Ecosyste.ms: Issues

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GitHub / dmis-lab/biobert issues and pull requests

#87 - Number of tokens mismatch in prediction and bert_pred outputs

Issue - State: closed - Opened by Sanjeev2487 almost 5 years ago - 4 comments

#86 - BioBERT Pre-trained Models for TF 2.0 or 1.15

Issue - State: closed - Opened by maziyarpanahi almost 5 years ago - 1 comment

#85 - _read_data function skipping the last sentence

Issue - State: open - Opened by ardakdemir almost 5 years ago

#84 - Will this fine tuning for tensorflow v2

Issue - State: closed - Opened by dhanushanthp almost 5 years ago - 1 comment

#83 - Bump tensorflow-gpu from 1.11.0 to 1.15.0

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago - 1 comment
Labels: dependencies

#82 - Update README.md

Pull Request - State: closed - Opened by jhyuklee almost 5 years ago

#81 - Update README.md

Pull Request - State: closed - Opened by jhyuklee almost 5 years ago

#80 - Update README.md

Pull Request - State: closed - Opened by jhyuklee almost 5 years ago

#78 - Problem with loading model

Issue - State: closed - Opened by Hedgehogues almost 5 years ago - 1 comment

#77 - How do I run NER predictions in pytorch?

Issue - State: closed - Opened by vasudhajain0 almost 5 years ago - 1 comment

#76 - finetuning

Issue - State: closed - Opened by Mayar2009 almost 5 years ago - 1 comment

#75 - How do I run predictions on a new passage for NER?

Issue - State: closed - Opened by pacejohn almost 5 years ago - 1 comment

#74 - Failed to get data set of ChemProt

Issue - State: closed - Opened by qiaoxiaosong almost 5 years ago - 1 comment

#73 - Serving input function

Issue - State: closed - Opened by sirisha-8 almost 5 years ago - 7 comments

#72 - How is Development set used during prediction time?

Issue - State: closed - Opened by ghost almost 5 years ago - 3 comments

#71 - Running run_ner.py

Issue - State: closed - Opened by vasudhajain0 almost 5 years ago - 1 comment

#70 - 'O' tag is hard-coded to be at position 3

Issue - State: closed - Opened by lfurrer almost 5 years ago - 2 comments

#69 - Fine-tuned NER not giving correct results

Issue - State: closed - Opened by shivanik96 almost 5 years ago - 4 comments

#67 - Do biobert support chinese?

Issue - State: closed - Opened by foreverwith almost 5 years ago - 1 comment

#66 - run_ner.py of huggingface

Issue - State: closed - Opened by vthost almost 5 years ago - 1 comment

#65 - Convert TF into Pytorch for Biobert

Issue - State: closed - Opened by yrf1 almost 5 years ago - 1 comment

#64 - Pre-processing text file

Issue - State: closed - Opened by ghost almost 5 years ago - 1 comment

#63 - Too much Prediction Time

Issue - State: closed - Opened by hegebharat almost 5 years ago - 1 comment

#62 - Laptop GPU overflow when fine-tuning NER

Issue - State: closed - Opened by zampierimatteo91 about 5 years ago - 2 comments

#61 - NER finetuning - checkpoint problem

Issue - State: closed - Opened by zampierimatteo91 about 5 years ago - 3 comments

#60 - How to ask specific questions?

Issue - State: closed - Opened by jsf0433 about 5 years ago - 6 comments

#59 - Raw Text named entity recognition prediction!

Issue - State: closed - Opened by AndreasSaka about 5 years ago - 1 comment

#58 - Strange Results with Huggingface

Issue - State: closed - Opened by vthost about 5 years ago - 17 comments

#57 - Unable to replicate the results shown for QA task

Issue - State: closed - Opened by ahmednasserswe about 5 years ago - 2 comments

#56 - NCBI-disease dataset

Issue - State: closed - Opened by ssavvi about 5 years ago - 1 comment

#55 - using wordpiece tokenizer for pre-training

Issue - State: closed - Opened by vr25 about 5 years ago - 1 comment

#54 - Unable to run NER in inference mode

Issue - State: closed - Opened by soumyavhasure about 5 years ago - 10 comments

#53 - Label leakage in construction of lines for run_ner.py?

Issue - State: closed - Opened by EthanSteinberg about 5 years ago - 1 comment

#52 - can't find `BioASQ-train-4b.json` for run_qa.py example

Issue - State: closed - Opened by ahmednasserswe about 5 years ago - 1 comment

#51 - pre-training from scratch

Issue - State: closed - Opened by vr25 about 5 years ago - 1 comment

#50 - NER predictions from pretrained models

Issue - State: closed - Opened by yrahul3910 about 5 years ago - 13 comments

#49 - Reproducing RE scores from the paper

Issue - State: closed - Opened by swethmandava about 5 years ago - 4 comments

#48 - NER dataset

Issue - State: closed - Opened by ibrahimishag about 5 years ago - 1 comment

#47 - NER and RE Prediction for raw sentence

Issue - State: closed - Opened by zhang-zeyu about 5 years ago - 2 comments

#46 - Pre-training vs fine-tuning?

Issue - State: closed - Opened by ghost about 5 years ago - 4 comments

#45 - Reproducing RE results using CHEMPROT datasets

Issue - State: closed - Opened by ibrahimishag about 5 years ago - 1 comment

#44 - biobert predicts only one class on test set

Issue - State: closed - Opened by vijay-srivas about 5 years ago - 6 comments

#43 - Question regarding BioASQ training dataset

Issue - State: closed - Opened by kuhanw about 5 years ago - 1 comment

#42 - What are the PubMed & PMC text that you've used?

