MT techniques in a retrieval system of semantically enriched patents

This paper focuses on how automatic translation techniques integrated in a patent retrieval system increase its capabilities and make possible extended features and functionalities. We describe 1) a novel methodology for natural language to SPARQL translation based on a grammar– ontology interoperability automation and a query grammar for the patents domain; 2) a devised strategy for statisticalbased translation of patents that allows to transfer semantic annotations to the target language; 3) a built-in knowledge representation infrastructure that uses multilingual semantic annotations; and 4) an online application that offers a multilingual search interface over structural knowledge databases (domain ontologies) and multilingual documents (biomedical patents) that have been automatically translated.Peer ReviewedPostprint (published version

Accelerating Innovation Through Analogy Mining

The availability of large idea repositories (e.g., the U.S. patent database) could significantly accelerate innovation and discovery by providing people with inspiration from solutions to analogous problems. However, finding useful analogies in these large, messy, real-world repositories remains a persistent challenge for either human or automated methods. Previous approaches include costly hand-created databases that have high relational structure (e.g., predicate calculus representations) but are very sparse. Simpler machine-learning/information-retrieval similarity metrics can scale to large, natural-language datasets, but struggle to account for structural similarity, which is central to analogy. In this paper we explore the viability and value of learning simpler structural representations, specifically, "problem schemas", which specify the purpose of a product and the mechanisms by which it achieves that purpose. Our approach combines crowdsourcing and recurrent neural networks to extract purpose and mechanism vector representations from product descriptions. We demonstrate that these learned vectors allow us to find analogies with higher precision and recall than traditional information-retrieval methods. In an ideation experiment, analogies retrieved by our models significantly increased people's likelihood of generating creative ideas compared to analogies retrieved by traditional methods. Our results suggest a promising approach to enabling computational analogy at scale is to learn and leverage weaker structural representations.Comment: KDD 201

Proposal Flow: Semantic Correspondences from Object Proposals

Finding image correspondences remains a challenging problem in the presence of intra-class variations and large changes in scene layout. Semantic flow methods are designed to handle images depicting different instances of the same object or scene category. We introduce a novel approach to semantic flow, dubbed proposal flow, that establishes reliable correspondences using object proposals. Unlike prevailing semantic flow approaches that operate on pixels or regularly sampled local regions, proposal flow benefits from the characteristics of modern object proposals, that exhibit high repeatability at multiple scales, and can take advantage of both local and geometric consistency constraints among proposals. We also show that the corresponding sparse proposal flow can effectively be transformed into a conventional dense flow field. We introduce two new challenging datasets that can be used to evaluate both general semantic flow techniques and region-based approaches such as proposal flow. We use these benchmarks to compare different matching algorithms, object proposals, and region features within proposal flow, to the state of the art in semantic flow. This comparison, along with experiments on standard datasets, demonstrates that proposal flow significantly outperforms existing semantic flow methods in various settings.Comment: arXiv admin note: text overlap with arXiv:1511.0506

Reply With: Proactive Recommendation of Email Attachments

Email responses often contain items-such as a file or a hyperlink to an external document-that are attached to or included inline in the body of the message. Analysis of an enterprise email corpus reveals that 35% of the time when users include these items as part of their response, the attachable item is already present in their inbox or sent folder. A modern email client can proactively retrieve relevant attachable items from the user's past emails based on the context of the current conversation, and recommend them for inclusion, to reduce the time and effort involved in composing the response. In this paper, we propose a weakly supervised learning framework for recommending attachable items to the user. As email search systems are commonly available, we constrain the recommendation task to formulating effective search queries from the context of the conversations. The query is submitted to an existing IR system to retrieve relevant items for attachment. We also present a novel strategy for generating labels from an email corpus---without the need for manual annotations---that can be used to train and evaluate the query formulation model. In addition, we describe a deep convolutional neural network that demonstrates satisfactory performance on this query formulation task when evaluated on the publicly available Avocado dataset and a proprietary dataset of internal emails obtained through an employee participation program.Comment: CIKM2017. Proceedings of the 26th ACM International Conference on Information and Knowledge Management. 201

Getting More out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/ outcome models in the UK’s largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors’ own group) who work in text processing for biomedicine and other areas. GATE is available online ,1. under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio