Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Add the DeepDDI model

See original GitHub issue

Dear @hzcheney,

  • Please read the paper first. It is here.
  • After that read the contributing guidelines.
  • If there is an existing open source version of the model please take a look.
  • ChemicalX is built on top of PyTorch 1.10. and torchdrug.
  • A similar model is which uses to generate drug representations. Take a look at the layer definition here.
  • The library heavily builds on top on torchdrug and molecules in batches are PackedGraphs.
  • There is already a model class under ./chemicalx/models/
  • Context features, drug level features and labels are all FloatTensors.
  • Look at the examples and tests under ./examples/ and ./tests/.
  • Add auxiliary layers as you see fit - please document these, add tests and add these layers to the main if needed.
  • Add typing to the initialisation and forward pass.
  • Non data dependent hyperparameters should have default values.
  • Please add tests under ./tests/ and make sure that your model/layer is tested with real data.
  • Write an example under ./examples/. What is the AUC on the test set? Is it reasonable?

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:13 (11 by maintainers)

github_iconTop GitHub Comments

cthoytcommented, Jan 27, 2022

So you could just submit the PR to take in whatever drug features are available from the data loader (currently Morgan fingerprints) and in future work we could add different featurizations to the data loader.

hzcheneycommented, Jan 28, 2022

@hzcheney Are you going to open a PR with your code?

@benedekrozemberczki Yeah! I have already opened a PR and please review it!

Read more comments on GitHub >

github_iconTop Results From Across the Web

Deep learning improves prediction of drug–drug and ... - PNAS
DNN of DeepDDI is a multilabel classification model that can predict multiple DDI types at the same time for a given drug pair....
Read more >
AttentionDDI: Siamese attention-based deep learning method ...
For instance, DeepDDI [6], a multilabel classification model, takes drug structure data as input along with drug names, in order to make DDI ......
Read more >
Drug-Drug Interaction Predicting by Neural Network Using ...
DeepDDI predicts DDIs from chemical structures and names of drugs in ... This model considers drug relationships with the word-embedding ...
Read more >
CNN-DDI: a learning-based method for predicting drug–drug ...
Two similarity-based models based on drug interaction profile ... DeepDDI was proposed [10] to classify the DDIs' events from DrugBank [24].
Read more >
Deep learning predicts drug-drug and drug-food interactions
Scientists have developed a computational framework, DeepDDI, that accurately predicts and generates 86 types of drug-drug and drug-food ...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Post

No results found

github_iconTop Related Hashnode Post

No results found