An inductive logic programming approach to learning which uORFs regulate gene expression.

Some upstream open reading frames (uORFs) regulate gene expression (i.e. they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not het fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of functional uORFs are needed. Unfortunately , lab experiments to verify that uORFs are functional are expensive. In this thesis, for the first time, the use of inductive logic programming (ILP) is explored for the task of learning which uORFs regulate gene expression in the yeast Saccharomyces cerevisiae. This work is directed to help select sets of candidate functional uORFs for experimental studies. With limited background knowledge, ILP can generate hypotheses which make the search for novel functional uORFs 17 times more efficient than random sampling. Adding mRNA secondary structure to the background knowledge results in hypotheses with significantly increased performance. This work is the first machine learning work to study both uORFs and mRNA secondary structures in the context of gene regulation. Using a novel combination of knowledge about biological conservation, gene ontology annotations and genes' response to different conditions results in hypotheses that are simple, informative, have an estimated sensitivity of 81% and provide provisional insights into biological characteristics of functional uORFs. The hypotheses predict 299 further genes to have 450 novel functional uORFs. A comparison with a related study suggests that 8 of these predicted functional uORFs (from 8 genes) are strong candidates for experimental studies

Inductive logic programming at 30

Inductive logic programming (ILP) is a form of logic-based machine learning. The goal of ILP is to induce a hypothesis (a logic program) that generalises given training examples and background knowledge. As ILP turns 30, we survey recent work in the field. In this survey, we focus on (i) new meta-level search methods, (ii) techniques for learning recursive programs that generalise from few examples, (iii) new approaches for predicate invention, and (iv) the use of different technologies, notably answer set programming and neural networks. We conclude by discussing some of the current limitations of ILP and discuss directions for future research.Comment: Extension of IJCAI20 survey paper. arXiv admin note: substantial text overlap with arXiv:2002.11002, arXiv:2008.0791

Explaining clusters with inductive logic programming and linked data

Knowledge Discovery consists in discovering hidden regularities in large amounts of data using data mining techniques. The obtained patterns require an interpretation that is usually achieved using some background knowledge given by experts from several domains. On the other hand, the rise of Linked Data has increased the number of connected cross-disciplinary knowledge, in the form of RDF datasets, classes and relationships. Here we show how Linked Data can be used in an Inductive Logic Programming process, where they provide background knowledge for finding hypotheses regarding the unrevealed connections between items of a cluster. By using an example with clusters of books, we show how different Linked Data sources can be used to automatically generate rules giving an underlying explanation to such clusters

Mathematical applications of inductive logic programming

Accepted versio

Predicate Invention in Inductive Logic Programming

The ability to recognise new concepts and incorporate them into our knowledge is an essential part of learning. From new scientific concepts to the words that are used in everyday conversation, they all must have at some point in the past, been invented and their definition defined. In this position paper, we discuss how a general framework for predicate invention could be made, by reasoning about the problem at the meta-level using an appropriate notion of top theory in inductive logic programming

Inductive Logic Programming as Abductive Search

We present a novel approach to non-monotonic ILP and its implementation called TAL (Top-directed Abductive Learning). TAL overcomes some of the completeness problems of ILP systems based on Inverse Entailment and is the first top-down ILP system that allows background theories and hypotheses to be normal logic programs. The approach relies on mapping an ILP problem into an equivalent ALP one. This enables the use of established ALP proof procedures and the specification of richer language bias with integrity constraints. The mapping provides a principled search space for an ILP problem, over which an abductive search is used to compute inductive solutions