Automated Scientific Discovery: From Equation Discovery to Autonomous Discovery Systems
Paper · 2023 · Stefan Kramer, Mattia Cerrato, Jannis Brugger et al.
Summary
This survey maps the field of automated scientific discovery along two strands that have so far developed largely apart. The first is the extraction of human-interpretable knowledge, mostly equations, from data. The second is automating and increasing the autonomy of the research process itself. The authors follow equation discovery and symbolic regression from the early BACON systems to grammar-guided and sparse-regression methods, and list open problems. They also examine the roles neural networks play: learning representations, guiding equation search, and serving as neural operators that give up interpretability entirely. They then turn to closed-loop systems, starting with the robot scientist Adam. Autonomy is framed with levels borrowed from self-driving cars, and the paper catalogues benchmarks and testbeds. The main conclusion is a clear gap: few systems both act autonomously and report their findings in formalisms scientists use, which would let humans steer the search. Bridging this gap is presented as necessary for the Nobel Turing Grand Challenge, which asks for AI scientists capable of Nobel-level discoveries by 2050.
Key points
- Lineage of equation discovery:
- BACON (built on PRISM, with versions BACON.2–5) rederived laws such as Kepler's third law by constructing new terms.
- Lagrange learned ODEs from observational data.
- Lagramge was the first system to constrain the search with a context-free grammar encoding domain knowledge.
- SINDy later applied sparse regression, and SINDy-SHRED extended it to nonlinear dynamics.
- Adam, the first robot scientist, automated hypothesis–experiment cycles in functional genomics; a third generation of robot scientists is now being developed.
- Autonomy is graded on five levels, as in autonomous driving; level five means scientific knowledge is produced with no human intervention.
- The paper cites Jan Zytkow's coupling of the FAHRENHEIT discovery system with real experiments as rare early work bridging both strands.
- Benchmarks reviewed include:
- ScienceWorld: 30 text-based tasks.
- DiscoveryBench: over 1,000 tasks, scored with an LLM judge.
- Open Catalyst 2020 (OC20): over a million DFT relaxations.
- Others: Feynman, Nguyen, ChemGymRL, BoxingGym, Science-Gym, Matbench, SCP-116K and The Well. Of these, only The Well is rated fully open-ended.
Institutions
Fields, topics and concepts
📚 Shelves 4The field of science this work belongs to (OpenAlex fields).Computer Science · 19,503 worksArtificial Intelligence · 18,805 worksMaterials Science · 58 worksMaterials Chemistry · 58 works
Cite
Cite as Stefan Kramer, Mattia Cerrato, Jannis Brugger, Sašo Džeroski and Ross King. 2023. Automated Scientific Discovery: From Equation Discovery to Autonomous Discovery Systems. arXiv:2305.02251 · Machine Learning (2026) 115:109.
@misc{kramer2023automated,
title = {{Automated Scientific Discovery: From Equation Discovery to Autonomous Discovery Systems}},
author = {Stefan Kramer, Mattia Cerrato, Jannis Brugger, Sašo Džeroski and Ross King},
year = {2023},
doi = {10.1007/s10994-025-06955-2},
eprint = {2305.02251},
archivePrefix = {arXiv},
url = {https://doi.org/10.1007/s10994-025-06955-2}
}References
- Langley, P.: Bacon: A production system that discovers empirical laws. In: Proceedings of the 5th International Joint Conference on Artificial Intelligence (IJCAI 1977), p. 344 (1977)
