{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/publicly-available-clinical-bert-embeddings","title":"Publicly Available Clinical BERT Embeddings","arxiv_id":"1904.03323","date":"2019-04-06","proceeding":"WS 2019 6","authors":["Emily Alsentzer","John R. Murphy","Willie Boag","Wei-Hung Weng","Di Jin","Tristan Naumann","Matthew B. A. McDermott"],"abstract":"Contextual word embedding models such as ELMo (Peters et al., 2018) and BERT (Devlin et al., 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such as clinical text; moreover, in the clinical domain, no publicly-available pre-trained BERT models yet exist. In this work, we address this need by exploring and releasing BERT models for clinical text: one for generic clinical text and another for discharge summaries specifically. We demonstrate that using a domain-specific model yields performance improvements on three common clinical NLP tasks as compared to nonspecific embeddings. These domain-specific models are not as performant on two clinical de-identification tasks, and argue that this is a natural consequence of the differences between de-identified source text and synthetically non de-identified task text.","url_abs":"https://arxiv.org/abs/1904.03323v3","url_pdf":"https://arxiv.org/pdf/1904.03323v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"publicly-available-clinical-bert-embeddings","repo_url":"https://github.com/EmilyAlsentzer/clinicalBERT","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"tf","reach":null},{"paper_slug":"publicly-available-clinical-bert-embeddings","repo_url":"https://github.com/ManasRMohanty/DS5500-capstone","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}},{"paper_slug":"publicly-available-clinical-bert-embeddings","repo_url":"https://github.com/obi-ml-public/ehr_deidentification","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"de-identification","task_name":"De-identification"}],"methods":[{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"attention-dropout","method_name":"Attention Dropout"},{"method_slug":"bert","method_name":"BERT"},{"method_slug":"bilstm","method_name":"BiLSTM"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"elmo","method_name":"ELMo"},{"method_slug":"lstm","method_name":"LSTM"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"linear-warmup-with-linear-decay","method_name":"Linear Warmup With Linear Decay"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"sigmoid-activation","method_name":"Sigmoid Activation"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"tanh-activation","method_name":"Tanh Activation"},{"method_slug":"weight-decay","method_name":"Weight Decay"},{"method_slug":"wordpiece","method_name":"WordPiece"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=1904.03323","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"1904.03323"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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