AccScience Publishing / IJB / Online First / DOI: 10.36922/IJB026350375
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REVIEW ARTICLE

Large language models for bioink knowledge extraction, design, and biofabrication workflow automation: A critical conceptual review

Yangyang Wang1 ,  Jiaxun Zhang1 ,  Haotian Bai1 ,  Yufei Ren1 ,  Yanning Yang1 ,  Jihan Wang2* ,  Jing Lv3*
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1 Department of Automation, School of Physics and Electronic Information, Yan’an University, Yan’an, Shaanxi , Chian
2 Department of Basic Medicine, Yan’an Medical College, Yan’an University, Yan’an, Shaanxi , China
3 Department of Clinical Laboratory, Honghui Hospital, Xi'an Jiaotong University, Xi’an, Shaanxi , China
Received: 27 August 2026 | Revised: 16 September 2026 | Accepted: 21 September 2026 | Published online: 21 September 2026
© 2026 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

Three-dimensional (3D) bioprinting offers precise spatial control for fabricating cell-laden constructs, yet bioink development remains constrained by labor-intensive trial-and-error experiments and fragmented reporting. Conventional machine-learning pipelines can support quantitative property prediction but generally require structured inputs and therefore do not natively use the formulation knowledge embedded in narrative literature. Large language models (LLMs), particularly when combined with domain-adapted information extraction, retrieval-augmented generation (RAG), and knowledge graphs, offer a complementary route for converting literature into traceable design evidence. This critical conceptual review examines how these technologies could support bioink knowledge extraction, formulation recommendation, and design-build-test-learn (DBTL) workflow coordination. Because direct experimental applications of LLMs to bioink design remain scarce, we explicitly distinguish demonstrated evidence in bioprinting from transferable evidence in biomedical natural-language processing, materials informatics, chemistry, and autonomous experimentation, and from prospective biofabrication concepts. We outline a provenance-aware Bioink Knowledge Graph (BioKG), clarify the complementary roles of LLMs, numerical generative models, Bayesian optimization, computer vision, and robotic control, and provide tissue-specific workflow scenarios and a minimum proof-of-concept evaluation framework. Key limitations include conflicting and heterogeneous evidence, cell-type-specific constraints, hallucination, limited benchmark datasets, and the absence of end-to-end validation. The resulting framework should therefore be interpreted as an evidence-bounded research roadmap rather than as a clinically or experimentally validated autonomous bioprinting system.

Keywords
Large language models
3D bioprinting
Bioink design
Inverse design
Design-Build-Test-Learn
Funding
This work was supported by the National Natural Science Foundation of China (No. 82560411), Shaanxi Natural Science Foundation of China (No. 2025JC-YBMS-916), and the Startup Foundation for Doctors of Yan’an University (No. YDBK2024-91 and No. YDZKBK2025-06).
Conflict of interest
The authors declare they have no competing interests.
