Abstract
Abductive reasoning plays an essential part in day-to-day problem-solving. It has been considered a powerful mechanism for hypothetical reasoning in the presence of incomplete knowledge; a form of “common sense” reasoning. In machine learning, abduction is viewed as a conceptual method in which data and the bond that jointly brings the different types of inference. The traditional Mode-Directed Inverse Entailment (MDIE) based systems such as Progol and Aleph for the abduction were not data-efficient since their execution time with the large dataset was too long. We present a new abductive learning procedure using Meta Inverse Entailment (MIE). MIE is similar to Mode-Directed Inverse Entailment (MDIE) but does not require user-defined mode declarations. In this paper, we use an implementation of MIE in Python called PyGol. We evaluate and compare this approach to reveal the microbial interactions in the ecosystem with state-of-art-of methods for abduction, such as Progol and Aleph. Our results show that PyGol has comparable predictive accuracies but is significantly faster than Progol and Aleph.
ILP 2022, 31st International Conference on Inductive Logic Programming, Cumberland Lodge, Windsor, UK.
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Notes
- 1.
Available from https://github.com/PyGol.
- 2.
Available from https://github.com/danyvarghese/IJCLR22-Abduction.
References
Adé, H., Malfait, B., De Raedt, L.: RUTH: an ILP theory revision system. In: Raś, Z.W., Zemankova, M. (eds.) ISMIS 1994. LNCS, vol. 869, pp. 336–345. Springer, Heidelberg (1994). https://doi.org/10.1007/3-540-58495-1_34
Barroso-Bergada, D., Tamaddoni-Nezhad, A., Muggleton, S.H., Vacher, C., Galic, N., Bohan, D.A.: Machine learning of microbial interactions using abductive ILP and hypothesis frequency/compression estimation. In: Katzouris, N., Artikis, A. (eds.) Inductive Logic Programming, ILP 2021. LNCS, vol. 13191, pp. 26–40. Springer, Cham (2022). https://doi.org/10.1007/978-3-030-97454-1_3
Cropper, A.: Efficiently learning efficient programs. Ph.D. thesis. Imperial College London, UK (2017)
De Raedt, L., Bruynooghe, M.: Interactive concept-learning and constructive induction by analogy. Mach. Learn. 8(2), 107–150 (1992)
Evans, R., Grefenstette, E.: Learning explanatory rules from noisy data. J. Artif. Int. Res. 61(1), 1–64 (2018)
França, M.V.M., Zaverucha, G., Garcez, A.: Fast relational learning using bottom clause propositionalization with artificial neural networks. Mach. Learn. 94(1), 81–104 (2014). https://doi.org/10.1007/s10994-013-5392-1. https://openaccess.city.ac.uk/id/eprint/3057/
Kakas, A., Tamaddoni, N.A., Muggleton, S., Chaleil, R.: Application of abductive ILP to learning metabolic network inhibition from temporal data. Mach. Learn. 64, 209–230 (2006). https://doi.org/10.1007/s10994-006-8988-x
Kakas, A.C., Kowalski, R.A., Toni., F.: Abduction in logic programming. J. Log. Comput. 2, 719–770 (1993)
Michalski, R.S.: A theory and methodology of inductive learning. Artif. Intell. 20(2), 111–161 (1983)
Michalski, R.S.: Inferential theory of learning as a conceptual basis for multistrategy learning. Mach. Learn. 11(2–3), 111–151 (1993)
Moyle, S.: Using theory completion to learn a robot navigation control program. In: Matwin, S., Sammut, C. (eds.) ILP 2002. LNCS (LNAI), vol. 2583, pp. 182–197. Springer, Heidelberg (2003). https://doi.org/10.1007/3-540-36468-4_12
Muggleton, S.: Inverse entailment and Progol. N. Gener. Comput. 13, 245–286 (1995)
Muggleton, S., Lin, D., Tamaddoni-Nezhad, A.: Meta-interpretive learning of higher-order dyadic datalog: predicate invention revisited. Mach. Learn. 100(1), 49–73 (2015). https://doi.org/10.1007/s10994-014-5471-y
