Skip to main content

Large-Scale Assessment of Deep Relational Machines

  • Conference paper
  • First Online:
Inductive Logic Programming (ILP 2018)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 11105))

Included in the following conference series:

Abstract

Deep Relational Machines (or DRMs) present a simple way for incorporating complex domain knowledge into deep networks. In a DRM this knowledge is introduced through relational features: in the original formulation of [1], the features are selected by an ILP engine using domain knowledge encoded as logic programs. More recently, in [2], DRMs appear to achieve good performance without the need of feature-selection by an ILP engine (the features are simply drawn randomly from a space of relevant features). The reports so far on DRMs though have been deficient on three counts: (a) They have been tested on very small amounts of data (7 datasets, not all independent, altogether with few 1000s of instances); (b) The background knowledge involved has been modest, involving few 10s of predicates; and (c) Performance assessment has been only on classification tasks. In this paper we rectify each of these shortcomings by testing on datasets from the biochemical domain involving 100s of 1000s of instances; industrial-strength background predicates involving multiple hierarchies of complex definitions; and on classification and regression tasks. Our results provide substantially reliable evidence of the predictive capabilities of DRMs; along with a significant improvement in predictive performance with the incorporation of domain knowledge. We propose the new datasets and results as updated benchmarks for comparative studies in neural-symbolic modelling.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    We have contacted the authors of [5] and [7] and are awaiting a response.

  2. 2.

    https://www.cancer.gov/.

  3. 3.

    https://www.ebi.ac.uk/chembl/.

  4. 4.

    Due to the page limit, we don’t show the hierarchy figure. This hierarchy is available on the web. Refer the Dataset availability section for more information.

  5. 5.

    Size refers to the number of neurons.

  6. 6.

    All the experiments (feature construction and deep learning) are conducted in Linux based machines with 64GB main memory, 16 processing cores, 2GB NVIDIA Graphics Processing Units. We used Python based Keras [27] with Tensorflow as backend [28] for implementing deep nets.

  7. 7.

    We are adopting this more conservative stand despite low P values for two reasons. First, we note that LRNNs only use the equivalent of the AB representation: we would, therefore, expect their performance to improve if provided with relations in the ABFR representation. Secondly, the reader is no doubt aware of the usual precautions when interpreting P-values obtained from multiple comparisons.

  8. 8.

    We have contacted the authors proposing ways to conduct this comparison.

References

  1. Lodhi, H.: Deep relational machines. In: Lee, M., Hirose, A., Hou, Z.-G., Kil, R.M. (eds.) ICONIP 2013. LNCS, vol. 8227, pp. 212–219. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-42042-9_27

    Chapter  Google Scholar 

  2. Vig, L., Srinivasan, A., Bain, M., Verma, A.: An Investigation into the role of domain-knowledge on the use of embeddings. In: Lachiche, N., Vrain, C. (eds.) ILP 2017. LNCS (LNAI), vol. 10759, pp. 169–183. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78090-0_12

    Chapter  Google Scholar 

  3. Towell, G.G., Shavlik, J.W.: Knowledge-based artificial neural networks. Artif. Intell. 70(1–2), 119–165 (1994)

    Article  Google Scholar 

  4. d’Avila Garcez, S., Broda, K.B., Gabbay, D.M.: Neural-symbolic Learning Systems: Foundations and Applications. Springer, London (2012). https://doi.org/10.1007/978-1-4471-0211-3

  5. Gust, H., Hagmayer, Y., Kuhnberger, K.U., Sloman, S.: Learning symbolic inferences with neural networks. In: Proceedings of the Annual Meeting of the Cognitive Science Society, vol. 27 (2005)

    Google Scholar 

  6. Sourek, G., Aschenbrenner, V., Zelezny, F., Kuzelka, O.: Lifted relational neural networks. arXiv preprint arXiv:1508.05128 (2015)

  7. Evans, R., Grefenstette, E.: Learning explanatory rules from noisy data. J. Artif. Intell. Res. 61, 1–64 (2018)

    Article  MathSciNet  Google Scholar 

  8. Lavrač, N., Džeroski, S., Grobelnik, M.: Learning nonrecursive definitions of relations with linus. In: Kodratoff, Y. (ed.) EWSL 1991. LNCS, vol. 482, pp. 265–281. Springer, Heidelberg (1991). https://doi.org/10.1007/BFb0017020

    Chapter  Google Scholar 

  9. Faruquie, T.A., Srinivasan, A., King, R.D.: Topic models with relational features for drug design. In: Riguzzi, F., Železný, F. (eds.) ILP 2012. LNCS (LNAI), vol. 7842, pp. 45–57. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-38812-5_4

    Chapter  Google Scholar 

  10. Joshi, S., Ramakrishnan, G., Srinivasan, A.: Feature construction using theory-guided sampling and randomised search. In: Železný, F., Lavrač, N. (eds.) ILP 2008. LNCS (LNAI), vol. 5194, pp. 140–157. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-85928-4_14

    Chapter  Google Scholar 

  11. Ramakrishnan, G., Joshi, S., Balakrishnan, S., Srinivasan, A.: Using ILP to construct features for information extraction from semi-structured text. In: Blockeel, H., Ramon, J., Shavlik, J., Tadepalli, P. (eds.) ILP 2007. LNCS (LNAI), vol. 4894, pp. 211–224. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-78469-2_22

    Chapter  Google Scholar 

  12. Saha, A., Srinivasan, A., Ramakrishnan, G.: What kinds of relational features are useful for statistical learning? In: Riguzzi, F., Železný, F. (eds.) ILP 2012. LNCS (LNAI), vol. 7842, pp. 209–224. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-38812-5_15

