External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway

This paper evaluates the impact of various event extraction systems on automatic pathway curation using the popular mTOR pathway. We quantify the impact of training data sets as well as different machine learning classifiers and show that some improve the quality of automatically extracted pathways

Supervised Typing of Big Graphs using Semantic Embeddings

We propose a supervised algorithm for generating type embeddings in the same semantic vector space as a given set of entity embeddings. The algorithm is agnostic to the derivation of the underlying entity embeddings. It does not require any manual feature engineering, generalizes well to hundreds of types and achieves near-linear scaling on Big Graphs containing many millions of triples and instances by virtue of an incremental execution. We demonstrate the utility of the embeddings on a type recommendation task, outperforming a non-parametric feature-agnostic baseline while achieving 15x speedup and near-constant memory usage on a full partition of DBpedia. Using state-of-the-art visualization, we illustrate the agreement of our extensionally derived DBpedia type embeddings with the manually curated domain ontology. Finally, we use the embeddings to probabilistically cluster about 4 million DBpedia instances into 415 types in the DBpedia ontology.Comment: 6 pages, to be published in Semantic Big Data Workshop at ACM, SIGMOD 2017; extended version in preparation for Open Journal of Semantic Web (OJSW

Long-tail Relation Extraction via Knowledge Graph Embeddings and Graph Convolution Networks

We propose a distance supervised relation extraction approach for long-tailed, imbalanced data which is prevalent in real-world settings. Here, the challenge is to learn accurate "few-shot" models for classes existing at the tail of the class distribution, for which little data is available. Inspired by the rich semantic correlations between classes at the long tail and those at the head, we take advantage of the knowledge from data-rich classes at the head of the distribution to boost the performance of the data-poor classes at the tail. First, we propose to leverage implicit relational knowledge among class labels from knowledge graph embeddings and learn explicit relational knowledge using graph convolution networks. Second, we integrate that relational knowledge into relation extraction model by coarse-to-fine knowledge-aware attention mechanism. We demonstrate our results for a large-scale benchmark dataset which show that our approach significantly outperforms other baselines, especially for long-tail relations.Comment: To be published in NAACL 201

Knowledge Base Population using Semantic Label Propagation

A crucial aspect of a knowledge base population system that extracts new facts from text corpora, is the generation of training data for its relation extractors. In this paper, we present a method that maximizes the effectiveness of newly trained relation extractors at a minimal annotation cost. Manual labeling can be significantly reduced by Distant Supervision, which is a method to construct training data automatically by aligning a large text corpus with an existing knowledge base of known facts. For example, all sentences mentioning both 'Barack Obama' and 'US' may serve as positive training instances for the relation born_in(subject,object). However, distant supervision typically results in a highly noisy training set: many training sentences do not really express the intended relation. We propose to combine distant supervision with minimal manual supervision in a technique called feature labeling, to eliminate noise from the large and noisy initial training set, resulting in a significant increase of precision. We further improve on this approach by introducing the Semantic Label Propagation method, which uses the similarity between low-dimensional representations of candidate training instances, to extend the training set in order to increase recall while maintaining high precision. Our proposed strategy for generating training data is studied and evaluated on an established test collection designed for knowledge base population tasks. The experimental results show that the Semantic Label Propagation strategy leads to substantial performance gains when compared to existing approaches, while requiring an almost negligible manual annotation effort.Comment: Submitted to Knowledge Based Systems, special issue on Knowledge Bases for Natural Language Processin