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Applying Inductive Logic Programming to Predicting Gene Function

AI Magazine

One of the fastest advancing areas of modern science is functional genomics. This science seeks to understand how the complete complement of molecular components of living organisms (nucleic acid, protein, small molecules, and so on) interact together to form living organisms. Functional genomics is of interest to AI because the relationship between machines and living organisms is central to AI and because the field is an instructive and fun domain to apply and sharpen AI tools and ideas, requiring complex knowledge representation, reasoning, learning, and so on. This article describes two machine learning (inductive logic programming [ILP])-based approaches to the bioinformatic problem of predicting protein function from amino acid sequence. The first approach is based on using ILP as a way of bootstrapping from conventional sequence-based homology methods.


Constraint Propagation for First-Order Logic and Inductive Definitions

arXiv.org Artificial Intelligence

Constraint propagation is one of the basic forms of inference in many logic-based reasoning systems. In this paper, we investigate constraint propagation for first-order logic (FO), a suitable language to express a wide variety of constraints. We present an algorithm with polynomial-time data complexity for constraint propagation in the context of an FO theory and a finite structure. We show that constraint propagation in this manner can be represented by a datalog program and that the algorithm can be executed symbolically, i.e., independently of a structure. Next, we extend the algorithm to FO(ID), the extension of FO with inductive definitions. Finally, we discuss several applications.


The Planning Spectrum - One, Two, Three, Infinity

Journal of Artificial Intelligence Research

Linear Temporal Logic (LTL) is widely used for defining conditions on the execution paths of dynamic systems. In the case of dynamic systems that allow for nondeterministic evolutions, one has to specify, along with an LTL formula f, which are the paths that are required to satisfy the formula. Two extreme cases are the universal interpretation A.f, which requires that the formula be satisfied for all execution paths, and the existential interpretation E.f, which requires that the formula be satisfied for some execution path. When LTL is applied to the definition of goals in planning problems on nondeterministic domains, these two extreme cases are too restrictive. It is often impossible to develop plans that achieve the goal in all the nondeterministic evolutions of a system, and it is too weak to require that the goal is satisfied by some execution. In this paper we explore alternative interpretations of an LTL formula that are between these extreme cases. We define a new language that permits an arbitrary combination of the A and E quantifiers, thus allowing, for instance, to require that each finite execution can be extended to an execution satisfying an LTL formula (AE.f), or that there is some finite execution whose extensions all satisfy an LTL formula (EA.f). We show that only eight of these combinations of path quantifiers are relevant, corresponding to an alternation of the quantifiers of length one (A and E), two (AE and EA), three (AEA and EAE), and infinity ((AE)* and (EA)*). We also present a planning algorithm for the new language that is based on an automata-theoretic approach, and study its complexity.


Blocksworld Revisited: Learning and Reasoning to Generate Event-Sequences from Image Pairs

arXiv.org Artificial Intelligence

The process of identifying changes or transformations in a scene along with the ability of reasoning about their causes and effects, is a key aspect of intelligence. In this work we go beyond recent advances in computational perception, and introduce a more challenging task, Image-based Event-Sequencing (IES). In IES, the task is to predict a sequence of actions required to rearrange objects from the configuration in an input source image to the one in the target image. IES also requires systems to possess inductive generalizability. Motivated from evidence in cognitive development, we compile the first IES dataset, the Blocksworld Image Reasoning Dataset (BIRD) which contains images of wooden blocks in different configurations, and the sequence of moves to rearrange one configuration to the other. We first explore the use of existing deep learning architectures and show that these end-to-end methods under-perform in inferring temporal event-sequences and fail at inductive generalization. We then propose a modular two-step approach: Visual Perception followed by Event-Sequencing, and demonstrate improved performance by combining learning and reasoning. Finally, by showing an extension of our approach on natural images, we seek to pave the way for future research on event sequencing for real world scenes.


Applying Inductive Logic Programming to Predicting Gene Function

AI Magazine

This science seeks to understand how the complete complement of molecular components of living organisms (nucleic acid, protein, small molecules, and so on) interact together to form living organisms. Functional genomics is of interest to AI because the relationship between machines and living organisms is central to AI and because the field is an instructive and fun domain to apply and sharpen AI tools and ideas, requiring complex knowledge representation, reasoning, learning, and so on. This article describes two machine learning (inductive logic programming [ILP])-based approaches to the bioinformatic problem of predicting protein function from amino acid sequence. The second approach used protein-functional ontologies to provide function classes and a hybrid ILP method to predict function directly from sequence.