biobert

There are 3 repositories under biobert topic.

covid-papers-browser
gsarti / covid-papers-browser
Browse Covid-19 & SARS-CoV-2 Scientific Papers with Transformers 🦠 📖
biobert bionlp covid-19 natural-language-processing scibert search-engine
Language:CSS 182
smitkiri / ehr-relation-extraction
NER and Relation Extraction from Electronic Health Records (EHR).
adverse-drug-events bert-relation-extraction bilstm-crf biobert ehr ehr-records n2c2 named-entity-recognition ner relation-extraction
Language:Python 83
acadTags / Explainable-Automated-Medical-Coding
Implementation and demo of explainable coding of clinical notes with Hierarchical Label-wise Attention Networks (HLAN)
attention-visualisation biobert cnn-att-models demo discharge-summaries hierarchical-attention-networks jupyter-notebook label-embeddings labelwise-attention medical-coding multi-label-classification simpletransformers
Language:Python 58
suamin / MIL-RBERT
MIL-RBERT: A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction (BioNLP @ ACL 2020)
bert biobert umls-metathesaurus medline multiple-instance-learning distant-supervision noisy-data relation-extraction bionlp
Language:Python 19
jgamper / biobert-pytorch
Ready to use BioBert pytorch weights for HuggingFace pytorch BertModel :relieved:
bert-model biobert huggingface-transformers pytorch
Language:Python 12
hushee69 / biobert-relation-extraction
Relation Extraction using BERT and BioBERT - using BERT, we achieved new state of the art results
bert-model biobert classification relation-extraction state-of-the-art
Language:Jupyter Notebook 10
Semantic-Search-Engine-for-COVID-19-literature
arnavsshah / Semantic-Search-Engine-for-COVID-19-literature
COVID-19 Open Research Dataset Challenge (CORD-19)
search-engine tf-idf information-retrieval biobert semantic-search-engine faiss sqlite3 cord-19 sentence-transformer
Language:Jupyter Notebook 6
covid
Aequivinius / covid
👑🦠 Annotating PMC and PubMed articles for Covid-related entities
biobert biomedical-text-mining pubannotation pmids
Language:Jupyter Notebook 5
Hugging-Face-Supporter / Multi-Label-Classification-of-Pubmed-Articles-Deployed-on-HuggingFace-Spaces
The traditional machine learning models give a lot of pain when we do not have sufficient labeled data for the specific task or domain we care about to train a reliable model. Transfer learning allows us to deal with these scenarios by leveraging the already existing labeled data of some related task or domain. We try to store this knowledge gained in solving the source task in the source domain and apply it to our problem of interest. In this work, I have utilized Transfer Learning utilizing BioBERT model. Also Applied RobertaForSequenceClassification and XLNetForSequenceClassification models for Fine-Tuning the Model. Model is live on Hugging Face Spaces
bert biobert deep-learning huggingface multilabel-classification nlp-machine-learning
Language:Jupyter Notebook 4
johndef64 / GRPM_system
Computational Strategies in Nutrigenetics: Constructing a Reference Dataset of Nutrition-Associated Genetic Polymorphisms https://doi.org/10.1101/2023.08.04.23293659
biobert data-integration gwas-catalog nutrigenomics personalized-nutrition semantic-similarity
Language:Jupyter Notebook 4
miladnouriezade / Ktrain-BioBert_NER
This repository contains data and BioBert based NER model monologg/biobert_v1.1_pubmed from community-uploaded Hugging Face models for detecting entities such as chemical and disease.
ner biomedical name named-entity-recognition ktrain spacy fasttext biobert huggingface nlp disease python bionlp
Language:Python 4
vkhamesi / proteins
🧬 Fine-Tuning Large Language and Protein Models on a single T4 GPU via Distillation, Quantization and Low-Rank Adaptation to run inference on proteins functions.
biobert bioinformatics biology deep-learning fine-tuning function-prediction gpu machine-learning natural-language-processing protbert proteins pytorch transformers
Language:Jupyter Notebook 3
adi5krish / Question-Answering-Tool-for-CliCR-Dataset
Question Answering tool for CliCR dataset developed using BERT and BioBERT
bert biobert python pytorch qatool tensorflow
Language:Jupyter Notebook 2
cosmoshsv / topiQAL
Topic+QA pipeLine
covid-19 kaggle-dataset topic-modeling bert-model biobert squad-dataset bioasq question-answering
Language:Jupyter Notebook 2
jcrossyale / biobert_analysis
Training and computational/visualization analysis of BERT and BioBERT using PyTorch and huggingface.
nlp transfer-learning machine-learning bert biobert medicine medical colab
Language:Python 2
matteotolloso / BioCograph
A tool capable of parsing datasets of papers from pubmed, annotating entities that appear using bio-BERT, creating a network of cooccurrences on which to perform analysis with various algorithms
biobert bioinformatics cooccurrence network-analysis networkx pubmed pubmed-parser python
Language:TeX 2
mobashgr / WeLT
