{"id":166764,"date":"2014-05-01T00:00:00","date_gmt":"2014-05-01T00:00:00","guid":{"rendered":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/msr-research-item\/annotating-clinical-events-in-text-snippets-for-phenotype-detection\/"},"modified":"2018-10-16T20:53:17","modified_gmt":"2018-10-17T03:53:17","slug":"annotating-clinical-events-in-text-snippets-for-phenotype-detection","status":"publish","type":"msr-research-item","link":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/publication\/annotating-clinical-events-in-text-snippets-for-phenotype-detection\/","title":{"rendered":"Annotating Clinical Events in Text Snippets for Phenotype Detection"},"content":{"rendered":"<div class=\"asset-content\">\n<p>Early detection and treatment of diseases that onset after a patient is admitted to a hospital, such as pneumonia, is critical to improving and reducing costs in healthcare. NLP systems that analyze the narrative data embedded in clinical artifacts such as x-ray reports can help support early detection. In this paper, we consider the importance of identifying the change of state for events\u2014in particular, clinical events that measure and compare the multiple states of a patients health across time. We propose a schema for event annotation comprised of five fields \u27e8location, attribute, value, change-of-state, reference\u27e9 and create preliminary annotation guidelines for annotators to apply the schema. We then train annotators, measure their performance, and finalize our guidelines. With the complete guidelines, we then annotate a corpus of snippets extracted from chest x-ray reports in order to integrate the annotations as a new source of features for classification tasks.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Early detection and treatment of diseases that onset after a patient is admitted to a hospital, such as pneumonia, is critical to improving and reducing costs in healthcare. NLP systems that analyze the narrative data embedded in clinical artifacts such as x-ray reports can help support early detection. In this paper, we consider the importance [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":null,"msr_publishername":"LREC","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"","msr_number":"","msr_organization":"","msr_pages_string":"","msr_page_range_start":"","msr_page_range_end":"","msr_series":"","msr_volume":"","msr_copyright":"","msr_conference_name":"","msr_doi":"","msr_arxiv_id":"","msr_s2_paper_id":"","msr_mag_id":"","msr_pubmed_id":"","msr_other_authors":"Meliha Yetisgen, Fei Xia, Prescott Klassen","msr_other_contributors":"","msr_speaker":"","msr_award":"","msr_affiliation":"","msr_institution":"","msr_host":"","msr_version":"","msr_duration":"","msr_original_fields_of_study":"","msr_release_tracker_id":"","msr_s2_match_type":"","msr_citation_count_updated":"","msr_published_date":"2014-05-01","msr_highlight_text":"","msr_notes":"","msr_longbiography":"","msr_publicationurl":"","msr_external_url":"","msr_secondary_video_url":"","msr_conference_url":"","msr_journal_url":"","msr_s2_pdf_url":"","msr_year":2014,"msr_citation_count":0,"msr_influential_citations":0,"msr_reference_count":0,"msr_s2_match_confidence":0,"msr_microsoftintellectualproperty":true,"msr_s2_open_access":false,"msr_s2_author_ids":[],"msr_pub_ids":[],"msr_hide_image_in_river":0,"footnotes":""},"msr-research-highlight":[],"research-area":[13553],"msr-publication-type":[193716],"msr-publisher":[],"msr-focus-area":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[],"msr-conference":[],"msr-journal":[],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-166764","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-medical-health-genomics","msr-locale-en_us"],"msr_publishername":"LREC","msr_edition":"","msr_affiliation":"","msr_published_date":"2014-05-01","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"","msr_number":"","msr_editors":"","msr_series":"","msr_issue":"","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":1,"msr_main_download":"204937","msr_publicationurl":"","msr_doi":"","msr_publication_uploader":[{"type":"file","title":"lrec_2014_final.pdf","viewUrl":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-content\/uploads\/2016\/02\/lrec_2014_final.pdf","id":204937,"label_id":0}],"msr_related_uploader":"","msr_citation_count":0,"msr_citation_count_updated":"","msr_s2_paper_id":"","msr_influential_citations":0,"msr_reference_count":0,"msr_arxiv_id":"","msr_s2_author_ids":[],"msr_s2_open_access":false,"msr_s2_pdf_url":null,"msr_attachments":[{"id":204937,"url":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-content\/uploads\/2016\/02\/lrec_2014_final.pdf"}],"msr-author-ordering":[{"type":"text","value":"Meliha Yetisgen","user_id":0,"rest_url":false},{"type":"user_nicename","value":"lucyv","user_id":32746,"rest_url":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=lucyv"},{"type":"text","value":"Fei Xia","user_id":0,"rest_url":false},{"type":"text","value":"Prescott Klassen","user_id":0,"rest_url":false}],"msr_impact_theme":[],"msr_research_lab":[],"msr_event":[],"msr_group":[],"msr_project":[393227],"publication":[],"video":[],"msr-tool":[],"msr_publication_type":"inproceedings","related_content":{"projects":[{"ID":393227,"post_title":"Biomedical Natural Language Processing","post_name":"biomedical-nlp","post_type":"msr-project","post_date":"2017-07-06 09:30:15","post_modified":"2017-07-14 12:37:01","post_status":"publish","permalink":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/project\/biomedical-nlp\/","post_excerpt":"The biomedical sciences are beginning to undergo a major transformation. Precision medicine has the potential to make treatments much more effective by better understanding patients, biological mechanisms, and therapeutic effects. However, current approaches only reach a small fraction of the patient population.\u00a0 Consider the molecular tumor board: dozens of highly paid specialists create a custom treatment plan for an individual patient, combing the research literature for research advances that are relevant to the cancer of&hellip;","_links":{"self":[{"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/393227"}]}}]},"_links":{"self":[{"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166764","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item"}],"about":[{"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-research-item"}],"version-history":[{"count":1,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166764\/revisions"}],"predecessor-version":[{"id":394706,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166764\/revisions\/394706"}],"wp:attachment":[{"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/media?parent=166764"}],"wp:term":[{"taxonomy":"msr-research-highlight","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-research-highlight?post=166764"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=166764"},{"taxonomy":"msr-publication-type","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-publication-type?post=166764"},{"taxonomy":"msr-publisher","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-publisher?post=166764"},{"taxonomy":"msr-focus-area","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-focus-area?post=166764"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=166764"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=166764"},{"taxonomy":"msr-field-of-study","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-field-of-study?post=166764"},{"taxonomy":"msr-conference","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-conference?post=166764"},{"taxonomy":"msr-journal","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-journal?post=166764"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=166764"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=166764"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}