References
  1. Mathur V, Agarwal P, Kasturi M, Srinivasan V, Seetharam RN, Vasanthan KS. Innovative bioinks for 3D bioprinting: Exploring technological potential and regulatory challenges. J Tissue Eng. 2025;16:20417314241308022. doi: 10.1177/20417314241308022
  2. Lee SJ, Jeong W, Atala A. 3D Bioprinting for Engineered Tissue Constructs and Patient-Specific Models: Current Progress and Prospects in Clinical Applications. Adv Mater. 2024;36(49):e2408032. doi: 10.1002/adma.202408032
  3. Prendergast ME, Burdick JA. Recent Advances in Enabling Technologies in 3D Printing for Precision Medicine. Adv Mater. 2020;32(13):e1902516. doi: 10.1002/adma.201902516
  4. Dey M, Ozbolat IT. 3D bioprinting of cells, tissues and organs. Sci Rep. 2020;10(1):14023. doi: 10.1038/s41598-020-70086-y
  5. Freeman S, Calabro S, Williams R, Jin S, Ye K. Bioink Formulation and Machine Learning-Empowered Bioprinting Optimization. Front Bioeng Biotechnol. 2022;10:913579. doi: 10.3389/fbioe.2022.913579
  6. Panwar A, Tan LP. Current Status of Bioinks for Micro-Extrusion-Based 3D Bioprinting. Molecules. 2016;21(6):685. doi: 10.3390/molecules21060685
  7. Yin J, Yan M, Wang Y, Fu J, Suo H. 3D Bioprinting of Low-Concentration Cell-Laden Gelatin Methacrylate (GelMA) Bioinks with a Two-Step Cross-linking Strategy. ACS Appl Mater Interfaces. 2018;10(8):6849-6857. doi: 10.1021/acsami.7b16059
  8. Jongprasitkul H, Turunen S, Parihar VS, Kellomäki M. Sequential Cross-linking of Gallic Acid-Functionalized GelMA-Based Bioinks with Enhanced Printability for Extrusion-Based 3D Bioprinting. Biomacromolecules. 2023;24(1):502-514. doi: 10.1021/acs.biomac.2c01418
  9. Zhang CY, Fu CP, Li XY, et al. Three-Dimensional Bioprinting of Decellularized Extracellular Matrix-Based Bioinks for Tissue Engineering. Molecules. 2022;27(11):3442. doi: 10.3390/molecules27113442
  10. Chen H, Liu Y, Balabani S, Hirayama R, Huang J. Machine Learning in Predicting Printable Biomaterial Formulations for Direct Ink Writing. Research (Wash D C). 2023;6:0197. doi: 10.34133/research.0197
  11. Theus AS, Ning L, Hwang B, et al. Bioprintability: Physiomechanical and Biological Requirements of Materials for 3D Bioprinting Processes. Polymers (Basel). 2020;12(10):2262. doi: 10.3390/polym12102262
  12. Schwab A, Levato R, D’Este M, Piluso S, Eglin D, Malda J. Printability and Shape Fidelity of Bioinks in 3D Bioprinting. Chem Rev. 2020;120(19):11028-11055. doi: 10.1021/acs.chemrev.0c00084
  13. Wang Y, Bai H, Ren Y, Yang Y, Wang J. Artificial intelligence-augmented bioprinting systems: Data-driven optimization and future applications in pharmacological research. Int J Bioprint. 2025;11(6):1-22. doi: 10.36922/ijb025350349
  14. Lee J, Oh SJ, An SH, Kim WD, Kim SH. Machine learning-based design strategy for 3D printable bioink: elastic modulus and yield stress determine printability. Biofabrication. 2020;12(3):035018. doi: 10.1088/1758-5090/ab8707
  15. Ramesh S, Deep A, Tamayol A, Kamaraj A, Mahajan C, Madihally S. Advancing 3D bioprinting through machine learning and artificial intelligence. Bioprint. 2024;38:e00331. doi: 10.1016/j.bprint.2024.e00331
  16. Zhou J, Li H, Chen S, Chen Z, Han Z, Gao X. Large language models in biomedicine and healthcare. npj Artif Intell. 2025;1(1):44. doi: 10.1038/s44387-025-00047-1
  17. Lin A, Ye J, Qi C, et al. Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics. Brief Bioinform. 2025;26(4):bbaf357. doi: 10.1093/bib/bbaf357
  18. Lehman E, Hernandez E, Mahajan D, et al. Do We Still Need Clinical Language Models? arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2302.08091
  19. Gao Y, Xiong Y, Gao X, et al. Retrieval-Augmented Generation for Large Language Models: A Survey. arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2312.10997
  20. Li W, Mao Z, Xiao Z, et al. Large language model for knowledge synthesis and AI-enhanced biomanufacturing. Trends Biotechnol. 2025;43(8):1864-1875. doi: 10.1016/j.tibtech.2025.02.008
  21. Zhou L, Ling H, Fu C, et al. Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics. arXiv.Preprint posted online 2025. doi: 10.48550/ARXIV.2510.09901
