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BioGPT: generative pre-trained transformer for biomedical text generation and mining

https://doi.org/10.1093/bib/bbac409
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19/19 checkable references clean · checked 2026-08-29

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

35 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

The 19 checked references that resolve
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining
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The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions
resolves10.18653/v1/D19-1259
PubMedQA: A Dataset for Biomedical Research Question Answering
resolves10.1093/bioinformatics/btv585
Automatic semantic classification of scientific literature according to the hallmarks of cancer
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MIMIC-III, a freely accessible critical care database
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Global-to-Local Neural Networks for Document-Level Relation Extraction
resolves10.18653/v1/2021.findings-emnlp.204
REBEL: Relation Extraction By End-to-end Language generation
resolves10.18653/v1/2022.bionlp-1.2
A sequence-to-sequence approach for document-level relation extraction
resolves10.18653/v1/2020.emnlp-main.523
LUKE: Deep Contextualized Entity Representations with Entity-aware Self-attention
resolves10.18653/v1/2022.acl-long.551
LinkBERT: Pretraining Language Models with Document Links
resolves10.1186/s12859-015-0564-6
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition
resolves10.18653/v1/2020.acl-main.207
SPECTER: Document-level Representation Learning using Citation-informed Transformers
resolves10.18653/v1/P16-2034
Attention-Based Bidirectional Long Short-Term Memory Networks for Relation Classification
resolves10.18653/v1/P19-1131
Joint Type Inference on Entities and Relations via Graph Convolutional Networks
resolves10.24963/ijcai.2020/561
A Relation-Specific Attention Network for Joint Entity and Relation Extraction
resolves10.18653/v1/2020.acl-main.136
A Novel Cascade Binary Tagging Framework for Relational Triple Extraction
resolves10.18653/v1/P18-1047
Extracting Relational Facts by an End-to-End Neural Model with Copy Mechanism
resolves10.18653/v1/2020.findings-emnlp.23
Minimize Exposure Bias of Seq2Seq Models in Joint Entity and Relation Extraction
resolves10.18653/v1/P16-1162
Neural Machine Translation of Rare Words with Subword Units
The 35 references without a DOI — listed, not checked
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no DOI — not checkedInternational Conference on Learning Representations
no DOI — not checkedImproving language understanding by generative pre-training
no DOI — not checkedLanguage models are unsupervised multitask learners
no DOI — not checkedLanguage models are few-shot learners
no DOI — not checkedProceedings of the 18th BioNLP Workshop and Shared Task
no DOI — not checkedDomain-specific language model pretraining for biomedical natural language processing
no DOI — not checkedGpt-3 models are poor few-shot learners in the biomedical domain
no DOI — not checkedThinking about gpt-3 in-context learning for biomedical ie? think again
no DOI — not checkedBioCreative V CDR task corpus: a resource for chemical disease relation extraction
no DOI — not checkedDiscovering drug-target interaction knowledge from biomedical literature
no DOI — not checkedProceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP)
no DOI — not checkedElectramed: a new pre-trained language representation model for biomedical nlp
no DOI — not checkedDare: Data augmented relation extraction with gpt-2
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no DOI — not checkedQanet: Combining local convolution with global self-attention for reading comprehension
no DOI — not checkedProceedings of the 20th Workshop on Biomedical Language Processing
no DOI — not checkedJoint European Conference on Machine Learning and Knowledge Discovery in Databases
no DOI — not checkedProceedings of COLING 2014, the 25th international conference on computational linguistics: technical papers
no DOI — not checkedProceedings of the Twenty-Ninth International Conference on International Joint Conferences on Artificial Intelligence
no DOI — not checkedProceedings of the 57th Annual Meeting of the Association for Computational Linguistics
no DOI — not checkedProceedings of the 28th International Conference on Computational Linguistics
no DOI — not checkedProceedings of the 2021 Conference on Empirical Methods in Natural Language Processing
no DOI — not checkedJoint entity and relation extraction with set prediction networks
no DOI — not checkedReinforced mnemonic reader for machine reading comprehension
no DOI — not checkedAttention is all you need
no DOI — not checkedPre-train, prompt, and predict: A systematic survey of prompting methods in natural language processing
no DOI — not checkedProceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers)
no DOI — not checkedProceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics (Demonstrations)
no DOI — not checkedInternational Conference on Learning Representations
no DOI — not checkedProceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: System Demonstrations
no DOI — not checkedProceedings of the 58th Annual Meeting of the Association for Computational Linguistics
no DOI — not checkedScifive: a text-to-text transformer model for biomedical literature
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