Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.
 We created a software tool that accurately removes all patient identifying information from various kinds of clinical data documents, including laboratory and narrative reports. We created the Medical De-identification System (MeDS), a software tool that de-identifies clinical documents, and performed 2 evaluations. Our first evaluation used 2,400 Health Level Seven (HL7) messages from 10 different HL7 message producers. After modifying the software based on the results of this first evaluation, we performed a second evaluation using 7,190 pathology report HL7 messages. We compared the results of MeDS de-identification process to a gold standard of human review to find identifying strings. For both evaluations, we calculated the number of successful scrubs, missed identifiers, and over-scrubs committed by MeDS and evaluated the readability and interpretability of the scrubbed messages. We categorized all missed identifiers into 3 groups: (1) complete HIPAA-specified identifiers, (2) HIPAA-specified identifier fragments, (3) non-HIPAA–specified identifiers (such as provider names and addresses). In the results of the first-pass evaluation, MeDS scrubbed 11,273 (99.06 ) of the 11,380 HIPAA-specified identifiers and 38,095 (98.26 ) of the 38,768 non-HIPAA–specified identifiers. In our second evaluation (status postmodification to the software), MeDS scrubbed 79,993 (99.47 ) of the 80,418 HIPAA-specified identifiers and 12,689 (96.93 ) of the 13,091 non-HIPAA–specified identifiers. Approximately 95 of scrubbed messages were both readable and interpretable. We conclude that MeDS successfully de-identified a wide range of medical documents from numerous sources and creates scrubbed reports that retain their interpretability, thereby maintaining their usefulness for research.   Electronic clinical documentation can be useful for activities such as public health surveillance, quality improvement, and research, but existing methods of de-identification may not provide sufficient protection of patient data. The general-purpose natural language processor MedLEE retains medical concepts while excluding the remaining text so, in addition to processing text into structured data, it may be able provide a secondary benefit of de-identification. Without modifying the system, the authors tested the ability of MedLEE to remove protected health information (PHI) by comparing 100 outpatient clinical notes with the corresponding XML-tagged output. Of 809 instances of PHI, 26 (3.2 ) were detected in output as a result of processing and identification errors. However, PHI in the output was highly transformed, much appearing as normalized terms for medical concepts, potentially making re-identification more difficult. The MedLEE processor may be a good enhancement to other de-identification systems, both removing PHI and providing coded data from clinical text.  Medical researchers are legally required to protect patients' privacy by removing personally identifiable information from medical records before sharing the data with other researchers. We present an evaluation of methods for computer-assisted removal and replacement of protected health information (PHI) from free-text nursing notes collected in the intensive care unit as part of the MIMIC II project. A semiautomated method was developed to allow clinicians to highlight PHI on the screen of a tablet PC and to compare and combine the selections of different experts reading the same notes. An analysis of the performance of three human expert de-identifiers and of an automated system is presented. Expert adjudication demonstrated that inter-human variability was high, with few false positives and many false negatives. The sensitivity of human experts working alone ranged from 0.63 to 0.93, with an average of 0.81, and the average positive predictive value was 0.98. An algorithm generated few false negatives but many false positives. Its sensitivity was 0.85, but its positive predictive value was only 0.37. The de-identified database of nursing notes was re-identified with realistic surrogate (but unprotected) dates, serial numbers, names, and phrases to provide a gold standard database of over 2600 notes (approximately 340,000 words) with over 1700 instances of PHI. This reference gold standard database of nursing notes and the Java source code used to evaluate algorithm performance will be made freely available on Physionet in order to facilitate the development and validation of future de-identification algorithms. Abstract We define a new approach to locating and replacing personally-identifying information in medical records that extends beyond straight search-and-replace procedures, and we provide techniques for minimizing risk to patient confidentiality. The straightforward approach of global search and replace properly located no more than 30-60 of all personally-identifying information that appeared explicitly in our sample database. On the other hand, our Scrub system found 99-100 of these references. Scrub uses detection algorithms that employ templates and specialized knowledge of what constitutes a name, address, phone number and so forth. We present an original system for locating and removing personally-identifying information in patient records. In this experiment, anonymization is seen as a particular case of knowledge extraction. We use natural language processing tools provided by the MEDTAG framework: a semantic lexicon specialized in medicine, and a toolkit for word-sense and morpho-syntactic tagging. The system finds 98-99 of all personally-identifying information. Abstract The ability to access large amounts of de-identified clinical data would facilitate epidemiologic and retrospective research. Previously described de-identification methods require knowledge of natural language processing or have not been made available to the public. We take advantage of the fact that the vast majority of proper names in pathology reports occur in pairs. In rare cases where one proper name is by itself, it is preceded or followed by an affix that identifies it as a proper name (Mrs., Dr., PhD). We created a tool based on this observation using substitution methods that was easy to implement and was largely based on publicly available data sources. We compiled a Clinical and Common Usage Word (CCUW) list as well as a fairly comprehensive proper name list. Despite the large overlap between these two lists, we were able to refine our methods to achieve accuracy similar to previous attempts at de-identification. Our method found 98.7 of 231 proper names in the narrative sections of pathology reports. Three single proper names were missed out of 1001 pathology reports (0.3 , no first name last name pairs). It is unlikely that identification could be implied from this information. We will continue to refine our methods, specifically working to improve the quality of our CCUW and proper name lists to obtain higher levels of accuracy.  