A cost-sensitive BERT that handles the class imbalance for the task of biomedical NER.
biomedical-applications cost-sensitive-learning ner biobert pubmed scibert bias bias-correction bioner bionlp
Language:Python 2
Overfitter / Know-Corona
🔍 Kaggle COVID-19 Open Research Dataset Challenge (CORD-19)
bert biobert nlp react transformers
Language:Jupyter Notebook 2
rrfsantos / Desafios-NLP
Bi Master - Grupo de desafios de NLP: Classificação Multiclasse, BIOBERT, spaCy, NER, POS, Tópicos, Geração de Texto, sentence-bert, Tensorflow USEm.
biobert lda multiclass-classification ner nlp nlp-machine-learning postagging questions-and-answers spacy tensorflow sentence-embeddings
Language:Jupyter Notebook 2
sushmita04 / ADR-detection-BioBERT
The repo consists of an ML model based on BioBERT by virtue of transfer learning, to detect adverse drug reactions (ADRs). It also consists of the data used by the model.
adverse-drug-reaction biobert deep-learning machine-learning transfer-learning
Language:Jupyter Notebook 2
bilalhameed248 / Patient-Most-Recent-Treatments-Similarity-Measuring
BioBert Enhanced Patient Treatment Similarity Analysis with Sentence Transformers
bert bert-fine-tuning bert-model biobert data-extraction data-preprocessing data-science deep-learning deep-neural-networks dnn python pytorch sentence-embeddings sentence-similarity sentence-transformers sentiment-analysis transformer
Language:Jupyter Notebook 1
Dimas263 / NLP_NER_BERT_Named_Entity_Recognition
NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT
bert-fine-tuning bert-model biobert biomedical-text-mining jupyter-notebook named-entity-recognition natural-language-processing plant-disease-classification python ner nlp pytorch transformer crf dimas dimas-dwi-putra dimas263 information-extraction relation-extraction
Language:Jupyter Notebook 1
esmailza / A-Recommendation-Model-for-Predicting-Alzheimer-s-Drugs-Mechanism-of-Action
A simple binary prediction model that gets the Alzheimer's drugs' description texts as input. It classifies the drugs into two Small Molecules (SM) and Disease modifying therapies (DMT) categories. The model utilizes BERT for word embeddings.
biobert natural-language-processing text-classification
Language:Python 1
imrandotkhan / medi_assit
BioBert for Q&A
bert-embeddings biobert deep-learning nlp-machine-learning question-answering
Language:Python 1
pinglab-intern / Cardio-NER-BioBERT
Ping Lab Intern Project, Summar, 2022: :octocat: Building Named Entity Recognition model with fine tuning BioBERT - a data engineering approach
biobert knowledgegraph ner
Language:Jupyter Notebook 1
bilalhameed248 / Delay-Reason-Extraction-Model
Efficient Delay Reason Extraction in Patient Appointments/Treatments Using BERT and Tensorflow. - Feb 2022 - Jun 2023
bert bert-fine-tuning bert-model biobert data-extraction data-preprocessing data-science deep-learning deep-neural-networks dnn pytorch semantic-analysis sentence-embeddings tensorflow transformer
Language:Python 0
Cartesian1671 / G4HSP-AI
Farida Hanna Campbell 2023
ai biobert genomics infectious-disease-models quadruplexes svm virus
Language:Jupyter Notebook 0
dsashulya / biobert-distillation
summer internship project @ JetBrains Research
biobert distillation ner token-classification transformers
Language:Python 0
dsashulya / diff-pruning
spring project @ JetBrains Research
pytorch nlp pruning ner bioner biobert
Language:Python 0
esmailza / Chemical-Gene-Chemical-Gene-Relation-Extraction-with-GNN
The model identifies chemical components and genes named entities and extracts the relations of the chemical-gene pair jointly. It utilizes the BioBERT model in the named entity recognition and the graphs neural networks for the RE subtasks.
biobert graphneuralnetwork named-entity-recognition natural-language-processing pytorch relation-extraction
Language:Python 0
gskdhiman / medical_qa
This project is a demo for Bert Question Answering on medical data.
bert biobert deep-learning medicalquestionanswering question-answering
Language:Python 0
jacons / LMining-Neurodegenerative
Literature Mining for Neurodegenerative disease
biobert dijkstra-algorithm knowledge-graph pagerank-algorithm wordtovec
Language:Jupyter Notebook 0
JuliusMaliwat / bachelor-thesis
A comparative study of SVM, Random Forest, and BioBERT models for enhancing medical meta-analysis through accurate literature classification.
biobert machine-learning python scikit-learn
Language:Jupyter Notebook 0
merishnaSuwal / bert-finetuning
Fine-tuning pre-trained BERT architectures from Hugging face
biobert medical-transcript question-answering
Language:Jupyter Notebook 0
daveramseymusic / biobert-bern
bern biobert biomedical-data-science
Language:Jupyter Notebook
rishivar / eHealth-clef-2020
Multi Label Text Classification of ICD-10-CM codes on the clinical record corpus for eHealth Lab CLEF - 2020
bert biobert clef ehealth electron multilabel-classification nlp roberta simple-transformers transformers
Language:Jupyter Notebook

