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Add SMILES string to data samples #321

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kshitij-v-mehta opened this issue Jan 28, 2025 · 0 comments
Open

Add SMILES string to data samples #321

kshitij-v-mehta opened this issue Jan 28, 2025 · 0 comments
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enhancement New feature or request

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Write the SMILES string for a data sample to the output dataset and read it back during training.
@kshitij-v-mehta kshitij-v-mehta added the enhancement New feature or request label Jan 28, 2025
@kshitij-v-mehta kshitij-v-mehta self-assigned this Jan 28, 2025
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
Set the smiles string in the object ORNL#321
5923068
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
creates a new attributes 'smiles' in the Data class ORNL#321
2ca1cab
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
Adds the smiles string to the Data object for the CSCE example ORNL#321
1859079
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
Writing smiles strings to ADIOS ORNL#321
29bc4d7
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
not adding smiles to list of keys in adios ORNL#321
2e0cfd9
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 6, 2025
adding smiles to 'keys' in adios output ORNL#321
5d72ea5
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 13, 2025
edits to smiles string writing. arrays renamed to smiles_data and smi…
65afae0 
…les_lengths ORNL#321
kshitij-v-mehta pushed a commit to kshitij-v-mehta/HydraGNN that referenced this issue Feb 13, 2025
function to read smiles strings ORNL#321
f285923
allaffa added a commit that referenced this issue Mar 15, 2025
@kshitij-v-mehta @allaffa
@jychoi-hpc @licj15 @streeve
Smiles strings 321 (#332)
e03feb3 
* adds dataset_name attribute to the base class and reads it into a data sample #319

* adds dataset_name to the Data class a kwarg #319

* dataset_name example for csce #319

* GraphGPS arguments added to JSON file for CSCE examplke

* formatting edits #319

* formatting #319

* isng model fixed

* Set the smiles string in the object #321

* checking to see if dataset_name is in keys before attempting to remove it #319

* creates a new attributes 'smiles' in the Data class #321

* Adds the smiles string to the Data object for the CSCE example #321

* Writing smiles strings to ADIOS #321

* not adding smiles to list of keys in adios #321

* adding smiles to 'keys' in adios output #321

* Not sure if smiles should be read this way

* edits to smiles string writing. arrays renamed to smiles_data and smiles_lengths #321

* function to read smiles strings #321

* update on smiles string in adios

* Add multidataset example with deepspeed support (#316)

* Add multidataset example with deepspeed support

* Change base.json to follow GPS' requirement

* update caching from v2 to v4 for CI workflows and fix formatting of deepspeed example  (#325)

* formatting of deepspeed python scripts fixed

* actions/cache upgrade from v2 to v4

* CI: run on ubuntu-latest (#330)

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Co-authored-by: Kshitij V. Mehta <[email protected]>
Co-authored-by: allaffa <[email protected]>
Co-authored-by: Choi <[email protected]>
Co-authored-by: Chaojian Li <[email protected]>
Co-authored-by: Sam Reeve <[email protected]>
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