dmis-lab/biobert issues and pull requests

#196 - Which BioBERT version is best?

Issue - State: open - Opened by Asaad-Pak 4 months ago - 1 comment

#195 - Hope the files can be numbered to guide me in the order of reading.

Issue - State: open - Opened by KKKlingyanqiu123 7 months ago

#194 - vocab.txt内容是啥，如何进行定义。

Issue - State: open - Opened by nibaba007 7 months ago

#193 - Can the server run BioBERT without a GPU?

Issue - State: open - Opened by Liwanglili about 1 year ago - 1 comment

#192 - remove dead link

Pull Request - State: open - Opened by bsenst over 1 year ago

#191 - The link of "this tool" is invalid

Issue - State: open - Opened by happycjksh over 1 year ago - 1 comment

#190 - error :replicating biobert exactly with NCbI dataset

Issue - State: open - Opened by ayodejioogunseye over 1 year ago - 1 comment

#189 - The Dataset link is invalid

Issue - State: open - Opened by Nick0821 over 1 year ago - 6 comments

#188 - Bump tensorflow-gpu from 1.15.2 to 2.12.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#187 - docker container and example notebook

Issue - State: open - Opened by skr3178 almost 2 years ago

#186 - How to convert biobert-large-cased-v1.1-squad to onnx

Issue - State: closed - Opened by yli223 almost 2 years ago

#185 - BioBert pre-trained weights and models are out of reach and download

Issue - State: closed - Opened by vahab-mspour almost 2 years ago - 4 comments

#184 - importing biobert_v1.1_pubmed ERROR 404: Not Found to Colab notebook

Issue - State: open - Opened by JaskaranKaurGill almost 2 years ago - 2 comments

#183 - Bump tensorflow-gpu from 1.15.2 to 2.9.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#182 - Difference among various pretrained huggingface models

Issue - State: closed - Opened by liulizuel about 2 years ago

#181 - Split for JNLPBA dataset.

Issue - State: open - Opened by siddharthtumre about 2 years ago

#180 - running the relation extraction model

Issue - State: open - Opened by engineernesma93 over 2 years ago - 1 comment

#179 - how to do Relation Extraction after using the components(BERN2:http://bern2.korea.ac.kr/) of this prediction entity.

Issue - State: closed - Opened by zhangweizhenGitHub over 2 years ago - 3 comments

#178 - Bump tensorflow-gpu from 1.15.2 to 2.7.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#177 - Bump tensorflow-gpu from 1.15.2 to 2.6.4

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#176 - How to "re-train" BioBert on a custom medical corpus?

Issue - State: open - Opened by peterphancong over 2 years ago

#175 - tokenizer.add_tokens() interfers with downstream NER task

Issue - State: open - Opened by laurens777 over 2 years ago

#174 - Why not filter out the [PAD] tokens when computing loss?

Issue - State: open - Opened by zdgithub over 2 years ago

#173 - How to use the RE model after training on GAD? I mean How to load the model and start to use it.??

Issue - State: open - Opened by uzair-balouch almost 3 years ago - 1 comment

#172 - Bump tensorflow-gpu from 1.15.2 to 2.5.3

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#171 - Add Dockerfile and fix requirements

Pull Request - State: open - Opened by leoramme about 3 years ago

#170 - Bump tensorflow-gpu from 1.15.2 to 2.5.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#169 - What are the output files in OUTPUT_DIR after fine-tuning BioBERT for NER?

Issue - State: open - Opened by sbi30 about 3 years ago - 1 comment

#168 - Bump tensorflow-gpu from 1.15.2 to 2.5.1

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#167 - Registering at BioASQ website

Issue - State: open - Opened by parvathysarat over 3 years ago - 1 comment

#166 - For custom RE dataset with entity marked in advanced

Issue - State: open - Opened by KennyNg-19 over 3 years ago - 1 comment

#165 - Training on multiple GPUs

Issue - State: closed - Opened by vinicius-cleves over 3 years ago - 2 comments

#164 - https://bern.korea.ac.kr/ not accessible

Issue - State: closed - Opened by luisafuss over 3 years ago - 3 comments

#163 - Issues with tokenizers

Issue - State: open - Opened by galsk87 over 3 years ago

#162 - RE datasets

Issue - State: open - Opened by luana-be over 3 years ago - 17 comments

#161 - Running biobert for pubmed classification on specific text

Issue - State: open - Opened by cartiksharma286 over 3 years ago - 1 comment

#160 - Not able to replicate result available in readme

Issue - State: open - Opened by Shailendra77 over 3 years ago

#159 - Can BioBERT be used for multilabel classification problem ?

