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I was wondering if there is a wish to also include temporal graph neural networks architectures in this repo or if that is preferred to be as a separate package?
There's PyTorch Geometric and PyTor…
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Opening up an issue to centralize discussion because I've been commenting on this topic in a number of PRs. We should think carefully about structuring the outputs of the chemprop CLI. Irrespective of…
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Hello,
I have a pretrained model using chemprop on a large dataset and I would like to use transfer learning to build a new model on a small dataset. To this end, I would like to keep the directed-me…
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**Describe the bug**
I'm having a runtimeError problem when running the training cell.
I'm using a dataset whose target is binary.
splitting randomly.
I'm not sure if this is a bug, but I was…
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- [x] function to score a structure using ProteinMPNN
- [x] allow moving a single chain away from the COM by 100 angstroms to roughly score ddG
- [x] score using this
- [x] check if this score has …
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Trying to train a classification model on my data results in error saying that I have -1 in target, while my data in target contains 0 and 1 only (please check screenshot).
```
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**Describe the bug**
`MPNN.encoding()` is designed to obtain the final hidden representations for the input molecules. However, when calling this function, an error will occur.
**Example(s)**
```…
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**Description:**
- DeepChem Version: 2.1.1
- Platform: MacOS 10.14.2
Encountered a dimensionality error when the model tried to reshape pair features. My sample code:
```
import deepche…
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Currently have some small-scale design setups for this, but should should be optimized:
Faster parameters
- [ ] num_recycles 1
- [ ] num_mpnn 10
- [ ] lower oligomer offset 1
- [ ] upper oligom…
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Hello,
I have a model using Chemprop for a big dataset and I would like to do transfer learning using "Pretraining" flag of chemprop for a related small dataset. Based on Chemprop, there are three wa…