laituan245 / bio_relex

Joint Biomedical Entity and Relation Extraction with Knowledge-Enhanced Collective Inference

Hi there 👋

I am a computer science Ph.D. student at the University of Illinois at Urbana-Champaign. My work focuses on deep learning for information extraction and natural language understanding. I completed my undergraduate degree in Computer Science at KAIST. I completed my Masters’s degree in Computer Science at the Purdue University.

bio_relex's Issues

Files other than datasets are not found in resources, can you give a detailed link?

How to get additional files in resources？

Dear Tuan Lai,

I am a researcher at the university of hong kong. I read your great work entitled 'Joint Biomedical Entity and Relation Extraction with knowledge-Enhanced Collective Inference'. I would like to try your great work by the code you provided at Github. However, I found that additional files in the resources folder can not be found.

Could you please help me with accessing them? Many thanks for your help! I will definitely cite your great work when I have some results.

Best,
Xiaolin Han

How to extract the five files in resource folder.

Hi! I'm a researcher from Central South University. Thanks for your great work. I'd like to learn from your work. I have UMLS and MetaMap installed on my device, but I don't know how to extract the five files in your resource folder.

--- umls_embs.pkl
--- umls_rels.txt
--- umls_reltypes.txt
--- umls_semtypes.txt
--- text2graph.pkl

Could you please teach me how to obtain these documents? It would be better if you could directly provide these documents to me. If our work comes to fruition, we will certainly cite your work​

关于umls数据问题

您好：
非常感谢您的代码分享，但是我在ulms中没有找到umls_embs.pkl，umls_rels.txt，umls_reltypes.txt， umls_semtypes.txt，text2graph.pkl这几个文件，希望您能分享一下，非常感谢。

Ade dataset

Hi ~ I would like to ask about the "relations" in each data dictionary in ADE dataset,
eg. "relations":[
{
"type": "Adverse-Effect",
"head": 0,
"tail": 1
}
"orig_id": 83
what does "head: 0" and "tail: 1" mean? and what is "orig_id" ?
Thanks!

How to calculate umls additional files

Hi,
I can't seem to find the scripts you used to calculate the additional UMLS related files and text2graph.pkl.
I also sent you an email on this matter.
I also hope you could give some insight on how to adapt your work on different datasets (like creating text2graph on different datasets).
Thank you for your work!

How to get umls file?

I found I couldn't find these five files --- umls_embs.pkl

--- umls_rels.txt
--- umls_reltypes.txt
--- umls_semtypes.txt
--- text2graph.pkl

I have download the UMLS-2020aa-fill file and installed in my device. But I don't know how to use it.
Can you tell me how to get additional files in resources? thank you.

I already send email to you email address. Looking forward to your reply.

How to get additional files in resources

I'm sorry to mention this issue，because I didn't find a way to use umls.Can you tell me how to get additional files in resources? thank you.