We used EHR data from two sites (MSHS and WCM) to develop the SS/SI NLP pipeline. First, we used 286,692 notes from 33,800 patients derived from the MSHS data warehouse. Notes are from psychiatric inpatient, psychiatric emergency department (ED), and psychiatry consult-liaison encounters between 2011 and 2020. Advantages of the corpus include relative consistency in documentation style and comprehensive biopsychosocial patient evaluations. Of note, the corpus also contains the occasional presence of clinical note templates (found in 14% of the notes) such as:‘lacks social support: yes/no/unknown.’ For this study, templates were removed while annotating and evaluating the NLP system; however, in the future, we will compare clinician responses in these templates to the gold-standard annotations.
Second, we used 48.98 million clinical notes from 558,133 patients derived from the WCM enterprise data warehouse. These notes from 2010 to 2023 comprise patients with any mental health diagnosis or antidepressant prescription from outpatient, inpatient, or ED visits. To align WCM data with the MSHS data, NLP development was restricted to psychiatric encounter notes only. The study was approved by the Institutional Review Boards (IRBs) at MSHS and WCM.
Authors:
(1) Braja Gopal Patra, Weill Cornell Medicine, New York, NY, USA and co-first authors;
(2) Lauren A. Lepow, Icahn School of Medicine at Mount Sinai, New York, NY, USA and co-first authors;
(3) Praneet Kasi Reddy Jagadeesh Kumar. Weill Cornell Medicine, New York, NY, USA;
(4) Veer Vekaria, Weill Cornell Medicine, New York, NY, USA;
(5) Mohit Manoj Sharma, Weill Cornell Medicine, New York, NY, USA;
(6) Prakash Adekkanattu, Weill Cornell Medicine, New York, NY, USA;
(7) Brian Fennessy, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
(8) Gavin Hynes, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
(9) Isotta Landi, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
(10) Jorge A. Sanchez-Ruiz, Mayo Clinic, Rochester, MN, USA;
(11) Euijung Ryu, Mayo Clinic, Rochester, MN, USA;
(12) Joanna M. Biernacka, Mayo Clinic, Rochester, MN, USA;
(13) Girish N. Nadkarni, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
(14) Ardesheer Talati, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA and New York State Psychiatric Institute, New York, NY, USA;
(15) Myrna Weissman, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA and New York State Psychiatric Institute, New York, NY, USA;
(16) Mark Olfson, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA, New York State Psychiatric Institute, New York, NY, USA, and Columbia University Irving Medical Center, New York, NY, USA;
(17) J. John Mann, Columbia University Irving Medical Center, New York, NY, USA;
(18) Alexander W. Charney, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
(19) Jyotishman Pathak, Weill Cornell Medicine, New York, NY, USA.
