Generative AI in Medicine

The increased capabilities of generative AI have dramatically expanded its possible use cases in medicine. We provide a comprehensive overview of generative AI use cases for clinicians, patients, clinical trial organizers, researchers, and trainees. We then discuss the many challenges -- including maintaining privacy and security, improving transparency and interpretability, upholding equity, and rigorously evaluating models -- which must be overcome to realize this potential, and the open research directions they give rise to.

Machine Learning for Health symposium 2023 -- Findings track

A collection of the accepted Findings papers that were presented at the 3rd Machine Learning for Health symposium (ML4H 2023), which was held on December 10, 2023, in New Orleans, Louisiana, USA. ML4H 2023 invited high-quality submissions on relevant problems in a variety of health-related disciplines including healthcare, biomedicine, and public health. Two submission tracks were offered: the archival Proceedings track, and the non-archival Findings track. Proceedings were targeted at mature work with strong technical sophistication and a high impact to health. The Findings track looked for new ideas that could spark insightful discussion, serve as valuable resources for the community, or could enable new collaborations. Submissions to the Proceedings track, if not accepted, were automatically considered for the Findings track. All the manuscripts submitted to ML4H Symposium underwent a double-blind peer-review process.

Coarse race data conceals disparities in clinical risk score performance

Healthcare data in the United States often records only a patient's coarse race group: for example, both Indian and Chinese patients are typically coded as ``Asian.'' It is unknown, however, whether this coarse coding conceals meaningful disparities in the performance of clinical risk scores across granular race groups. Here we show that it does. Using data from 418K emergency department visits, we assess clinical risk score performance disparities across granular race groups for three outcomes, five risk scores, and four performance metrics. Across outcomes and metrics, we show that there are significant granular disparities in performance within coarse race categories. In fact, variation in performance metrics within coarse groups often exceeds the variation between coarse groups. We explore why these disparities arise, finding that outcome rates, feature distributions, and the relationships between features and outcomes all vary significantly across granular race categories. Our results suggest that healthcare providers, hospital systems, and machine learning researchers should strive to collect, release, and use granular race data in place of coarse race data, and that existing analyses may significantly underestimate racial disparities in performance.

Improved Text Classification via Test-Time Augmentation

Test-time augmentation -- the aggregation of predictions across transformed examples of test inputs -- is an established technique to improve the performance of image classification models. Importantly, TTA can be used to improve model performance post-hoc, without additional training. Although test-time augmentation (TTA) can be applied to any data modality, it has seen limited adoption in NLP due in part to the difficulty of identifying label-preserving transformations. In this paper, we present augmentation policies that yield significant accuracy improvements with language models. A key finding is that augmentation policy design -- for instance, the number of samples generated from a single, non-deterministic augmentation -- has a considerable impact on the benefit of TTA. Experiments across a binary classification task and dataset show that test-time augmentation can deliver consistent improvements over current state-of-the-art approaches.

Data Augmentation for Electrocardiograms

Neural network models have demonstrated impressive performance in predicting pathologies and outcomes from the 12-lead electrocardiogram (ECG). However, these models often need to be trained with large, labelled datasets, which are not available for many predictive tasks of interest. In this work, we perform an empirical study examining whether training time data augmentation methods can be used to improve performance on such data-scarce ECG prediction problems. We investigate how data augmentation strategies impact model performance when detecting cardiac abnormalities from the ECG. Motivated by our finding that the effectiveness of existing augmentation strategies is highly task-dependent, we introduce a new method, TaskAug, which defines a flexible augmentation policy that is optimized on a per-task basis. We outline an efficient learning algorithm to do so that leverages recent work in nested optimization and implicit differentiation. In experiments, considering three datasets and eight predictive tasks, we find that TaskAug is competitive with or improves on prior work, and the learned policies shed light on what transformations are most effective for different tasks. We distill key insights from our experimental evaluation, generating a set of best practices for applying data augmentation to ECG prediction problems.

