biobert | trained biomedical language representation model | Natural Language Processing library

by dmis-lab Python Version: v20200409 License: Non-SPDX

X-Ray Key Features Code Snippets(3)Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | biobert Summary

biobert is a Python library typically used in Artificial Intelligence, Natural Language Processing, Pytorch, Bert applications. biobert has no bugs, it has no vulnerabilities, it has build file available and it has medium support. However biobert has a Non-SPDX License. You can download it from GitHub.

This repository provides the code for fine-tuning BioBERT, a biomedical language representation model designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details. This project is done by DMIS-Lab.

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Security

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biobert has a medium active ecosystem.

It has 1651 star(s) with 426 fork(s). There are 58 watchers for this library.

It had no major release in the last 6 months.

There are 48 open issues and 121 have been closed. On average issues are closed in 76 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of biobert is v20200409

Quality

biobert has 0 bugs and 0 code smells.

Security

biobert has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

biobert code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

biobert has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

biobert releases are not available. You will need to build from source code and install.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

biobert saves you 2398 person hours of effort in developing the same functionality from scratch.

It has 5227 lines of code, 272 functions and 18 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed biobert and discovered the below as its top functions. This is intended to give you an instant insight into biobert implemented functionality, and help decide if they suit your requirements.

Writes prediction results
Get the final prediction
Get the n - best logits from a list of logits
Compute softmax
Convert examples into features
Truncate a sequence pair
Return a string representation of text
Convert a single example
Validate flags
Check if the case matches the given checkpoint
Convert a golden path to CoNLL form
Tokenize text
Write examples to examples
Embedding postprocessor
Read squad examples from a file
Check whether the case matches the given checkpoint
Detokenize predicted tokens
Compute word embedding
Builds a function that builds a file - based input
Create training instances
Creates a attention mask from input_tensor
Convert examples into TFRecord
Process feature
Reads examples from input_file
Builds input_fn
Transformer transformer model
Build a function for TPUEstimator

Get all kandi verified functions for this library.

biobert Key Features

No Key Features are available at this moment for biobert.

biobert Examples and Code Snippets

MLT-DFKI at CLEF eHealth Task 1: Multi-label Classification with BERT,Running BERT Models

Python

Lines of Code : 32

License : No License

Copy

python convert_tf_checkpoint_to_pytorch.py \
    --tf_checkpoint_path $BERT_MODEL/biobert_model.ckpt \
    --bert_config_file $BERT_MODEL/bert_config.json \
    --pytorch_dump_path $BERT_MODEL/pytorch_model.bin

export DATA_DIR=exps-data/data
export

Clinical Reading Comprehension (CliniRC),Train and Test a QA model,BERT

Python

Lines of Code : 31

License : Permissive (Apache-2.0)

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$ chmod +x download_pretrained_models.sh; ./download_pretrained_models.sh

$ CUDA_VISIBLE_DEVICES=0 python ./BERT/run_squad.py \
    --vocab_file=./pretrained_bert_models/clinicalbert/vocab.txt \
    --bert_config_file=./pretrained_bert_models/clinic

BioBert Embeddings,Examples

Python

Lines of Code : 27

License : Permissive (MIT)

Copy

from biobert_embedding.embedding import BiobertEmbedding

## Example 1
text = "Breast cancers with HER2 amplification have a higher risk of CNS metastasis and poorer prognosis."\

# Class Initialization (You can set default 'model_path=None' as your

Community Discussions

Trending Discussions on biobert

How to Run Pytorch Bert with AMD

How to get BioBERT embeddings

Unable to install pandas 0.23

QUESTION

How to Run Pytorch Bert with AMD

Asked 2022-Mar-30 at 22:31

github code: https://github.com/bellowman/Deep-Learning-Practice/blob/main/BioBert%20for%20Multi%20Label%20AMD.ipynb

Hello everyone,

I am a beginner with pytorch, tensorflow, and BERT. I have a machine at home with an AMD Ryzen 7 1800x and a Radeon RX 6600 video card.

I am trying to run a bioBERT model at home. I have trouble leveraging my model to use my AMD card. I posted my github notebook. I have troubles in cell 3 and 9.

First Question: In cell 3,I am trying to convert the bioBERT weight to PyTorch with transformmer-cli. I get the warning of "Could not load dynamic library 'cudart64_110.dll'". Does this affect performance later?
Second Question: In cell 9, My model load is really slow because it is using just the CPU. How can I get the model to run on my AMD GPU

...

