Iterative refinement and goal articulation to optimize large language models for clinical information extraction.

Lindsay G. Cowell

David Hein Alana Christie Michael J. Holcomb Bingqing Xie Aj Jain Joseph Vento Dinesh Rakheja Ameer Hamza Shakur Scott Christley Lindsay G. Cowell James Brugarolas Andrew R. Jamieson Payal Kapur Iterative refinement and goal articulation to optimize large language models for clinical information extraction. 2025 8 npj Digit. Medicine 1 https://doi.org/10.1038/s41746-025-01686-z db/journals/npjdm/npjdm8.html#HeinCHXJVRSCCBJK25 streams/journals/npjdm

John Beverley Yongqun He Barry Smith 0001 Shane Babcock Eric Merrell Lindsay G. Cowell Regina Hurley Sebastian Deusing Coordinating Coronavirus Research: The Virus Infectious Disease Ontology. 1-14 2022 ICBO https://ceur-ws.org/Vol-3805/ICBO-2022_paper_3877.pdf conf/icbo/2022 db/conf/icbo/icbo2022.html#BeverleyH0BMCHD22

Shane Babcock John Beverley Lindsay G. Cowell Barry Smith 0001 The Infectious Disease Ontology in the age of COVID-19. 13 2021 12 J. Biomed. Semant. 1 https://doi.org/10.1186/s13326-021-00245-1 https://www.wikidata.org/entity/Q112778988 db/journals/biomedsem/biomedsem12.html#BabcockBCS21

Milena Pavlovic Lonneke Scheffer Keshav Motwani Chakravarthi Kanduri Radmila Kompova Nikolay Vazov Knut Waagan Fabian L. M. Bernal Alexandre Almeida Costa Brian Corrie Rahmad Akbar Ghadi S. Al Hajj Gabriel Balaban Todd M. Brusko Maria Chernigovskaya Scott Christley Lindsay G. Cowell Robert Frank 0006 Ivar Grytten Sveinung Gundersen Ingrid Hobæk Haff Eivind Hovig Ping-Han Hsieh Günter Klambauer Marieke L. Kuijjer Christin Lund-Andersen Antonio Martini 0001 Thomas Minotto Johan Pensar Knut D. Rand Enrico Riccardi Philippe A. Robert Artur Rocha Andrei Slabodkin Igor Snapkov Ludvig Magne Sollid Dmytro Titov Cédric R. Weber Michael Widrich Gur Yaari Victor Greiff Geir Kjetil Sandve The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. 936-944 2021 3 Nat. Mach. Intell. 11 https://doi.org/10.1038/s42256-021-00413-z db/journals/natmi/natmi3.html#PavlovicSMKKVWB21

Jared Ostmeyer Scott Christley Lindsay G. Cowell Dynamic Kernel Matching for Non-conforming Data: A Case Study of T-cell Receptor Datasets. 2021 abs/2103.10472 CoRR https://arxiv.org/abs/2103.10472 db/journals/corr/corr2103.html#abs-2103-10472

Scott Christley Ademar Aguiar George Blanck Felix Breden Syed Ahmad Chan Bukhari Christian E. Busse Jerome Jaglale Srilakshmy L. Harikrishnan Uri Laserson Bjoern Peters Artur Rocha Chaim A. Schramm Sarah Taylor Jason A. Vander Heiden Bojan Zimonja Corey T. Watson Brian Corrie Lindsay G. Cowell The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. 22 2020 3 Frontiers Big Data https://doi.org/10.3389/fdata.2020.00022 https://www.wikidata.org/entity/Q112726310 db/journals/fdata/fdata3.html#ChristleyABBBBJ20

Jared Ostmeyer Lindsay G. Cowell Machine learning on sequential data using a recurrent weighted average. 281-288 2019 331 Neurocomputing https://doi.org/10.1016/j.neucom.2018.11.066 https://www.wikidata.org/entity/Q91871525 db/journals/ijon/ijon331.html#OstmeyerC19

Jared Ostmeyer Scott Christley William Rounds Inimary T. Toby Benjamin M. Greenberg Nancy Monson Lindsay G. Cowell Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. 401:1-401:10 2017 18 BMC Bioinform. 1 https://doi.org/10.1186/s12859-017-1814-6 https://www.wikidata.org/entity/Q41590849 db/journals/bmcbi/bmcbi18.html#OstmeyerCRTGMC17

Scott Christley Mikhail K. Levin Inimary T. Toby John M. Fonner Nancy Monson William Rounds Florian Rubelt Walter Scarborough Richard H. Scheuermann Lindsay G. Cowell VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. 448:1-448:5 2017 18 BMC Bioinform. 1 https://doi.org/10.1186/s12859-017-1853-z https://www.wikidata.org/entity/Q42375167 db/journals/bmcbi/bmcbi18.html#ChristleyLTFMRR17