- Langley, P.W., Simon, H.A., Bradshaw, G., Zytkow, J.M.: Scientific Discovery: Computational Explorations of the Creative Process. MIT Press, Cambridge, MA, USA (1987) find
- Džeroski, S., Todorovski, L.: Discovering dynamics. In: Proceedings of the Tenth International Conference on Machine Learning, pp. 97–103. Morgan Kaufmann, Amherst, MA, USA (1993) find
- Koza, J.R.: Genetic programming as a means for programming computers by natural selection. Statistics and Computing 4, 87–112 (1994) find
- Li, Z., Ji, J., Zhang, Y.: From kepler to newton: Explainable ai for science. arXiv preprint arXiv:2111.12210 (2021) https://doi.org/10.48550/arXiv.2111.12210 — [doi:10.48550/arxiv.2111.12210](https://doi.org/10.48550/arxiv.2111.12210) ↗
- King, R.D., Rowland, J., Oliver, S.G., Young, M., Aubrey, W., Byrne, E., Liakata, M., Markham, M., Pir, P., Soldatova, L.N., Sparkes, A., Whelan, K.E., Clare, A.: The automation of science. Science 324(5923), 85–89 (2009) find
- Cohn, D.A., Ghahramani, Z., Jordan, M.I.: Active learning with statistical models. Journal of Artificial Intelligence Research 4, 129–145 (1996) find
- Sutton, R., Barto, A.: Reinforcement Learning: An Introduction. MIT Press, Cambridge, MA, USA (2018) find
- Zytkow, J.M., Zhu, J., Hussam, A.: Automated discovery in a chemistry laboratory. In: Proceedings of the 8th National Conference on Artificial Intelligence (AAAI 1990), pp. 889–894. AAAI Press / MIT Press, Boston, MA, USA (1990) find
- Huang, K.-M., Zytkow, J.M.: Discovering empirical equations from robot-collected data. In: Proceedings of the 10th International Symposium on Foundations of Intelligent Systems (ISMIS 1997), pp. 287–297. Springer, Charlotte, North Carolina, USA (1997) find
- Makke, N., Chawla, S.: Interpretable scientific discovery with symbolic regression: a reviews. Artificial Intelligence Review 57(2) (2024) find
- Musslick, S., Bartlett, L.K., Chandramouli, S.H., Dubova, M., Gobet, F., Griffiths, T.L., Hullman, J., King, R.D., Kutz, J.N., Lucas, C.G., Mahesh, S., Pestilli, F., Sloman, S.J., Holmes, W.R.: Automating the practice of science: Opportunities, challenges, and implications. PNAS 122(5) (2025) find
- Gao, S., Fang, A., Huang, Y., Giunchiglia, V., Noori, A., Schwarz, J.R., Ektefaie, Y., Kondic, J., Zitnik, M.: Empowering biomedical discovery with ai agents. Cell 187(22), 6125–6151 (2024)
- Langley, P.: Agents of exploration and discovery. AI Magazine 42(4), 72–82 (2022) find
- Langley, P.: Integrated systems for computational scientific discovery. In: Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), pp. 22598–22606. AAAI Press, Vancouver, Canada (2024) find
- Todorovski, L., Džeroski, S.: Declarative bias in equation discovery. In: Proceedings of the Fourteenth International Conference on Machine Learning, pp. 376–384. Morgan Kaufmann, San Francisco, CA (1997) find
- Brence, J., Todorovski, L., Džeroski, S.: Probabilistic grammars for equation discovery. Knowledge Based Systems 224, 107077 (2021) find
- Schmidt, M., Lipson, H.: Distilling free-form natural laws from experimental data. Science 324(5923), 81–85 (2009) find
- Brunton, S.L., Proctor, J.L., Kutz, J.N.: Discovering governing equations from data by sparse identification of nonlinear dynamical systems. PNAS 113, 3932– 3937 (2016) find
- Gao, M.L., Williams, J.P., Kutz, J.N.: Sparse identification of nonlinear dynamics and Koopman operators with Shallow Recurrent Decoder Networks (2025). https://arxiv.org/abs/2501.13329 — [arXiv:2501.13329](https://arxiv.org/abs/2501.13329) ↗
