Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a ‘landscape’ representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems ‘hard’, but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the ‘best’ experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes

Computational Discovery of Communicable Scientific Knowledge

In this paper we distinguish between two computational paradigms for knowledge discovery that share the notion of heuristic search, but dier in the importance they place on using scientific formalisms to state discovered knowledge. We also report progress on computational methods for discovering such communicable knowledge in two domains, one involving the regulation of photosynthesis in phytoplankton and the other involving carbon production by vegetation in the Earth ecosystem. In each case, we describe a representation for models, methods for using data to revise existing models, and some initial results. In closing, we discuss related work on the computational discovery of communicable scientific knowledge and outline directions for future research