Comments (3)
chc273
commented on June 18, 2024
Hi @tawe141,
By default, MEGNet model takes the atom feature for each atom to be just the atomic number (integer). Here, the MolecularGraphBatchGenerator generated a specific molecular graph where the atom features for each atom is a vector. Therefore you need to set nfeat_node in MEGNetModel initializer.
The nfeat_node should be set to train_generator[0][0][0].shape[-1]. Please see if this solves your problem. Otherwise please share a minimal dataset that I can work with to solve the issue.
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chc273
commented on June 18, 2024
@tawe141 please also check the example for molecule graphs and model training
https://github.com/materialsvirtuallab/megnet/blob/master/notebooks/molecule_example.ipynb
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tawe141
commented on June 18, 2024
Perfect! Thanks @chc273
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Related Issues (20)
- Can MEGNet be made end-to-end differentiable wrt atomic positions of atoms? HOT 8
- import pybel error HOT 1
- Multi-output Regression HOT 4
- could you please provide an example to predict disordered structure? HOT 12
- Multi classification task HOT 5
- installation issue (RDKit and openbabel must be installed) HOT 3
- Might be nice to see MEGNet on matbench HOT 7
- unlockNN module for uncertainty quantification of MEGNet HOT 5
- code in pytorch? HOT 3
- Problem with load molecule data from ase HOT 4
- how does megnet paper address possible data leakage HOT 1
- Return history of the model using .train_from_graphs HOT 1
- Using megnet for systems having atoms apart from "H", "C", "N", "O", "F" HOT 4
- Breaking up a big molecule into two parts; making predictions from graphs of the two separate "molecular" parts
- Unable to understand the shape of the target/output tensor for example in "Customized Graph Network Models"
- List index out of range while training the NN
- Web App HOT 2
- Web App Access HOT 1
- Review request for disordered structure example HOT 2
- ImportError: cannot import name 'ReduceLRUponNan' from 'megnet.callbacks' in multifidelity/train.py
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