Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0)

Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0). Jagannatha, A., Liu, F., Liu, W., & Yu, H. Drug Safety, January, 2019.
doi abstract bibtex

INTRODUCTION: This work describes the Medication and Adverse Drug Events from Electronic Health Records (MADE 1.0) corpus and provides an overview of the MADE 1.0 2018 challenge for extracting medication, indication, and adverse drug events (ADEs) from electronic health record (EHR) notes. OBJECTIVE: The goal of MADE is to provide a set of common evaluation tasks to assess the state of the art for natural language processing (NLP) systems applied to EHRs supporting drug safety surveillance and pharmacovigilance. We also provide benchmarks on the MADE dataset using the system submissions received in the MADE 2018 challenge. METHODS: The MADE 1.0 challenge has released an expert-annotated cohort of medication and ADE information comprising 1089 fully de-identified longitudinal EHR notes from 21 randomly selected patients with cancer at the University of Massachusetts Memorial Hospital. Using this cohort as a benchmark, the MADE 1.0 challenge designed three shared NLP tasks. The named entity recognition (NER) task identifies medications and their attributes (dosage, route, duration, and frequency), indications, ADEs, and severity. The relation identification (RI) task identifies relations between the named entities: medication-indication, medication-ADE, and attribute relations. The third shared task (NER-RI) evaluates NLP models that perform the NER and RI tasks jointly. In total, 11 teams from four countries participated in at least one of the three shared tasks, and 41 system submissions were received in total. RESULTS: The best systems F1 scores for NER, RI, and NER-RI were 0.82, 0.86, and 0.61, respectively. Ensemble classifiers using the team submissions improved the performance further, with an F1 score of 0.85, 0.87, and 0.66 for the three tasks, respectively. CONCLUSION: MADE results show that recent progress in NLP has led to remarkable improvements in NER and RI tasks for the clinical domain. However, some room for improvement remains, particularly in the NER-RI task.

@article{jagannatha_overview_2019,
	title = {Overview of the {First} {Natural} {Language} {Processing} {Challenge} for {Extracting} {Medication}, {Indication}, and {Adverse} {Drug} {Events} from {Electronic} {Health} {Record} {Notes} ({MADE} 1.0)},
	issn = {1179-1942},
	doi = {10.1007/s40264-018-0762-z},
	abstract = {INTRODUCTION: This work describes the Medication and Adverse Drug Events from Electronic Health Records (MADE 1.0) corpus and provides an overview of the MADE 1.0 2018 challenge for extracting medication, indication, and adverse drug events (ADEs) from electronic health record (EHR) notes.
OBJECTIVE: The goal of MADE is to provide a set of common evaluation tasks to assess the state of the art for natural language processing (NLP) systems applied to EHRs supporting drug safety surveillance and pharmacovigilance. We also provide benchmarks on the MADE dataset using the system submissions received in the MADE 2018 challenge.
METHODS: The MADE 1.0 challenge has released an expert-annotated cohort of medication and ADE information comprising 1089 fully de-identified longitudinal EHR notes from 21 randomly selected patients with cancer at the University of Massachusetts Memorial Hospital. Using this cohort as a benchmark, the MADE 1.0 challenge designed three shared NLP tasks. The named entity recognition (NER) task identifies medications and their attributes (dosage, route, duration, and frequency), indications, ADEs, and severity. The relation identification (RI) task identifies relations between the named entities: medication-indication, medication-ADE, and attribute relations. The third shared task (NER-RI) evaluates NLP models that perform the NER and RI tasks jointly. In total, 11 teams from four countries participated in at least one of the three shared tasks, and 41 system submissions were received in total.
RESULTS: The best systems F1 scores for NER, RI, and NER-RI were 0.82, 0.86, and 0.61, respectively. Ensemble classifiers using the team submissions improved the performance further, with an F1 score of 0.85, 0.87, and 0.66 for the three tasks, respectively.
CONCLUSION: MADE results show that recent progress in NLP has led to remarkable improvements in NER and RI tasks for the clinical domain. However, some room for improvement remains, particularly in the NER-RI task.},
	language = {eng},
	number = {1},
	journal = {Drug Safety},
	author = {Jagannatha, Abhyuday and Liu, Feifan and Liu, Weisong and Yu, Hong},
	month = jan,
	year = {2019},
	pmid = {30649735 PMCID: PMC6860017},
	pages = {99--111},
}