    Chapter  Google Scholar 

  13. Specia, L., Srinivasan, A., Joshi, S., Ramakrishnan, G., das Graças Volpe Nunes, M.: An investigation into feature construction to assist word sense disambiguation. Mach. Learn. 76(1), 109–136 (2009). https://doi.org/10.1007/s10994-009-5114-x

  14. Srinivasan, A., King, R.D.: Feature construction with inductive logic programming: a study of quantitative predictions of biological activity by structural attributes. In: Muggleton, S. (ed.) ILP 1996. LNCS, vol. 1314, pp. 89–104. Springer, Heidelberg (1997). https://doi.org/10.1007/3-540-63494-0_50

    Chapter  Google Scholar 

  15. França, M.V.M., Zaverucha, G., Garcez, A.: Neural relational learning through semi-propositionalization of bottom clauses. In: AAAI Spring Symposium Series (2015)

    Google Scholar 

  16. Muggleton, S.: Inverse entailment and progol. New Gener. Comput. 13(3–4), 245–286 (1995)

    Article  Google Scholar 

  17. Plotkin, G.: Automatic Methods of Inductive Inference. Ph.D. thesis, Edinburgh University, August 1971

    Google Scholar 

  18. Marx, K.A., O’Neil, P., Hoffman, P., Ujwal, M.: Data mining the NCI cancer cell line compound GI50 values: identifying quinone subtypes effective against melanoma and leukemia cell classes. J. Chem. Inf. Comput. Sci. 43(5), 1652–1667 (2003)

    Article  Google Scholar 

  19. Ralaivola, L., Swamidass, S.J., Saigo, H., Baldi, P.: Graph kernels for chemical informatics. Neural Netw. 18(8), 1093–1110 (2005)

    Article  Google Scholar 

  20. Olier, I., Sadawi, N., Bickerton, G.R., Vanschoren, J., Grosan, C., Soldatova, L., King, R.D.: Meta-QSAR: a large-scale application of meta-learning to drug design and discovery. Mach. Learn., pp. 1–27 (2018)

    Google Scholar 

  21. Van Craenenbroeck, E.; Vandecasteele, H.D.L.: Dmax’s functional group and ring library (2002). https://dtai.cs.kuleuven.be/software/dmax/

  22. Ando, H.Y., Dehaspe, L., Luyten, W., Van Craenenbroeck, E., Vandecasteele, H., Van Meervelt, L.: Discovering h-bonding rules in crystals with inductive logic programming. Mol. Pharm. 3(6), 665–674 (2006)

    Article  Google Scholar 

  23. Grave, K.D., Costa, F.: Molecular graph augmentation with rings and functional groups. J. Chem. Inf. Model. 50(9), 1660–1668 (2010)

    Article  Google Scholar 

  24. Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)

  25. Bianchini, M., Scarselli, F.: On the complexity of shallow and deep neural network classifiers. In: ESANN (2014)

    Google Scholar 

  26. Rogers, D., Hahn, M.: Extended-connectivity fingerprints. J. Chem. Inf. Model. 50(5), 742–754 (2010)

    Article  Google Scholar 

  27. Chollet, F., et al.: Keras (2015). https://keras.io

  28. Abadi, M., Agarwal, A., et al.: TensorFlow: Large-scale machine learning on heterogeneous systems (2015), Software available from tensorflow.org. https://www.tensorflow.org/

  29. McCreath, E., Sharma, A.: Lime: a system for learning relations. In: Richter, M.M., Smith, C.H., Wiehagen, R., Zeugmann, T. (eds.) ALT 1998. LNCS (LNAI), vol. 1501, pp. 336–374. Springer, Heidelberg (1998). https://doi.org/10.1007/3-540-49730-7_25

    Chapter  Google Scholar 

  30. Lodhi, H., Muggleton, S.: Is mutagenesis still challenging. In: Proceedings of the 15th International Conference on Inductive Logic Programming, ILP, pp. 35–40. Citeseer (2005)

    Google Scholar 

  31. Dash, T., Joshi, R.S., Baskar, A., Srinivasan, A.: Some distributional results for discrete stochastic search. In: Submitted to Asian Conference on Machine Learning (ACML) (2018)

    Google Scholar 

  32. Srinivasan, A., Ramakrishnan, G.: Parameter screening and optimisation for ILP using designed experiments. J. Mach. Learn. Res. 12, 627–662 (2011). http://portal.acm.org/citation.cfm?id=1953067

Download references

Acknowledgments

A.S. is a Visiting Professorial Fellow, School of CSE, UNSW Sydney. A.S. is supported by the SERB grant EMR/2016/002766. RDK is supported by Indian National Science Academy’s Dr. V. Ramalingaswamy Chair award. We thank the following for their invaluable assistance: researchers at the DTAI, University of Leuven, for suggestions on how to use the background knowledge within DMAX; Ing. Gustav Sourek (Czech Technical University, Prague) and Dr. Ivan Olier Caparroso (Liverpool John Moores University, UK) for providing the dataset information and scores.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Tirtharaj Dash or Ashwin Srinivasan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Dash, T., Srinivasan, A., Vig, L., Orhobor, O.I., King, R.D. (2018). Large-Scale Assessment of Deep Relational Machines. In: Riguzzi, F., Bellodi, E., Zese, R. (eds) Inductive Logic Programming. ILP 2018. Lecture Notes in Computer Science(), vol 11105. Springer, Cham. https://doi.org/10.1007/978-3-319-99960-9_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-99960-9_2

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-99959-3

  • Online ISBN: 978-3-319-99960-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics