Ranking Medical Subject Headings using a factor graph model.

Automatically assigning MeSH (Medical Subject Headings) to articles is an active research topic. Recent work demonstrated the feasibility of improving the existing automated Medical Text Indexer (MTI) system, developed at the National Library of Medicine (NLM). Encouraged by this work, we propose a novel data-driven approach that uses semantic distances in the MeSH ontology for automated MeSH assignment. Specifically, we developed a graphical model to propagate belief through a citation network to provide robust MeSH main heading (MH) recommendation. Our preliminary results indicate that this approach can reach high Mean Average Precision (MAP) in some scenarios

Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models

Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble method that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper adaptation of the algorithms used to deal with this challenging classification task. Results: The ensemble method we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. During the BioASQ 2014 challenge we obtained the first place during the first batch and the third in the two following batches. Our success in the BioASQ challenge proved that a fully automated machine-learning approach, which does not implement any heuristics and rule-based approaches, can be highly competitive and outperform other approaches in similar challenging contexts

International conference on software engineering and knowledge engineering: Session chair

The Thirtieth International Conference on Software Engineering and Knowledge Engineering (SEKE 2018) will be held at the Hotel Pullman, San Francisco Bay, USA, from July 1 to July 3, 2018. SEKE2018 will also be dedicated in memory of Professor Lofti Zadeh, a great scholar, pioneer and leader in fuzzy sets theory and soft computing. The conference aims at bringing together experts in software engineering and knowledge engineering to discuss on relevant results in either software engineering or knowledge engineering or both. Special emphasis will be put on the transference of methods between both domains. The theme this year is soft computing in software engineering & knowledge engineering. Submission of papers and demos are both welcome

Stable Feature Selection for Biomarker Discovery

Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this article, we review existing stable feature selection methods for biomarker discovery using a generic hierarchal framework. We have two objectives: (1) providing an overview on this new yet fast growing topic for a convenient reference; (2) categorizing existing methods under an expandable framework for future research and development

Structural Embedding of Syntactic Trees for Machine Comprehension

Deep neural networks for machine comprehension typically utilizes only word or character embeddings without explicitly taking advantage of structured linguistic information such as constituency trees and dependency trees. In this paper, we propose structural embedding of syntactic trees (SEST), an algorithm framework to utilize structured information and encode them into vector representations that can boost the performance of algorithms for the machine comprehension. We evaluate our approach using a state-of-the-art neural attention model on the SQuAD dataset. Experimental results demonstrate that our model can accurately identify the syntactic boundaries of the sentences and extract answers that are syntactically coherent over the baseline methods

Exploiting prior knowledge and latent variable representations for the statistical modeling and probabilistic querying of large knowledge graphs

Large knowledge graphs increasingly add great value to various applications that require machines to recognize and understand queries and their semantics, as in search or question answering systems. These applications include Google search, Bing search, IBM’s Watson, but also smart mobile assistants as Apple’s Siri, Google Now or Microsoft’s Cortana. Popular knowledge graphs like DBpedia, YAGO or Freebase store a broad range of facts about the world, to a large extent derived from Wikipedia, currently the biggest web encyclopedia. In addition to these freely accessible open knowledge graphs, commercial ones have also evolved including the well-known Google Knowledge Graph or Microsoft’s Satori. Since incompleteness and veracity of knowledge graphs are known problems, the statistical modeling of knowledge graphs has increasingly gained attention in recent years. Some of the leading approaches are based on latent variable models which show both excellent predictive performance and scalability. Latent variable models learn embedding representations of domain entities and relations (representation learning). From these embeddings, priors for every possible fact in the knowledge graph are generated which can be exploited for data cleansing, completion or as prior knowledge to support triple extraction from unstructured textual data as successfully demonstrated by Google’s Knowledge-Vault project. However, large knowledge graphs impose constraints on the complexity of the latent embeddings learned by these models. For graphs with millions of entities and thousands of relation-types, latent variable models are required to exploit low dimensional embeddings for entities and relation-types to be tractable when applied to these graphs. The work described in this thesis extends the application of latent variable models for large knowledge graphs in three important dimensions. First, it is shown how the integration of ontological constraints on the domain and range of relation-types enables latent variable models to exploit latent embeddings of reduced complexity for modeling large knowledge graphs. The integration of this prior knowledge into the models leads to a substantial increase both in predictive performance and scalability with improvements of up to 77% in link-prediction tasks. Since manually designed domain and range constraints can be absent or fuzzy, we also propose and study an alternative approach based on a local closed-world assumption, which derives domain and range constraints from observed data without the need of prior knowledge extracted from the curated schema of the knowledge graph. We show that such an approach also leads to similar significant improvements in modeling quality. Further, we demonstrate that these two types of domain and range constraints are of general value to latent variable models by integrating and evaluating them on the current state of the art of latent variable models represented by RESCAL, Translational Embedding, and the neural network approach used by the recently proposed Google Knowledge Vault system. In the second part of the thesis it is shown that the just mentioned three approaches all perform well, but do not share many commonalities in the way they model knowledge graphs. These differences can be exploited in ensemble solutions which improve the predictive performance even further. The third part of the thesis concerns the efficient querying of the statistically modeled knowledge graphs. This thesis interprets statistically modeled knowledge graphs as probabilistic databases, where the latent variable models define a probability distribution for triples. From this perspective, link-prediction is equivalent to querying ground triples which is a standard functionality of the latent variable models. For more complex querying that involves e.g. joins and projections, the theory on probabilistic databases provides evaluation rules. In this thesis it is shown how the intrinsic features of latent variable models can be combined with the theory of probabilistic databases to realize efficient probabilistic querying of the modeled graphs

Correcting Knowledge Base Assertions

The usefulness and usability of knowledge bases (KBs) is often limited by quality issues. One common issue is the presence of erroneous assertions, often caused by lexical or semantic confusion. We study the problem of correcting such assertions, and present a general correction framework which combines lexical matching, semantic embedding, soft constraint mining and semantic consistency checking. The framework is evaluated using DBpedia and an enterprise medical KB