Hierarchical inference applied to Cyc

Hierarchical graphs are a frequent solution for capturing symbolic data due the importance of hierarchies for defining knowledge. In these graphs, relations among elements may contain large portions of the element’s semantics. However, knowledge discovery based on analyzing the patterns of hierarchical relations is rarely used. We outline four inference based algorithms exploiting semantic properties of hierarchically represented knowledge for producing new links, and test one of them on a generalization of Cyc’s KB. Finally, we argue why such algorithms can be useful for unsupervised learning and supervised analysis of a KBPeer ReviewedPostprint (author’s final draft

Link prediction in very large directed graphs: Exploiting hierarchical properties in parallel

Link prediction is a link mining task that tries to find new edges within a given graph. Among the targets of link prediction there is large directed graphs, which are frequent structures nowadays. The typical sparsity of large graphs demands of high precision predictions in order to obtain usable results. However, the size of those graphs only permits the execution of scalable algorithms. As a trade-off between those two problems we recently proposed a link prediction algorithm for directed graphs that exploits hierarchical properties. The algorithm can be classified as a local score, which entails scalability. Unlike the rest of local scores, our proposal assumes the existence of an underlying model for the data which allows it to produce predictions with a higher precision. We test the validity of its hierarchical assumptions on two clearly hierarchical data sets, one of them based on RDF. Then we test it on a non-hierarchical data set based on Wikipedia to demonstrate its broad applicability. Given the computational complexity of link prediction in very large graphs we also introduce some general recommendations useful to make of link prediction an efficiently parallelized problem.Peer ReviewedPostprint (published version

Understanding Science Through Knowledge Organizers: An Introduction

We propose, in this paper, a teaching program based on a grammar of scientific language borrowed mostly from the area of knowledge representation in computer science and logic. The paper introduces an operationizable framework for understanding knowledge using knowledge representation (KR) methodology. We start with organizing concepts based on their cognitive function, followed by assigning valid and authentic semantic relations to the concepts. We propose that in science education, students can understand better if they organize their knowledge using the KR principles. The process, we claim, can help them to align their conceptual framework with that of experts which we assume is the goal of science education

Planar Ultrametric Rounding for Image Segmentation

We study the problem of hierarchical clustering on planar graphs. We formulate this in terms of an LP relaxation of ultrametric rounding. To solve this LP efficiently we introduce a dual cutting plane scheme that uses minimum cost perfect matching as a subroutine in order to efficiently explore the space of planar partitions. We apply our algorithm to the problem of hierarchical image segmentation

Some Issues on Ontology Integration

The word integration has been used with different meanings in the ontology field. This article aims at clarifying the meaning of the word “integration” and presenting some of the relevant work done in integration. We identify three meanings of ontology “integration”: when building a new ontology reusing (by assembling, extending, specializing or adapting) other ontologies already available; when building an ontology by merging several ontologies into a single one that unifies all of them; when building an application using one or more ontologies. We discuss the different meanings of “integration”, identify the main characteristics of the three different processes and proposethree words to distinguish among those meanings:integration, merge and use

Latent protein trees

Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated intensities for each sample. Subsets of features within the data are from the same peptide, subsets of peptides are from the same protein, and subsets of proteins are in the same biological pathways, therefore, there is the potential for very complex and informative correlational structure inherent in these data. Recent attempts to utilize this data often focus on the identification of single features that are associated with a particular phenotype that is relevant to the experiment. However, to date, there have been no published approaches that directly model what we know to be multiple different levels of correlation structure. Here we present a hierarchical Bayesian model which is specifically designed to model such correlation structure in unbiased, label-free proteomics. This model utilizes partial identification information from peptide sequencing and database lookup as well as the observed correlation in the data to appropriately compress features into latent proteins and to estimate their correlation structure. We demonstrate the effectiveness of the model using artificial/benchmark data and in the context of a series of proteomics measurements of blood plasma from a collection of volunteers who were infected with two different strains of viral influenza.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS639 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Knowledge Representation and WordNets

Knowledge itself is a representation of “real facts”. Knowledge is a logical model that presents facts from “the real world” witch can be expressed in a formal language. Representation means the construction of a model of some part of reality. Knowledge representation is contingent to both cognitive science and artificial intelligence. In cognitive science it expresses the way people store and process the information. In the AI field the goal is to store knowledge in such way that permits intelligent programs to represent information as nearly as possible to human intelligence. Knowledge Representation is referred to the formal representation of knowledge intended to be processed and stored by computers and to draw conclusions from this knowledge. Examples of applications are expert systems, machine translation systems, computer-aided maintenance systems and information retrieval systems (including database front-ends).knowledge, representation, ai models, databases, cams

Massive ontology interface

This paper describes the Massive Ontology Interface (MOI), a web portal which facilitates interaction with a large ontology (over 200,000 concepts and 1.6M assertions) that is built automatically using OpenCyc as a backbone. The aim of the interface is to simplify interaction with the massive amounts of information and guide the user towards understanding the ontology’s data. Using either a text or graph-based representation, users can discuss and edit the ontology. Social elements utilizing gamification techniques are included to encourage users to create and collaborate on stored knowledge as part of a web community. An evaluation by 30 users comparing MOI with OpenCyc’s original interface showed significant improvements in user understanding of the ontology, although full testing of the interface’s social elements lies in the future