journal article·2025-06-30Open access

Data Imputation Based on Retrieval-Augmented Generation

Xiaojun Shi, Jiacheng Wang, Gregorius Justin Chung, Derick Julian, Lianpeng Qiao

Applied Sciences· Volume 15· Issue 13

Abstract

Modern organizations collect increasing volumes of data to drive decision-making, often stored in centralized repositories such as data lakes, which consist of diverse structured and unstructured datasets. However, these repositories often suffer from issues such as incomplete, inconsistent, and low-quality data, which hinder data-driven insights. Existing methods for data imputation, including statistical techniques and machine learning approaches, often rely heavily on large amounts of labeled data and domain-specific knowledge, making them labor-intensive and limited in handling semantic heterogeneity across data formats. To address these challenges, this study proposes a novel retrieval-augmented generation (RAG) framework for data imputation that effectively combines the strengths of retrieval mechanisms and large language models (LLMs). This approach constructs semantic-based indexes for heterogeneous data, employs a recall and re-ranking strategy to enhance retrieval relevance, and proposes a method to reduce inference cost while ensuring imputation quality. Extensive experiments on real-world datasets demonstrate that the proposed framework significantly outperforms machine learning and deep learning approaches.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Recommender Systems and Techniques · Data Management and Algorithms · Data Mining Algorithms and Applications

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

School of Computer Science & Technolohy, Beijing Institute of Technology, Beijing 100081, China

Funding

National Key R&D Program of China · NSFC

References (100+)

Show source-provided references
1. Big Data sources and methods for social and economic analyses10.1016/j.techfore.2017.07.027 ↗
2. Can, U., and Alatas, B. (2017). Big social network data and sustainable economic development. Sustainability, 9.10.3390/su9112027 ↗
3. Arora, A., Vats, P., Tomer, N., Kaur, R., Saini, A.K., Shekhawat, S.S., and Roopak, M. (2023). Data-Driven Decision Support Systems in E-Governance: Leveraging AI for Policymaking. Proceedings of the International Conference on Artificial Intelligence on Textile and Apparel, Springer.10.1007/978-981-99-8479-4_17 ↗
4. Linkov, I., Trump, B.D., Poinsatte-Jones, K., and Florin, M.V. (2018). Governance strategies for a sustainable digital world. Sustainability, 10.10.3390/su10020440 ↗
5. van Veenstra, A.F., and Kotterink, B. (2017, January 4–7). Data-driven policy making: The policy lab approach. Proceedings of the Electronic Participation: 9th IFIP WG 8.5 International Conference, ePart 2017, St. Petersburg, Russia. Proceedings 9.
6. Rendle, S. (2010, January 13–17). Factorization machines. Proceedings of the 2010 IEEE International Conference on Data Mining, Sydney, Australia.10.1109/ICDM.2010.127 ↗
7. He, X., and Chua, T.S. (2017, January 7–11). Neural factorization machines for sparse predictive analytics. Proceedings of the 40th International ACM SIGIR conference on Research and Development in Information Retrieval, Tokyo, Japan.10.1145/3077136.3080777 ↗
8. Jiang, P., Xiao, C., Cross, A., and Sun, J. (2023). Graphcare: Enhancing healthcare predictions with personalized knowledge graphs. arXiv.
9. Stage-aware hierarchical attentive relational network for diagnosis prediction10.1109/TKDE.2023.3310478 ↗
10. Ye, M., Cui, S., Wang, Y., Luo, J., Xiao, C., and Ma, F. (2021, January 19–23). Medpath: Augmenting health risk prediction via medical knowledge paths. Proceedings of the Web Conference, Ljubljana, Slovenia.10.1145/3442381.3449860 ↗
11. Yang, K., Xu, Y., Zou, P., Ding, H., Zhao, J., Wang, Y., and Xie, B. (2023, January 7–14). KerPrint: Local-global knowledge graph enhanced diagnosis prediction for retrospective and prospective interpretations. Proceedings of the AAAI Conference on Artificial Intelligence, Washington, DC, USA.10.1609/aaai.v37i4.25667 ↗
12. Cui, C., Wang, W., Zhang, M., Chen, G., Luo, Z., and Ooi, B.C. (2021, January 20–25). Alphaevolve: A learning framework to discover novel alphas in quantitative investment. Proceedings of the 2021 International Conference on Management of Data, Xi’an, China.10.1145/3448016.3457324 ↗
13. Zhou, H., Zhang, S., Peng, J., Zhang, S., Li, J., Xiong, H., and Zhang, W. (2021, January 2–9). Informer: Beyond efficient transformer for long sequence time-series forecasting. Proceedings of the AAAI Conference on Artificial Intelligence, Virtually.10.1609/aaai.v35i12.17325 ↗
14. Ren, Y., Chen, Y., Liu, S., Wang, B., Yu, H., and Cui, Z. (2024). TPLLM: A traffic prediction framework based on pretrained large language models. arXiv.
15. A comprehensive survey on imputation of missing data in internet of things10.1145/3533381 ↗
16. Little, R.J., and Rubin, D.B. (2019). Statistical Analysis with Missing Data, John Wiley & Sons.10.1002/9781119482260 ↗
17. A novel framework for imputation of missing values in databases10.1109/TSMCA.2007.902631 ↗
18. An introduction to kernel and nearest-neighbor nonparametric regression10.1080/00031305.1992.10475879 ↗
19. Missing data imputation using statistical and machine learning methods in a real breast cancer problem10.1016/j.artmed.2010.05.002 ↗
20. Twala, B., Cartwright, M., and Shepperd, M. (2005, January 17–18). Comparison of various methods for handling incomplete data in software engineering databases. Proceedings of the IEEE 2005 International Symposium on Empirical Software Engineering, Noosa Heads, Australia.
21. Gondara, L., and Wang, K. (2017). Multiple imputation using deep denoising autoencoders. arXiv.10.1007/978-3-319-93040-4_21 ↗
22. Mattei, P.A., and Frellsen, J. (2019, January 9–15). MIWAE: Deep generative modelling and imputation of incomplete data sets. Proceedings of the International Conference on Machine Learning, Long Beach, CA, USA.
23. Methodologies for cross-domain data fusion: An overview10.1109/TBDATA.2015.2465959 ↗
24. Lv, F., Liang, T., Chen, X., and Lin, G. (2020, January 14–19). Cross-domain semantic segmentation via domain-invariant interactive relation transfer. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Seattle, WA, USA.10.1109/CVPR42600.2020.00439 ↗
25. Combining heterogeneous classifiers for relational databases10.1016/j.patcog.2012.06.015 ↗
26. Sayyadian, M., LeKhac, H., Doan, A., and Gravano, L. (2006, January 15–20). Efficient keyword search across heterogeneous relational databases. Proceedings of the 2007 IEEE 23rd International Conference on Data Engineering, Istanbul, Turkey.10.1109/ICDE.2007.367880 ↗
27. Drutsa, A., Fedorova, V., Ustalov, D., Megorskaya, O., Zerminova, E., and Baidakova, D. (2020, January 14–19). Crowdsourcing practice for efficient data labeling: Aggregation, incremental relabeling, and pricing. Proceedings of the 2020 ACM SIGMOD International Conference on Management of Data, Portland, OR, USA.10.1145/3318464.3383127 ↗
28. Zhang, C., Zhong, H., Zhang, K., Chai, C., Wang, R., Zhuang, X., Bai, T., Qiu, J., Cao, L., and Fan, J. (2024). Harnessing Diversity for Important Data Selection in Pretraining Large Language Models. arXiv.
29. Language models are few-shot learners
30. Narayan, A., Chami, I., Orr, L., Arora, S., and Ré, C. (2022). Can foundation models wrangle your data?. arXiv.10.14778/3574245.3574258 ↗
31. Wei, J., Bosma, M., Zhao, V.Y., Guu, K., Yu, A.W., Lester, B., Du, N., Dai, A.M., and Le, Q.V. (2021). Finetuned language models are zero-shot learners. arXiv.
32. Few-shot task-agnostic neural architecture search for distilling large language models
33. Consistent meta-regularization for better meta-knowledge in few-shot learning10.1109/TNNLS.2021.3084733 ↗
34. Chain-of-thought prompting elicits reasoning in large language models
35. Tree of thoughts: Deliberate problem solving with large language models
36. Qahtan, A.A., Elmagarmid, A., Castro Fernandez, R., Ouzzani, M., and Tang, N. (2018, January 19–23). FAHES: A robust disguised missing values detector. Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, London, UK.10.1145/3219819.3220109 ↗
37. Supporting ranking queries on uncertain and incomplete data10.1007/s00778-009-0176-8 ↗
38. Discovery of genuine functional dependencies from relational data with missing values10.14778/3204028.3204032 ↗
39. LSTM-based traffic flow prediction with missing data10.1016/j.neucom.2018.08.067 ↗
40. Where’s my data? evaluating visualizations with missing data10.1109/TVCG.2018.2864914 ↗
41. Embedded functional dependencies and data-completeness tailored database design10.14778/3342263.3342626 ↗
42. Forgetting of unused classes in missing data environment using automatically generated data: Application to on-line handwritten gesture command recognition10.1016/j.patcog.2017.08.007 ↗
43. Zhao, B., Wu, B., Wu, T., and Wang, Y. (2017, January 22–29). Zero-shot learning posed as a missing data problem. Proceedings of the IEEE International Conference on Computer Vision Workshops, Venice, Italy.10.1109/ICCVW.2017.310 ↗
44. TRIP: An interactive retrieving-inferring data imputation approach10.1109/TKDE.2015.2411276 ↗
45. Enriching data imputation under similarity rule constraints10.1109/TKDE.2018.2883103 ↗
46. Imputation of missing data in industrial databases10.1023/A:1008334909089 ↗
47. Wahl, S., Boulesteix, A.L., Zierer, A., Thorand, B., and van de Wiel, M.A. (2016). Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation. BMC Med Res. Methodol., 16.10.1186/s12874-016-0239-7 ↗
48. Accounting for misclassified outcomes in binary regression models using multiple imputation with internal validation data10.1093/aje/kws340 ↗
49. Thiesmeier, R., Bottai, M., and Orsini, N. (2024). Imputing missing values with external data. arXiv.