  22. Zhang S, Liang D, Lei Y, Luo Y, Shi R. Artificial intelligence-assisted smart hydrogel bioinks in 3D bioprinting: design, optimization, and construct validation for functional tissue engineering. Front Bioeng Biotechnol. 2026;14:1898243. doi: 10.3389/fbioe.2026.1898243
  23. Liu S, Kaur N, Song DH, Moses JC, Ozbolat IT. Self-driving bioprinting laboratories. Biofabrication. 2026;18(1):013001. doi: 10.1088/1758-5090/ae3645
  24. Lee J, Yoon W, Kim S, et al. BioBERT: a pre-trained biomedical language representation model for biomedical text mining. Bioinformatics. 2020;36(4):1234-1240. doi: 10.1093/bioinformatics/btz682
  25. Devlin J, Chang MW, Lee K, Toutanova K. BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding. In: Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers). Association for Computational Linguistics; 2019:4171-4186. doi: 10.18653/v1/n19-1423
  26. Beltagy I, Lo K, Cohan A. SciBERT: A Pretrained Language Model for Scientific Text. In: Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). Association for Computational Linguistics; 2019:3613-3618. doi: 10.18653/v1/d19-1371
  27. Gu Y, Tinn R, Cheng H, et al. Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing. ACM Trans Comput Healthcare. 2021;3(1):1-23. doi: 10.1145/3458754
  28. Shetty P, Rajan AC, Kuenneth C, et al. A general-purpose material property data extraction pipeline from large polymer corpora using natural language processing. npj Comput Mater. 2023;9(1):52. doi: 10.1038/s41524-023-01003-w
  29. Gupta T, Zaki M, Krishnan NMA, Mausam. MatSciBERT: A materials domain language model for text mining and information extraction. npj Comput Mater. 2022;8(1):102. doi: 10.1038/s41524-022-00784-w
  30. Li M, Zhuang Y, Hou Y, et al. Integrating graph convolutional networks with large language models for structured biomedical material knowledge representation. Regen Biomater. 2025;12:rbaf083. doi: 10.1093/rb/rbaf083
  31. Chimene D, Lennox KK, Kaunas RR, Gaharwar AK. Advanced Bioinks for 3D Printing: A Materials Science Perspective. Ann Biomed Eng. 2016;44(6):2090-2102. doi: 10.1007/s10439-016-1638-y
  32. Moroni L, Boland T, Burdick JA, et al. Biofabrication: A Guide to Technology and Terminology. Trends Biotechnol. 2018;36(4):384-402. doi: 10.1016/j.tibtech.2017.10.015
  33. Zhang W, Zhang J. Hallucination Mitigation for Retrieval-Augmented Large Language Models: A Review. Mathematics. 2025;13(5):856. doi: 10.3390/math13050856
  34. M Bran A, Cox S, Schilter O, Baldassari C, White AD, Schwaller P. Augmenting large language models with chemistry tools. Nat Mach Intell. 2024;6(5):525-535. doi: 10.1038/s42256-024-00832-8
  35. Boiko DA, MacKnight R, Kline B, Gomes G. Autonomous chemical research with large language models. Nature. 2023;624(7992):570-578. doi: 10.1038/s41586-023-06792-0
  36. AI4Science MR, Quantum MA. The Impact of Large Language Models on Scientific Discovery: a Preliminary Study using GPT-4. arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2311.07361
  37. Qi B, Zhang K, Li H, et al. Large Language Models are Zero Shot Hypothesis Proposers. arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2311.05965
  38. Abdel-Rehim A, Zenil H, Orhobor O, et al. Scientific hypothesis generation by large language models: laboratory validation in breast cancer treatment. J R Soc Interface. 2025;22(227):20240674. doi: 10.1098/rsif.2024.0674
  39. Labrak Y, Rouvier M, Dufour R. A Zero-shot and Few-shot Study of Instruction-Finetuned Large Language Models Applied to Clinical and Biomedical Tasks. arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2307.12114
  40. Wei J, Wang X, Schuurmans D, et al. Chain-Of-Thought Prompting Elicits Reasoning in Large Language Models. Adv Neural Inf Process Syst. 2022:24824-24837. doi: 10.52202/068431-1800
  41. Lewis P, Perez E, Piktus A, et al. Retrieval-augmented generation for knowledge-intensive NLP tasks. In: Proceedings of the 34th International Conference on Neural Information Processing Systems. 2020:9459-9474.
