Table of Links Abstract and 1. Introduction Abstract and 1. Introduction 2 Data 2.1 Data Sources 2.1 Data Sources 2.2 SS and SI Categories 2.2 SS and SI Categories 3 Methods 3.1 Lexicon Creation and Expansion 3.1 Lexicon Creation and Expansion 3.2 Annotations 3.2 Annotations 3.3 System Description 3.3 System Description 4 Results 4.1 Demographics and 4.2 System Performance 4.1 Demographics and 4.2 System Performance 5 Discussion 5 Discussion 5.1 Limitations 5.1 Limitations 6 Conclusion, Reproducibility, Funding, Acknowledgments, Author Contributions, and References 6 Conclusion, Reproducibility, Funding, Acknowledgments, Author Contributions, and References SUPPLEMENTARY SUPPLEMENTARY Guidelines for Annotating Social Support and Social Isolation in Clinical Notes Guidelines for Annotating Social Support and Social Isolation in Clinical Notes Other Supervised Models Other Supervised Models 6 CONCLUSION We offer two open-source NLP systems with different approaches, as well as a manual annotation guideline for identifying SS and SI. The rule-based approach and the LLM approach each have strengths and limitations in performing this challenging task of creating a portable system to identify fine and coarse-grained categories of SS and SI in psychiatric patients. REPRODUCIBILITY All code for rule- and LLM-based systems are available on GitHub. Link: https://github.com/CornellMHILab/Social Support Social Isolation Extraction. Link The annotation guidelines and lexicons are available in the supplementary files. FUNDING This study was funded in part by grants from the National Institutes of Health (R01 MH119177, R01 MH121907, and R01 MH121922). ACKNOWLEDGEMENTS This work was supported in part through the computational and data resources and staff expertise provided by Scientific Computing and Data at the Icahn School of Medicine at Mount Sinai Health System and supported by the Clinical and Translational Science Awards (CTSA) grant UL1TR004419 from the National Center for Advancing Translational Sciences. Research reported in this publication was also supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD026880 and S10OD030463. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. AUTHOR CONTRIBUTIONS BGP and LAL worked on planning, data collection, data annotation, data extraction, software development, writing, and editing. PR worked on LLM implementation and editing. VV helped in data annotation, writing, and editing. MMS, BF, and GH helped in data annotation. JP and PA helped in planning, advising, and editing. MW, JJM, and MO helped in initial category identification, lexicon development, advising, and editing. JASR, ER, JMB, IL, GNN, AT, and AWC helped in advising and editing. JP and AWC provided resources and funding. REFERENCES [1] World Health Organization. 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[46] Haokun Liu, Derek Tam, Mohammed Muqeeth, Jay Mohta, Tenghao Huang, Mohit Bansal, and Colin A Raffel. Few-shot parameter-efficient fine-tuning is better and cheaper than incontext learning. Advances in Neural Information Processing Systems, 35:1950–1965, 2022. This paper is available on arxiv under CC BY 4.0 DEED license. This paper is available on arxiv under CC BY 4.0 DEED license. available on arxiv 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. Authors: 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.

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Guidelines for Annotating Social Support and Social Isolation in Clinical Notes

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Open-Source NLP Systems for Identifying Social Support and Isolation in Psychiatric Notes

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