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Jeffrey Tan

GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning

May 08, 2023
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein

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This paper presents our contribution to the MEDIQA-2023 Dialogue2Note shared task, encompassing both subtask A and subtask B. We approach the task as a dialogue summarization problem and implement two distinct pipelines: (a) a fine-tuning of a pre-trained dialogue summarization model and GPT-3, and (b) few-shot in-context learning (ICL) using a large language model, GPT-4. Both methods achieve excellent results in terms of ROUGE-1 F1, BERTScore F1 (deberta-xlarge-mnli), and BLEURT, with scores of 0.4011, 0.7058, and 0.5421, respectively. Additionally, we predict the associated section headers using RoBERTa and SciBERT based classification models. Our team ranked fourth among all teams, while each team is allowed to submit three runs as part of their submission. We also utilize expert annotations to demonstrate that the notes generated through the ICL GPT-4 are better than all other baselines. The code for our submission is available.

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Deep Learning vs. Human Graders for Classifying Severity Levels of Diabetic Retinopathy in a Real-World Nationwide Screening Program

Oct 18, 2018
Paisan Raumviboonsuk, Jonathan Krause, Peranut Chotcomwongse, Rory Sayres, Rajiv Raman, Kasumi Widner, Bilson J L Campana, Sonia Phene, Kornwipa Hemarat, Mongkol Tadarati, Sukhum Silpa-Acha, Jirawut Limwattanayingyong, Chetan Rao, Oscar Kuruvilla, Jesse Jung, Jeffrey Tan, Surapong Orprayoon, Chawawat Kangwanwongpaisan, Ramase Sukulmalpaiboon, Chainarong Luengchaichawang, Jitumporn Fuangkaew, Pipat Kongsap, Lamyong Chualinpha, Sarawuth Saree, Srirat Kawinpanitan, Korntip Mitvongsa, Siriporn Lawanasakol, Chaiyasit Thepchatri, Lalita Wongpichedchai, Greg S Corrado, Lily Peng, Dale R Webster

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Deep learning algorithms have been used to detect diabetic retinopathy (DR) with specialist-level accuracy. This study aims to validate one such algorithm on a large-scale clinical population, and compare the algorithm performance with that of human graders. 25,326 gradable retinal images of patients with diabetes from the community-based, nation-wide screening program of DR in Thailand were analyzed for DR severity and referable diabetic macular edema (DME). Grades adjudicated by a panel of international retinal specialists served as the reference standard. Across different severity levels of DR for determining referable disease, deep learning significantly reduced the false negative rate (by 23%) at the cost of slightly higher false positive rates (2%). Deep learning algorithms may serve as a valuable tool for DR screening.

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