  42. Fan W, Ding Y, Ning L, et al. A Survey on RAG Meeting LLMs: Towards Retrieval-Augmented Large Language Models. In: Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2024:6491-6501. doi: 10.1145/3637528.3671470
  43. Neha F, Bhati D, Shukla DK. Retrieval-Augmented Generation (RAG) in Healthcare: A Comprehensive Review. AI. 2025;6(9):226. doi: 10.3390/ai6090226
  44. Xu S, Yan Z, Dai C, Wu F. MEGA-RAG: a retrieval-augmented generation framework with multi-evidence guided answer refinement for mitigating hallucinations of LLMs in public health. Front Public Health. 2025;13:1635381. doi: 10.3389/fpubh.2025.1635381
  45. Edge D, Trinh H, Cheng N, et al. From Local to Global: A Graph RAG Approach to Query-Focused Summarization. arXiv. Preprint posted online 2024. doi: 10.48550/ARXIV.2404.16130
  46. Peng B, Zhu Y, Liu Y, et al. Graph Retrieval-Augmented Generation: A Survey. ACM Trans Inf Syst. 2025;44(2):35. doi: 10.1145/3777378
  47. Xu S, Chen M, Chen S. Enhancing Retrieval-Augmented Generation Models with Knowledge Graphs: Innovative Practices Through a Dual-Pathway Approach. In: Huang DS, Si Z, Chen W, eds. Advanced Intelligent Computing Technology and Applications. Singapore: Springer Nature Singapore; 2024:398-409. doi: 10.1007/978-981-97-5678-0_34
  48. Xu L, Xie H, Qin SJ, Tao X, Wang FL. Parameter-Efficient Fine-Tuning Methods for Pretrained Language Models: A Critical Review and Assessment. IEEE Trans Pattern Anal Mach Intell. 2026;48(6):6107-6126. doi: 10.1109/TPAMI.2026.3657354
  49. Hu EJ, Shen Y, Wallis P, et al. LoRA: Low-Rank Adaptation of Large Language Models. In: ICLR 2022. 2022. Accessed July 29, 2026. https://www.microsoft.com/en-us/research/publication/lora-low-rank-adaptation-of-large-language-models/
  50. Shao J, Khan AN, Brett C, Berg T, Li X, Yao B. Multi-Task LLM with LoRA Fine-Tuning for Automated Cancer Staging and Biomarker Extraction. arXiv. Preprint posted online 2026. doi: 10.48550/ARXIV.2604.13328
  51. Silva Robazzi JV, Derman ID, Gupta D, et al. The Synergy of Artificial Intelligence and 3D Bioprinting: Unlocking New Frontiers in Precision and Tissue Fabrication. Adv Funct Mater. 2026;36(1):e09530. doi: 10.1002/adfm.202509530
  52. Sarah R, Schimmelpfennig K, Rohauer R, Lewis CL, Limon SM, Habib A. Characterization and Machine Learning-Driven Property Prediction of a Novel Hybrid Hydrogel Bioink Considering Extrusion-Based 3D Bioprinting. Gels. 2025;11(1):45. doi: 10.3390/gels11010045
  53. Luo Y, Yang Z, Meng F, Li Y, Zhou J, Zhang Y. An Empirical Study of Catastrophic Forgetting in Large Language Models During Continual Fine-tuning. arXiv. Preprint posted online 2023. doi: 10.48550/ARXIV.2308.08747
  54. Perera N, Dehmer M, Emmert-Streib F. Named Entity Recognition and Relation Detection for Biomedical Information Extraction. Front Cell Dev Biol. 2020;8:673. doi: 10.3389/fcell.2020.00673
  55. Nasar Z, Jaffry SW, Malik MK. Named Entity Recognition and Relation Extraction. ACM Comput Surv. 2022;54(1):20. doi: 10.1145/3445965
  56. Grouin C, Grabar N. Year 2023 in Biomedical Natural Language Processing: a Tribute to Large Language Models and Generative AI. Yearb Med Inform. 2024;33(1):241-248. doi: 10.1055/s-0044-1800751
