Machine Learning Methods to Extract Documentation of Breast Cancer Symptoms From Electronic Health Records

Journal of Pain and Symptom Management
Alexander W ForsythCharlotta Lindvall

Abstract

Clinicians document cancer patients' symptoms in free-text format within electronic health record visit notes. Although symptoms are critically important to quality of life and often herald clinical status changes, computational methods to assess the trajectory of symptoms over time are woefully underdeveloped. To create machine learning algorithms capable of extracting patient-reported symptoms from free-text electronic health record notes. The data set included 103,564 sentences obtained from the electronic clinical notes of 2695 breast cancer patients receiving paclitaxel-containing chemotherapy at two academic cancer centers between May 1996 and May 2015. We manually annotated 10,000 sentences and trained a conditional random field model to predict words indicating an active symptom (positive label), absence of a symptom (negative label), or no symptom at all (neutral label). Sentences labeled by human coder were divided into training, validation, and test data sets. Final model performance was determined on 20% test data unused in model development or tuning. The final model achieved precision of 0.82, 0.86, and 0.99 and recall of 0.56, 0.69, and 1.00 for positive, negative, and neutral symptom labels, respectively. The mo...Continue Reading

References

May 19, 2007·Journal of Pain and Symptom Management·Saskia C C M TeunissenAlexander de Graeff
May 12, 2009·Journal of the American Board of Family Medicine : JABFM·Karl A LorenzSteven M Asch
Sep 8, 2010·The New England Journal of Medicine·Jennifer S TemelThomas J Lynch
May 21, 2013·Journal of the American Medical Informatics Association : JAMIA·Kirk RobertsSanda M Harabagiu
Dec 11, 2013·Journal of Educational Evaluation for Health Professions·Matt Vassar, Matthew Holzmann
Feb 3, 2015·Annals of Internal Medicine·Adam E SingerKarl A Lorenz
Jul 18, 2015·Science·M I Jordan, T M Mitchell
Aug 9, 2015·Journal of the American Medical Informatics Association : JAMIA·Mahnoosh KholghiAnthony Nguyen
Nov 18, 2015·Circulation·Rahul C Deo
Feb 18, 2016·Nordic Journal of Psychiatry·Mia Gall GrandahlSidse Marie Arnfred
Apr 29, 2016·JAMA Oncology·Wen-Wai YimSharon W Kwan
Jul 28, 2016·Journal of Palliative Medicine·Adam E SingerKarl A Lorenz
Nov 9, 2016·Breast Cancer Research and Treatment·Adam YalaKevin S Hughes
Jun 7, 2017·JAMA : the Journal of the American Medical Association·Ethan BaschDeborah Schrag

❮ Previous
Next ❯

Citations

Apr 6, 2019·Journal of Medical Internet Research·Andreas K Triantafyllidis, Athanasios Tsanas
Feb 6, 2020·JMIR Medical Informatics·Emily R PfaffAshok Krishnamurthy
Dec 19, 2018·BMC Emergency Medicine·Diane L LorenzettiCynthia A Beck
Feb 25, 2019·Quality of Life Research : an International Journal of Quality of Life Aspects of Treatment, Care and Rehabilitation·Yuelin LiBernard H Bochner
Apr 2, 2020·JMIR Medical Informatics·Irena Spasic, Goran Nenadic
Jun 3, 2018·Journal of Medical Toxicology : Official Journal of the American College of Medical Toxicology·Kei OuchiEdward W Boyer
Sep 22, 2020·Journal of Healthcare Engineering·Z Faizal Khan, Sultan Refa Alotaibi

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

International Journal of Methods in Psychiatric Research
George KarystianisGoran Nenadic
AMIA ... Annual Symposium Proceedings
Quang NguyenMilos Hauskrecht
© 2022 Meta ULC. All rights reserved