', 1), ('I', 2), ('I', 3)?

Oh I see. Uh... There is no particular ordering I think... The order doesn't change the result and I don't remember why there are in this order...

GPU memory growth

Hi, You can try three things: 1. reduce batch size 2. reduce hidden size from 450 -> 300, for instance. 2. In chemutils.py, change `MAX_NCAND` to smaller value. Please also...

Bug on icml18-jtnn/fast_jtnn/chemutils.py", line 324, in check_aroma

Hi, I didn't find the line aenzynes in fast_jtnn/chemutils.py. Could you pull the latest version from github? Wengong

fast molopt

Currently not. In terms of conditional optimization, we developed a new method called graph-to-graph translation that performs much better than running gradient ascent over VAE latent space. The paper and...

Default argument value is mutable

Hi, Thanks for pointing out this issue. It is NOT on purpose (or used as a trick). For MolTreeNode class, I really meant to set default value of `clique=[]`.

Default argument value is mutable

Hi, I did some quick check: For `MolTreeNode()` constructor, I tested the line `super_root = MolTreeNode("")` by printing `super_root.clique`, it always prints `[]` as desired. For `enum_assemble()` function, I tested...

Default argument value is mutable

I don't think this problem will cause memory issues.