  57. Kalyan KS, Rajasekharan A, Sangeetha S. AMMU: A survey of transformer-based biomedical pretrained language models. J Biomed Inform. 2022;126:103982. doi: 10.1016/j.jbi.2021.103982
  58. Foppiano L, Lambard G, Amagasa T, Ishii M. Mining experimental data from materials science literature with large language models: an evaluation study. Sci Technol Adv Mater Methods. 2024;4(1):2356506. doi: 10.1080/27660400.2024.2356506
  59. Dagdelen J, Dunn A, Lee S, et al. Structured information extraction from scientific text with large language models. Nat Commun. 2024;15(1):1418. doi: 10.1038/s41467-024-45563-x
  60. Kyle S, Jessop ZM, Al-Sabah A, Whitaker IS. ‘Printability’ of Candidate Biomaterials for Extrusion Based 3D Printing: State-of-the-Art. Adv Healthc Mater. 2017;6(16):1700264. doi: 10.1002/adhm.201700264
  61. Paxton N, Smolan W, Böck T, Melchels F, Groll J, Jungst T. Proposal to assess printability of bioinks for extrusion-based bioprinting and evaluation of rheological properties governing bioprintability. Biofabrication. 2017;9(4):044107. doi: 10.1088/1758-5090/aa8dd8
  62. Malda J, Visser J, Melchels FP, et al. 25th anniversary article: Engineering hydrogels for biofabrication. Adv Mater. 2013;25(36):5011-5028. doi: 10.1002/adma.201302042
  63. Gillispie G, Prim P, Copus J, et al. Assessment methodologies for extrusion-based bioink printability. Biofabrication. 2020;12(2):022003. doi: 10.1088/1758-5090/ab6f0d
  64. Ai Q, Meng F, Shi J, Pelkie B, Coley CW. Extracting structured data from organic synthesis procedures using a fine-tuned large language model. Digit Discov. 2024;3(9):1822-1831. doi: 10.1039/d4dd00091a
  65. Shi Y, Rampal N, Zhao C, et al. Comparison of LLMs in extracting synthesis conditions and generating Q&A datasets for metal–organic frameworks. Digit Discov. 2025;4(10):2676-2683. doi: 10.1039/d5dd00081e
  66. Rajamohan BP, Bradley ACH, Tran VD, et al. Materials Data Science Ontology(MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science. Sci Data. 2025;12(1):628. doi: 10.1038/s41597-025-04938-5
  67. Wilkinson MD, Dumontier M, Aalbersberg IJ, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3:160018. doi: 10.1038/sdata.2016.18
  68. Venugopal V, Olivetti E. MatKG: An autonomously generated knowledge graph in Material Science. Sci Data. 2024;11(1):217. doi: 10.1038/s41597-024-03039-z
  69. Ye Y, Ren J, Wang S, et al. Construction and Application of Materials Knowledge Graph in Multidisciplinary Materials Science via Large Language Model. Adv Neural Inf Process Syst 37. 2024:56878-56897. doi: 10.52202/079017-1812
  70. Stocker M, Oelen A, Jaradeh MY, et al. FAIR scientific information with the Open Research Knowledge Graph. FAIR Connect. 2023;1(1):19-21. doi: 10.3233/fc-221513
  71. Grijalva Garces D, Strauß S, Gretzinger S, et al. On the reproducibility of extrusion-based bioprinting: round robin study on standardization in the field. Biofabrication. 2023;16(1):015002. doi: 10.1088/1758-5090/acfe3b
  72. Skardal A, Atala A. Biomaterials for integration with 3-D bioprinting. Ann Biomed Eng. 2015;43(3):730-746. doi: 10.1007/s10439-014-1207-1
  73. Zimmerling A, Zhou Y, Chen X. Synthesis of Alginate/Collagen Bioink for Bioprinting Respiratory Tissue Models. J Funct Biomater. 2024;15(4):90. doi: 10.3390/jfb15040090
