Qualitative System Identification from Imperfect Data

Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as differential equations. Quantitative modelling works best when the structure of the model (i.e., the form of the equations) is known; and the primary concern is one of estimating the values of the parameters in the model. For complex biological systems, the model-structure is rarely known and the modeler has to deal with both model-identification and parameter-estimation. In this paper we are concerned with providing automated assistance to the first of these problems. Specifically, we examine the identification by machine of the structural relationships between experimentally observed variables. These relationship will be expressed in the form of qualitative abstractions of a quantitative model. Such qualitative models may not only provide clues to the precise quantitative model, but also assist in understanding the essence of that model. Our position in this paper is that background knowledge incorporating system modelling principles can be used to constrain effectively the set of good qualitative models. Utilising the model-identification framework provided by Inductive Logic Programming (ILP) we present empirical support for this position using a series of increasingly complex artificial datasets. The results are obtained with qualitative and quantitative data subject to varying amounts of noise and different degrees of sparsity. The results also point to the presence of a set of qualitative states, which we term kernel subsets, that may be necessary for a qualitative model-learner to learn correct models. We demonstrate scalability of the method to biological system modelling by identification of the glycolysis metabolic pathway from data

On the Implementation of the Probabilistic Logic Programming Language ProbLog

The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with probabilities. These facts are treated as mutually independent random variables that indicate whether these facts belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.Comment: 28 pages; To appear in Theory and Practice of Logic Programming (TPLP

Low Size-Complexity Inductive Logic Programming: The East-West Challenge Considered as a Problem in Cost-Sensitive Classification

The Inductive Logic Programming community has considered proof-complexity and model-complexity, but, until recently, size-complexity has received little attention. Recently a challenge was issued "to the international computing community" to discover low size-complexity Prolog programs for classifying trains. The challenge was based on a problem first proposed by Ryszard Michalski, 20 years ago. We interpreted the challenge as a problem in cost-sensitive classification and we applied a recently developed cost-sensitive classifier to the competition. Our algorithm was relatively successful (we won a prize). This paper presents our algorithm and analyzes the results of the competition

A Multi-Engine Approach to Answer Set Programming

Answer Set Programming (ASP) is a truly-declarative programming paradigm proposed in the area of non-monotonic reasoning and logic programming, that has been recently employed in many applications. The development of efficient ASP systems is, thus, crucial. Having in mind the task of improving the solving methods for ASP, there are two usual ways to reach this goal: $(i)$ extending state-of-the-art techniques and ASP solvers, or $(ii)$ designing a new ASP solver from scratch. An alternative to these trends is to build on top of state-of-the-art solvers, and to apply machine learning techniques for choosing automatically the "best" available solver on a per-instance basis. In this paper we pursue this latter direction. We first define a set of cheap-to-compute syntactic features that characterize several aspects of ASP programs. Then, we apply classification methods that, given the features of the instances in a {\sl training} set and the solvers' performance on these instances, inductively learn algorithm selection strategies to be applied to a {\sl test} set. We report the results of a number of experiments considering solvers and different training and test sets of instances taken from the ones submitted to the "System Track" of the 3rd ASP Competition. Our analysis shows that, by applying machine learning techniques to ASP solving, it is possible to obtain very robust performance: our approach can solve more instances compared with any solver that entered the 3rd ASP Competition. (To appear in Theory and Practice of Logic Programming (TPLP).)Comment: 26 pages, 8 figure