- Ganzert, S., Guttmann, J., Steinmann, D., Kramer, S.: Equation discovery for model identification in respiratory mechanics of the mechanically ventilated human lung. In: Proceedings of the 13th International Conference on Discovery Science (DS 2010), pp. 296–310. Springer, Berlin, Heidelberg (2010) find
- Washio, T., Motoda, H.: Discovering admissible models of complex systems based on scale-types and identity constraints. In: Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence (IJCAI 1997), pp. 810–819 (1997) find
- Brence, J., Todorovski, L., Džeroski, S.: Dimensionally consistent equation discovery through probabilistic attribute grammars. Information Sciences (2023) find
- Chaushevska, M., Todorovski, L., Brence, J., Džeroski, S.: Learning the probabilities in probabilistic context-free grammars for arithmetical expressions from equation corpora. In: Proceedings of the Slovenian Conference on Artificial Intelligence (2022) find
- Džeroski, S., Petrovski, I.: Discovering dynamics with genetic programming. In: Proceedings of the Seventh European Conference on Machine Learning, pp. 347– 350. Springer, Berlin, Heidelberg (1994) find
- Todorovski, L., Džeroski, S.: Integrating knowledge-driven and data-driven approaches to modeling. Ecological Modelling 194, 3–13 (2006) find
- Bridewell, W., Langley, P., Todorovski, L., Džeroski, S.: Inductive process modeling. Machine Learning 71, 1–32 (2008) find
- Čerepnalkoski, D., Taškova, K., Todorovski, L., Atanasova, N., Džeroski, S.: The influence of parameter fitting methods on model structure selection in automated modeling of aquatic ecosystems. Ecological Modelling 45, 136–165 (2012) find
- Guimerà, R., Reichardt, I., Aguilar-Mogas, A., Massucci, F.A., Miranda, M., Pallarès, J., Sales-Pardo, M.: A bayesian machine scientist to aid in the solution of challenging scientific problems. Science Advances 6, 6971 (2020) find
- Cranmer, M.D.: Interpretable machine learning for science with pysr and symbolicregression.jl. CoRR abs/2305.01582 (2023) 2305.01582
- Bychkov, A., Issan, I., Pogudin, G., Krämer, B.: Exact and optimal quadratiza-tion of nonlinear finite-dimensional non-autonomous dynamical systems. SIAM Journal on Applied Dynamical Systems 23(1), 982–1016 (2024) find
- Jiang, N., Xue, Y.: Symbolic regression via control variable genetic programming. In: Proc. of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2023), pp. 178–195. Springer, Berlin, Heidelberg (2023) find
- Udrescu, S.-M., Tan, A., Feng, J., Neto, O., Wu, T., Tegmark, M.: Ai feynman 2.0: Pareto-optimal symbolic regression exploiting graph modularity. In: Advances in Neural Information Processing Systems 33 (2020) find
- Lusch, B., Kutz, J.N., Brunton, S.L.: Deep learning for universal linear embeddings of nonlinear dynamics. Nature communications 9(1), 4950 (2018) find
- Mežnar, S., Džeroski, S., Todorovski, L.: Efficient generator of mathematical expressions for symbolic regression. Machine Learning 112(11), 4563–4596 (2023) find
- Mundhenk, T.N., Landajuela, M., Glatt, R., Santiago, C.P., Faissol, D.M., Petersen, B.K.: Symbolic regression via neural-guided genetic programming population seeding. arXiv preprint arXiv:2111.00053 (2021) — [arXiv:2111.00053](https://arxiv.org/abs/2111.00053) find