  74. F04 Committee. ASTM F3659-24: Standard Guide for Bioinks Used in Bioprinting. ASTM International; 2024. doi: 10.1520/F3659-24
  75. Kearnes SM, Maser MR, Wleklinski M, et al. The Open Reaction Database. J Am Chem Soc. 2021;143(45):18820-18826. doi: 10.1021/jacs.1c09820
  76. Krotkov NA, Sbytov DA, Chakhoyan AA, et al. Nanostructured Material Design via a Retrieval-Augmented Generation (RAG) Approach: Bridging Laboratory Practice and Scientific Literature. J Chem Inf Model. 2025;65(20):11064-11078. doi: 10.1021/acs.jcim.5c01897
  77. Hassan T, Karim MF, Jeelani H, Behnam E, Green R, Syed FJ. Optimizing Medical Question-Answering Systems: A Comparative Study of Fine-Tuned and Zero-Shot Large Language Models with RAG Framework. arXiv. Preprint posted online 2025. doi: 10.48550/ARXIV.2512.05863
  78. Asai A, Wu Z, Wang Y, Sil A, Hajishirzi H. Self-RAG: Learning to Retrieve, Generate, and Critique through Self-Reflection. In: ICLR 2024. 2024:9112-9141. Accessed July 29, 2026. https://proceedings.iclr.cc/paper_files/paper/2024/file/25f7be9694d7b32d5cc670927b8091e1-Paper-Conference.pdf
  79. Wang S, Yang H, Liu W. Research on the construction and application of retrieval enhanced generation (RAG) model based on knowledge graph. Sci Rep. 2025;15(1):40425. doi: 10.1038/s41598-025-21222-z
  80. Mohammad S, Akand R, Cook KM, Nilufar S, Chowdhury F. Leveraging Deep Learning and Generative AI for Predicting Rheological Properties and Material Compositions of 3D Printed Polyacrylamide Hydrogels. Gels. 2024;10(10):660. doi: 10.3390/gels10100660
  81. Park H, Li Z, Walsh A. Has generative artificial intelligence solved inverse materials design? Matter. 2024;7(7):2355-2367. doi: 10.1016/j.matt.2024.05.017
  82. Zeni C, Pinsler R, Zügner D, et al. A generative model for inorganic materials design. Nature. 2025;639(8055):624-632. doi: 10.1038/s41586-025-08628-5
  83. Zhang Z, Tao ZZ, Du R, Huo R, Zheng X. Artificial Intelligence Informed Hydrogel Biomaterials in Additive Manufacturing. Gels. 2025;11(12):981. doi: 10.3390/gels11120981
  84. Lim KS, Galarraga JH, Cui X, Lindberg GCJ, Burdick JA, Woodfield TBF. Fundamentals and Applications of Photo-Cross-Linking in Bioprinting. Chem Rev. 2020;120(19):10662-10694. doi: 10.1021/acs.chemrev.9b00812
  85. Chen Z, Yuan X, Zhang J, et al. LABO: LLM-Accelerated Bayesian Optimization through Broad Exploration and Selective Experimentation. arXiv. Preprint posted online 2026. doi: 10.48550/ARXIV.2605.22054
  86. Malekpour A, Chen X. Printability and Cell Viability in Extrusion-Based Bioprinting from Experimental, Computational, and Machine Learning Views. J Funct Biomater. 2022;13(2):40. doi: 10.3390/jfb13020040
  87. Elango J, Zamora-Ledezma C. Rheological, Structural, and Biological Trade-Offs in Bioink Design for 3D Bioprinting. Gels. 2025;11(8):659. doi: 10.3390/gels11080659
  88. Shahriari B, Swersky K, Wang Z, Adams RP, de Freitas N. Taking the Human Out of the Loop: A Review of Bayesian Optimization. In: Proc IEEE. 2016;104:148-175. doi: 10.1109/JPROC.2015.2494218
