Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT

no code implementations • EMNLP 2020 • Akshay Smit, Saahil Jain, Pranav Rajpurkar, Anuj Pareek, Andrew Ng, Matthew Lungren

The extraction of labels from radiology text reports enables large-scale training of medical imaging models.

Feature Engineering

On the Opportunities and Risks of Foundation Models

2 code implementations • 16 Aug 2021 • Rishi Bommasani, Drew A. Hudson, Ehsan Adeli, Russ Altman, Simran Arora, Sydney von Arx, Michael S. Bernstein, Jeannette Bohg, Antoine Bosselut, Emma Brunskill, Erik Brynjolfsson, Shyamal Buch, Dallas Card, Rodrigo Castellon, Niladri Chatterji, Annie Chen, Kathleen Creel, Jared Quincy Davis, Dora Demszky, Chris Donahue, Moussa Doumbouya, Esin Durmus, Stefano Ermon, John Etchemendy, Kawin Ethayarajh, Li Fei-Fei, Chelsea Finn, Trevor Gale, Lauren Gillespie, Karan Goel, Noah Goodman, Shelby Grossman, Neel Guha, Tatsunori Hashimoto, Peter Henderson, John Hewitt, Daniel E. Ho, Jenny Hong, Kyle Hsu, Jing Huang, Thomas Icard, Saahil Jain, Dan Jurafsky, Pratyusha Kalluri, Siddharth Karamcheti, Geoff Keeling, Fereshte Khani, Omar Khattab, Pang Wei Koh, Mark Krass, Ranjay Krishna, Rohith Kuditipudi, Ananya Kumar, Faisal Ladhak, Mina Lee, Tony Lee, Jure Leskovec, Isabelle Levent, Xiang Lisa Li, Xuechen Li, Tengyu Ma, Ali Malik, Christopher D. Manning, Suvir Mirchandani, Eric Mitchell, Zanele Munyikwa, Suraj Nair, Avanika Narayan, Deepak Narayanan, Ben Newman, Allen Nie, Juan Carlos Niebles, Hamed Nilforoshan, Julian Nyarko, Giray Ogut, Laurel Orr, Isabel Papadimitriou, Joon Sung Park, Chris Piech, Eva Portelance, Christopher Potts, aditi raghunathan, Rob Reich, Hongyu Ren, Frieda Rong, Yusuf Roohani, Camilo Ruiz, Jack Ryan, Christopher Ré, Dorsa Sadigh, Shiori Sagawa, Keshav Santhanam, Andy Shih, Krishnan Srinivasan, Alex Tamkin, Rohan Taori, Armin W. Thomas, Florian Tramèr, Rose E. Wang, William Wang, Bohan Wu, Jiajun Wu, Yuhuai Wu, Sang Michael Xie, Michihiro Yasunaga, Jiaxuan You, Matei Zaharia, Michael Zhang, Tianyi Zhang, Xikun Zhang, Yuhui Zhang, Lucia Zheng, Kaitlyn Zhou, Percy Liang

AI is undergoing a paradigm shift with the rise of models (e. g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks.

Transfer Learning

Q-Pain: A Question Answering Dataset to Measure Social Bias in Pain Management

no code implementations • 3 Aug 2021 • Cécile Logé, Emily Ross, David Yaw Amoah Dadey, Saahil Jain, Adriel Saporta, Andrew Y. Ng, Pranav Rajpurkar

Recent advances in Natural Language Processing (NLP), and specifically automated Question Answering (QA) systems, have demonstrated both impressive linguistic fluency and a pernicious tendency to reflect social biases.

Decision Making Experimental Design +2

RadGraph: Extracting Clinical Entities and Relations from Radiology Reports

1 code implementation • 28 Jun 2021 • Saahil Jain, Ashwin Agrawal, Adriel Saporta, Steven QH Truong, Du Nguyen Duong, Tan Bui, Pierre Chambon, Yuhao Zhang, Matthew P. Lungren, Andrew Y. Ng, Curtis P. Langlotz, Pranav Rajpurkar

We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14, 579 entities and 10, 889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets.

Relation Extraction

Effect of Radiology Report Labeler Quality on Deep Learning Models for Chest X-Ray Interpretation

no code implementations • 1 Apr 2021 • Saahil Jain, Akshay Smit, Andrew Y. Ng, Pranav Rajpurkar

Next, after training image classification models using labels generated from the different radiology report labelers on one of the largest datasets of chest X-rays, we show that an image classification model trained on labels from the VisualCheXbert labeler outperforms image classification models trained on labels from the CheXpert and CheXbert labelers.

Classification General Classification +1

VisualCheXbert: Addressing the Discrepancy Between Radiology Report Labels and Image Labels

1 code implementation • 23 Feb 2021 • Saahil Jain, Akshay Smit, Steven QH Truong, Chanh DT Nguyen, Minh-Thanh Huynh, Mudit Jain, Victoria A. Young, Andrew Y. Ng, Matthew P. Lungren, Pranav Rajpurkar

We also find that VisualCheXbert better agrees with radiologists labeling chest X-ray images than do radiologists labeling the corresponding radiology reports by an average F1 score across several medical conditions of between 0. 12 (95% CI 0. 09, 0. 15) and 0. 21 (95% CI 0. 18, 0. 24).

CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT

7 code implementations • 20 Apr 2020 • Akshay Smit, Saahil Jain, Pranav Rajpurkar, Anuj Pareek, Andrew Y. Ng, Matthew P. Lungren

The extraction of labels from radiology text reports enables large-scale training of medical imaging models.

Feature Engineering