AYNEC: All you need for evaluating completion techniques in knowledge graphs

The popularity of knowledge graphs has led to the development of techniques to refine them and increase their quality. One of the main refinement tasks is completion (also known as link prediction for knowledge graphs), which seeks to add missing triples to the graph, usually by classifying potential ones as true or false. While there is a wide variety of graph completion techniques, there is no standard evaluation setup, so each proposal is evaluated using different datasets and metrics. In this paper we present AYNEC, a suite for the evaluation of knowledge graph completion techniques that covers the entire evaluation workflow. It includes a customisable tool for the generation of datasets with multiple variation points related to the preprocessing of graphs, the splitting into training and testing examples, and the generation of negative examples. AYNEC also provides a visual summary of the graph and the optional exportation of the datasets in an open format for their visualisation. We use AYNEC to generate a library of datasets ready to use for evaluation purposes based on several popular knowledge graphs. Finally, it includes a tool that computes relevant metrics and uses significance tests to compare each pair of techniques. These open source tools, along with the datasets, are freely available to the research community and will be maintained.Ministerio de Economía y Competitividad TIN2016-75394-

Evaluation Measures for Hierarchical Classification: a unified view and novel approaches

Hierarchical classification addresses the problem of classifying items into a hierarchy of classes. An important issue in hierarchical classification is the evaluation of different classification algorithms, which is complicated by the hierarchical relations among the classes. Several evaluation measures have been proposed for hierarchical classification using the hierarchy in different ways. This paper studies the problem of evaluation in hierarchical classification by analyzing and abstracting the key components of the existing performance measures. It also proposes two alternative generic views of hierarchical evaluation and introduces two corresponding novel measures. The proposed measures, along with the state-of-the art ones, are empirically tested on three large datasets from the domain of text classification. The empirical results illustrate the undesirable behavior of existing approaches and how the proposed methods overcome most of these methods across a range of cases.Comment: Submitted to journa

Random geometric complexes

We study the expected topological properties of Cech and Vietoris-Rips complexes built on i.i.d. random points in R^d. We find higher dimensional analogues of known results for connectivity and component counts for random geometric graphs. However, higher homology H_k is not monotone when k > 0. In particular for every k > 0 we exhibit two thresholds, one where homology passes from vanishing to nonvanishing, and another where it passes back to vanishing. We give asymptotic formulas for the expectation of the Betti numbers in the sparser regimes, and bounds in the denser regimes. The main technical contribution of the article is in the application of discrete Morse theory in geometric probability.Comment: 26 pages, 3 figures, final revisions, to appear in Discrete & Computational Geometr

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013