  89. Snoek J, Larochelle H, Adams RP. Practical Bayesian Optimization of Machine Learning Algorithms. Adv Neural Inf Process Syst 25. 2012. Accessed July 29, 2026. https://proceedings.neurips.cc/paper_files/paper/2012/file/05311655a15b75fab86956663e1819cd-Paper.pdf
  90. Liang Q, Gongora AE, Ren Z, et al. Benchmarking the performance of Bayesian optimization across multiple experimental materials science domains. npj Comput Mater. 2021;7(1):188. doi: 10.1038/s41524-021-00656-9
  91. Gupta R, Hartford J, Liu B. LLMs for Bayesian Optimization in Scientific Domains: Are We There Yet? arXiv. Preprint posted online 2025. doi: 10.48550/ARXIV.2509.21403
  92. Han D, Ai Z, Cai P, et al. ChemBOMAS: Accelerated BO in Chemistry with LLM-Enhanced Multi-Agent System. arXiv. Preprint posted online 2025. doi: 10.48550/ARXIV.2509.08736
  93. Kumbhar S, Mishra V, Coutinho K, Handa D, Iquebal A, Baral C. Hypothesis Generation for Materials Discovery and Design Using Goal-Driven and Constraint-Guided LLM Agents. arXiv. Preprint posted online 2025. doi: 10.48550/ARXIV.2501.13299
  94. Vanlauwe F, Dermaux C, Shamieva S, Vermeiren S, Van Vlierberghe S, Blondeel P. Small molecular weight alginate gel porogen for the 3D bioprinting of microvasculature. Front Bioeng Biotechnol. 2024;12:1452477. doi: 10.3389/fbioe.2024.1452477
  95. Mazari-Arrighi E, Lépine M, Ayollo D, et al. Self-Organization of Long-Lasting Human Endothelial Capillary-Like Networks Guided by DLP Bioprinting. Adv Healthc Mater. 2024;13(14):e2302830. doi: 10.1002/adhm.202302830
  96. Zhou W, Gao L, Wu M, Liu J. AI-assisted interdisciplinary integration of multimodal CT/MRI imaging and 3D printing in medicine: Technical advancements, clinical translations, and future perspectives. Int J Bioprint. 2026;12(1):125-144. doi: 10.36922/ijb025390404
  97. Kelly D, Sergis V, Ventura i Blanco L, Mason K, Daly AC. Autonomous Control of Extrusion Bioprinting Using Convolutional Neural Networks. Adv Funct Mater. 2025;35(30):2424553. doi: 10.1002/adfm.202424553
  98. Jin Z, Zhang Z, Shao X, Gu GX. Monitoring Anomalies in 3D Bioprinting with Deep Neural Networks. ACS Biomater Sci Eng. 2023;9(7):3945-3952. doi: 10.1021/acsbiomaterials.0c01761
  99. Sergis V, Kelly D, Pramanick A, Britchfield G, Mason K, Daly AC. In-situ quality monitoring during embedded bioprinting using integrated microscopy and classical computer vision. Biofabrication. 2025;17(2):025004. doi: 10.1088/1758-5090/adaa22
  100. Ke D. AI-driven closed-loop extrusion-based bioprinting system: from dynamic regulation to medical translation. Bioprinting. 2026;54:e00459. doi: 10.1016/j.bprint.2025.e00459
  101. Spannenkrebs JB, Eiermann A, Zoll T, Hackenschmidt S, Kabisch J. Closing the loop: establishing an autonomous test-learn cycle to optimize induction of bacterial systems using a robotic platform. Front Bioeng Biotechnol. 2025;12:1528224. doi: 10.3389/fbioe.2024.1528224
  102. Hatem S, Khoriba G, Gad-Elrab MH, ElHelw M. Up To Date: Automatic Updating Knowledge Graphs Using LLMs. Procedia Comput Sci. 2024;244:327-334. doi: 10.1016/j.procs.2024.10.206
  103. Shi H, Xu Z, Wang H, et al. Continual Learning of Large Language Models: A Comprehensive Survey. ACM Comput Surv. 2025;58(5):1-42. doi: 10.1145/3735633
