IP Library Granted Patent US 12,462,911
Granted Patent B2
US 12,462,911 · App. 17/207,582 · Granted Nov 4, 2025

Clinical concept identification, extraction, and prediction system and related methods

Inventors: Michael Lucas (Chicago, IL); Jonathan Ozeran (Chicago, IL); Jason Taylor (Chicago, IL); Louis Fernandes (Chicago, IL)
Assignee: TEMPUS AI, INC.
G16H15/00G06F40/295G06F40/30G16H10/20G16H10/60G16H70/00
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,462,911
App. No.
17/207,582
Granted
Nov 4, 2025
Kind
B2
Abstract

A method for determining whether a patient may be enrolled into a clinical trial includes the steps of examining the patient's medical record from an electronic health record system, deriving a plurality of first concepts from the medical record, normalizing each concept in the plurality of first concepts to produce, for each normalization, a normalized concept, comparing each normalized concept to a list of study criteria, to indicate if the normalized concept meets the criteria, and if each criteria is met, indicating that the patient is not ineligible for enrollment in the clinical trial

Claims (56)

1 . A computer-implemented method for determining whether a subject may be enrolled into a clinical trial, the computer-implemented method comprising:

storing, via one or more processors, a plurality of abstraction categories in a database wherein each abstraction category includes a plurality of fields and each field corresponds to a concept type;

accessing, via one or more processors, a medical record of a subject from an electronic health record system wherein the medical record includes a plurality of text words;

deriving, via one or more processors, a plurality of first concepts from the medical record by:

(i) identifying, via one or more processors, a match to a first concept in the plurality of first concepts, the plurality of first concepts not designated as a predetermined authority and including two or more tiers of concepts;

(ii) referencing, via one or more processors, the first concept with an entity in a database of related concepts;

(iii) identifying, via one or more processors, a match from the entity to a second concept in a second list of concepts designated in the predetermined authority, wherein the second concept is included in one of the two or more tiers of concepts, and wherein the predetermined authority is not directly linked to the plurality of first concepts except by a relationship to the entity;

(iv) retrieving, via one or more processors, a degree of specificity comprising selection criteria identifying one or more tiers of the two or more tiers of concepts, other than the one tier including the second concept; and

(v) normalizing, via one or more processors, the second concept to a third concept, of a plurality of third concepts, included in the one or more tiers of the two or more tiers of concepts, based at least in part on the second concept not satisfying the selection criteria;

comparing, via one or more processors, a list of study criteria associated with the clinical trial to the plurality of third concepts, to indicate if the subject meets the list of study criteria; and

generating, via one or more processors, an indication of eligibility of the subject for enrollment in the clinical trial based on the comparing.

2 . The computer-implemented method of claim 1 , wherein deriving the plurality of first concepts from the medical record comprises using a constituency tree.

3 . The computer-implemented method of claim 1 , wherein deriving the plurality of first concepts from the medical record comprises using a name entity recognition model.

4 . The computer-implemented method of claim 3 , wherein the name entity recognition model comprises a conditional random field.

5 . The computer-implemented method of claim 3 , wherein the name entity recognition model comprises a convolutional neural network.

6 . A computer-implemented method for determining whether a subject may be enrolled into a clinical trial, comprising:

examining, via one or more processors, a medical record of the subject from an electronic health record system;

deriving, via one or more processors, a plurality of first concepts from the medical record by:

(i) identifying, via one or more processors, a match to a first concept in the plurality of first concepts, the plurality of first concepts not designated as a predetermined authority and including two or more tiers of concepts;

(ii) referencing, via one or more processors, the first concept with an entity in a database of related concepts;

(iii) identifying, via one or more processors, a match from the entity to a second concept in a second list of concepts designated in the predetermined authority, wherein the second concept is included in one of the two or more tiers of concepts, and wherein the predetermined authority is not directly linked to the plurality of first concepts except by a relationship to the entity;

(iv) retrieving, via one or more processors, a degree of specificity comprising selection criteria identifying one or more tiers of the two or more tiers of concepts, other than the one tier including the second concept; and

(v) normalizing, via one or more processors, the second concept to a third concept, of a plurality of third concepts, included in the one or more tiers of the two or more tiers of concepts, based at least in part on the second concept not satisfying the selection criteria;

comparing, via one or more processors, a list of study criteria associated with the clinical trial to the plurality of third concepts, to indicate if the subject meets the list of study criteria; and

generating, via one or more processors, an indication of eligibility of the subject for enrollment in the clinical trial based on the comparing.

7 . The computer-implemented method of claim 6 , wherein deriving the plurality of first concepts from the medical record comprises using a constituency tree.

8 . The computer-implemented method of claim 6 , wherein deriving the plurality of first concepts from the medical record comprises using a name entity recognition model.

9 . The computer-implemented method of claim 8 , wherein the name entity recognition model comprises a conditional random field.

10 . The computer-implemented method of claim 8 , wherein the name entity recognition model comprises a convolutional neural network.