ANSWER

Answered 2021-Dec-09 at 07:58

Thank you to chrispresso

AMD ROCm seems to be the way to go, but it requires one to run under linux

Source https://stackoverflow.com/questions/70279801

QUESTION

How to get BioBERT embeddings

Asked 2021-Feb-21 at 09:46

I have field within a pandas dataframe with a text field for which I want to generate BioBERT embeddings. Is there a simple way with which I can generate the vector embeddings? I want to use them within another model.

here is a hypothetical sample of the data frame

Visit Code Problem Assessment 1234 ge reflux working diagnosis well 4567 medication refill order working diagnosis note called in brand benicar 5mg qd 30 prn refill

I have tried this package, but receive an error upon installation https://pypi.org/project/biobert-embedding

Error:

...

ANSWER

Answered 2021-Feb-21 at 09:46

Try to install it as follows:

Source https://stackoverflow.com/questions/66284360

QUESTION

Unable to install pandas 0.23

Asked 2020-Oct-05 at 09:26

I need to install BioBERT for my project and according to the requirements.txt document, I need to install pandas version 0.23. Using command prompt, I ran the following command: pip install pandas==0.23. However, I keep getting the following errors:

Running setup.py install for pandas ... - WARNING: Subprocess output does not appear to be encoded as cp1252

and then...

ERROR: Command errored out with exit status 1: command: 'c:\users\username\appdata\local\programs\python\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\username\AppData\Local\Temp\pip-install-b7c7z3mn\pandas\setup.py'"'"'; file='"'"'C:\Users\username\AppData\Local\Temp\pip-install-b7c7z3mn\pandas\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\username\AppData\Local\Temp\pip-record-23blwwjr\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\users\username\appdata\local\programs\python\python37\Include\pandas' cwd: C:\Users\username\AppData\Local\Temp\pip-install-b7c7z3mn\pandas\

Then it tries to build wheel for pandas (setup.py) which results in another "Error":

ERROR: Command errored out with exit status 1: 'c:\users\username\appdata\local\programs\python\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\username\AppData\Local\Temp\pip-install-b7c7z3mn\pandas\setup.py'"'"'; file='"'"'C:\Users\username\AppData\Local\Temp\pip-install-b7c7z3mn\pandas\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\username\AppData\Local\Temp\pip-record-23blwwjr\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\users\username\appdata\local\programs\python\python37\Include\pandas' Check the logs for full command output.

In case needed: python version: 3.7.9 tensorflow version: 1.15.0 tensorflow-gpu version: 1.15.2

I would appreciate any help!

Regards

...

ANSWER

Answered 2020-Oct-05 at 09:26

There might not be a wheel for Pandas 0.23.0 on Python 3.7 on Windows, and your box is lacking the tools necessary to compile it.

Try a nearby version, such as

Source https://stackoverflow.com/questions/64205851

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install biobert

We provide five versions of pre-trained weights. Pre-training was based on the original BERT code provided by Google, and training details are described in our paper. Currently available versions of pre-trained weights are as follows:.
BioBERT-Base v1.1 (+ PubMed 1M) - based on BERT-base-Cased (same vocabulary)
BioBERT-Large v1.1 (+ PubMed 1M) - based on BERT-large-Cased (custom 30k vocabulary), NER/QA Results
BioBERT-Base v1.0 (+ PubMed 200K) - based on BERT-base-Cased (same vocabulary)
BioBERT-Base v1.0 (+ PMC 270K) - based on BERT-base-Cased (same vocabulary)
BioBERT-Base v1.0 (+ PubMed 200K + PMC 270K) - based on BERT-base-Cased (same vocabulary)
Sections below describe the installation and the fine-tuning process of BioBERT based on Tensorflow 1 (python version <= 3.7). For PyTorch version of BioBERT, you can check out this repository. If you are not familiar with coding and just want to recognize biomedical entities in your text using BioBERT, please use this tool which uses BioBERT for multi-type NER and normalization.

Support

Web-based biomedical NER + normalization using BioBERT. BioBERT based real-time question answering model for COVID-19. Code for the seventh BioASQ challenge winning model (factoid/yesno/list). Paper link with BibTeX (Bioinformatics).

Find more information at: