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biobert
Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text miningbiobert-pytorch
PyTorch Implementation of BioBERTbern
A neural named entity recognition and multi-type normalization tool for biomedical text miningBERN2
BERN2: an advanced neural biomedical namedentity recognition and normalization toolBioSyn
ACL'2020: Biomedical Entity Representations with Synonym Marginalizationhats
HATS: A Hierarchical Graph Attention Network for Stock Movement Predictionbioasq-biobert
Pre-trained Language Model for Biomedical Question AnsweringGeNER
Simple Questions Generate Named Entity Recognition Datasets (EMNLP 2022)KitcheNette
KitcheNette: Predicting and Recommending Food Ingredient Pairings using Siamese Neural NetworkscovidAsk
covidAsk: Answering Questions on COVID-19 in Real-TimeBioLAMA
EMNLP'2021: Can Language Models be Biomedical Knowledge Bases?ReSimNet
Implementation of ReSimNet for drug response similarity predictionOLAPH
OLAPH: Improving Factuality in Biomedical Long-form Question AnsweringPerceiverCPI
Bioinformatics'2022 PerceiverCPI: A nested cross-attention network for compound-protein interaction predictionself-biorag
ISMB'24 "Self-BioRAG: Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language Models"excord
Learn to Resolve Conversational Dependency: A Consistency Training Framework for Conversational Question Answering (Kim et al., ACL 2021)position-bias
EMNLP'2020: Look at the First Sentence: Position Bias in Question AnsweringTouR
Findings of ACL'2023: Optimizing Test-Time Query Representations for Dense Retrievalnesa
NESA: Neural Event Scheduling AssistantLIQUID
LIQUID: A Framework for List Question Anwering Dataset Generation (AAAI 2023)tbinet
TBiNet: A deep neural network for predicting transcription factor binding sites using attention mechanismdemographic-prediction
Predicting Multiple Demographic Attributes with Task Specific Embedding Transformation and Attention NetworkVAECox
ISMB 2020: Improved survival analysis by learning shared genomic information from pan-cancer dataANGEL
Learning from Negative samples for Biomedical Generative Entity Linkingmoable
Predicting mechanism of action of novelcompounds using compound structure andtranscriptomic signature co-embeddingcookingsense
CookingSense: A Culinary Knowledgebase with Multidisciplinary Assertions (LREC-COLING 2024)ConNER
Bioinformatics'2023: Consistency Enhancement of Model Prediction on Document-level Named Entity RecognitionSeqTagQA
Sequence Tagging for Biomedical Extractive Question Answering (Bioinformatics'2020)ArkDTA
bioasq8b
Transferability of Natural Language Inference to Biomedical Question AnsweringAdvSR
Adversarial Subword Regularization forRobust Neural Machine TranslationMulinforCPI
MulinforCPI: enhancing precision of compound-protein interaction prediction through novel perspectives on multi-level information integrationRecipeMind
RecipeMind: Guiding Ingredient Choices from Food Pairing to Recipe Completition using Cascaded Set Transformer (Mogan Gim et al., 2022)KAZU-NER-module
EMNLP 2022: Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu FrameworkCRADLE-VAE
trnet
TRNet: A neural network model for predicting drug induced gene expression profilesKitchenScale
KitchenScale: Learning Food Numeracy from Recipes through Context-Aware Ingredient Quantity Predictionbioner-generalization
How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?bc7-chem-id
DMIS at BioCreative VII NLMChem TrackMolPLA
bioasq9b-dmis
KU-DMIS at BioASQ 9GLIT
GLIT: A Graph Neural Network for Drug-inducedLiver Injury Prediction using Transcriptome DataParaCLIP
Fine-tuning CLIP Text Encoders with Two-step Paraphrasing (EACL 2024, Findings)arpnet
ARPNet: Antidepressant Response Prediction Network for Major Depressive Disorderbio-entity-extractor
SMURF
SMURF: Machine learning pipeline for discovering cancer type specific driver mutations and diagnostic markersLAPIS
RAG2
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