awslabs / awslabs/graphstorm

[Feature request] Support nodes transform and with multiple textual fields

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Dominant language
Python
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452
Forks
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Description

Some nodes may contain more than one fields of texts (e.g. title, key words, description). The current best practices is to concatenate them before tokenization. However, there are cases where concatenation is infeasible: leading to long texts beyond LM's receptive fields; and mixed types of languages:

```
{
"node_type": "drug",
"format": {
"name": "parquet"
},
"files": [... ],
"node_id_col": "ent idx",
"features": [
{
"feature_col": "name",
"feature_name": "name",
"transform": {
"name": "tokenize_hf",
"bert_model": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext",
"max_seq_length": 256
}
},
{
"feature_col": "SMILES_string",
"feature_name": "SMILES_string",
"transform": {
"name": "tokenize_hf",
"bert_model": "DeepChem/ChemBERTa-77M-MLM",
"max_seq_length": 256
}
}
]
}
```

Contributor guide

Open the contributing guide

Research direction

No files, tests, or entry points are named in the issue. Start by locating the existing node feature transformation and tokenization configuration, then determine how multiple textual feature fields can retain separate transforms; done means fields such as name and SMILES_string can be processed independently without concatenation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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