BioREx
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ncbi
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...
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...
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...
**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...
I used AIONER output to extract relations, but it didn't work. Went through the issues and found the example to be in BioRED repo. Want to know how to create...
I've encountered an issue where I'm unable to reproduce the relationship extraction results from the PubTator3 website (example: [19394258](https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publication/19394258/export/pubtator)) using BioREx. When I run the tool using the suggested model,...
Hi @potinglai , PyTorch 2.7.0 just came out. Any chance BioRex can be updated to this latest version? Thanks!
Hey there! I saw in the BioREx paper that 'DrugProt-Chem' is used as an entity type, but in the merged BioREx _train.tsv_ I only see the value of 'Chemical'. Was...
Hello.. It is important for a study that we are conducting to be sure about the directionality of the relations in BioRex. Some of then are easy to see but...