Trygve E. Bakken Lindsay G. Cowell Brian D. Aevermann Mark Novotny Rebecca D. Hodge Jeremy A. Miller Alexandra Lee Ivan Chang Jamison M. McCorrison Bali Pulendran Yu Qian Nicholas J. Schork Roger S. Lasken Ed S. Lein Richard H. Scheuermann Cell type discovery and representation in the era of high-content single cell phenotyping. 7-16 2017 18 BMC Bioinform. S-17 https://doi.org/10.1186/s12859-017-1977-1 https://www.wikidata.org/entity/Q47870911 db/journals/bmcbi/bmcbi18S.html#BakkenCANHMLCMP17

Jared Ostmeyer Lindsay G. Cowell Machine Learning on Sequential Data Using a Recurrent Weighted Average. 2017 abs/1703.01253 CoRR http://arxiv.org/abs/1703.01253 db/journals/corr/corr1703.html#OstmeyerC17

Inimary T. Toby Mikhail K. Levin Edward Salinas Scott Christley Sanchita Bhattacharya Felix Breden Adam Buntzman Brian Corrie John M. Fonner Namita T. Gupta Uri Hershberg Nishanth Marthandan Aaron M. Rosenfeld William Rounds Florian Rubelt Walter Scarborough Jamie K. Scott Mohamed Uduman Jason A. Vander Heiden Richard H. Scheuermann Nancy Monson Steven H. Kleinstein Lindsay G. Cowell VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. 333 2016 17 BMC Bioinform. S-13 https://doi.org/10.1186/s12859-016-1214-3 https://www.wikidata.org/entity/Q28843105 db/journals/bmcbi/bmcbi17S.html#TobyLSCBBBCFGHM16

Mikhail K. Levin Lindsay G. Cowell owlcpp: a C++ library for working with OWL ontologies. 35 2015 6 J. Biomed. Semant. https://doi.org/10.1186/s13326-015-0035-z https://www.wikidata.org/entity/Q35781707 db/journals/biomedsem/biomedsem6.html#LevinC15

Albert Goldfain Barry Smith 0001 Lindsay G. Cowell Ontological Representation of CDC Active Bacterial Core Surveillance Case Reports. 74-77 2014 ICBO https://ceur-ws.org/Vol-1327/icbo2014_paper_51.pdf conf/icbo/2014 db/conf/icbo/icbo2014.html#GoldfainSC14 Claire L. Gordon Stephanie Pouch Lindsay G. Cowell Mary Regina Boland Heather L. Platt Albert Goldfain Chunhua Weng Design and Evaluation of a Bacterial Clinical Infectious Diseases Ontology. 2013 AMIA https://knowledge.amia.org/amia-55142-a2013e-1.580047/t-09-1.582024/f-009-1.582025/a-133-1.582125/a-182-1.582120 conf/amia/2013 db/conf/amia/amia2013.html#GordonPCBPGW13 Albert Goldfain Lindsay G. Cowell Barry Smith 0001 Constructing a Lattice of Infectious Disease Ontologies from a Staphylococcus aureus Isolate Repository. 2012 ICBO https://ceur-ws.org/Vol-897/session1-paper03.pdf conf/icbo/2012 db/conf/icbo/icbo2012.html#GoldfainCS12

Terrence F. Meehan Anna Maria Masci Amina Abdulla Lindsay G. Cowell Judith A. Blake Christopher J. Mungall Alexander D. Diehl Logical Development of the Cell Ontology. 6 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-6 https://www.wikidata.org/entity/Q33786317 db/journals/bmcbi/bmcbi12.html#MeehanMACBMD11

Albert Goldfain Barry Smith 0001 Lindsay G. Cowell Towards an ontological representation of resistance: The case of MRSA. 35-41 2011 44 J. Biomed. Informatics 1 https://doi.org/10.1016/j.jbi.2010.02.008 https://www.wikidata.org/entity/Q34092218 db/journals/jbi/jbi44.html#GoldfainSC11

Alexander D. Diehl Alison Deckhut Augustine Judith A. Blake Lindsay G. Cowell Elizabeth S. Gold Timothy A. Gondré-Lewis Anna Maria Masci Terrence F. Meehan Penelope A. Morel Anastasia Nijnik Bjoern Peters Bali Pulendran Richard H. Scheuermann Q. Alison Yao Martin S. Zand Christopher J. Mungall Hematopoietic cell types: Prototype for a revised cell ontology. 75-79 2011 44 J. Biomed. Informatics 1 https://doi.org/10.1016/j.jbi.2010.01.006 https://www.wikidata.org/entity/Q33940690 db/journals/jbi/jbi44.html#DiehlABCGGMMMNPPSYZM11

