Comparing Rule-based, Feature-based and Deep Neural Methods for De-identification of Dutch Medical Records

Unstructured information in electronic health records provide an invaluable resource for medical research. To protect the confidentiality of patients and to conform to privacy regulations, de-identification methods automatically remove personally identifying information from these medical records. However, due to the unavailability of labeled data, most existing research is constrained to English medical text and little is known about the generalizability of de-identification methods across languages and domains. In this study, we construct a varied dataset consisting of the medical records of 1260 patients by sampling data from 9 institutes and three domains of Dutch healthcare. We test the generalizability of three de-identification methods across languages and domains. Our experiments show that an existing rule-based method specifically developed for the Dutch language fails to generalize to this new data. Furthermore, a state-of-the-art neural architecture performs strongly across languages and domains, even with limited training data. Compared to feature-based and rule-based methods the neural method requires significantly less configuration effort and domain-knowledge. We make all code and pre-trained de-identification models available to the research community, allowing practitioners to apply them to their datasets and to enable future benchmarks.Comment: Proceedings of the 1st ACM WSDM Health Search and Data Mining Workshop (HSDM2020), 202

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

There is a great and growing need to ascertain what exactly is the state of a patient, in terms of disease progression, actual care practices, pathology, adverse events, and much more, beyond the paucity of data available in structured medical record data. Ascertaining these harder-to-reach data elements is now critical for the accurate phenotyping of complex traits, detection of adverse outcomes, efficacy of off-label drug use, and longitudinal patient surveillance. Clinical notes often contain the most detailed and relevant digital information about individual patients, the nuances of their diseases, the treatment strategies selected by physicians, and the resulting outcomes. However, notes remain largely unused for research because they contain Protected Health Information (PHI), which is synonymous with individually identifying data. Previous clinical note de-identification approaches have been rigid and still too inaccurate to see any substantial real-world use, primarily because they have been trained with too small medical text corpora. To build a new de-identification tool, we created the largest manually annotated clinical note corpus for PHI and develop a customizable open-source de-identification software called Philter ("Protected Health Information filter"). Here we describe the design and evaluation of Philter, and show how it offers substantial real-world improvements over prior methods

De-identification of patient notes with recurrent neural networks

Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of electronic health record databases, the limited number of researchers with access to non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value. Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset. Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall of 97.38 and a precision of 98.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall of 99.25 and a precision of 99.21. Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no manual feature engineering

Extracting adverse drug reactions and their context using sequence labelling ensembles in TAC2017

Adverse drug reactions (ADRs) are unwanted or harmful effects experienced after the administration of a certain drug or a combination of drugs, presenting a challenge for drug development and drug administration. In this paper, we present a set of taggers for extracting adverse drug reactions and related entities, including factors, severity, negations, drug class and animal. The systems used a mix of rule-based, machine learning (CRF) and deep learning (BLSTM with word2vec embeddings) methodologies in order to annotate the data. The systems were submitted to adverse drug reaction shared task, organised during Text Analytics Conference in 2017 by National Institute for Standards and Technology, archiving F1-scores of 76.00 and 75.61 respectively.Comment: Paper describing submission for TAC ADR shared tas

Comparing Rule-based, Feature-based and Deep Neural Methods for De-identification of Dutch Medical Records

Unstructured information in electronic health records provide an invaluable resource for medical research. To protect the confidentiality of patients and to conform to privacy regulations, de-identification methods automatically remove personally identifying information from these medical records. However, due to the unavailability of labeled data, most existing research is constrained to English medical text and little is known about the generalizability of de-identification methods across languages and domains. In this study, we construct a varied dataset consisting of the medical records of 1260 patients by sampling data from 9 institutes and three domains of Dutch healthcare. We test the generalizability of three de-identification methods across languages and domains. Our experiments show that an existing rule-based method specifically developed for the Dutch language fails to generalize to this new data. Furthermore, a state-of-the-art neural architecture performs strongly across languages and domains, even with limited training data. Compared to feature-based and rule-based methods the neural method requires significantly less configuration effort and domain-knowledge. We make all code and pre-trained de-identification models available to the research community, allowing practitioners to apply them to their datasets and to enable future benchmarks