mlsanityData to 14 Oct 2026

An evaluation of DeepSeek Models in Biomedical Natural Language Processing

arXiv 2503.00624 ↗First posted 1 Mar 2025cs.CL cs.AIcited by 6

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Abstract (arXiv)

The advancement of Large Language Models (LLMs) has significantly impacted biomedical Natural Language Processing (NLP), enhancing tasks such as named entity recognition, relation extraction, event extraction, and text classification. In this context, the DeepSeek series of models have shown promising potential in general NLP tasks, yet their capabilities in the biomedical domain remain underexplored. This study evaluates multiple DeepSeek models (Distilled-DeepSeek-R1 series and Deepseek-LLMs) across four key biomedical NLP tasks using 12 datasets, benchmarking them against state-of-the-art alternatives (Llama3-8B, Qwen2.5-7B, Mistral-7B, Phi-4-14B, Gemma-2-9B). Our results reveal that while DeepSeek models perform competitively in named entity recognition and text classification, challenges persist in event and relation extraction due to precision-recall trade-offs. We provide task-specific model recommendations and highlight future research directions. This evaluation underscores the strengths and limitations of DeepSeek models in biomedical NLP, guiding their future deployment and optimization.

Key facts. Cited by 6 papers in the map (data through 14 Oct 2026). Builds on 31 of its 56 references that are in the map. First posted on arXiv 1 Mar 2025.

Builds on

31 of 56 references.

References · 31

  1. 2017Attention Is All You Needcited by 60,361
  2. 2024The Llama 3 Herd of Modelscited by 14,715
  3. 2021LoRA: Low-Rank Adaptation of Large Language Modelscited by 14,380
  4. 2020Retrieval-Augmented Generation for Knowledge-Intensive NLP Taskscited by 9,297
  5. 2025DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learningcited by 6,330
  6. 2024Qwen2.5 Technical Reportcited by 4,942
  7. 2024Gemma 2: Improving Open Language Models at a Practical Sizecited by 1,998
  8. 2022Large Language Models Encode Clinical Knowledgecited by 1,830
  9. 2024DeepSeek-Coder: When the Large Language Model Meets Programming -- The Rise of Code Intelligencecited by 1,181
  10. 2024DeepSeek-VL: Towards Real-World Vision-Language Understandingcited by 733
  11. 2023Capabilities of GPT-4 on Medical Challenge Problemscited by 638
  12. 2022GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Recordscited by 238
19 more
  1. 2023BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Taskscited by 201
  2. 2023A Study of Generative Large Language Model for Medical Research and Healthcarecited by 163
  3. 2017PubMed 200k RCT: a Dataset for Sequential Sentence Classification in Medical Abstractscited by 124
  4. 2022BioRED: A Rich Biomedical Relation Extraction Datasetcited by 85
  5. 2021Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processingcited by 57
  6. 2024Autonomous LLM-driven research from data to human-verifiable research paperscited by 53
  7. 2024Large Language Models for Disease Diagnosis: A Scoping Reviewcited by 51
  8. 2023Enhancing Knowledge Graph Construction Using Large Language Modelscited by 44
  9. 2022PHEE: A Dataset for Pharmacovigilance Event Extraction from Textcited by 37
  10. 2021Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Reviewcited by 35
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  13. 2025MMRAG: Multi-Mode Retrieval-Augmented Generation with Large Language Models for Biomedical In-Context Learningcited by 13
  14. 2024Benchmarking Retrieval-Augmented Large Language Models in Biomedical NLP: Application, Robustness, and Self-Awarenesscited by 11
  15. 2024RAMIE: Retrieval-Augmented Multi-task Information Extraction with Large Language Models on Dietary Supplementscited by 11
  16. 2024A Survey on Symbolic Knowledge Distillation of Large Language Modelscited by 9
  17. 2024Chain-of-Though (CoT) prompting strategies for medical error detection and correctioncited by 7
  18. 2024Towards Better Multi-task Learning: A Framework for Optimizing Dataset Combinations in Large Language Modelscited by 6
  19. 2024Development and Testing of a Novel Large Language Model-Based Clinical Decision Support Systems for Medication Safety in 12 Clinical Specialtiescited by 5

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 3; 2026: 3.

6 papers.

  1. 2025Towards Reasoning Era: A Survey of Long Chain-of-Thought for Reasoning Large Language Modelscited by 384
  2. 2025Benchmarking GPT-5 for biomedical natural language processingcited by 5
  3. 2025Quantized Large Language Models in Biomedical Natural Language Processing: Evaluation and Recommendationcited by 3
  4. 2026Can Large Language Models Self-Correct in Medical Question Answering? An Exploratory Studycited by 3
  5. 2026To Reason or Not to: Selective Chain-of-Thought in Medical Question Answeringcited by 0
  6. 2026Let LLMs Judge Each Other: Multi-Agent Peer-Reviewed Reasoning for Medical Question Answeringcited by 0

Similar, not cited

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  1. 2024LLMs in Biomedicine: A study on clinical Named Entity Recognition
  2. 2024LLMs are not Zero-Shot Reasoners for Biomedical Information Extraction
  3. 2023Benchmarking large language models for biomedical natural language processing applications and recommendations
  4. 2023Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition
  5. 2024A Survey for Large Language Models in Biomedicine
  6. 2024LLM-IE: A Python Package for Generative Information Extraction with Large Language Models
  7. 2023Evaluation of ChatGPT Family of Models for Biomedical Reasoning and Classification
  8. 2024Large Language Models Struggle in Token-Level Clinical Named Entity Recognition