Downloads: 0

{"_id":"x5iuwBzdYTDYD5Ert","bibbaseid":"jagannatha-liu-liu-yu-overviewofthefirstnaturallanguageprocessingchallengeforextractingmedicationindicationandadversedrugeventsfromelectronichealthrecordnotesmade10-2019","author_short":["Jagannatha, A.","Liu, F.","Liu, W.","Yu, H."],"bibdata":{"bibtype":"article","type":"article","title":"Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0)","issn":"1179-1942","doi":"10.1007/s40264-018-0762-z","abstract":"INTRODUCTION: This work describes the Medication and Adverse Drug Events from Electronic Health Records (MADE 1.0) corpus and provides an overview of the MADE 1.0 2018 challenge for extracting medication, indication, and adverse drug events (ADEs) from electronic health record (EHR) notes. OBJECTIVE: The goal of MADE is to provide a set of common evaluation tasks to assess the state of the art for natural language processing (NLP) systems applied to EHRs supporting drug safety surveillance and pharmacovigilance. We also provide benchmarks on the MADE dataset using the system submissions received in the MADE 2018 challenge. METHODS: The MADE 1.0 challenge has released an expert-annotated cohort of medication and ADE information comprising 1089 fully de-identified longitudinal EHR notes from 21 randomly selected patients with cancer at the University of Massachusetts Memorial Hospital. Using this cohort as a benchmark, the MADE 1.0 challenge designed three shared NLP tasks. The named entity recognition (NER) task identifies medications and their attributes (dosage, route, duration, and frequency), indications, ADEs, and severity. The relation identification (RI) task identifies relations between the named entities: medication-indication, medication-ADE, and attribute relations. The third shared task (NER-RI) evaluates NLP models that perform the NER and RI tasks jointly. In total, 11 teams from four countries participated in at least one of the three shared tasks, and 41 system submissions were received in total. RESULTS: The best systems F1 scores for NER, RI, and NER-RI were 0.82, 0.86, and 0.61, respectively. Ensemble classifiers using the team submissions improved the performance further, with an F1 score of 0.85, 0.87, and 0.66 for the three tasks, respectively. CONCLUSION: MADE results show that recent progress in NLP has led to remarkable improvements in NER and RI tasks for the clinical domain. However, some room for improvement remains, particularly in the NER-RI task.","language":"eng","number":"1","journal":"Drug Safety","author":[{"propositions":[],"lastnames":["Jagannatha"],"firstnames":["Abhyuday"],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Feifan"],"suffixes":[]},{"propositions":[],"lastnames":["Liu"],"firstnames":["Weisong"],"suffixes":[]},{"propositions":[],"lastnames":["Yu"],"firstnames":["Hong"],"suffixes":[]}],"month":"January","year":"2019","pmid":"30649735 PMCID: PMC6860017","pages":"99–111","bibtex":"@article{jagannatha_overview_2019,\n\ttitle = {Overview of the {First} {Natural} {Language} {Processing} {Challenge} for {Extracting} {Medication}, {Indication}, and {Adverse} {Drug} {Events} from {Electronic} {Health} {Record} {Notes} ({MADE} 1.0)},\n\tissn = {1179-1942},\n\tdoi = {10.1007/s40264-018-0762-z},\n\tabstract = {INTRODUCTION: This work describes the Medication and Adverse Drug Events from Electronic Health Records (MADE 1.0) corpus and provides an overview of the MADE 1.0 2018 challenge for extracting medication, indication, and adverse drug events (ADEs) from electronic health record (EHR) notes.\nOBJECTIVE: The goal of MADE is to provide a set of common evaluation tasks to assess the state of the art for natural language processing (NLP) systems applied to EHRs supporting drug safety surveillance and pharmacovigilance. We also provide benchmarks on the MADE dataset using the system submissions received in the MADE 2018 challenge.\nMETHODS: The MADE 1.0 challenge has released an expert-annotated cohort of medication and ADE information comprising 1089 fully de-identified longitudinal EHR notes from 21 randomly selected patients with cancer at the University of Massachusetts Memorial Hospital. Using this cohort as a benchmark, the MADE 1.0 challenge designed three shared NLP tasks. The named entity recognition (NER) task identifies medications and their attributes (dosage, route, duration, and frequency), indications, ADEs, and severity. The relation identification (RI) task identifies relations between the named entities: medication-indication, medication-ADE, and attribute relations. The third shared task (NER-RI) evaluates NLP models that perform the NER and RI tasks jointly. In total, 11 teams from four countries participated in at least one of the three shared tasks, and 41 system submissions were received in total.\nRESULTS: The best systems F1 scores for NER, RI, and NER-RI were 0.82, 0.86, and 0.61, respectively. Ensemble classifiers using the team submissions improved the performance further, with an F1 score of 0.85, 0.87, and 0.66 for the three tasks, respectively.\nCONCLUSION: MADE results show that recent progress in NLP has led to remarkable improvements in NER and RI tasks for the clinical domain. However, some room for improvement remains, particularly in the NER-RI task.},\n\tlanguage = {eng},\n\tnumber = {1},\n\tjournal = {Drug Safety},\n\tauthor = {Jagannatha, Abhyuday and Liu, Feifan and Liu, Weisong and Yu, Hong},\n\tmonth = jan,\n\tyear = {2019},\n\tpmid = {30649735 PMCID: PMC6860017},\n\tpages = {99--111},\n}\n\n","author_short":["Jagannatha, A.","Liu, F.","Liu, W.","Yu, H."],"key":"jagannatha_overview_2019","id":"jagannatha_overview_2019","bibbaseid":"jagannatha-liu-liu-yu-overviewofthefirstnaturallanguageprocessingchallengeforextractingmedicationindicationandadversedrugeventsfromelectronichealthrecordnotesmade10-2019","role":"author","urls":{},"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"http://fenway.cs.uml.edu/papers/pubs-all.bib","dataSources":["TqaA9miSB65nRfS5H"],"keywords":[],"search_terms":["overview","first","natural","language","processing","challenge","extracting","medication","indication","adverse","drug","events","electronic","health","record","notes","made","jagannatha","liu","liu","yu"],"title":"Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0)","year":2019,"downloads":1}