11 . A computing system for determining whether a subject may be enrolled into a clinical trial, the computing system comprising:

a computer including a processing device, the processing device configured to:

examine a medical record of the subject from an electronic health record system;

derive a plurality of first concepts from the medical record by:

(i) identifying a match to a first concept in the plurality of first concepts, the plurality of first concepts not designated as a predetermined authority and including two or more tiers of concepts;

(ii) referencing the first concept with an entity in a database of related concepts;

(iii) identifying a match from the entity to a second concept in a second list of concepts designated in the predetermined authority, wherein the second concept is included in one of the two or more tiers of concepts, and wherein the predetermined authority is not directly linked to the plurality of first concepts except by a relationship to the entity;

(iv) retrieving a degree of specificity comprising selection criteria identifying one or more tiers of the two or more tiers of concepts, other than the one tier including the second concept; and

v) normalizing the second concept to a third concept, of a plurality of third concepts, included in the one or more tiers of the two or more tiers of concepts, based at least in part on the second concept not satisfying the selection criteria;

compare a list of study criteria associated with the clinical trial to the plurality of third concepts, to indicate if the subject meets the list of study criteria; and

generate an indication of eligibility of the subject for enrollment in the clinical trial based on the comparing.

12 . The computing system of claim 11 , wherein the processing device is further configured to:

use a constituency tree.

13 . The computing system of claim 11 , wherein the processing device is further configured to:

use a name entity recognition model.

14 . The computing system of claim 13 , wherein the name entity recognition model comprises a conditional random field.

15 . The computing system of claim 13 , wherein the name entity recognition model comprises a convolutional neural network.

16 . A non-transitory computer-readable storage medium having stored thereon program code instructions that, when executed by a processor, cause the processor to:

examine a medical record of a subject from an electronic health record system;

derive a plurality of first concepts from the medical record by:

(i) identifying a match to a first concept in a plurality of first concepts, the plurality of first concepts not designated as a predetermined authority and including two or more tiers of concepts;

(ii) referencing the first concept with an entity in a database of related concepts;

(iii) identifying a match from the entity to a second concept in a second list of concepts designated in the predetermined authority, wherein the second concept is included in one of the two or more tiers of concepts, and wherein the predetermined authority is not directly linked to the plurality of first concepts except by a relationship to the entity;

(iv) retrieving, via one or more processors, a degree of specificity comprising selection criteria identifying one or more tiers of the two or more tiers of concepts, other than the one tier including the second concept; and

(v) normalizing the second concept to a third concept, of a plurality of third concepts, included in the one or more tiers of the two or more tiers of concepts, based at least in part on the second concept not satisfying the selection criteria; and

compare a list of study criteria associated with a clinical trial to the plurality of third concepts, to indicate if the subject meets the list of study criteria; and

generate an indication of eligibility of the subject for enrollment in the clinical trial based on the comparing.