- Petersen, B.K., Larma, M.L., Mundhenk, T.N., Santiago, C.P., Kim, S.K., Kim, J.T.: Deep symbolic regression: Recovering mathematical expressions from data via risk-seeking policy gradients. In: Proceedings of the 9th International Conference on Learning Representations (ICLR 2021) (2021) find
- Biggio, L., Bendinelli, T., Neitz, A., Lucchi, A., Parascandolo, G.: Neural symbolic regression that scales. In: Meila, M., Zhang, T. (eds.) Proceedings of the 38th International Conference on Machine Learning, ICML 2021, 18-24 July 2021, Virtual Event. Proceedings of Machine Learning Research, vol.… find
- Valipour, M., You, B., Panju, M., Ghodsi, A.: SymbolicGPT: A Generative Transformer Model for Symbolic Regression. arXiv. arXiv:2106.14131 [cs] version: 1 (2021). https://doi.org/10.48550/arXiv.2106.14131 . http://arxiv.org/abs/2106.14131 — [doi:10.48550/arxiv.2106.14131](https://doi.org/10.48550/arxiv.2106.14131) ↗
- Kamienny, P., d’Ascoli, S., Lample, G., Charton, F.: End-to-end symbolic regression with transformers. In: Koyejo, S., Mohamed, S., Agarwal, A., Belgrave, D., Cho, K., Oh, A. (eds.) Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022,…
- Brugger, J., Cerrato, M., Richter, D., Derstroff, C., Maninger, D., Mezini, M., Kramer, S.: Neural-Guided Equation Discovery (2025). https://arxiv.org/abs/2503.16953 — [arXiv:2503.16953](https://arxiv.org/abs/2503.16953) ↗
- Shojaee, P., Meidani, K., Farimani, A.B., Reddy, C.K.: Transformer-based Planning for Symbolic Regression (2023) https://doi.org/10.48550/ARXIV.2303.06833 . Publisher: arXiv Version Number: 4. Accessed 2023-08-09 — [doi:10.48550/arxiv.2303.06833](https://doi.org/10.48550/arxiv.2303.06833) ↗
- Kamienny, P., Lample, G., Lamprier, S., Virgolin, M.: Deep generative symbolic regression with monte-carlo-tree-search. In: Krause, A., Brunskill, E., Cho, K., Engelhardt, B., Sabato, S., Scarlett, J. (eds.) International Conference on Machine Learning, ICML 2023, 23-29 July 2023. Proceedings of Mac… find
- Sahoo, S., Lampert, C., Martius, G.: Learning Equations for Extrapolation and Control. In: Proceedings of the 35th International Conference on Machine Learning, pp. 4442–4450. PMLR, Stockholm, Sweden (2018). ISSN: 2640-3498. https://proceedings.mlr.press/v80/sahoo18a.html Accessed 2024-02-19 ↗
- Liu, Z., Wang, Y., Vaidya, S., Ruehle, F., Halverson, J., Soljačić, M., Hou, T.Y., Tegmark, M.: Kan: Kolmogorov-arnold networks. arXiv preprint arXiv:2404.19756 (2024) — [arXiv:2404.19756](https://arxiv.org/abs/2404.19756) find
- Merler, M., Haitsiukevich, K., Dainese, N., Marttinen, P.: In-Context Symbolic Regression: Leveraging Large Language Models for Function Discovery. In: Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (Volume 4: Student Research Workshop), pp. 589–606. Associat… find
- Sharlin, S., Josephson, T.R.: In Context Learning and Reasoning for Symbolic Regression with Large Language Models. arXiv. Version Number: 2 (2024). https://doi.org/10.48550/ARXIV.2410.17448 . https://arxiv.org/abs/2410.17448 Accessed 2025-03-17 ↗
- Shojaee, P., Meidani, K., Gupta, S., Farimani, A.B., Reddy, C.K.: LLM-SR: Scientific Equation Discovery via Programming with Large Language Models. arXiv. Version Number: 2 (2024). https://doi.org/10.48550/ARXIV.2404.18400 . https://arxiv.org/abs/2404.18400 Accessed 2024-08-05 ↗
- Meyerson, E., Nelson, M.J., Bradley, H., Gaier, A., Moradi, A., Hoover, A.K., Lehman, J.: Language Model Crossover: Variation through Few-Shot Prompting. arXiv. Version Number: 3 (2023). https://doi.org/10.48550/ARXIV.2302.12170 . https://arxiv.org/abs/2302.12170 Accessed 2025-03-27 — [doi:10.48550/arxiv.2302.12170](https://doi.org/10.48550/arxiv.2302.12170) ↗
