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Khresmoi Multilingual Medical Text Analysis, Search and Machine Translation Connected in a Thriving Data-Value Chain

Deliverables

Requirements for Medical Record Analysis and Search

This deliverable will summarise the interactions and decisions made during the requirements specification process for the medical record analysis and search.

Initial Data Management Plan

The Data Management Plan will describe the data that KConnect will generate, whether and how it will be exploited or made accessible for verification and re-use, and how it will be curated and preserved.

Ethics Approvals

This deliverable responds to the Ethics Screening Report. It will include copies of ethical approvals for the collection of personal data by the competent University Data Protection Officer / National Data Protection authority, and detailed information on the procedures that will be implemented for data collection, storage, protection, retention and destruction, as well as confirmation that they comply with national and EU legislation.

Updated Data Management Plan

The Data Management Plan will describe the data that KConnect will generate, whether and how it will be exploited or made accessible for verification and re-use, and how it will be curated and preserved.

Component Interoperability Architecture

This deliverable will describe the KConnect cloud infrastructure and design the service interface of key project services.

Requirements for Vertical Search Solutions

This deliverable will summarise the interactions and decisions made during the requirements specification process for the vertical search solutions.

Final KConnect web site

The final version of the KConnect web site as described in Task 5.1.

Initial KConnect web site

The initial version of the KConnect web site as described in Task 5.1.

Log Analysis and Document Classification Toolkit (First Version)

This toolkit will comprise the cross-lingual medical document classification tools for a number of useful classes such as readability, trustability and target audience, as well as cross-lingual medical search log analysis tools with interesting behaviour patterns available. Tools and guidelines for adding new classes and behaviours will also be part of this toolkit.

Toolkit and Report for Translator Adaptation to New Languages (Final Version)

A set of tools allowing easy addition of new languages to the Khresmoi Translator by exploiting various training resources, decision support tools to assist in the choice of resources to include based on their price or effort to expected increase in translation performance, and a user guide on how to add a new language.

Toolkit and Report for Translator Adaptation to New Languages (First Version)

A set of tools allowing easy addition of new languages to the Khresmoi Translator by exploiting various training resources, decision support tools to assist in the choice of resources to include based on their price or effort to expected increase in translation performance, and a user guide on how to add a new language.

Adaptation to Hungarian, Swedish, and Polish

Khresmoi Translator adapted to translation from English to Hungarian, Swedish, Polish and vice versa based on publicly available resources and data automatically harvested from the web.

Semantic Annotation Toolkit (First Version)

This toolkit will comprise processes for adapters to follow when moving KConnect to a new language, and the tools required to make this shift. It will include tools for configuring the annotation pipeline, and for integrating terminologies. Documentation will include guides for sourcing the required resources and for adapting them where neccesary.

Log Analysis and Document Classification Toolkit (Final Version)

This toolkit will comprise the cross-lingual medical document classification tools for a number of useful classes such as readability, trustability and target audience, as well as cross-lingual medical search log analysis tools with interesting behaviour patterns available. Tools and guidelines for adding new classes and behaviours will also be part of this toolkit.

Semantic Annotation Toolkit (Final Version)

This toolkit will comprise processes for adapters to follow when moving KConnect to a new language, and the tools required to make this shift. It will include tools for configuring the annotation pipeline, and for integrating terminologies. Documentation will include guides for sourcing the required resources and for adapting them where neccesary.

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Publications

Language Independent Tokenization vs. Stemming in Automated Detection of Health Websites’ HONcode Conformity: An Evaluation

Author(s): Célia Boyer, Ljiljana Dolamic, Gilles Falquet
Published in: Procedia Computer Science, Issue 64, 2015, Page(s) 224-231, ISSN 1877-0509
DOI: 10.1016/j.procs.2015.08.484

Automated Detection of HONcode Website Conformity Compared to Manual Detection: An Evaluation

Author(s): Célia Boyer, Ljiljana Dolamic
Published in: Journal of Medical Internet Research, Issue 17/6, 2015, Page(s) e135, ISSN 1438-8871
DOI: 10.2196/jmir.3831

How users search and what they search for in the medical domain

Author(s): João Palotti, Allan Hanbury, Henning Müller, Charles E. Kahn
Published in: Information Retrieval Journal, Issue 19/1-2, 2016, Page(s) 189-224, ISSN 1386-4564
DOI: 10.1007/s10791-015-9269-8

Negative symptoms in schizophrenia: a study in a large clinical sample of patients using a novel automated method