Assignments (4)
RELEASE OF SECURITY INTEREST Recorded May 13, 2026
From: ARES CAPITAL CORPORATION, AS COLLATERAL AGENT
To: TEMPUS AI, INC. (F/K/A TEMPUS LABS, INC.)
Reel/Frame 075608/0784 →
CHANGE OF NAME Recorded Feb 9, 2024
From: TEMPUS LABS, INC.
To: TEMPUS AI, INC.
Reel/Frame 066544/0110 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Oct 27, 2022
From: LUCAS, MICHAEL; TAYLOR, JASON; OZERAN, JONATHAN; FERNANDES, LOUIS
To: TEMPUS LABS, INC.
Reel/Frame 061557/0437 →
SECURITY INTEREST Recorded Sep 22, 2022
From: TEMPUS LABS, INC.
To: ARES CAPITAL CORPORATION, AS COLLATERAL AGENT
Reel/Frame 061506/0316 →
Continuity (3)
Continuation 16702510 · Dec 3, 2019
Provisional Application 62774854 · Dec 3, 2018
Related Publication 20210210184A1 · Jul 8, 2021
References Cited (258)
US 5804656A · Eichenauer et al. · 1998 [cited by applicant]
US 6804656B1 · Rosenfeld · 2004 [cited by applicant]
US 9031926B2 · Milward · 2015 [cited by applicant]
US 9208217B2 · Milward · 2015 [cited by applicant]
US 9424532B1 · Abedini · 2016 [cited by applicant]
US 10553308B2 · Baldwin · 2020 [cited by applicant]
US 11145390B2 · Will et al. · 2021 [cited by applicant]
US 11257571B2 · Will et al. · 2022 [cited by applicant]
US 11742064B2 · Ozeran et al. · 2023 [cited by applicant]
US 20010051353A1 · Kornblith · 2001 [cited by applicant]
US 20020173702A1 · Lebel · 2002 [cited by applicant]
US 20030143572A1 · Lu et al. · 2003 [cited by applicant]
US 20030144886A1 · Taira · 2003 [cited by applicant]
US 20040122790A1 · Walker · 2004 [cited by applicant]
US 20040220895A1 · Carus · 2004 [cited by examiner]
US 20050125256A1 · Schoenberg et al. · 2005 [cited by applicant]
US 20070005621A1 · Lesh · 2007 [cited by applicant]
US 20070294111A1 · Settimi · 2007 [cited by examiner]
US 20080162393A1 · Iliff · 2008 [cited by applicant]
US 20080195600A1 · Deakter · 2008 [cited by applicant]
US 20090319244A1 · West · 2009 [cited by applicant]
US 20100029498A1 · Gnirke · 2010 [cited by applicant]
US 20100076780A1 · Mahesh et al. · 2010 [cited by applicant]
US 20110117545A1 · Stacey et al. · 2011 [cited by applicant]
US 20110255790A1 · Duggan · 2011 [cited by applicant]
US 20110288877A1 · Ofek · 2011 [cited by applicant]
US 20120110016A1 · Phillips · 2012 [cited by applicant]
US 20120123184A1 · Otto · 2012 [cited by applicant]
US 20120173585A1 · Pan · 2012 [cited by examiner]
US 20120179696A1 · Charlot · 2012 [cited by examiner]
US 20120231959A1 · Elton et al. · 2012 [cited by applicant]
US 20120265544A1 · Hwang · 2012 [cited by applicant]
US 20120310899A1 · Wasserman et al. · 2012 [cited by applicant]
US 20130024382A1 · Dala et al. · 2013 [cited by applicant]
US 20130060793A1 · Bandyopadhyay · 2013 [cited by examiner]
US 20130073214A1 · Hyland et al. · 2013 [cited by applicant]
US 20130096947A1 · Shah · 2013 [cited by applicant]
US 20130185089A1 · Michelson et al. · 2013 [cited by applicant]
US 20130246049A1 · Mirhaji · 2013 [cited by applicant]
US 20130268474A1 · Nizzari et al. · 2013 [cited by applicant]
US 20130332191A1 · Hoffman et al. · 2013 [cited by applicant]
US 20140046926A1 · Walton · 2014 [cited by applicant]
US 20140122117A1 · Masarie · 2014 [cited by applicant]
US 20140244625A1 · Seghezzi · 2014 [cited by applicant]
US 20140249761A1 · Carroll · 2014 [cited by applicant]
US 20140278461A1 · Artz · 2014 [cited by applicant]
US 20140280353A1 · Delany · 2014 [cited by applicant]
US 20140330583A1 · Madhavan et al. · 2014 [cited by applicant]
US 20140364481A1 · Elenitoba-Johnson et al. · 2014 [cited by applicant]
US 20140365242A1 · Neff · 2014 [cited by applicant]
US 20150006558A1 · Leighton · 2015 [cited by applicant]
US 20150106125A1 · Farooq · 2015 [cited by applicant]
US 20150178386A1 · Oberkampf · 2015 [cited by applicant]
US 20150213194A1 · Wolf · 2015 [cited by applicant]
US 20150324527A1 · Siegel · 2015 [cited by applicant]
US 20150331909A1 · Sundquist · 2015 [cited by applicant]
US 20160019351A1 · Ober, Jr. · 2016 [cited by examiner]
US 20160019365A1 · Ober, Jr. · 2016 [cited by examiner]
US 20160019666A1 · Amarasingham · 2016 [cited by applicant]
US 20160210427A1 · Mynhier et al. · 2016 [cited by applicant]
US 20160224893A1 · Parker, Jr · 2016 [cited by examiner]
US 20170046425A1 · Tonkin · 2017 [cited by applicant]
US 20170076046A1 · Barnes et al. · 2017 [cited by applicant]
US 20170103163A1 · Emanuel · 2017 [cited by examiner]
US 20170109502A1 · Labkoff · 2017 [cited by applicant]
US 20170177597A1 · Asimenos · 2017 [cited by applicant]
US 20170177822A1 · Fogel · 2017 [cited by applicant]
US 20170193175A1 · Madabhushi et al. · 2017 [cited by applicant]
US 20170193197A1 · Randhawa · 2017 [cited by examiner]
US 20170199965A1 · Dekel · 2017 [cited by applicant]
US 20170237805A1 · Worley · 2017 [cited by applicant]
US 20170351816A1 · Fink · 2017 [cited by examiner]
US 20180045727A1 · Spetzler et al. · 2018 [cited by applicant]
US 20180046753A1 · Shelton · 2018 [cited by applicant]
US 20180046764A1 · Katwala · 2018 [cited by applicant]
US 20180046780A1 · Graiver et al. · 2018 [cited by applicant]
US 20180060482A1 · Nadauld et al. · 2018 [cited by applicant]
US 20180060523A1 · Farh · 2018 [cited by applicant]
US 20180068083A1 · Cohen · 2018 [cited by applicant]
US 20180085015A1 · Crowder · 2018 [cited by applicant]
US 20180089373A1 · Matsuguchi et al. · 2018 [cited by applicant]
