This paper firstly provides a re-appraisal of the development of techniques for inverting deduction, secondly introduces Mode-Directed Inverse Entailment (MDIE) as a generalisation and enhancement of previous approaches and thirdly describes an implementation of MDIE in the Progol system. Progol is implemented in C and available by anonymous ftp. The re-assessment of previous techniques in terms of inverse entailment leads to new results for learning from positive data and inverting implication between pairs of clauses.

Hybrid learning methods use theoretical knowledge of a domain and a set of classified examples to develop a method for accurately classifying examples not seen during training. The challenge of hybrid learning systems is to use the information provided by one source of information to offset information missing from the other source. By so doing, a hybrid learning system should learn more effectively than systems that use only one of the information sources. KBANN(Knowledge-Based Artificial Neural Networks) is a hybrid learning system built on top of connectionist learning techniques. It maps problem-specific "domain theories", represented in propositional logic, into neural networks and then refines this reformulated knowledge using backpropagation. KBANN is evaluated by extensive empirical tests on two problems from molecular biology. Among other results, these tests show that the networks created by KBANN generalize better than a wide variety of learning systems, as well as several t...

This paper describes the use of Inductive Logic Programming as a scientific assistant. In particular, it details the application of the ILP system Progol to discovering structural features that can result in mutagenicity in small molecules. To discover these concepts, Progol only had access to the atomic and bond structure of the molecules. With such a primitive description and no further assistance from chemists, Progol corroborated some existing knowledge and proposed a new structural alert for mutagenicity in compounds. In the process, the experiments act as a case study in which, even with extremely limited background knowledge, an Inductive Logic Programming tool firstly, complements a complex statistical model developed by skilled chemists, and secondly, continues to provide understandable theories when the statistical model fails. The experiments also constitute the first demonstrations of a prototype of the Progol system. Progol allows the construction of hypotheses with bounded non-determinacy by performing a best-first search within the subsumption lattice. The results here provide evidence that such searches are both viable and desirable. 1

. A novel approach to learning first order logic formulae from positive and negative examples is presented. Whereas present inductive logic programming systems employ examples as true and false ground facts (or clauses), we view examples as interpretations which are true or false for the target theory. This viewpoint allows to reconcile the inductive logic programming paradigm with classical attribute value learning in the sense that the latter is a special case of the former. Because of this property, we are able to adapt AQ and CN2 type algorithms in order to enable learning of full first order formulae. However, whereas classical learning techniques have concentrated on concept representations in disjunctive normal form, we will use a clausal representation, which corresponds to a conjuctive normal form where each conjunct forms a constraint on positive examples. This representation duality reverses also the role of positive and negative examples, both in the heuristics and in the a...

A relational instance-based learning algorithm, called Ribl, is motivated and developed in this paper. We argue that instancebased methods o#er solutions to the often unsatisfactory behavior of current inductive logic programming #ILP# approaches in domains with continuous attribute values and in domains with noisy attributes and#or examples. Three research issues that emerge when a propositional instance-based learner is adapted to a #rst-order representation are identi#ed: #1# construction of cases from the knowledge base, #2# computation of similaritybetween arbitrarily complex cases, and #3# estimation of the relevance of predicates and attributes. Solutions to these issues are developed. Empirical results indicate that Ribl is able to achieve high classi#cation accuracy in a variety of domains. to appear in: Proc. 13th International Conference on Machine Learning, L. Saitta #ed.#, Morgan Kaufmann, 1996 1 Introduction The #eld of Inductive Logic Programming ...

In this paper we study the problem of classifying chemical compound datasets. We present a sub-structure-based classification algorithm that decouples the sub-structure discovery process from the classification model construction and uses frequent subgraph discovery algorithms to find all topological and geometric sub-structures present in the dataset. The advantage of our approach is that during classification model construction, all relevant sub-structures are available allowing the classifier to intelligently select the most discriminating ones. The computational scalability is ensured by the use of highly efficient frequent subgraph discovery algorithms coupled with aggressive feature selection. Our experimental evaluation on eight different classification problems shows that our approach is computationally scalable and outperforms existing schemes by 10% to 35%, on the average.

Recently, computer programs developed within the field of Inductive Logic Programming have received some attention for their ability to construct restricted first-order logic solutions using problem-specific background knowledge. Prominent applications of such programs have been concerned with determining "structure-activity" relationships in the areas of molecular biology and chemistry. Typically the task here is to predict the "activity" of a compound, like toxicity, from its chemical structure.

This paper is a case study of a machine aided knowledge discovery process within the general area of drug design. More specifically, the paper describes a sequence of experiments in which an Inductive Logic Programming(ILP) system is used for pharmacophore discovery. Within drug design, a pharmacophore is a description of the substructure of a ligand (a small molecule) which is responsible for medicinal activity. This medicinal activity is produced by interaction between the ligand and a binding site on a target protein. ILP was chosen by the domain expert (first author) at Pfizer since active molecules are most naturally described, in relational terms, as requiring a substructure (pharmacophore) with various 3-D relations which hold among the atoms involved. The results described in this paper build on previous investigations into prediction of mutagenicity using ILP with a 2-D (bond connectivity only) representation of molecules. The case study supports general lessons for knowledge discovery, as well as more specific lessons for pharmacophorediscovery, the use of ILP for 3-D problems, and for the particular medicinal activity of ACE inhibition, a treatment for hypertension.

An important test-bed for Inductive Logic Programming (ILP) systems has been the task of relating the activity of chemical compounds to their structure. In this paper we examine the structure-activity problems that have been addressed by ILP, and evaluate empirically the extent to which a first-order representation was required. This is done by comparing ILP theories against those constructed by standard linear regression and a decision-tree learner. When propositional encodings are feasible for the feature-based algorithms, we present evidence that they are capable of matching the predictive accuracies of an ILP theory. However, as the diversity of compounds considered increases, propositional encodings become intractable. In such cases, our results provide support for the claim that ILP programs will continue to construct accurate, understandable theories. Based on this evidence, we propose future work to realise fully the potential of ILP in structure-activity problems. 1

Machine Learning algorithms are being increasingly used for knowledge discovery tasks. Approaches can be broadly divided by distinguishing discovery of procedural from that of declarative knowledge. Client requirements determine which of these is appropriate. This paper discusses an experimental application of machine learning in an area related to drug design. The bottleneck here is in finding appropriate constraints to reduce the large number of candidate molecules to be synthesisedand tested. Such constraints canbe viewed as declarative specifications of the structural elements necessary for high medicinal activity and low toxicity. The first-order representation used within Inductive Logic Programming (ILP) provides an appropriate description language for such constraints. Within this application area knowledge accreditation requires not only a demonstration of predictive accuracy but also, and crucially, a certification of novel insight into the structural chemistry. Thi...