Issue - State: closed - Opened by yonatanbitton about 5 years ago - 2 comments

#41 - i2b2 dataset results

Issue - State: closed - Opened by andreasgrv about 5 years ago - 2 comments

#40 - Distilled Version of biobert

Issue - State: closed - Opened by leonweber about 5 years ago - 3 comments

#39 - NER predict only mode

Issue - State: closed - Opened by UrszulaCzerwinska over 5 years ago - 2 comments

#38 - BioBert NER only for Prediction

Issue - State: closed - Opened by PHAllenChen over 5 years ago

#37 - Can't get word embedding

Issue - State: closed - Opened by happypanda5 over 5 years ago - 4 comments

#36 - Why BioBERT is not up on paperswithcode SOTA leaderboard

Issue - State: closed - Opened by shreyashub over 5 years ago - 2 comments

#35 - NER datasets

Issue - State: closed - Opened by shreyashub over 5 years ago - 1 comment

#34 - Reproducing BioASQ Results

Issue - State: closed - Opened by suamin over 5 years ago - 10 comments

#33 - ChemProt trainset, develop set, test set in Re_data ?

Issue - State: closed - Opened by CV2014 over 5 years ago - 1 comment

#32 - run_ner lines 154-164. Why '30'?

Issue - State: closed - Opened by ypapanik over 5 years ago - 4 comments

#31 - BioASQ-test issues

Issue - State: closed - Opened by LauSama over 5 years ago - 1 comment

#30 - What version of tensorflow/CUDA was used?

Issue - State: closed - Opened by bgriffen over 5 years ago - 1 comment

#29 - BioASQ datasets issues

Issue - State: closed - Opened by LauSama over 5 years ago - 1 comment

#28 - An analysis paper of BioBERT and BioELMo

Issue - State: closed - Opened by Andy-jqa over 5 years ago - 1 comment

#27 - adding additional features for QA task

Issue - State: closed - Opened by telukuntla over 5 years ago - 1 comment

#25 - extract_features.py

Issue - State: closed - Opened by telukuntla over 5 years ago - 1 comment

#24 - BERT Large or BERT Base?

Issue - State: closed - Opened by telukuntla over 5 years ago - 7 comments

#23 - Retreiving Embedding vector

Issue - State: closed - Opened by pyturn over 5 years ago - 16 comments

#22 - word embedding vector

Issue - State: closed - Opened by telukuntla over 5 years ago - 4 comments

#21 - Fine tuning BioBERT on CPU

Issue - State: closed - Opened by vkramdev over 5 years ago

#20 - python file to run for fine-tuning on Squad

Issue - State: closed - Opened by telukuntla over 5 years ago - 2 comments

#19 - training on Squad

Issue - State: closed - Opened by telukuntla over 5 years ago - 4 comments

#18 - DDI

Issue - State: closed - Opened by lucaputelli over 5 years ago - 1 comment

#17 - fix path for label2id.pkl

Pull Request - State: closed - Opened by cbhyphen over 5 years ago - 1 comment

#16 - Biobert text classification

Issue - State: closed - Opened by dongfang91 over 5 years ago - 5 comments

#15 - Replication of Relation Extraction results - share finetuning parameters

Issue - State: closed - Opened by ypapanik over 5 years ago - 5 comments

#14 - Fine tune BioBERT on multiple new categories for NER task

Issue - State: closed - Opened by kormilitzin over 5 years ago - 7 comments

#13 - Is it possible to output probability score for each token?

Issue - State: closed - Opened by gccome over 5 years ago - 5 comments

#12 - Dimension size must be evenly divisible by N but is M for 'loss/Reshape_1'

Issue - State: closed - Opened by gccome over 5 years ago - 16 comments

#11 - downloading datasets

Issue - State: closed - Opened by EmilyAlsentzer over 5 years ago - 4 comments

#10 - Pre-training for SQUAD and fine-tuning for BIOASQ

Issue - State: closed - Opened by rsanjaykamath almost 6 years ago - 3 comments

#9 - Extra checkpoint initialisation in run_ner.py (Minor)

Issue - State: closed - Opened by antonyscerri almost 6 years ago - 1 comment

#8 - BioBERT base model files

Issue - State: closed - Opened by antonyscerri almost 6 years ago - 2 comments

#7 - Task Fine Tuning Parameters

Issue - State: closed - Opened by antonyscerri almost 6 years ago - 4 comments

#6 - fixed minor typo in README.md

Pull Request - State: closed - Opened by Mohan-Zhang-u almost 6 years ago - 1 comment

#5 - ner_detokenize

Issue - State: closed - Opened by phu5ion almost 6 years ago - 2 comments

#4 - Why does vocab not appear to be medically oriented?

Issue - State: closed - Opened by mikerossgithub almost 6 years ago - 1 comment

#3 - What Metric exactly is reported/computed for NER?

Issue - State: closed - Opened by Iwontbecreative almost 6 years ago - 7 comments

#2 - BioBert for Pytorch

Issue - State: closed - Opened by dpappas almost 6 years ago - 3 comments

#1 - Simplify convert_to_unicode() in tokenization.py

Pull Request - State: closed - Opened by cclauss almost 6 years ago