US 20180101584A1 · Pattnaik et al. · 2018 [cited by applicant]
US 20180121618A1 · Smith · 2018 [cited by applicant]
US 20180144003A1 · Formoso · 2018 [cited by applicant]
US 20180211725A1 · Purdie et al. · 2018 [cited by applicant]
US 20180301205A1 · Mao · 2018 [cited by applicant]
US 20180311224A1 · Hedley · 2018 [cited by applicant]
US 20180373844A1 · Ferrandez-Escamez · 2018 [cited by applicant]
US 20190006024A1 · Kapoor · 2019 [cited by examiner]
US 20190006048A1 · Gupta et al. · 2019 [cited by applicant]
US 20190050530A1 · De La Vega · 2019 [cited by applicant]
US 20190057774A1 · Velez · 2019 [cited by applicant]
US 20190108898A1 · Gulati · 2019 [cited by applicant]
US 20190108912A1 · Spurlock, III · 2019 [cited by applicant]
US 20190206524A1 · Baldwin · 2019 [cited by applicant]
US 20190214145A1 · Kurek et al. · 2019 [cited by applicant]
US 20190304574A1 · Weinstock et al. · 2019 [cited by applicant]
US 20190311787A1 · Graiver et al. · 2019 [cited by applicant]
US 20200005461A1 · Yip · 2020 [cited by applicant]
US 20200005906A1 · Wang · 2020 [cited by examiner]
US 20200065374A1 · Gao · 2020 [cited by examiner]
US 20200075139A1 · Master · 2020 [cited by examiner]
US 20200118644A1 · Khan · 2020 [cited by applicant]
US 20200126642A1 · Kenna · 2020 [cited by examiner]
US 20200176098A1 · Lucas · 2020 [cited by applicant]
US 20200219619A1 · Feczko · 2020 [cited by applicant]
US 20200234801A1 · Mao · 2020 [cited by examiner]
US 20210043275A1 · Landau et al. · 2021 [cited by applicant]
US 20210115519A1 · Pitroda et al. · 2021 [cited by applicant]
US 20210174025A1 · Hu · 2021 [cited by examiner]
US 20210208131A1 · Kretzschmar et al. · 2021 [cited by applicant]
US 20230267553A1 · Colley et al. · 2023 [cited by applicant]
AU 2012225666A1 · 2013 [cited by applicant]
AU 2015213399A1 · 2016 [cited by applicant]
WO 2004027706A1 · 2004 [cited by applicant]
WO 2019132685A1 · 2019 [cited by applicant]
WO 2020023420 · 2020 [cited by applicant]
Gkotsis et al., Don't Let Notes Be Misunderstood: A Negation Detection Method for Assessing Risk of Suicide in Mental Health Records, 2016, Proceedings of the 3rd Workshop on Computational Linguistics and Clinical Psych… [cited by examiner]
Damen et al., Pastel: A Semantic Platform for Assisted Clinical Trial Patient Recruitment, 2013, IEEE International Conference on Healthcare Informatics (Year: 2013). [cited by examiner]
Lee et al., A Semantic Framework for Intelligent Matchmaking for Clinical Trial Eligibility Critiera, Sep. 2013, ACM Transactions on Intelligent Systems and Technology, vol. 4, No. 4, Article 71 (Year: 2013). [cited by examiner]
Kopcke, Employing Computers for the Recruitment into Clinical Trials: A Comprehensive Systematic Review, Jul. 2014, J Med Internet Res 16(7) (Year: 2014). [cited by examiner]
Ni et al., Increasing the efficiency of trail-patient matching: automated clinical trial eligibility Pre-screening for pediatric oncology patients, 2015, BMC Medical Informatics and Decision Making (Year: 2015). [cited by examiner]
“Algorithm Implementation/Strings/Levenshtein distance,” Wikibooks, last edited on Jan. 5, 2019, 39 pages. Retrieved from Internet. URL: https://en.wikibooks.org/wiki/Algorithm_Implementation/Strings/Levenshtein_distanc… [cited by applicant]
“Amazon Textract—Easily extract text and data from virtually any document,” Amazon, Nov. 28, 2018, 6 pages. Retrieved from Internet. URL: https://aws.amazon.com/textract/. [cited by applicant]
“CliNER,” Text Machine Lab 2014, Nov. 10, 2017, 2 pages. Retrieved from Internet. URL: http://text-machine.cs.uml.edu/cliner/. [cited by applicant]
“Clinithink Clix CNLP (Harness unstructured data to drive value across the healthcare continuum),” Clinithink Limited, 2015, 1 page. Retrieved from Internet. URL: http://clinithink.com/wp-content/uploads//2015/01/Clinit… [cited by applicant]
“Evernote Scannable on the App Store,” Jun. 18, 2018, 3 pages. Retrieved from Internet. URL: https://itunes.apple.com/us/app/evernote-scannable/id883338188?mt=8. [cited by applicant]
“12E: The world's leading Text Mining platform,” 2019 Linguamatics, Aug. 14, 2018, 5 pages. Retrieved from Internet. URL: https://www.linguamatics.com/products-services/about-i2e. [cited by applicant]
“PHP: levenshtein—Manual,” latest comment dated in 2014, 32 pages. Retrieved from Internet. URL: http://www.php.net/levenshtein. [cited by applicant]
“Talk:Algorithm Implementation/Strings/Levenshtein distance,” Wikibooks, last edited on Nov. 2, 2016, 2 pages. Retrieved from Internet. URL: https://en.wikibooks.org/wiki/Talk:Algorithm_Implementation/Strings/Levenshtei… [cited by applicant]
“Why cTAKES? See the animation below for a sampling of cTAKES capabilities,” The Apache Software Foundation, Apr. 25, 2017, 1 page. Retrieved from Internet. URL: http://ctakes.apache.org/whycTAKES.html. [cited by applicant]
AACR Project Genie Consortium. AACR Project Genie: Powering Precision Medicine through an International Consortium. Cancer Discov. 7, 818-831 (2017). [cited by applicant]
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013). [cited by applicant]
Allen, J. et al. Barriers to Patient Enrollment in Therapeutic Clinical Trials for Cancer: A Landscape Report. (2018). [cited by applicant]