Author(s): Rashmi Patel, Nishamali Jayatilleke, Matthew Broadbent, Chin-Kuo Chang, Nadia Foskett, Genevieve Gorrell, Richard D Hayes, Richard Jackson, Caroline Johnston, Hitesh Shetty, Angus Roberts, Philip McGuire, Robert Stewart
Published in: BMJ Open, Issue 5/9, 2015, Page(s) e007619, ISSN 2044-6055
DOI: 10.1136/bmjopen-2015-007619

Extracting antipsychotic polypharmacy data from electronic health records: developing and evaluating a novel process

Author(s): Giouliana Kadra, Robert Stewart, Hitesh Shetty, Richard G. Jackson, Mark A. Greenwood, Angus Roberts, Chin-Kuo Chang, James H. MacCabe, Richard D. Hayes
Published in: BMC Psychiatry, Issue 15/1, 2015, ISSN 1471-244X
DOI: 10.1186/s12888-015-0557-z

Making sense of big data in health research: Towards an EU action plan

Author(s): Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek, Norbert Graf, Vera Grimm, Henk-Jan Guchelaar, Yi-Ke Guo, Ivo Glynne Gut, Allan Hanbury, Shahid Hanif, Ralf-Dieter Hilgers, Ángel Ho
Published in: Genome Medicine, Issue 8/1, 2016, ISSN 1756-994X
DOI: 10.1186/s13073-016-0323-y

Neural Monkey: An Open-source Tool for Sequence Learning

Author(s): Jindřich Helcl, Jindřich Libovický
Published in: The Prague Bulletin of Mathematical Linguistics, Issue 107/1, 2017, Page(s) 5-17, ISSN 0032-6585
DOI: 10.1515/pralin-2017-0001

Natural language processing to extract symptoms of severe mental illness from clinical text: the Clinical Record Interactive Search Comprehensive Data Extraction (CRIS-CODE) project

Author(s): Richard G Jackson, Rashmi Patel, Nishamali Jayatilleke, Anna Kolliakou, Michael Ball, Genevieve Gorrell, Angus Roberts, Richard J Dobson, Robert Stewart
Published in: BMJ Open, Issue 7/1, 2017, Page(s) e012012, ISSN 2044-6055
DOI: 10.1136/bmjopen-2016-012012

Automated PDF highlighting to support faster curation of literature for Parkinson’s and Alzheimer’s disease

Author(s): Honghan Wu, Anika Oellrich, Christine Girges, Bernard de Bono, Tim J.P. Hubbard, Richard J.B. Dobson
Published in: Database, Issue 2017/1, 2017, ISSN 1758-0463
DOI: 10.1093/database/bax027

Language, Structure, and Reuse in the Electronic Health Record

Author(s): Angus Roberts
Published in: The AMA Journal of Ethic, Issue 19/3, 2017, Page(s) 281-288, ISSN 2376-6980
DOI: 10.1001/journalofethics.2017.19.3.stas1-1703

The Influence of Pre-processing on the Estimation of Readability of Web Documents

Author(s): João Rafael de Moura Palotti, Guido Zuccon, Allan Hanbury
Published in: Proceedings of the 24th ACM International on Conference on Information and Knowledge Management, 2015, Page(s) 1763-1766

CUNI in WMT15: Chimera Strikes Again

Author(s): Ondřej Bojar, Aleš Tamchyna
Published in: Proceedings of the Tenth Workshop on Statistical Machine Translation, 2015, Page(s) 79-83
DOI: 10.18653/v1/W15-3006

CLEF eHealth Evaluation Lab 2015, Task 2: Retrieving Information About Medical Symptoms

Author(s): Joao Palotti, Guido Zuccon, Lorraine Goeuriot, Liadh Kelly, Allan Hanbury, Gareth Jones, Mihai Lupu, Pavel Pecina
Published in: Working Notes of CLEF 2015 - Conference and Labs of the Evaluation forum, 2015

CUNI at the CLEF 2015 eHealth Lab Task 2

Author(s): Shadi Saleh, Feraena Bibyna, Pavel Pecina
Published in: Working Notes of CLEF 2015 - Conference and Labs of the Evaluation forum, 2015

What a Transfer-Based System Brings to the Combination with PBMT

Author(s): Aleš Tamchyna, Ondrej Bojar
Published in: Proceedings of the Fourth Workshop on Hybrid Approaches to Translation (HyTra), 2015, Page(s) 11-20
DOI: 10.18653/v1/W15-4103

UFPRSheffield: Contrasting Rule-based and Support Vector Machine Approaches to Time Expression Identification in Clinical TempEval