Mikhail K. Levin Alan Ruttenberg Anna Maria Masci Lindsay G. Cowell <i>owl_cpp</i>, a C++ Library for Working with OWL Ontologies. 2011 ICBO https://ceur-ws.org/Vol-833/paper40.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#LevinRMC11 Anna Maria Masci Mikhail K. Levin Alan Ruttenberg Lindsay G. Cowell Connecting Ontologies for the Representation of Biological Pathways. 2011 ICBO https://ceur-ws.org/Vol-833/paper74.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#MasciLRC11 Anna Maria Masci Jeffrey Roach Bernard de Bono Pierre Grenon Lindsay G. Cowell Bridging Multiple Ontologies: Representation of the Liver Immune Response. 2011 ICBO https://ceur-ws.org/Vol-833/paper75.pdf conf/icbo/2011 db/conf/icbo/icbo2011.html#MasciRBGC11 Albert Goldfain Barry Smith 0001 Lindsay G. Cowell Dispositions and the Infectious Disease Ontology. 400-413 2010 FOIS https://doi.org/10.3233/978-1-60750-535-8-400 conf/fois/2010 db/conf/fois/fois2010.html#GoldfainSC10

Anna Maria Masci Cecilia N. Arighi Alexander D. Diehl Anne E. Lieberman Chris Mungall Richard H. Scheuermann Barry Smith 0001 Lindsay G. Cowell An improved ontological representation of dendritic cells as a paradigm for all cell types. 2009 10 BMC Bioinform. https://doi.org/10.1186/1471-2105-10-70 https://www.wikidata.org/entity/Q21284365 db/journals/bmcbi/bmcbi10.html#MasciADLMSSC09

Joseph M. Volpe Lindsay G. Cowell Thomas B. Kepler SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. 438-444 2006 22 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btk004 https://www.wikidata.org/entity/Q33229588 db/journals/bioinformatics/bioinformatics22.html#VolpeCK06

Amina Abdulla Brian D. Aevermann Ademar Aguiar Rahmad Akbar Cecilia N. Arighi Alison Deckhut Augustine Shane Babcock Trygve E. Bakken Gabriel Balaban Fabian L. M. Bernal John Beverley Sanchita Bhattacharya Judith A. Blake George Blanck Mary Regina Boland Bernard de Bono Felix Breden James Brugarolas Todd M. Brusko Syed Ahmad Chan Bukhari Adam Buntzman Christian E. Busse Ivan Chang Maria Chernigovskaya Alana Christie Scott Christley Brian Corrie Alexandre Almeida Costa Sebastian Deusing Alexander D. Diehl John M. Fonner Robert Frank 0006 Elizabeth S. Gold Albert Goldfain Timothy A. Gondré-Lewis Claire L. Gordon Benjamin M. Greenberg Victor Greiff Pierre Grenon Ivar Grytten Sveinung Gundersen Namita T. Gupta Ingrid Hobæk Haff Ghadi S. Al Hajj Srilakshmy L. Harikrishnan Yongqun He Jason A. Vander Heiden David Hein Uri Hershberg Rebecca D. Hodge Michael J. Holcomb Eivind Hovig Ping-Han Hsieh Regina Hurley Jerome Jaglale Aj Jain Andrew R. Jamieson Chakravarthi Kanduri Payal Kapur Thomas B. Kepler Günter Klambauer Steven H. Kleinstein Radmila Kompova Marieke L. Kuijjer Uri Laserson Roger S. Lasken Alexandra Lee Ed S. Lein Mikhail K. Levin Anne E. Lieberman Christin Lund-Andersen Nishanth Marthandan Antonio Martini 0001 Anna Maria Masci Jamison M. McCorrison Terrence F. Meehan Eric Merrell Jeremy A. Miller Thomas Minotto Nancy Monson Penelope A. Morel Keshav Motwani Chris MungallChristopher J. Mungall Anastasia Nijnik Mark Novotny Jared Ostmeyer Milena Pavlovic Johan Pensar Björn PetersBjoern Peters Heather L. Platt Stephanie Pouch Bali Pulendran Yu Qian Dinesh Rakheja Knut D. Rand Enrico Riccardi Jeffrey Roach Philippe A. Robert Artur Rocha Aaron M. Rosenfeld William Rounds Florian Rubelt Alan Ruttenberg Edward Salinas Geir Kjetil Sandve Walter Scarborough Lonneke Scheffer Richard H. Scheuermann Nicholas J. Schork Chaim A. Schramm Jamie K. Scott Ameer Hamza Shakur Andrei Slabodkin Barry Smith 0001 Igor Snapkov Ludvig Magne Sollid Sarah Taylor Dmytro Titov Inimary T. Toby Mohamed Uduman Nikolay Vazov Joseph Vento Joseph M. Volpe Knut Waagan Corey T. Watson Cédric R. Weber Chunhua Weng Michael Widrich Bingqing Xie Gur Yaari Q. Alison Yao Martin S. Zand Bojan Zimonja