- Cranmer, M.D., Sanchez-Gonzalez, A., Battaglia, P.W., Xu, R., Cranmer, K., Spergel, D.N., Ho, S.: Discovering symbolic models from deep learning with inductive biases. In: Advances in Neural Information Processing Systems 33 (2020)
- Garcon, A., Vexler, J., Budker, D., Kramer, S.: Deep neural networks to recover unknown physical parameters from oscillating time series. PLoS ONE 17(5), 0268439 (2022) find
- Chen, B., Huang, K., Raghupathi, S., Chandratreya, I., Du, Q., Lipson, H.: Automated discovery of fundamental variables hidden in experimental data. Nature Computational Science 2, 433–442 (2022) find
- Levina, E., Bickel, P.J.: Maximum likelihood estimation of intrinsic dimension. In: Advances in Neural Information Processing Systems 17, pp. 777–784 (2004) find
- Kovachki, N., Li, Z., Liu, B., Azizzadenesheli, K., Bhattacharya, K., Stuart, A.M., Anandkumar, A.: Neural operator: Learning maps between function spaces with applications to pdes. Journal of Machine Learning Research 24, 1–97 (2023) find
- Lu, L., Jin, P., Pang, G., Zhang, Z., Karniadakis, G.E.: Learning nonlinear operators via deeponet based on the universal approximation theorem of operators. Nature Machine Intelligence 3(3), 218–229 (2021) find
- Li, Z., Kovachki, N.B., Azizzadenesheli, K., Liu, B., Bhattacharya, K., Stuart, A.M., Anandkumar, A.: Fourier neural operator for parametric partial differential equations. In: Proceedings of the 9th International Conference on Learning Representations (ICLR 2021) (2021) find
- Eisenstein, M.: Self-driving laboratories, advanced immunotherapies and five more technologies to watch in 2025. Nature 637, 1008–1011 (2025) https://doi.org/10.1038/d41586-025-00075-6 — [doi:10.1038/d41586-025-00075-6](https://doi.org/10.1038/d41586-025-00075-6) ↗
- Sparkes, A., Aubrey, W., Byrne, E., Clare, A., Khan, M.N., Liakata, M., Markham, M., Rowland, J., Soldatova, L.N., Whelan, K.E., Young, M., King, R.D.: Towards robot scientists for autonomous scientific discovery. Automated Experimentation 2(1) (2021) find
- Williams, K., Bilsland, E., Sparkes, A., Aubrey, W., Young, M., Soldatova, L.N., Grave, K.D., Ramon, J., Clare, M., Sirawaraporn, W., Oliver, S.G., King, R.D.: Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases. Journal of the Royal Society In… find
- Williams, K., Bilsland, E., Sparkes, A., Aubrey, W., Young, M., Soldatova, L.N., De Grave, K., Ramon, J., Clare, M., Sirawaraporn, W., Oliver, S.G., King, R.D.: Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases. Journal of the Royal Society I… — [doi:10.1098/rsif.2014.1289](https://doi.org/10.1098/rsif.2014.1289) find
- Roper, K., Abdel-Rehim, A., Hubbard, S., Carpenter, M., Rzhetsky, A., Soldatova, L.N., King, R.D.: Testing the reproducibility and robustness of the cancer biology literature by robot. Journal of the Royal Society Interface 19(189), 20210821 (2022) https://doi.org/10.1098/rsif.2021.0821 — [doi:10.1098/rsif.2021.0821](https://doi.org/10.1098/rsif.2021.0821) ↗
- Burger, B., Maffettone, P.M., Gusev, V.V., Aitchison, C.M., Bai, Y., Wang, X., Li, X., Alston, B.M., Li, B., Clowes, R., Rankin, N., Harris, B., Sprick, R.S., Cooper, A.I.: A mobile robotic chemist. Nature 583(7815), 237–241 (2020) https://doi.org/10.1038/s41586-020-2442-2 — [doi:10.1038/s41586-020-2442-2](https://doi.org/10.1038/s41586-020-2442-2) ↗
