TADPLOT program, version 2.0: User's guide

The TADPLOT Program, Version 2.0 is described. The TADPLOT program is a software package coordinated by a single, easy-to-use interface, enabling the researcher to access several standard file formats, selectively collect specific subsets of data, and create full-featured publication and viewgraph quality plots. The user-interface was designed to be independent from any file format, yet provide capabilities to accommodate highly specialized data queries. Integrated with an applications software network, data can be assessed, collected, and viewed quickly and easily. Since the commands are data independent, subsequent modifications to the file format will be transparent, while additional file formats can be integrated with minimal impact on the user-interface. The graphical capabilities are independent of the method of data collection; thus, the data specification and subsequent plotting can be modified and upgraded as separate functional components. The graphics kernel selected adheres to the full functional specifications of the CORE standard. Both interface and postprocessing capabilities are fully integrated into TADPLOT

Overview of BioCreative II gene mention recognition.

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions

Figure mining for biomedical research

Motivation: Figures from biomedical articles contain valuable information difficult to reach without specialized tools. Currently, there is no search engine that can retrieve specific figure types. Results: This study describes a retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid computational and experimental research. Availability: http://iossifovlab.cshl.edu/figurome Contact: [email protected]

A line-based representation for matching words in historical manuscripts

Cataloged from PDF version of article.In this study, we propose a new method for retrieving and recognizing words in historical documents. We represent word images with a set of line segments. Then we provide a criterion for word matching based on matching the lines. We carry out experiments on a benchmark dataset consisting of manuscripts by George Washington, as well as on Ottoman manuscripts. (C) 2011 Elsevier B.V. All rights reserved

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

SpellMapper: A non-autoregressive neural spellchecker for ASR customization with candidate retrieval based on n-gram mappings

Contextual spelling correction models are an alternative to shallow fusion to improve automatic speech recognition (ASR) quality given user vocabulary. To deal with large user vocabularies, most of these models include candidate retrieval mechanisms, usually based on minimum edit distance between fragments of ASR hypothesis and user phrases. However, the edit-distance approach is slow, non-trainable, and may have low recall as it relies only on common letters. We propose: 1) a novel algorithm for candidate retrieval, based on misspelled n-gram mappings, which gives up to 90% recall with just the top 10 candidates on Spoken Wikipedia; 2) a non-autoregressive neural model based on BERT architecture, where the initial transcript and ten candidates are combined into one input. The experiments on Spoken Wikipedia show 21.4% word error rate improvement compared to a baseline ASR system.Comment: Accepted by INTERSPEECH 202