biobert

gsarti / covid-papers-browser

smitkiri / ehr-relation-extraction

acadTags / Explainable-Automated-Medical-Coding

suamin / MIL-RBERT

jgamper / biobert-pytorch

hushee69 / biobert-relation-extraction

arnavsshah / Semantic-Search-Engine-for-COVID-19-literature

Aequivinius / covid

Hugging-Face-Supporter / Multi-Label-Classification-of-Pubmed-Articles-Deployed-on-HuggingFace-Spaces

johndef64 / GRPM_system

miladnouriezade / Ktrain-BioBert_NER

vkhamesi / proteins

adi5krish / Question-Answering-Tool-for-CliCR-Dataset

cosmoshsv / topiQAL

jcrossyale / biobert_analysis

matteotolloso / BioCograph

mobashgr / WeLT

Overfitter / Know-Corona

rrfsantos / Desafios-NLP

sushmita04 / ADR-detection-BioBERT

bilalhameed248 / Patient-Most-Recent-Treatments-Similarity-Measuring

Dimas263 / NLP_NER_BERT_Named_Entity_Recognition

esmailza / A-Recommendation-Model-for-Predicting-Alzheimer-s-Drugs-Mechanism-of-Action

imrandotkhan / medi_assit

pinglab-intern / Cardio-NER-BioBERT

bilalhameed248 / Delay-Reason-Extraction-Model

Cartesian1671 / G4HSP-AI

dsashulya / biobert-distillation

dsashulya / diff-pruning

esmailza / Chemical-Gene-Chemical-Gene-Relation-Extraction-with-GNN

gskdhiman / medical_qa

jacons / LMining-Neurodegenerative

JuliusMaliwat / bachelor-thesis

merishnaSuwal / bert-finetuning

daveramseymusic / biobert-bern

rishivar / eHealth-clef-2020