- King, R., Peter, O., Courtney, P.: Robot scientists: From adam to eve to genesis. In: Science, T., Innovation, O. (eds.) Artificial Intelligence in Science: Challenges, Opportunities and the Future of Research, pp. 127–138. OECD Publishing, Paris (2023) find
- Wilczek, F., Devine, B.: Fantastic Realities: 49 Mind Journeys and a Trip to Stockholm. World Scientific, Singapore (2006) find
- Kitano, H.: Nobel turing challenge: Creating the engine for scientific discovery. npj Systems Biology and Applications 7(29) (2021) find
- Uy, N.Q., Hoai, N.X., O’Neill, M., McKay, R.I., Galván-López, E.: Semantically-based crossover in genetic programming: application to real-valued symbolic regression. Genetic Programming and Evolvable Machines 12, 91–119 (2011) find
- Udrescu, S.-M., Tegmark, M.: Ai feynman: A physics-inspired method for symbolic regression. Science advances 6(16), 2631 (2020)
- Dunn, A., Wang, Q., Ganose, A., Dopp, D., Jain, A.: Benchmarking materials property prediction methods: the matbench test set and automatminer reference algorithm. npj Computational Materials 6, 138 (2020) find
- Lu, D., Tan, X., Xu, R., Yao, T., Qu, C., Chu, W., Xu, Y., Qi, Y.: SCP-116K: A High-Quality Problem-Solution Dataset and a Generalized Pipeline for Automated Extraction in the Higher Education Science Domain (2025). https://arxiv.org/abs/2501.15587 — [arXiv:2501.15587](https://arxiv.org/abs/2501.15587) ↗
- Ohana, R., McCabe, M., Meyer, L.T., Morel, R., Agocs, F.J., Beneitez, M., Berger, M., Burkhart, B., Dalziel, S.B., Fielding, D.B., Fortunato, D., Goldberg, J.A., Hirashima, K., Jiang, Y.-F., Kerswell, R., Maddu, S., Miller, J.M., Mukhopadhyay, P., Nixon, S.S., Shen, J., Watteaux, R., Blancard, B.R.-… find
- Wang, R., Jansen, P., Côté, M.-A., Ammanabrolu, P.: ScienceWorld: Is your Agent Smarter than a 5th Grader? (2022). https://arxiv.org/abs/2203.07540 ↗
- Jansen, P.e.a.: DiscoveryWorld: A Virtual Environment for Developing and Evaluating Automated Scientific Discovery Agents (2024)
- Beeler, C., Subramanian, S.G., Sprague, K., Baula, M., Chatti, N., Dawit, A., Li, X., Paquin, N., Shahen, M., Yang, Z., Bellinger, C., Crowley, M., Tamblyn, I.: Chemgymrl: A customizable interactive framework for reinforcement learning for digital chemistry. Digital Discovery 3, 742–758 (2024) https… — [doi:10.1039/d3dd00183k](https://doi.org/10.1039/d3dd00183k) find
- Majumder, B.P., Surana, H., Agarwal, D., Dalvi Mishra, B., Meena, A., Prakhar, A., Vora, T., Khot, T., Sabharwal, A., Clark, P.: DiscoveryBench: Towards Data-Driven Discovery with Large Language Models. Dataset and code available on GitHub (https://github.com/allenai/discoverybench) and HuggingFace…
- Gandhi, K., Li, M.Y., Goodyear, L., Li, L., Bhaskar, A., Zaman, M., Goodman, N.D.: BoxingGym: Benchmarking Progress in Automated Experimental Design and Model Discovery. Project page with environments: https://github.com/kanishkg/boxing-gym (2025) ↗
- Cerrato, M., Schmitt, N., Baur, L., Finkelstein, E., Jukic, S., Münzel, L., Paul, F.P., Pfannes, P., Rohr, B., Schellenberg, J., Wolf, P., Kramer, S.: Science-Gym: A simple testbed for ai-driven scientific discovery. In: Proceedings of the 26th International Conference on Discovery Science (DS). Le… — [doi:10.1007/978-3-031-78977-9](https://doi.org/10.1007/978-3-031-78977-9) find
- Chanussot, L.e.a.: The open catalyst 2020 (oc20) dataset and community challenges. ACS Catalysis 11(10), 6059–6072 (2021) find
Updated
This page in Markdown → https://md.research.elamur.ai/free/en/papers/kramer-2023-automated-scientific-discovery-equation/