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References from Developing foundations for biomedical knowledgebases from literature using large language models – A systematic assessment. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1146/annurev-biodatasci-072018-021321
10.1146/annurev-biodatasci-072018-021321 · External reference
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database
10.1186/s13073-019-0686-y · 2019 · External reference
Cancer Hallmarks Analytics Tool (CHAT): A text mining approach to organize and evaluate scientific literature on cancer
10.1093/bioinformatics/btx454 · 2017 · External reference
CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer
10.1038/s41592-019-0422-y · 2019 · External reference
10.1016/j.jbi.2012.10.007
10.1016/j.jbi.2012.10.007 · External reference
Structured information extraction from scientific text with large language models
10.1038/s41467-024-45563-x · 2024 · External reference
Flexible, model-agnostic method for materials data extraction from text using general purpose language models
10.1039/d4dd00016a · 2024 · External reference
An extensive benchmark study on biomedical text generation and mining with ChatGPT
10.1093/bioinformatics/btad557 · 2023 · External reference
Privacy-preserving large language models for structured medical information retrieval
10.1038/s41746-024-01233-2 · 2024 · External reference
Optimization of hepatological clinical guidelines interpretation by large language models: a retrieval augmented generation-based framework
10.1038/s41746-024-01091-y · 2024 · External reference
Large language models to identify social determinants of health in electronic health records
10.1038/s41746-023-00970-0 · 2024 · External reference
10.1038/s41591-023-02448-8
10.1038/s41591-023-02448-8 · External reference
10.1016/j.ccell.2020.07.004
10.1016/j.ccell.2020.07.004 · External reference
10.1146/annurev-pathol-042020-042741
10.1146/annurev-pathol-042020-042741 · External reference
Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer
2018 · External reference
Organ-specific metastatic landscape dissects PD-(L)1 blockade efficacy in advanced non-small cell lung cancer: applicability from clinical trials to real-world practice
2022 · External reference
Molecular correlates of clinical response and resistance to atezolizumab in combination with bevacizumab in advanced hepatocellular carcinoma
2022 · External reference
ICI efficacy information portal: a knowledgebase for responder prediction to immune checkpoint inhibitors
10.1093/narcan/zcad012 · 2023 · External reference
BLEU: A method for automatic evaluation of machine translation
2002 · External reference
Rouge: A package for automatic evaluation of summaries
2004 · External reference
Bertscore: Evaluating text generation with bert
2019 · External reference
10.18653/v1/2022.emnlp-main.759
10.18653/v1/2022.emnlp-main.759 · External reference
Fantastically Ordered Prompts and Where to Find Them: Overcoming Few-Shot Prompt Order Sensitivity
2022 · External reference
Calibrate Before Use: Improving Few-Shot Performance of Language Models
2021 · External reference
Self-discover: Large language models self-compose reasoning structures
2024 · External reference
10.18653/v1/2023.emnlp-main.723
10.18653/v1/2023.emnlp-main.723 · External reference
Evaluating large language models on medical evidence summarization
10.1038/s41746-023-00896-7 · 2023 · External reference
MTAS: A Reference-Free Approach for Evaluating Abstractive Summarization Systems
10.1145/3660820 · 2024 · External reference
& others. Comparative Evaluation of Large Language Models for Abstractive Summarization. in 2024 14th International Conference on Cloud Computing
2024 · External reference
Evaluating the state-of-the-art of End-to-End Natural Language Generation: The E2E NLG challenge
10.1016/j.csl.2019.06.009 · 2020 · External reference
10.18653/v1/d18-1235
10.18653/v1/d18-1235 · External reference
Benchmarking large language models for biomedical natural language processing applications and recommendations
10.1038/s41467-025-56989-2 · 2025 · External reference
Gsm-symbolic: Understanding the limitations of mathematical reasoning in large language models
2024 · External reference
A scientific-article key-insight extraction system based on multi-actor of fine-tuned open-source large language models
10.1038/s41598-025-85715-7 · 2025 · External reference
LitSumm: large language models for literature summarization of noncoding RNAs
10.1093/database/baaf006 · 2025 · External reference
10.1038/s41591-024-03423-7
10.1038/s41591-024-03423-7 · External reference
Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset XML Dataset
10.21105/joss.01979 · 2020 · External reference
Towards reasoning era: A survey of long chain-of-thought for reasoning large language models
2025 · External reference
Deepseek-R1: Incentivizing reasoning capability in LLMs via reinforcement learning
2025 · External reference
Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma
10.1172/jci.insight.121522 · 2018 · External reference
Deberta: Decoding-enhanced bert with disentangled attention
2021 · External reference
