Open Access Research article

Self organising hypothesis networks: a new approach for representing and structuring SAR knowledge

Thierry Hanser*, Chris Barber, Edward Rosser, Jonathan D Vessey, Samuel J Webb and Stéphane Werner

Author Affiliations

Lhasa Limited, Leeds, UK

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Journal of Cheminformatics 2014, 6:21  doi:10.1186/1758-2946-6-21

Published: 8 May 2014

Abstract

Background

Combining different sources of knowledge to build improved structure activity relationship models is not easy owing to the variety of knowledge formats and the absence of a common framework to interoperate between learning techniques. Most of the current approaches address this problem by using consensus models that operate at the prediction level. We explore the possibility to directly combine these sources at the knowledge level, with the aim to harvest potentially increased synergy at an earlier stage. Our goal is to design a general methodology to facilitate knowledge discovery and produce accurate and interpretable models.

Results

To combine models at the knowledge level, we propose to decouple the learning phase from the knowledge application phase using a pivot representation (lingua franca) based on the concept of hypothesis. A hypothesis is a simple and interpretable knowledge unit. Regardless of its origin, knowledge is broken down into a collection of hypotheses. These hypotheses are subsequently organised into hierarchical network. This unification permits to combine different sources of knowledge into a common formalised framework. The approach allows us to create a synergistic system between different forms of knowledge and new algorithms can be applied to leverage this unified model. This first article focuses on the general principle of the Self Organising Hypothesis Network (SOHN) approach in the context of binary classification problems along with an illustrative application to the prediction of mutagenicity.

Conclusion

It is possible to represent knowledge in the unified form of a hypothesis network allowing interpretable predictions with performances comparable to mainstream machine learning techniques. This new approach offers the potential to combine knowledge from different sources into a common framework in which high level reasoning and meta-learning can be applied; these latter perspectives will be explored in future work.

Keywords:
Machine learning; Knowledge discovery; Data mining; SAR; QSAR; SOHN; Interpretable model; Confidence metric; Hypothesis Network

Graphical abstract