50. Flexibly accounting for exposure misclassification with external validation data10.1093/aje/kwaa011 ↗
51. Salgado, C.M., Azevedo, C., Proença, H., and Vieira, S.M. (2016). Missing data. Secondary Analysis of Electronic Health Records, Springer.10.1007/978-3-319-43742-2_13 ↗
52. Muzellec, B., Josse, J., Boyer, C., and Cuturi, M. (2020, January 13–18). Missing data imputation using optimal transport. Proceedings of the International Conference on Machine Learning, Virtual.
53. Pattern classification with missing data: A review10.1007/s00521-009-0295-6 ↗
54. MissForest—non-parametric missing value imputation for mixed-type data10.1093/bioinformatics/btr597 ↗
55. Zhang, A., Song, S., Sun, Y., and Wang, J. (2019, January 8–11). Learning individual models for imputation. Proceedings of the 2019 IEEE 35th International Conference on Data Engineering (ICDE), Macao, China.10.1109/ICDE.2019.00023 ↗
56. Variational autoencoders for missing data imputation with application to a simulated milling circuit10.1016/j.ifacol.2018.09.406 ↗
57. Handling incomplete heterogeneous data using vaes10.1016/j.patcog.2020.107501 ↗
58. Missing data imputation with adversarially-trained graph convolutional networks10.1016/j.neunet.2020.06.005 ↗
59. Yoon, J., Jordon, J., and Schaar, M. (2018, January 10–15). Gain: Missing data imputation using generative adversarial nets. Proceedings of the International Conference on Machine Learning, Stockholm, Sweden.
60. Chen, T., and Guestrin, C. (2016, January 13–17). Xgboost: A scalable tree boosting system. Proceedings of the 22nd ACM Sigkdd International Conference on Knowledge Discovery and Data Mining, San Francisco, CA, USA.10.1145/2939672.2939785 ↗
61. Multiple imputation by chained equations (MICE): Implementation in Stata10.18637/jss.v045.i04 ↗
62. Spectral regularization algorithms for learning large incomplete matrices
63. Lee, D., and Seung, H.S. (2000). Algorithms for non-negative matrix factorization. Adv. Neural Inf. Process. Syst., 13.
64. Multiple imputation in principal component analysis10.1007/s11634-011-0086-7 ↗
65. Doersch, C. (2016). Tutorial on variational autoencoders. arXiv.
66. Germain, M., Gregor, K., Murray, I., and Larochelle, H. (2015, January 6–11). Made: Masked autoencoder for distribution estimation. Proceedings of the International Conference on Machine Learning, Lille, France.
67. Arjovsky, M., Chintala, S., and Bottou, L. (2017, January 6–11). Wasserstein generative adversarial networks. Proceedings of the International Conference on Machine Learning, Sydney, Australia.
68. Customizable text generation via conditional text generative adversarial network10.1016/j.neucom.2018.12.092 ↗
69. Mei, Y., Song, S., Fang, C., Yang, H., Fang, J., and Long, J. (2021, January 19–22). Capturing semantics for imputation with pre-trained language models. Proceedings of the 2021 IEEE 37th International Conference on Data Engineering (ICDE), Chania, Greece.10.1109/ICDE51399.2021.00013 ↗
70. Chen, Y., Wang, X., and Xu, G. (2023). Gatgpt: A pre-trained large language model with graph attention network for spatiotemporal imputation. arXiv.
71. Ding, Z., Tian, J., Wang, Z., Zhao, J., and Li, S. (2024). Data imputation using large language model to accelerate recommendation system. arXiv.
72. Radford, A. (2025, June 10). Improving Language Understanding by Generative Pre-Training. Available online: https://www.mikecaptain.com/resources/pdf/GPT-1.pdf.
73. Ruder, S., Peters, M.E., Swayamdipta, S., and Wolf, T. (2019, January 2–7). Transfer learning in natural language processing. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Tutorials, Minneapolis, MN, USA.10.18653/v1/N19-5004 ↗
74. Luo, G., Han, Y.T., Mou, L., and Firdaus, M. (2023). Prompt-based editing for text style transfer. arXiv.10.18653/v1/2023.findings-emnlp.381 ↗
75. Atlas: Few-shot learning with retrieval augmented language models
76. Transtab: Learning transferable tabular transformers across tables