Issue - State: open - Opened by coolcoder001 over 3 years ago - 3 comments

#158 - Provide QA BioASQ previous version

Issue - State: open - Opened by abdallah197 almost 4 years ago - 1 comment

#157 - Bump tensorflow-gpu from 1.15.2 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#156 - NER: Model pre-trained for BertForTokenClassification task

Issue - State: open - Opened by mshtelma almost 4 years ago

#155 - Hugginface demo not working | Issue with AutoModel for BioBERT-squad

Issue - State: open - Opened by tanmaylaud almost 4 years ago

#154 - Questions about the NER dataset

Issue - State: open - Opened by nowhyun almost 4 years ago

#153 - Questionable training labels in GAD RE dataset

Issue - State: open - Opened by amirkdv almost 4 years ago - 2 comments

#152 - How do I specify a certain GPU for training when I fine-tuned NER?

Issue - State: closed - Opened by Crucialer almost 4 years ago - 1 comment

#151 - time to train

Issue - State: open - Opened by ShreyasVarun almost 4 years ago

#150 - how to modify the code and run on GPU?

Issue - State: open - Opened by yangxia605 almost 4 years ago

#149 - RE finetune using custom dataset, taskname?

Issue - State: open - Opened by ChloeJKim almost 4 years ago - 3 comments

#148 - chemprot dataset problem with run_re.py script

Issue - State: open - Opened by ghost almost 4 years ago - 3 comments

#147 - Error when Running Biobert on a variety of biomedical corpora

Issue - State: open - Opened by JinweiZhu almost 4 years ago - 1 comment

#146 - for the RE,How to fine-tune for a multi-label classification task,but not binary?

Issue - State: closed - Opened by yangxia605 almost 4 years ago - 1 comment

#145 - Biobert & spacy

Issue - State: closed - Opened by joseberlines about 4 years ago - 1 comment

#144 - RE Fine-tuning issue

Issue - State: closed - Opened by LedaguenelArthur about 4 years ago - 1 comment

#143 - Bump tensorflow-gpu from 1.15.2 to 2.3.1

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#142 - F1 metrics for NCBI dataset:token level or entity level?

Issue - State: closed - Opened by zhiyuanpeng about 4 years ago

#141 - Addition of new tokens in vocabulary while pre-training BioBERT

Issue - State: closed - Opened by pg427 about 4 years ago - 4 comments

#140 - What is in train.csv in the NER datasets?

Issue - State: closed - Opened by Santosh-Gupta about 4 years ago - 1 comment

#139 - Bump tensorflow-gpu from 1.15.2 to 1.15.4

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#138 - cased vs uncased model

Issue - State: closed - Opened by mchari about 4 years ago - 1 comment

#137 - NER label

Issue - State: open - Opened by kellyquek about 4 years ago

#136 - Help required with NER

Issue - State: open - Opened by Orneyfish about 4 years ago - 3 comments

#135 - How to load fine-tuned model and to predict?

Issue - State: open - Opened by leeivan about 4 years ago - 2 comments

#134 - Benchmark Dataset Preprocessing (QA)

Issue - State: closed - Opened by etetteh over 4 years ago - 1 comment

#133 - relation extraction task

Issue - State: closed - Opened by JehadAldahdooh over 4 years ago - 11 comments

#132 - Biobert for ICD/ CPT/ CDT code extraction

Issue - State: open - Opened by NarenInD over 4 years ago - 1 comment

#131 - Results on NER datasets

Issue - State: open - Opened by ardakdemir over 4 years ago

#130 - Is there a Tensorflow-hub version of the BioBERT model?

Issue - State: open - Opened by ibrahimishag over 4 years ago - 1 comment

#129 - ./download.sh Unrecognized archive format

Issue - State: open - Opened by MiraWelner over 4 years ago

#128 - Another Languages Steps

Issue - State: closed - Opened by lbolanos over 4 years ago - 1 comment

#127 - Ways to reduce BioBert high CPU usage and prediction time except quantisation

Issue - State: open - Opened by Abl1405 over 4 years ago

#126 - .

Issue - State: closed - Opened by Cairo-RxLogix over 4 years ago

#125 - Cosine Similarity is high when created sentence embeddings for 'asthma' (medical domain) and another with non-medical domain. Why ?

Issue - State: open - Opened by Sumedh1505 over 4 years ago

#113 - "ERROR: No matching distribution found for tensorflow-gpu==1.11.0 (from -r requirements.txt (line 1))" while installing requirements.txt

Issue - State: open - Opened by jamshaidsohail5 over 4 years ago - 5 comments

GitHub / dmis-lab/biobert issues and pull requests