Quantifying Inequality in Underreported Medical Conditions

Estimating the prevalence of a medical condition, or the proportion of the population in which it occurs, is a fundamental problem in healthcare and public health. Accurate estimates of the relative prevalence across groups -- capturing, for example, that a condition affects women more frequently than men -- facilitate effective and equitable health policy which prioritizes groups who are disproportionately affected by a condition. However, it is difficult to estimate relative prevalence when a medical condition is underreported. In this work, we provide a method for accurately estimating the relative prevalence of underreported medical conditions, building upon the positive unlabeled learning framework. We show that under the commonly made covariate shift assumption -- i.e., that the probability of having a disease conditional on symptoms remains constant across groups -- we can recover the relative prevalence, even without restrictive assumptions commonly made in positive unlabeled learning and even if it is impossible to recover the absolute prevalence. We provide a suite of experiments on synthetic and real health data that demonstrate our method's ability to recover the relative prevalence more accurately than do baselines, and the method's robustness to plausible violations of the covariate shift assumption.

Learning to Limit Data Collection via Scaling Laws: Data Minimization Compliance in Practice

Data minimization is a legal obligation defined in the European Union's General Data Protection Regulation (GDPR) as the responsibility to process an adequate, relevant, and limited amount of personal data in relation to a processing purpose. However, unlike fairness or transparency, the principle has not seen wide adoption for machine learning systems due to a lack of computational interpretation. In this paper, we build on literature in machine learning and law to propose the first learning framework for limiting data collection based on an interpretation that ties the data collection purpose to system performance. We formalize a data minimization criterion based on performance curve derivatives and provide an effective and interpretable piecewise power law technique that models distinct stages of an algorithm's performance throughout data collection. Results from our empirical investigation offer deeper insights into the relevant considerations when designing a data minimization framework, including the choice of feature acquisition algorithm, initialization conditions, as well as impacts on individuals that hint at tensions between data minimization and fairness.

When and Why Test-Time Augmentation Works

Test-time augmentation (TTA)---the aggregation of predictions across transformed versions of a test input---is a common practice in image classification. In this paper, we present theoretical and experimental analyses that shed light on 1) when test time augmentation is likely to be helpful and 2) when to use various test-time augmentation policies. A key finding is that even when TTA produces a net improvement in accuracy, it can change many correct predictions into incorrect predictions. We delve into when and why test-time augmentation changes a prediction from being correct to incorrect and vice versa. Our analysis suggests that the nature and amount of training data, the model architecture, and the augmentation policy all matter. Building on these insights, we present a learning-based method for aggregating test-time augmentations. Experiments across a diverse set of models, datasets, and augmentations show that our method delivers consistent improvements over existing approaches.

Unsupervised Domain Adaptation in the Absence of Source Data

Current unsupervised domain adaptation methods can address many types of distribution shift, but they assume data from the source domain is freely available. As the use of pre-trained models becomes more prevalent, it is reasonable to assume that source data is unavailable. We propose an unsupervised method for adapting a source classifier to a target domain that varies from the source domain along natural axes, such as brightness and contrast. Our method only requires access to unlabeled target instances and the source classifier. We validate our method in scenarios where the distribution shift involves brightness, contrast, and rotation and show that it outperforms fine-tuning baselines in scenarios with limited labeled data.

Image segmentation of liver stage malaria infection with spatial uncertainty sampling

Global eradication of malaria depends on the development of drugs effective against the silent, yet obligate liver stage of the disease. The gold standard in drug development remains microscopic imaging of liver stage parasites in in vitro cell culture models. Image analysis presents a major bottleneck in this pipeline since the parasite has significant variability in size, shape, and density in these models. As with other highly variable datasets, traditional segmentation models have poor generalizability as they rely on hand-crafted features; thus, manual annotation of liver stage malaria images remains standard. To address this need, we develop a convolutional neural network architecture that utilizes spatial dropout sampling for parasite segmentation and epistemic uncertainty estimation in images of liver stage malaria. Our pipeline produces high-precision segmentations nearly identical to expert annotations, generalizes well on a diverse dataset of liver stage malaria parasites, and promotes independence between learned feature maps to model the uncertainty of generated predictions.