  104. Basara G, Ozcebe SG, Ellis BW, Zorlutuna P. Tunable Human Myocardium Derived Decellularized Extracellular Matrix for 3D Bioprinting and Cardiac Tissue Engineering. Gels. 2021;7(2):70. doi: 10.3390/gels7020070
  105. Lim KS, Abinzano F, Bernal PN, et al. One-Step Photoactivation of a Dual-Functionalized Bioink as Cell Carrier and Cartilage-Binding Glue for Chondral Regeneration. Adv Healthc Mater. 2020;9(15):e1901792. doi: 10.1002/adhm.201901792
  106. Zhe M, Wu X, Yu P, et al. Recent Advances in Decellularized Extracellular Matrix-Based Bioinks for 3D Bioprinting in Tissue Engineering. Materials. 2023;16(8):3197. doi: 10.3390/ma16083197
  107. Kim BS, Das S, Jang J, Cho DW. Decellularized Extracellular Matrix-based Bioinks for Engineering Tissue- and Organ-specific Microenvironments. Chem Rev. 2020;120(19):10608-10661. doi: 10.1021/acs.chemrev.9b00808
  108. Zhang M, Zhang C, Li Z, Fu X, Huang S. Advances in 3D skin bioprinting for wound healing and disease modeling. Regen Biomater. 2022;10:rbac105. doi: 10.1093/rb/rbac105
  109. Cavallo A, Al Kayal T, Mero A, et al. Fibrinogen-Based Bioink for Application in Skin Equivalent 3D Bioprinting. J Funct Biomater. 2023;14(9):459. doi: 10.3390/jfb14090459
  110. Saul D, Kosinsky RL. Spatial transcriptomics herald a new era of transcriptome research. Clin Transl Med. 2023;13(5):e1264. doi: 10.1002/ctm2.1264
  111. Du L, Yang H. Spatial omics in 3D culture model systems: decoding cellular positioning mechanisms and microenvironmental dynamics. J Transl Med. 2025;23(1):1356. doi: 10.1186/s12967-025-07390-6
  112. Rodrigues DB, Reis RL, Pirraco RP. Modelling the complex nature of the tumor microenvironment: 3D tumor spheroids as an evolving tool. J Biomed Sci. 2024;31(1):13. doi: 10.1186/s12929-024-00997-9
  113. Zanoni M, Piccinini F, Arienti C, et al. 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained. Sci Rep. 2016;6:19103. doi: 10.1038/srep19103
  114. Yi HG, Jeong YH, Kim Y, et al. A bioprinted human-glioblastoma-on-a-chip for the identification of patient-specific responses to chemoradiotherapy. Nat Biomed Eng. 2019;3(7):509-519. doi: 10.1038/s41551-019-0363-x
  115. Rizzo M, Veneri A, Marcuzzo M, et al. Machine learning models explanations as interpretations of evidence: a theoretical framework of explainability and its implications on high-stakes biomedical decision-making. BMC Med Res Methodol. 2025;25(S1):282. doi: 10.1186/s12874-025-02703-1
  116. Amann J, Blasimme A, Vayena E, Frey D, Madai VI; Precise4Q consortium. Explainability for artificial intelligence in healthcare: a multidisciplinary perspective. BMC Med Inform Decis Mak. 2020;20(1):310. doi: 10.1186/s12911-020-01332-6
  117. Yang T, Xiao Y, Bao Z, Hao J, Peng J. The rise and potential opportunities of large language model agents in bioinformatics and biomedicine. Brief Bioinform. 2025;26(6):bbaf601. doi: 10.1093/bib/bbaf601
  118. Omiye JA, Lester JC, Spichak S, Rotemberg V, Daneshjou R. Large language models propagate race-based medicine. NPJ Digit Med. 2023;6(1):195. doi: 10.1038/s41746-023-00939-z
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International Journal of Bioprinting, Electronic ISSN: 2424-8002 Print ISSN: 2424-7723, Published by AccScience Publishing