There is an urgent need to make drug discovery cheaper and faster. This will enable the development of treatments for diseases currently neglected for economic reasons, such as tropical and orphan diseases, and generally increase the supply of new drugs. Here, we report the Robot Scientist ‘Eve’ designed to make drug discovery more economical. A Robot Scientist is a laboratory automation system that uses artificial intelligence (AI) techniques to discover scientific knowledge through cycles of experimentation. Eve integrates and automates library-screening, hit-confirmation, and lead generation through cycles of quantitative structure activity relationship learning and testing. Using econometric modelling we demonstrate that the use of AI to select compounds economically outperforms standard drug screening. For further efficiency Eve uses a standardized form of assay to compute Boolean functions of compound properties. These assays can be quickly and cheaply engineered using synthetic biology, enabling more targets to be assayed for a given budget. Eve has repositioned several drugs against specific targets in parasites that cause tropical diseases. One validated discovery is that the anti-cancer compound TNP-470 is a potent inhibitor of dihydrofolate reductase from the malaria-causing parasite Plasmodium vivax.

Inductive logic programming, or relational learning, is a powerful paradigm for machine learning or data mining. However, in order for ILP to become practically useful, the efficiency of ILP systems must improve substantially. To this end, the notion of a query pack is introduced: it structures sets of similar queries. Furthermore, a mechanism is described for executing such query packs. A complexity analysis shows that considerable efficiency improvements can be achieved through the use of this query pack execution mechanism. This claim is supported by empirical results obtained by incorporating support for query pack execution in two existing learning systems.

Trypsin is the workhorse protease in mass spectrometry-based proteomics experiments and is used to digest proteins into more readily analyzable peptides. To identify these peptides after mass spectrometric analysis, the actual digestion has to be mimicked as faithfully as possible in silico. In this paper we introduce CP-DT (Cleavage Prediction with Decision Trees), an algorithm based on a decision tree ensemble that was learned on publicly available peptide identification data from the PRIDE repository. We demonstrate that CP-DT is able to accurately predict tryptic cleavage: tests on three independent data sets show that CP-DT significantly outperforms the Keil rules that are currently used to predict tryptic cleavage. Moreover, the trees generated by CP-DT can make predictions efficiently and are interpretable by domain experts.

Computerization in healthcare in general, and in the operating room (OR) and intensive care unit (ICU) in particular, is on the rise. This leads to large patient databases, with specific properties. Machine learning techniques are able to examine and to extract knowledge from large databases in an automatic way. Although the number of potential applications for these techniques in medicine is large, few medical doctors are familiar with their methodology, advantages and pitfalls. A general overview of machine learning techniques, with a more detailed discussion of some of these algorithms, is presented in this review.

Measuring the similarity or distance between sets of points in a metric space is an important problem in machine learning and has also applications in other disciplines e.g. in computational geometry, philosophy of science, methods for updating or changing theories, . . . . Recently Eiter and Mannila have proposed a new measure which is computable in polynomial time. However, it is not a distance function in the mathematical sense because it does not satisfy the triangle inequality. We introduce a new measure which is a metric while being computable in polynomial time. We also present a variant which computes a normalised metric and a variant which can associate different weights with the points in the set.