Patrick R. Alba

dblp:168/7629 · DBLP profile ↗
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14ranked-venue papers
5as first author
4since 2021 · last 2024
0000-0002-5176-5447ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 14 · 5 first-author · 4 since 2021
YearPublicationVenuePosition
2024 Strategies for secondary use of real-world clinical and administrative data for outcome ascertainment in pragmatic clinical trials
Cynthia Hau, Patricia A. Woods, Amanda S. Guski, Srihari I. Raju, Patrick R. Alba, William C. Cushman, Peter A. Glassman, Areef Ishani, Addison A. Taylor, Ryan E. Ferguson, Sarah Leatherman
J. Biomed. Informatics6
2023 A deep learning approach for medication disposition and corresponding attributes extraction
abstract
OBJECTIVE: This article summarizes our approach to extracting medication and corresponding attributes from clinical notes, which is the focus of track 1 of the 2022 National Natural Language Processing (NLP) Clinical Challenges(n2c2) shared task. METHODS: The dataset was prepared using Contextualized Medication Event Dataset (CMED), including 500 notes from 296 patients. Our system consisted of three components: medication named entity recognition (NER), event classification (EC), and context classification (CC). These three components were built using transformer models with slightly different architecture and input text engineering. A zero-shot learning solution for CC was also explored. RESULTS: Our best performance systems achieved micro-average F1 scores of 0.973, 0.911, and 0.909 for the NER, EC, and CC, respectively. CONCLUSION: In this study, we implemented a deep learning-based NLP system and demonstrated that our approach of (1) utilizing special tokens helps our model to distinguish multiple medications mentions in the same context; (2) aggregating multiple events of a single medication into multiple labels improves our model's performance.
Qiwei Gan, Mengke Hu, Kelly S. Peterson, Hannah Eyre, Patrick R. Alba, Annie E. Bowles, Johnathan C. Stanley, Scott L. DuVall, Jianlin Shi
J. Biomed. Informatics5
2021 Vaping at the VA: Developing an Annotated Corpus of Electronic Cigarette Mentions in Clinical Notes at the Department of Veterans Affairs
Mike Conway, Patrick R. Alba, Shu-Hong Zhu, Olga V. Patterson
AMIA2
2021 Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python
Hannah Eyre, Alec B. Chapman, Kelly S. Peterson, Jianlin Shi, Patrick R. Alba, Makoto Jones, Tamara L. Box, Scott L. DuVall, Olga V. Patterson
AMIA5
2020 A Decade of Vaping: Identifying Shifts in Clinical Documentation and Terminology in the Department of Veterans Affairs (2010-2020)
Patrick R. Alba, Olga V. Patterson, Mike Conway
AMIA1
2020 Removing barriers to clinical text processing with MedSpaCy
Hannah Eyre, Olga V. Patterson, Jianlin Shi, Kelly S. Peterson, Alec B. Chapman, Patrick R. Alba, Scott L. DuVall
AMIA6
2018 Ankle Brachial Index Extraction System
Patrick R. Alba, Scott L. DuVall, Daniel Norvell, Kathryn P. Moore, Joseph M. Czerniecki, Olga V. Patterson
AMIA1
2018 A User-Friendly Interface for Concept Dictionary Expansion Using Word Embeddings and SNOMED-CT
Alec B. Chapman, Patrick R. Alba, Brian T. Bucher, Scott L. DuVall, Olga V. Patterson
AMIA2
2018 Fast and Accurate Adverse Drug Event labeling without a GPU
Kelly S. Peterson, Alec B. Chapman, Patrick R. Alba, Scott L. DuVall, Olga V. Patterson
AMIA3
2017 Pathology Information Extraction in Bladder Cancer Surveillance
Patrick R. Alba, Scott L. DuVall, Terri Elizabeth Workman, Florian Schroeck, Olga V. Patterson
AMIA1
2016 The Super Annotator: A Method of Semi-Automated Rare Event Identification for Large Clinical Data Sets
Patrick R. Alba, Olga V. Patterson, Benjamin Viernes, Daniel W. Denhalter, Nicole Bailey, Aaron W. C. Kamauu, Scott L. DuVall
AMIA1
2016 Large Scale Clinical Text Processing and Process Optimization
Scott L. DuVall, Patrick R. Alba, Olga V. Patterson
AMIA2
2016 An Introduction to Natural Language Processing Methods in Clinical Research
Olga V. Patterson, Patrick R. Alba, Scott L. DuVall
AMIA2
2015 Knowledge Base Acquisition For Rare Concepts Using Manual Bootstrapping
Patrick R. Alba, Scott L. DuVall, Joanne LaFleur, Adam Bress, Olga V. Patterson
AMIA1