BioREx

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Some rows contain ''None" labels.

1

When I run `bash scripts/build_biorex_datasets.sh`, the error occurs. https://github.com/ncbi/BioREx/blob/0031c52d2dd0d7fb8e3b84e256d8fbf73c4bd463/src/run_ncbi_rel_exp.py#L112 Here, the code emits an error, because it cannot find a label when the label is ''. I think the https://github.com/ncbi/BioREx/blob/0031c52d2dd0d7fb8e3b84e256d8fbf73c4bd463/src/run_ncbi_rel_exp.py#L148...

dongheechoi

run_biorex_exp.sh doesn't seem to use GPU

1

I tried to run the script but I don't think it is using a GPU. I stopped the code before this line (https://github.com/ncbi/BioREx/blob/0031c52d2dd0d7fb8e3b84e256d8fbf73c4bd463/src/tf_wrapper.py#L199C28-L200C1), and check it whether using GPU or...

dongheechoi

Can you proivde a script or an explanation to reproduce scores in your paper?

2

In the paper (https://arxiv.org/abs/2306.11189), you wrote the scores below. Can you kindly provide a way to reproduce this?   For example, with the model you provided in the repo...

dongheechoi

Loaded 0 parameters in the TF 2.0 model. Some weights of the model were not used when initializing the TF 2.0 model TFBertForSequenceClassification

1

**I tried to run ’scripts/run_biorex_exp.sh‘ to reproduce your results, but ran into the following trouble: When I test directly with microsoft pre-trained models, the warning prompts:** > [INFO|modeling_tf_utils.py:2830] 2024-02-29 20:59:44,616...

lou-yimin