Aronson, Alan “MetaMap—A Tool For Recognizing UMLS Concepts in Text,” Jan. 11, 2019, 2 pages. Retrieved from Internet. URL: https://metamap.nlm.nih.gov/. [cited by applicant]
Ayers, M. et al. IFN-?-related mRNA profile predicts clinical response to PD-1 blockade. J. Clin. Invest. 127, 2930-2940 (2017). [cited by applicant]
Balatero, David (dbalatero/levenshtein-ffi) “Fast string edit distance computation, using the Damerau-Levenshtein algorithm,” GitHub, Inc., latest comment dated on Aug. 10, 2014, 2 pages. Retrieved from Internet. URL: h… [cited by applicant]
Beaubier, N. et al. Clinical Validation of the Tempus xT Next-Generation Sequencing Targeted Oncology Assay. Oncotarget 10, 2384-2396 (2019). [cited by applicant]
Bertsimas, D., et al. “Personalized diabetes management using electronic medical records.” Diabetes care 40.2 (2017): 210-217. [cited by applicant]
Caris Life Sciences. Code: Comprehensive Oncology Data Explorer. Slideshow May 2017. Accessed on Dec. 16, 2020 at https://www.karmanos.org/Uploads/Public/Documents/Karmanos/CODE%20slides_5.2017.pptx%20. [cited by applicant]
Chae, Y. K. et al. Association of tumor mutational burden with DNA repair mutations and response to anti-PD-1/PD-L1 therapy in non-small cell lung cancer. Clin. Lung Cancer (2018). doi: 10.1016/J.CLLC.2018.09.008. [cited by applicant]
Chatterjee, P. et al. The TMPRSS2-ERG Gene Fusion Blocks XRCC4-Mediated Nonhomologous End-Joining Repair and Radiosensitizes Prostate Cancer Cells to PARP Inhibition. Mol. Cancer Ther. 14, 1896-1906 (2015). [cited by applicant]
Chen, Huizhong et al. “Robust Text Detection in Natural Images With Edge-Enhanced Maximally Stable Extremal Regions,” 2011 18th IEEE International Conference on Image Processing, Sep. 11-14, 2011, 4 pages. [cited by applicant]
Choi, Edward et al. “Coarse-to-Fine Question Answering for Long Documents,” Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, Vancouver, Canada, Jul. 30-Aug. 4, 2017, pp. 209-220. [cited by applicant]
Choi, Edward et al. “Doctor AI: Predicting Clinical Events via Recurrent Neural Networks,” Proceedings of Machine Learning for Healthcare 2016, JMLR W&C Track vol. 56, 2016, pp. 1-18. [cited by applicant]
Collobert, Ronan et al. “Natural Language Processing (Almost) from Scratch,” Journal of Machine Learning Research 12, (2011) pp. 2493-2537. [cited by applicant]
Conneau, Alexis et al. “Very Deep Convolutional Networks for Text Classification,” arXiv:1606.01781 [cs.CL], Jan. 27, 2017, 10 pages. [cited by applicant]
Conway, J. R., et al. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938-2940 (2017). [cited by applicant]
Coutinho, A. D., et al. “Real-world treatment patterns and outcomes of patients with small cell lung cancer progressing after 2 lines of therapy.” Lung Cancer 127 (2019): 53-58. [cited by applicant]
Cristescu, R. et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science 362, eaar3593 (2018). [cited by applicant]
Darvin, P., et al. Immune checkpoint inhibitors: recent progress and potential biomarkers. Exp. Mol. Med. 50, 165 (2018). [cited by applicant]
Das, Rajarshi et al. “Chains of Reasoning over Entities, Relations, and Text using Recurrent Neural Networks,” Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics:… [cited by applicant]
De Bruijn, Berry et al. “Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010,” 18 J. Am. Med. Inform. Assoc. 2011, May 12, 2011, pp. 557-562. [cited by applicant]
Dempster, A.P. et al. (1977). “Maximum Likelihood from Incomplete Data via the EM Algorithm”. Journal of the Royal Statistical Society, Series B. 39 (1): 1-38. [cited by applicant]
Desrichard, A., et al. Cancer Neoantigens and Applications for Immunotherapy. (2016). doi:10.1158/1078-0432. CCR-14-3175. [cited by applicant]
Dhir, M. et al. Impact of genomic profiling on the treatment and outcomes of patients with advanced gastrointestinal malignancies. Cancer Med. 6, 195-206 (2017). [cited by applicant]
Dienstmann, R. et al. Standardized decision support in next generation sequencing reports of somatic cancer variants. Mol. Oncol. 8, 859-873 (2014). [cited by applicant]
Dienstmann, R., et al. “Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors.” Cancer discovery 5.2 (2015): 118-123. [cited by applicant]
Dnanexus. Working with UK Biobank: A Research Guide. Accessed online on Dec. 31, 2020. Available at https://web.archive.org/save/https://dna-nexus-prod-s3-assets-51tcpaqcp0pd.s3.amazonaws.com/images/files/DNAnexus_White… [cited by applicant]
Dobin, A. et al. Star: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013). [cited by applicant]
Dozat, Timothy et al. “Deep Biaffine Attention for Neural Dependency Parsing,” Published as a conference paper at ICLR 2017, arXiv:1611.01734 [cs.CL], Mar. 10, 2017, pp. 1-8. [cited by applicant]
Faust, G. G. et al. Samblaster: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503-2505 (2014). [cited by applicant]
Fernandes, G. et al. Next-generation Sequencing-based genomic profiling: Fostering innovation in cancer care? Clinics 72, 588-594 (2017). [cited by applicant]
Finan, C. et al. The druggable genome and support for target identification and validation in drug development. Sci. Transl. Med. 9, eaag1166 (2017). [cited by applicant]
Flaig, T. W., et al. “Treatment evolution for metastatic castration-resistant prostate cancer with recent introduction of novel agents: retrospective analysis of real-world data.” Cancer Medicine 5.2 (2016): 182. [cited by applicant]