77. Yang, C., Luo, Y., Cui, C., Fan, J., Chai, C., and Tang, N. (2025, June 10). Retrieval Augmented Imputation Using Data Lake Tables. Available online: https://openreview.net/forum?id=EyW92b6DyY.
78. Deep neural networks and tabular data: A survey10.1109/TNNLS.2022.3229161 ↗
79. Carballo, K.V., Na, L., Ma, Y., Boussioux, L., Zeng, C., Soenksen, L.R., and Bertsimas, D. (2022). TabText: A Flexible and Contextual Approach to Tabular Data Representation. arXiv.
80. Ren, W., Zhao, T., Huang, Y., and Honavar, V. (2025). Deep Learning within Tabular Data: Foundations, Challenges, Advances and Future Directions. arXiv.
81. Yi, Z., Ouyang, J., Liu, Y., Liao, T., Xu, Z., and Shen, Y. (2024). A Survey on Recent Advances in LLM-Based Multi-turn Dialogue Systems. arXiv.
82. Bai, G., Liu, J., Bu, X., He, Y., Liu, J., Zhou, Z., Lin, Z., Su, W., Ge, T., and Zheng, B. (2024). Mt-bench-101: A fine-grained benchmark for evaluating large language models in multi-turn dialogues. arXiv.10.18653/v1/2024.acl-long.401 ↗
83. Gao, Y., Xiong, Y., Gao, X., Jia, K., Pan, J., Bi, Y., Dai, Y., Sun, J., and Wang, H. (2023). Retrieval-augmented generation for large language models: A survey. arXiv.
84. Retrieval-augmented generation for knowledge-intensive nlp tasks
85. Wu, Y., Zhao, Y., Hu, B., Minervini, P., Stenetorp, P., and Riedel, S. (2022). An efficient memory-augmented transformer for knowledge-intensive nlp tasks. arXiv.10.18653/v1/2022.emnlp-main.346 ↗
86. Jiang, Z., Xu, F.F., Gao, L., Sun, Z., Liu, Q., Dwivedi-Yu, J., Yang, Y., Callan, J., and Neubig, G. (2023). Active retrieval augmented generation. arXiv.10.18653/v1/2023.emnlp-main.495 ↗
87. Guu, K., Lee, K., Tung, Z., Pasupat, P., and Chang, M. (2020, January 13–18). Retrieval augmented language model pre-training. Proceedings of the International Conference on Machine Learning, Virtual Event.
88. Zhuang, X., Peng, J., Ma, R., Wang, Y., Bai, T., Wei, X., Qiu, J., Zhang, C., Qian, Y., and He, C. (2025). Meta-rater: A Multi-dimensional Data Selection Method for Pre-training Language Models. arXiv.
89. In-context retrieval-augmented language models10.1162/tacl_a_00605 ↗
90. Li, P., He, Y., Yashar, D., Cui, W., Ge, S., Zhang, H., Fainman, D.R., Zhang, D., and Chaudhuri, S. (2023). Table-gpt: Table-tuned gpt for diverse table tasks. arXiv.10.1145/3654979 ↗
91. Table-GPT: Table Fine-tuned GPT for Diverse Table Tasks
92. Zhang, D., Yin, C., Zeng, J., Yuan, X., and Zhang, P. (2020). Combining structured and unstructured data for predictive models: A deep learning approach. BMC Med. Inform. Decis. Mak., 20.10.1186/s12911-020-01297-6 ↗
93. Alessandro, M.D., Calabrés, E., and Elkano, M. (2024). A Modular End-to-End Multimodal Learning Method for Structured and Unstructured Data. arXiv.
94. Bai, T., Yang, L., Wong, Z.H., Peng, J., Zhuang, X., Zhang, C., Wu, L., Qiu, J., Zhang, W., and Yuan, B. (2024). Multi-Agent Collaborative Data Selection for Efficient LLM Pretraining. arXiv.
95. Ebrahimi, S., Arik, S.O., Dong, Y., and Pfister, T. (2023). Lanistr: Multimodal learning from structured and unstructured data. arXiv.
96. Yang, S., Zhang, R., Erfani, S.M., and Lau, J.H. (2021, January 19–27). UniMF: A Unified Framework to Incorporate Multimodal Knowledge Bases intoEnd-to-End Task-Oriented Dialogue Systems. Proceedings of the IJCAI, Montreal, QC, Canada.10.24963/ijcai.2021/548 ↗
97. The impact of heterogeneous distance functions on missing data imputation and classification performance10.1016/j.engappai.2022.104791 ↗
98. Guțu, B.M., and Popescu, N. (2024). Exploring Data Analysis Methods in Generative Models: From Fine-Tuning to RAG Implementation. Computers, 13.10.3390/computers13120327 ↗
99. Naeem, Z.A., Ahmad, M.S., Eltabakh, M., Ouzzani, M., and Tang, N. (2024). RetClean: Retrieval-Based Data Cleaning Using Foundation Models and Data Lakes. arXiv.10.14778/3685800.3685890 ↗
100. Deng, X., Sun, H., Lees, A., Wu, Y., and Yu, C. (2020). TURL: Table Understanding through Representation Learning. arXiv.10.14778/3430915.3430921 ↗