All Publications


  • Cross-Modal Data Programming Enables Rapid Medical Machine Learning. Patterns (New York, N.Y.) Dunnmon, J. A., Ratner, A. J., Saab, K., Khandwala, N., Markert, M., Sagreiya, H., Goldman, R., Lee-Messer, C., Lungren, M. P., Rubin, D. L., Re, C. 2020; 1 (2)

    Abstract

    A major bottleneck in developing clinically impactful machine learning models is a lack of labeled training data for model supervision. Thus, medical researchers increasingly turn to weaker, noisier sources of supervision, such as leveraging extractions from unstructured text reports to supervise image classification. A key challenge in weak supervision is combining sources of information that may differ in quality and have correlated errors. Recently, a statistical theory of weak supervision called data programming has shown promise in addressing this challenge. Data programming now underpins many deployed machine-learning systems in the technology industry, even for critical applications. We propose a new technique for applying data programming to the problem of cross-modal weak supervision in medicine, wherein weak labels derived from an auxiliary modality (e.g., text) are used to train models over a different target modality (e.g., images). We evaluate our approach on diverse clinical tasks via direct comparison to institution-scale, hand-labeled datasets. We find that our supervision technique increases model performance by up to 6 points area under the receiver operating characteristic curve (ROC-AUC) over baseline methods by improving both coverage and quality of the weak labels. Our approach yields models that on average perform within 1.75 points ROC-AUC of those supervised with physician-years of hand labeling and outperform those supervised with physician-months of hand labeling by 10.25 points ROC-AUC, while using only person-days of developer time and clinician work-a time saving of 96%. Our results suggest that modern weak supervision techniques such as data programming may enable more rapid development and deployment of clinically useful machine-learning models.

    View details for DOI 10.1016/j.patter.2020.100019

    View details for PubMedID 32776018

  • Weak supervision as an efficient approach for automated seizure detection in electroencephalography. NPJ digital medicine Saab, K. n., Dunnmon, J. n., Ré, C. n., Rubin, D. n., Lee-Messer, C. n. 2020; 3 (1): 59

    Abstract

    Automated seizure detection from electroencephalography (EEG) would improve the quality of patient care while reducing medical costs, but achieving reliably high performance across patients has proven difficult. Convolutional Neural Networks (CNNs) show promise in addressing this problem, but they are limited by a lack of large labeled training datasets. We propose using imperfect but plentiful archived annotations to train CNNs for automated, real-time EEG seizure detection across patients. While these weak annotations indicate possible seizures with precision scores as low as 0.37, they are commonly produced in large volumes within existing clinical workflows by a mixed group of technicians, fellows, students, and board-certified epileptologists. We find that CNNs trained using such weak annotations achieve Area Under the Receiver Operating Characteristic curve (AUROC) values of 0.93 and 0.94 for pediatric and adult seizure onset detection, respectively. Compared to currently deployed clinical software, our model provides a 31% increase (18 points) in F1-score for pediatric patients and a 17% increase (11 points) for adult patients. These results demonstrate that weak annotations, which are sustainably collected via existing clinical workflows, can be leveraged to produce clinically useful seizure detection models.

    View details for DOI 10.1038/s41746-020-0264-0

    View details for PubMedID 33597644

  • Weak supervision as an efficient approach for automated seizure detection in electroencephalography. NPJ digital medicine Saab, K. n., Dunnmon, J. n., Ré, C. n., Rubin, D. n., Lee-Messer, C. n. 2020; 3: 59

    Abstract

    Automated seizure detection from electroencephalography (EEG) would improve the quality of patient care while reducing medical costs, but achieving reliably high performance across patients has proven difficult. Convolutional Neural Networks (CNNs) show promise in addressing this problem, but they are limited by a lack of large labeled training datasets. We propose using imperfect but plentiful archived annotations to train CNNs for automated, real-time EEG seizure detection across patients. While these weak annotations indicate possible seizures with precision scores as low as 0.37, they are commonly produced in large volumes within existing clinical workflows by a mixed group of technicians, fellows, students, and board-certified epileptologists. We find that CNNs trained using such weak annotations achieve Area Under the Receiver Operating Characteristic curve (AUROC) values of 0.93 and 0.94 for pediatric and adult seizure onset detection, respectively. Compared to currently deployed clinical software, our model provides a 31% increase (18 points) in F1-score for pediatric patients and a 17% increase (11 points) for adult patients. These results demonstrate that weak annotations, which are sustainably collected via existing clinical workflows, can be leveraged to produce clinically useful seizure detection models.

    View details for DOI 10.1038/s41746-020-0264-0

    View details for PubMedID 32352037

    View details for PubMedCentralID PMC7170880

  • Shuffled Linear Regression with Erroneous Observations Saab, S. S., Saab, K., Saab, S. S., IEEE IEEE. 2019