Forbes, S. A et al. Cosmic: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777-D783 (2017). [cited by applicant]
Gangul, R. Line of Therapy Analytics: A key to commercial drug success. Feb. 15, 2017. Available online https://www.saama.com/blog/line-therapy-analytics-key-commercial-drug-success/. [cited by applicant]
Genthial, Guillaum “Sequence Tagging with Tensorflow (bi-LSTM + CRF with character embeddings for NER and POS),” Guillaume Genthial blog, Apr. 5, 2017, 23 pages. [cited by applicant]
Goldman, M. et al. The UCSC Xena platform for public and private cancer genomics data visualization and interpretation. bioRxiv 326470 (2019). doi:10.1101/326470. [cited by applicant]
Gong, J. et al. Value-based genomics. Oncotarget 9, 15792-15815 (2018). [cited by applicant]
Goodman, A. M. et al. Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers. Mol. Cancer Ther. 16, 2598-2608 (2017). [cited by applicant]
Griffith, M. et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat. Genet. 49, 170-174 (2017). [cited by applicant]
Rokach L., Maimon O., Decision Trees, 2005, Data Mining and Knowledge Discovery Handbook, pp. 165-192 (Year: 2005). [cited by applicant]
Robinson, D. R. et al. Integrative clinical genomics of metastatic cancer. Nature 548, 297-303 (2017). [cited by applicant]
Rooney, M. S. et al. Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity. Cell 160, 48-61 (2015). [cited by applicant]
Rosenthal, R., et al. deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 17, (2016). [cited by applicant]
Roufas, C. et al. The Expression and Prognostic Impact of Immune Cytolytic Activity-Related Markers in Human Malignancies: A Comprehensive Meta-analysis. Front. Oncol. 8, 27 (2018). [cited by applicant]
Sager, Naomi et al. “Natural Language Processing and the Representation of Clinical Data,” Journal of the American Medical Informatics Association, vol. 1, No. 2, Mar./Apr. 1994, pp. 142-160. [cited by applicant]
Sambyal, Nitigya et al. “Automatic Text Extraction and Character Segmentation Using Maximally Stable Extremal Regions,” arXiv:1608.03374 [cs.CV], Aug. 11, 2016, 6 pages. [cited by applicant]
Savova, et al., “Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications”, J Am Med Inform Assoc 2010;17: 507-513., retrieved from the internet at: https… [cited by applicant]
Sheng, Q. et al. An Activated ErbB3/NRG1 Autocrine Loop Supports In Vivo Proliferation in Ovarian Cancer Cells. Cancer Cell 17, 298-310 (2010). [cited by applicant]
Solomon, B., et al. ALK Gene Rearrangements: A New Therapeutic Target in a Molecularly Defined Subset of Non-small Cell Lung Cancer. J. Thorac. Oncol. 4, 1450-1454 (2009). [cited by applicant]
Szolek, A. et al. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 30, 3310-3316 (2014). [cited by applicant]
Teer, J. K. et al. Evaluating somatic tumor mutation detection without matched normal samples. Hum. Genomics 11, 22 (2017). [cited by applicant]
The ASCO Post. 2018 ASCO: IMPACT Trial Matches Treatment to Genetic Changes in the Tumor to Improve Survival Across Multiple Cancer Types—The ASCO Post. Jun. 6, 2018 (2018). Available at: http://www.ascopost.com/News/58… [cited by applicant]
Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644-648 (2005). [cited by applicant]
Tsang, J-P. Deploying Machine Learning for Commercial Analytics. PMSA.net. Version accessed Dec. 15, 2018. Available online at https://web.archive.org/web/20181215152550/http://www.pmsa.net/jpmsa-vol06-article09. [cited by applicant]
Tsou, Ching-Huei et al. “Watson for Patient Record Analytics (aka Watson Emra),” IBM Research, Aug. 2017, 5 pages. Retrieved from Internet. URL: https://researcher.watson.ibm.com/researcher/view_group.php?id=7664. [cited by applicant]
Unger, J. M., et al. Systematic Review and Meta-Analysis of the Magnitude of Structural, Clinical, and Physician and Patient Barriers to Cancer Clinical Trial Participation. J. Natl. Inst. 111, 245-255 (2019). [cited by applicant]
Wang, Z. et al. Significance of the TMPRSS2:ERG gene fusion in prostate cancer. Mol. Med. Rep. 16, 5450-5458 (2017). [cited by applicant]
Wheler, J. J. et al. Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study. Cancer Res. 76, 3690-3701 (2016). [cited by applicant]
Wilson, T. R., et al. Neuregulin-1-Mediated Autocrine Signaling Underlies Sensitivity to HER2 Kinase Inhibitors in a Subset of Human Cancers. Cancer Cell 20, 158-172 (2011). [cited by applicant]
Wu, Yonghui et al. “A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text,” AMIA Annual Symp. Proc. 2015; Published online Nov. 5, 2015, pp. 1326-1333. [cited by applicant]
Yan, M. et al. HER2 expression status in diverse cancers: review of results from 37,992 patients. Cancer Metastasis Rev. 34, 157-64 (2015). [cited by applicant]
Yang, L. et al. NRG1-dependent activation of HER3 induces primary resistance to trastuzumab in HER2-overexpressing breast cancer cells. Int. J. Oncol. 51, 1553-1562 (2017). [cited by applicant]
Yonesaka, K. et al. Activation of ERBB2 Signaling Causes Resistance to the EGFR-Directed Therapeutic Antibody Cetuximab. Sci. Transl. Med. 3, 99ra86-99ra86 (2011). [cited by applicant]
Yong, W P, et al. “The role of pharmacogenetics in cancer therapeutics.” British journal of clinical pharmacology 62.1 (2006): 35-46. [cited by applicant]