Muggleton, S.: Learning from positive data. In: Muggleton, S. (ed.) ILP 1996. LNCS, vol. 1314, pp. 358–376. Springer, Heidelberg (1997). https://doi.org/10.1007/3-540-63494-0_65
Muggleton, S.H., Bryant, C.H.: Theory completion using inverse entailment. In: Cussens, J., Frisch, A. (eds.) ILP 2000. LNCS (LNAI), vol. 1866, pp. 130–146. Springer, Heidelberg (2000). https://doi.org/10.1007/3-540-44960-4_8
Muggleton, S., de Raedt, L.: Inductive logic programming: Theory and methods. J. Log. Program. 19–20, 629–679 (1994). Special Issue: Ten Years of Logic Programming
Nienhuys-Cheng, S.-H., de Wolf, R.: Foundations of Inductive Logic Programming. LNCS, vol. 1228. Springer, Heidelberg (1997). https://doi.org/10.1007/3-540-62927-0
Ourston, D., Mooney, R.J.: Theory refinement combining analytical and empirical methods. Artif. Intell. 66(2), 273–309 (1994)
Ray, O., Broda, K., Russo, A.: Hybrid Abductive inductive learning: a generalisation of Progol. In: Horváth, T., Yamamoto, A. (eds.) ILP 2003. LNCS (LNAI), vol. 2835, pp. 311–328. Springer, Heidelberg (2003). https://doi.org/10.1007/978-3-540-39917-9_21
Srinivasan, A.: A learning engine for proposing hypotheses (Aleph) (2001). https://www.cs.ox.ac.uk/activities/programinduction/Aleph/aleph.html
Tamaddoni-Nezhad, A., Lin, D., Watanabe, H., Chen, J., Muggleton, S.: Machine Learning of Biological Networks Using Abductive ILP, pp. 363–401. Wiley, Hoboken (2014). https://doi.org/10.1002/9781119005223.ch10
Tamaddoni-Nezhad, A., Bohan, D., Raybould, A., Muggleton, S.: Towards machine learning of predictive models from ecological data. In: Davis, J., Ramon, J. (eds.) ILP 2014. LNCS (LNAI), vol. 9046, pp. 154–167. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-23708-4_11
Varghese, D., Bauer, R., Baxter-Beard, D., Muggleton, S., Tamaddoni-Nezhad, A.: Human-like rule learning from images using one-shot hypothesis derivation. In: Katzouris, N., Artikis, A. (eds.) Inductive Logic Programming, ILP 2021. LNCS, vol. 13191, pp. pp 234–250. Springer, Cham (2022). https://doi.org/10.1007/978-3-030-97454-1_17
Varghese, D., Tamaddoni-Nezhad, A.: One-shot rule learning for challenging character recognition. In: Proceedings of the 14th International Rule Challenge, August 2020, Oslo, Norway, vol. 2644, pp. 10–27 (2020)
Varghese, D., Tamaddoni-Nezhad, A.: Pyilp (2022). https://github.com/danyvarghese/PyILP/
Yamamoto, A.: Revising the logical foundations of inductive logic programming systems with ground reduced programs. New Gener. Comput. 17, 119–127 (1998). https://cir.nii.ac.jp/crid/1571417125491386240
Yamamoto, A.: Which hypotheses can be found with inverse entailment? In: Lavrač, N., Džeroski, S. (eds.) ILP 1997. LNCS, vol. 1297, pp. 296–308. Springer, Heidelberg (1997). https://doi.org/10.1007/3540635149_58
Yamamoto, A.: Using abduction for induction based on bottom generalization. In: Flach, P.A., Kakas, A.C. (eds.) Abduction and Induction. Applied Logic Series, vol. 18, pp. 267–280. Springer, Dordrecht (2000). https://doi.org/10.1007/978-94-017-0606-3_17
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Varghese, D., Barroso-Bergada, D., Bohan, D.A., Tamaddoni-Nezhad, A. (2024). Efficient Abductive Learning of Microbial Interactions Using Meta Inverse Entailment. In: Muggleton, S.H., Tamaddoni-Nezhad, A. (eds) Inductive Logic Programming. ILP 2022. Lecture Notes in Computer Science(), vol 13779. Springer, Cham. https://doi.org/10.1007/978-3-031-55630-2_10
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