Author(s): Hegler Tissot, Genevieve Gorrell, Angus Roberts, Leon Derczynski, Marcos Didonet Del Fabro
Published in: Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), 2015, Page(s) 835-839
DOI: 10.18653/v1/S15-2141

Effect of the Named Entity Recognition and Sliding Window on the HONcode Automated Detection of HONcode Criteria for Mass Health Online Content

Author(s): Celia Boyer, Ljiljana Dolamic, Patrick Ruch, Gilles Falquet
Published in: Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, 2016, Page(s) 151-158
DOI: 10.5220/0005644301510158

Encoding Medication Episodes for Adverse Drug Event Prediction

Author(s): Honghan Wu, Zina M. Ibrahim, Ehtesham Iqbal, Richard J. B. Dobson
Published in: 2016, Page(s) 245-250
DOI: 10.1007/978-3-319-47175-4_18

Adapting SMT Query Translation Reranker to New Languages in Cross-Lingual Information Retrieval

Author(s): Pecina, Pavel; Saleh, Shadi
Published in: Issue 6, 2016

Overview of the CLEF eHealth Evaluation Lab 2016

Author(s): Liadh Kelly, Lorraine Goeuriot, Hanna Suominen, Aurélie Névéol, João Palotti, Guido Zuccon
Published in: 2016, Page(s) 255-266
DOI: 10.1007/978-3-319-44564-9_24

Task3 Patient-Centred Information Retrieval: Team CUNI

Author(s): Pecina, Pavel; Saleh, Shadi
Published in: Issue 1, 2017

Assessors Agreement: A Case Study across Assessor Type, Payment Levels, Query Variations and Relevance Dimensions

Author(s): Joao Palotti, Guido Zuccon, Johannes Bernhardt, Allan Hanbury, Lorraine Goeuriot
Published in: 2016, Page(s) 40-53
DOI: 10.1007/978-3-319-44564-9_4

TUW @ TREC Clinical Decision Support Track 2015

Author(s): Joao Palotti, Allan Hanbury
Published in: Text Retrieval Conference, 2015

Task3 Patient-Centred Information Retrieval: Team CUNI

Author(s): Saleh Shadi, Pavel Pecina
Published in: CLEF 2016 Working Notes, 2016, Page(s) 123-129

Does Online Evaluation Correspond to Offline Evaluation in Query Auto Completion?

Author(s): Alexandros Bampoulidis, João Palotti, Mihai Lupu, Jon Brassey, Allan Hanbury
Published in: 2017, Page(s) 713-719
DOI: 10.1007/978-3-319-56608-5_70

Ranking Health Web Pages with Relevance and Understandability

Author(s): Joao Palotti, Lorraine Goeuriot, Guido Zuccon, Allan Hanbury
Published in: Proceedings of the 39th International ACM SIGIR conference on Research and Development in Information Retrieval - SIGIR '16, 2016, Page(s) 965-968
DOI: 10.1145/2911451.2914741

The IR Task at the CLEF eHealth Evaluation Lab 2016: User-centred Health Information Retrieval

Author(s): Pecina, Pavel; Deacon, Anthony; Lupu, Mihai; Zuccon, Guido; Kelly, Liadh; Palotti, João; Goeuriot, Lorraine; Müller, Henning; Budaher, Julie
Published in: Issue 4, 2016

CUNI System for WMT16 Automatic Post-Editing and Multimodal Translation Tasks

Author(s): Jindřich Libovický, Jindřich Helcl, Marek Tlustý, Ondřej Bojar, Pavel Pecina
Published in: Proceedings of the First Conference on Machine Translation: Volume 2, Shared Task Papers, 2016, Page(s) 646-654
DOI: 10.18653/v1/W16-2361

Reranking Hypotheses of Machine-Translated Queries for Cross-Lingual Information Retrieval

Author(s): Pecina, Pavel; Saleh, Shadi
Published in: Experimental IR Meets Multilinguality, Multimodality, and Interaction 7th International Conference of the CLEF Association, Issue 5, 2016, Page(s) 54-66

Interactive exploration of healthcare queries

Author(s): Alexandras Bampoulidis, Mihai Lupu, Joao Palotti, Sokratis Metallidis, Jon Brassey, Allan Hanbury
Published in: 2016 14th International Workshop on Content-Based Multimedia Indexing (CBMI), 2016, Page(s) 1-4
DOI: 10.1109/cbmi.2016.7500275

Using Health Statistics to Improve Medical and Health Search

Author(s): Tawan Sierek, Allan Hanbury
Published in: Experimental IR Meets Multilinguality, Multimodality, and Interaction, 2015, Page(s) 287-292
DOI: 10.1007/978-3-319-24027-5_30