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Journal Article
Advancing the application and evaluation of large language models in health and biomedicine
Journal of the American Medical Informatics Association, Volume 32, Issue 4, April 2025, Pages 603–604, https://doi.org/10.1093/jamia/ocaf043
Published: 17 April 2025
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Permutation importance of classification model features. Bars indicate the ... Get access
Published: 15 April 2025
Figure 2.
Permutation importance of classification model features. Bars indicate the mean loss in area under the receiver operating characteristic curve across numerous train-test splits and random permutations of that feature alone in the test data. The black lines indicate the standard deviation across trai
Journal Article
Recovering missing electronic health record mortality data with a machine learning-enhanced data linkage process Get access
Journal of the American Medical Informatics Association, ocaf060, https://doi.org/10.1093/jamia/ocaf060
Published: 15 April 2025
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Flowchart of data linkage process. Diagram summarizing the data linkage ... Get access
Published: 15 April 2025
Figure 1.
Flowchart of data linkage process. Diagram summarizing the data linkage process. EHR and state death records are obtained. Then, records are linked by algorithms to find potential matches. Then, in stage 1 of classification, potential matches are scored and a score threshold applied. Then, in sta
Journal Article
Detecting emergencies in patient portal messages using large language models and knowledge graph-based retrieval-augmented generation
Journal of the American Medical Informatics Association, ocaf059, https://doi.org/10.1093/jamia/ocaf059
Published: 12 April 2025
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The screenshot of a patient message indicating a potential medical emergenc...
Published: 12 April 2025
Figure 1.
The screenshot of a patient message indicating a potential medical emergency. The form includes a warning to call 911 or visit the emergency department for emergencies, followed by text fields for “Enter a subject...” (filled in with “Headache”) and “Enter your message...” (containing a detailed not
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Study overview. A flowchart showing a study overview where a knowledge grap...
Published: 12 April 2025
Figure 2.
Study overview. A flowchart showing a study overview where a knowledge graph, developed using a GPT-4–powered nurse triage book, feeds into three RAG methods (naive, local, global) and a prompt‐only approach, with all outputs evaluated via statistical tests on key performance metrics. (RAG: retrieva
Journal Article
Revisions to the Safety Assurance Factors for Electronic Health Record Resilience (SAFER) Guides to update national recommendations for safe use of electronic health records
Journal of the American Medical Informatics Association, Volume 32, Issue 4, April 2025, Pages 755–760, https://doi.org/10.1093/jamia/ocaf018
Published: 12 April 2025
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Distribution of health literacy scores among All of Us participant... Get access
Published: 11 April 2025
Figure 1.
Distribution of health literacy scores among All of Us participants. A histogram displaying a graphical representation of the distribution of health literacy scores among All of Us participants. The histogram is skewed to the right, showing a higher number of participants as health literacy sco
Journal Article
Assessing health literacy and diversity within the All of Us Research Program Get access
Journal of the American Medical Informatics Association, ocae225, https://doi.org/10.1093/jamia/ocae225
Published: 11 April 2025
Journal Article
Letter to the Editor in response to “Application of a digital quality measure for cancer diagnosis in Epic Cosmos” Get access
Journal of the American Medical Informatics Association, ocaf025, https://doi.org/10.1093/jamia/ocaf025
Published: 10 April 2025
Journal Article
Evaluating the effectiveness of biomedical fine-tuning for large language models on clinical tasks Get access
Journal of the American Medical Informatics Association, ocaf045, https://doi.org/10.1093/jamia/ocaf045
Published: 07 April 2025
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Comparative performance of selected general-purpose vs biomedical LLMs with... Get access
in
Evaluating the effectiveness of biomedical fine-tuning for large language models on clinical tasks
Published: 07 April 2025
Figure 1.
Comparative performance of selected general-purpose vs biomedical LLMs with longer context size. This figure presents heatmaps showing the performance of selected general-purpose and biomedical LLMs across various clinical tasks. The models are divided into two panels based on size: (A) (7B/8B model
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Comparative performance of the domain specific and general-purpose base mod... Get access
in
Evaluating the effectiveness of biomedical fine-tuning for large language models on clinical tasks
Published: 07 April 2025
Figure 2.
Comparative performance of the domain specific and general-purpose base models on the two clinical case vignette series (A), LongHealth (B), MeDiSumQA (C), MedNLI (D), MeQSum (E), ProblemSummary (F), and MeDiSumCode (G). Bars represent the respective metric and error bars represent 95% confidence in
Journal Article
Beyond Phecodes: leveraging PheMAP to identify patients lacking diagnosis codes in electronic health records Get access
Journal of the American Medical Informatics Association, ocaf055, https://doi.org/10.1093/jamia/ocaf055
Published: 29 March 2025
Journal Article
DiMB-RE: mining the scientific literature for diet-microbiome associations
Journal of the American Medical Informatics Association, ocaf054, https://doi.org/10.1093/jamia/ocaf054
Published: 27 March 2025
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Flowchart for the inclusion and exclusion criteria. Flowchart illustrati... Get access
Published: 27 March 2025
Figure 1.
Flowchart for the inclusion and exclusion criteria. Flowchart illustrating the selection of patients for the study using EHR, Fitbit and genomic data. Out of 963 patients who underwent one of eight surgeries and shared Fitbit data, 601 were excluded for only sharing post-surgery data. Of the rema
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Annotation of a sentence from a PubMed abstract (PMID: 33509667). Entity me...
Published: 27 March 2025
Figure 1.
Annotation of a sentence from a PubMed abstract (PMID: 33509667). Entity mentions are shown in colored boxes and triggers and the corresponding relations are highlighted in brown. Relations are assigned certainty levels. Abbreviations: F, Factual; N, Negated. A diagram showing the annotation of e
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AUC for 4 models with genetic data integration for chronic opioid use outco... Get access
Published: 27 March 2025
Figure 2.
AUC for 4 models with genetic data integration for chronic opioid use outcome. AUC evaluated on the test set is plotted for the dataset with genomic data. Legends for each model are given at the bottom right with the AUC values. The diagonal blue dotted line represents the performance of a model mak
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Illustrative examples of ATLAS output in 2 patients with COPD who reported ...
Published: 27 March 2025
Figure 1.
Illustrative examples of ATLAS output in 2 patients with COPD who reported the same peak leg effort and dyspnea scores (5/10 according to the Borg score). Patient #1 (A) is a 58-year-old man with mild-to-moderate COPD-based on resting functional data showing a peak work rate of 115 W. In this case,