Yun, S. et al. Clinical significance of overexpression of NRG1 and its receptors, HER3 and HER4, in gastric cancer patients. Gastric Cancer 21, 225-236 (2018). [cited by applicant]
Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23, 703-713 (2017). [cited by applicant]
Zeng, et al., “Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system”, BMC Medical Informatics and Decision Making 2006, 6:30, retrieved … [cited by applicant]
Zhang, Yuan et al. “Aspect-augmented Adversarial Networks for Domain Adaptation” sentiarXiv:1701.00188v2 [cs. CL], Sep. 25, 2017, 14 pages. [cited by applicant]
International Searching Authority. International Search Report and Written Opinion for application PCT/US2020/047704. Mailed on Nov. 20, 2020. 9 pages. [cited by applicant]
Han, M.-E. et al. Overexpression of NRG1 promotes progression of gastric cancer by regulating the self-renewal of cancer stem cells. J. Gastroenterol. 50, 645-656 (2015). [cited by applicant]
Hartmaier, R. J. et al. High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis. Cancer Res. 77, 2464-2475 (2017). [cited by applicant]
He, Dafang et al. “Multi-scale Multi-task FCN for Semantic Page Segmentation and Table Detection,” IEEE, 2017 14th IAPR International Conference on Document Analysis and Recognition, Nov. 9-15, 2017, pp. 254-261. [cited by applicant]
He, Luheng et al. “Deep Semantic Role Labeling: WhatWorks and What's Next” Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, Vancouver, Canada, Jul. 30-Aug. 4, 2017, pp. 473-483. [cited by applicant]
Hegde, G. V. et al. Blocking NRG1 and Other Ligand-Mediated Her4 Signaling Enhances the Magnitude and Duration of the Chemotherapeutic Response of Non-Small Cell Lung Cancer. Sci. Transl. Med. 5, 171ra18-171ra18 (2013). [cited by applicant]
Institute of Medicine of the National Academies. Clinical Trials in Cancer. Chapter 6 in Transforming Clinical Research In the United States: Challenges and Opportunities: Workshop Summary (ed. Institute of Medicine (US… [cited by applicant]
International Searching Authority, International Search Report and Written Opinion for application PCT/US2019/056713. Mailed on Feb. 27, 2020. [cited by applicant]
International Searching Authority, International Search Report and Written Opinion for application PCT/US2019/064329. Mailed on Apr. 1, 2020. [cited by applicant]
International Searching Authority. International Search Report and Written Opinion for application PCT/US2021/017517. Mailed on Apr. 29, 2021. 11 pages. [cited by applicant]
Kavasidis, I. et al. “A Saliency-based Convolutional Neural Network for Table and Chart Detection in Digitized Documents,” Submitted to IEEE Transactions on Multimedia, Apr. 17, 2018, pp. 1-13. [cited by applicant]
Kim, Youngjun et al. “A Study of Concept Extraction Across Different Types of Clinical Notes,” AMIA Annu Symp Proc. 2015; Nov. 5, 2015, pp. 737-746. [cited by applicant]
Afferty, John et al. “Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data,” Proceedings of the 18th International Conference on Machine Learning 2001 (ICML 2001), Jun. 28, 2001, pp.… [cited by applicant]
Lample, Guillaume et al. “Neural Architectures for Named Entity Recognition,” Association for Computational Linguistics, Proceedings of NAACL-HLT 2016, San Diego, California, Jun. 12-17, 2016, pp. 260-270. [cited by applicant]
Lang, Francois-Michel et al. “Increasing UMLS Coverage and Reducing Ambiguity via Automated Creation of Synonymous Terms: First Steps toward Filling UMLS Synonymy Gaps,” Semantic Scholar, 2017, pp. 1-26. [cited by applicant]
Laserson, Jonathan et al. “TextRay: Mining Clinical Reports to Gain a Broad Understanding of Chest X-rays,” arXiv: 1806.02121 [cs.CV], Jun. 6, 2018, 13 pages. [cited by applicant]
Lau, D., et al. RNA Sequencing of the Tumor Microenvironment in Precision Cancer Immunotherapy. Trends in Cancer 5, 149-156 (2019). [cited by applicant]
Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013). [cited by applicant]
Layer, R. M., et al. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014). [cited by applicant]
Le, D. T. et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science 357, 409-413 (2017). [cited by applicant]
Lee, Kenton et al. “End-to-end Neural Coreference Resolution,” arXiv:1707.07045 [cs.CL], Dec. 15, 2017, 10 pages. [cited by applicant]
Lei, Tao et al. “Rationalizing Neural Predictions,” arXiv:1606.04155 [cs.CL], Nov. 2, 2016, 11 pages. [cited by applicant]
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285-291 (2016). [cited by applicant]
Li, H. et al. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009). [cited by applicant]
Li, M. M. et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer. J. Mol. Diagnostics 19, 4-23 (2017). [cited by applicant]
Liao, Y., et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014). [cited by applicant]
Ling, Yuan et al. “Learning to Diagnose: Assimilating Clinical Narratives using Deep Reinforcement Learning,” Proceedings of the The 8th International Joint Conference on Natural Language Processing, Taipei, Taiwan, Nov… [cited by applicant]
Lipton, Zachary et al. “Learning to Diagnose With LSTM Recurrent Neural Networks,” ICLR 2016, arXiv:1511.03677 [cs.LG], pp. 1-18. [cited by applicant]
Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585 (2013). [cited by applicant]
Luraghi, P. et al. A Molecularly Annotated Model of Patient-Derived Colon Cancer Stem-Like Cells to Assess Genetic and Nongenetic Mechanisms of Resistance to Anti-EGFR Therapy. Clin. Cancer Res. 24, 807-820 (2018). [cited by applicant]
Ma, Xuezhe et al. “End-to-end Sequence Labeling via Bi-directional LSTM-CNNs-CRF,” arXiv: 1603.01354v5 [cs.LG], May 29, 2016, 12 pages. [cited by applicant]
Mackenzie, Andrei (andrei-m/levenshtein.js) “Levenshtein distance between two given strings implemented in JavaScript and usable as a Node.js module, ” GitHub, Inc., latest comment dated on Feb. 2, 2018, 9 pages. Retrie… [cited by applicant]
Madhavan, S. et al. ClinGen Cancer Somatic Working Group—standardizing and democratizing access to cancer molecular diagnostic data to drive translational research. Pac. Symp. Biocomput. 23, 247-258 (2018). [cited by applicant]
Malangone-Monaco, E., et al. “Prescribing patterns of oral antineoplastic therapies observed in the treatment of patients with advanced prostate cancer between 2012 and 2014: results of an oncology EMR analysis.” Clinic… [cited by applicant]
Maxwell, K. N. et al. BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers. Nat. Commun. 8, 319 (2017). [cited by applicant]
Mendell, J. et al. Clinical Translation and Validation of a Predictive Biomarker for Patritumab, an Anti-human Epidermal Growth Factor Receptor 3 (HER3) Monoclonal Antibody, in Patients With Advanced Non-small Cell Lung… [cited by applicant]
Mihalcea, Rada et al. “Part IV Graph-Based Natural Language Processing” excerpted from a book “Graph-Based Natural Language Processing and Information Retrieval,” Cambridge University Press, First published 2011 (Reprin… [cited by applicant]
Miller, A. et al. High somatic mutation and neoantigen burden are correlated with decreased progression-free survival in multiple myeloma. Blood Cancer J. 7, e612 (2017). [cited by applicant]
Mysore, Sheshera S. “Segmentation of Non-text Objects with Connected Operators” Msheshera, May 21, 2017, 2 pages. Retrieved from Internet. URL: http://msheshera.github.io/non-text-segment-connected-operators.html. [cited by applicant]
Narasimhan, Karthik et al. “Improving Information Extraction by Acquiring External Evidence with Reinforcement Learning,” arXiv: 1603.07954v3 [cs.CL], Sep. 27, 2016, 12 pages. [cited by applicant]
Neelakantan, Arvind et al. “Learning Dictionaries for Named Entity Recognition using Minimal Supervision,” Proceedings of the 14th Conference of the European Chapter of the Association for Computational Linguistics, Got… [cited by applicant]
Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453-7 (2015). [cited by applicant]
Newton, Y. et al. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer Res. 77, e111-e114 (2017). [cited by applicant]
Optum. Determining Lines of Therapy (LOT) in Oncology in Claims Databases. 2017. Available online at https://cdn-aem.optum.com/content/dam/optum3/optum/en/resources/white-papers/wf520768_guidelines-for-determining-lines… [cited by applicant]
Peng, L. et al. Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types. Sci. Rep. 5, 13413 (2015). [cited by applicant]
Peters, Matthew. E. et al. “Semi-supervised sequence tagging with bidirectional language models,” arXiv:1705.00108v1 [cs.CL], Apr. 29, 2017, 10 pages. [cited by applicant]
Prakash, Aaditya et al. “Condensed Memory Networks for Clinical Diagnostic Inferencing,” arXiv:1612.01848v2 [cs.CL], Jan. 3, 2017, 8 pages. [cited by applicant]
Radovich, M. et al. Clinical benefit of a precision medicine based approach for guiding treatment of refractory cancers. Oncotarget 7, 56491-56500 (2016). [cited by applicant]
Rajkumar, S. V., et al. “Guidelines for determination of the number of prior lines of therapy in multiple myeloma.” Blood, The Journal of the American Society of Hematology 126.7 (2015): 921-922. [cited by applicant]
Reiman, D. et al. Integrating RNA expression and visual features for immune infiltrate prediction. Biocomputing 2019, 284-295 (2018). [cited by applicant]
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Patho… [cited by applicant]
European Patent Application No. 20812660.7, Extended European Search Report, dated May 16, 2023. [cited by applicant]
International Searching Authority. International Search Report and Written Opinion for application PCT/US2020/035624. Mailed on Nov. 4, 2020. 13 pages. [cited by applicant]
Learning Eligibility in Cancer Clinical Trials using Deep Neural Networks, Aurelia Bustos, Antonio Pertusa, Preprint submitted to Applied Sciences, Jul. 26, 2018 (Year: 2018). [cited by applicant]
Natural Language Processing for EHR-Based Computational Phenotyping, Zexian Zeng, Yu Deng, Xiaoyu Li, Tristan Naumann, Yuan Luo, IEEE Transactions on Computational Biology and Bioinformatics (Year: 2018). [cited by applicant]
Sayitoglu M. Clinical Interpretation of Genomic Variations. Genomik Varyasyonlarin Klinik Yorumlanmasi. Turk J Haematol. 2016, 33(3): 172-179. doi:10.4274/tjh.2016.0149 (Year: 2016). [cited by applicant]
Shu Y, Wu X, Tong X, Wang X, Chang Z, Mao Y, Chen X, Sun J, Wang Z, Hong Z, Zhu L, Zhu C, Chen J, Liang Y, Shao H, Shao YW. Circulating Tumor DNA Mutation Profiling by Targeted Next Generation Sequencing Provides Guidan… [cited by applicant]