Related papers: De-identification of Unstructured Clinical Texts f…
The increasing availability of sensitive textual data has created an urgent need for robust de-identification methods that enable compliant data sharing while preserving downstream utility. This paper presents DeID-Clinic, a multi-layered…
Deep learning approaches exhibit promising performances on various text tasks. However, they are still struggling on medical text classification since samples are often extremely imbalanced and scarce. Different from existing mainstream…
With a neural sequence generation model, this study aims to develop a method of writing the patient clinical texts given a brief medical history. As a proof-of-a-concept, we have demonstrated that it can be workable to use medical concept…
Background: Electronic health records (EHRs) are a valuable resource for data-driven medical research. However, the presence of protected health information (PHI) makes EHRs unsuitable to be shared for research purposes. De-identification,…
Clinical text classification is an important problem in medical natural language processing. Existing studies have conventionally focused on rules or knowledge sources-based feature engineering, but only a few have exploited effective…
In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a disease mention in free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language…
International Classification of Diseases (ICD) are the de facto codes used globally for clinical coding. These codes enable healthcare providers to claim reimbursement and facilitate efficient storage and retrieval of diagnostic…
Many models are pretrained on redacted text for privacy reasons. Clinical foundation models are often trained on de-identified text, which uses special syntax (masked) text in place of protected health information. Even though these models…
We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at…
Unstructured textual data is at the heart of healthcare systems. For obvious privacy reasons, these documents are not accessible to researchers as long as they contain personally identifiable information. One way to share this data while…
In this work, we investigate unsupervised representation learning on medical time series, which bears the promise of leveraging copious amounts of existing unlabeled data in order to eventually assist clinical decision making. By evaluating…
Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence…
Recent research advances achieve human-level accuracy for de-identifying free-text clinical notes on research datasets, but gaps remain in reproducing this in large real-world settings. This paper summarizes lessons learned from building a…
De-identification is the task of detecting protected health information (PHI) in medical text. It is a critical step in sanitizing electronic health records (EHRs) to be shared for research. Automatic de-identification classifierscan…
Named entity recognition often fails in idiosyncratic domains. That causes a problem for depending tasks, such as entity linking and relation extraction. We propose a generic and robust approach for high-recall named entity recognition. Our…
Unsupervised person re-identification (re-ID) has become an important topic due to its potential to resolve the scalability problem of supervised re-ID models. However, existing methods simply utilize pseudo labels from clustering for…
Clinical text provides essential information to estimate the acuity of a patient during hospital stays in addition to structured clinical data. In this study, we explore how clinical text can complement a clinical predictive learning task.…
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…
Exploiting natural language processing in the clinical domain requires de-identification, i.e., anonymization of personal information in texts. However, current research considers de-identification and downstream tasks, such as concept…
Unstructured information comprises a valuable source of data in clinical records. For text mining in clinical records, concept extraction is the first step in finding assertions and relationships. This study presents a system developed for…