ARTIFICIAL INTELLIGENCE AND DIGITAL METHODS IN BIOLOGICAL RESEARCH
DOI:
https://doi.org/10.5281/Keywords:
artificial intelligence, machine learning, deep learning, bioinformatics, genomics, , digital microscopy, biodiversity monitoring, laboratory automationAbstract
High-throughput sequencing, single-cell omics, digital microscopy, remote sensing, and automated sensors have dramatically increased the volume and complexity of data generated in biological research. This literature review aims to systematize the main applications of artificial intelligence and digital methods in biological research, their scientific potential, and the conditions required for their reliable use. A thematic synthesis of peer-reviewed studies demonstrates that artificial intelligence delivers significant results in genomic variant detection, cell segmentation, protein structure prediction, single-cell data integration, screening of novel molecules, biodiversity monitoring, and laboratory workflow automation. However, high predictive performance does not establish that a biological mechanism has been proven: data leakage, sampling bias, domain shifts, limited interpretability, and the lack of transparency of code and models hinder the generalizability of results. The literature synthesis indicates that artificial intelligence should be regarded not as a tool for replacing biologists, but as a research infrastructure governed by data quality control, external validation, domain expertise, and reproducibility standards.
References
1. Bernett, J., Blumenthal, D. B., Grimm, D. G., Haselbeck, F., Joeres, R., Kalinina, O. V., & List, M. (2024). Guiding questions to avoid data leakage in biological machine learning applications. Nature Methods, 21, 1444–1453. https://doi.org/10.1038/s41592-024-02362-y
2. Borowiec, M. L., Dikow, R. B., Frandsen, P. B., McKeeken, A., Valentini, G., & White, A. E. (2022). Deep learning as a tool for ecology and evolution. Methods in Ecology and Evolution, 13(8), 1640–1660. https://doi.org/10.1111/2041-210X.13901
3. Christin, S., Hervet, É., & Lecomte, N. (2019). Applications for deep learning in ecology. Methods in Ecology and Evolution, 10(10), 1632–1644. https://doi.org/10.1111/2041-210X.13256
4. Cui, H., Wang, C., Maan, H., Pang, K., Luo, F., Duan, N., & Wang, B. (2024). scGPT: Toward building a foundation model for single-cell multi-omics using generative AI. Nature Methods, 21, 1470–1480. https://doi.org/10.1038/s41592-024-02201-0
5. Eraslan, G., Avsec, Ž., Gagneur, J., & Theis, F. J. (2019). Deep learning: New computational modelling techniques for genomics. Nature Reviews Genetics, 20, 389–403. https://doi.org/10.1038/s41576-019-0122-6
6. Greener, J. G., Kandathil, S. M., Moffat, L., & Jones, D. T. (2022). A guide to machine learning for biologists. Nature Reviews Molecular Cell Biology, 23, 40–55. https://doi.org/10.1038/s41580-021-00407-0
7. Heil, B. J., Hoffman, M. M., Markowetz, F., Lee, S.-I., Greene, C. S., & Hicks, S. C. (2021). Reproducibility standards for machine learning in the life sciences. Nature Methods, 18, 1132–1135. https://doi.org/10.1038/s41592-021-01256-7
8. Jumper, J., Evans, R., Pritzel, A., et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2
9. King, R. D., Rowland, J., Oliver, S. G., Young, M., Aubrey, W., Byrne, E., et al. (2009). The automation of science. Science, 324(5923), 85–89. https://doi.org/10.1126/science.1165620
10. LeCun, Y., Bengio, Y., & Hinton, G. (2015). Deep learning. Nature, 521, 436–444. https://doi.org/10.1038/nature14539
11. Lopez, R., Regier, J., Cole, M. B., Jordan, M. I., & Yosef, N. (2018). Deep generative modeling for single-cell transcriptomics. Nature Methods, 15, 1053–1058. https://doi.org/10.1038/s41592-018-0229-2
12. Moen, E., Bannon, D., Kudo, T., Graf, W., Covert, M., & Van Valen, D. (2019). Deep learning for cellular image analysis. Nature Methods, 16, 1233–1246. https://doi.org/10.1038/s41592-019-0403-1
13. Norouzzadeh, M. S., Nguyen, A., Kosmala, M., Swanson, A., Palmer, M. S., Packer, C., & Clune, J. (2018). Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning. Proceedings of the National Academy of Sciences, 115(25), E5716–E5725. https://doi.org/10.1073/pnas.1719367115
14. Pachitariu, M., & Stringer, C. (2022). Cellpose 2.0: How to train your own model. Nature Methods, 19, 1634–1641. https://doi.org/10.1038/s41592-022-01663-4
15. Pichler, M., & Hartig, F. (2023). Machine learning and deep learning– A review for ecologists. Methods in Ecology and Evolution, 14(4), 994–1016. https://doi.org/10.1111/2041-210X.14061
16. Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., et al. (2018). A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology, 36, 983–987. https://doi.org/10.1038/nbt.4235
17. Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., et al. (2020). A deep learning approach to antibiotic discovery. Cell, 180(4), 688–702.e13. https://doi.org/10.1016/j.cell.2020.01.021
18. Stowell, D. (2022). Computational bioacoustics with deep learning: A review and roadmap. PeerJ, 10, e13152. https://doi.org/10.7717/peerj.13152
19. Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: A generalist algorithm for cellular segmentation. Nature Methods, 18, 100–106. https://doi.org/10.1038/s41592-020-01018-x
20. Tunyasuvunakool, K., Adler, J., Wu, Z., et al. (2021). Highly accurate protein structure prediction for the human proteome. Nature, 596, 590–596. https://doi.org/10.1038/s41586-021-03828-1
21. Vamathevan, J., Clark, D., Czodrowski, P., Dunham, I., Ferran, E., Lee, G., et al. (2019). Applications of machine learning in drug discovery and development. Nature Reviews Drug Discovery, 18, 463–477. https://doi.org/10.1038/s41573-019-0024-5
22. Varadi, M., Anyango, S., Deshpande, M., et al. (2022). AlphaFold Protein Structure Database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research, 50(D1), D439–D444. https://doi.org/10.1093/nar/gkab1061
23. Wäldchen, J., & Mäder, P. (2018). Machine learning for image based species identification. Methods in Ecology and Evolution, 9(11), 2216–2225. https://doi.org/10.1111/2041-210X.13075
24. Walsh, I., Fishman, D., Garcia-Gasulla, D., et al. (2021). DOME: Recommendations for supervised machine learning validation in biology. Nature Methods, 18, 1122–1127. https://doi.org/10.1038/s41592-021-01205-4
25. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18
Published
Issue
Section
License
Copyright (c) 2026 Жанел Рысбекова, М.Н. Мәулен (Автор)

This work is licensed under a Creative Commons Attribution 4.0 International License.
Articles are distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) license.