Automating Weak Label Generation for Data Programming with Clinicians in the Loop

TL;DR

This paper introduces a novel approach to generate weak labels for medical data by selecting representative samples for expert labeling, improving data programming accuracy in high-dimensional medical datasets.

Contribution

It proposes a distance-based sampling algorithm that efficiently captures dataset distribution for weak label generation, enhancing data programming in high-dimensional medical data.

Findings

17-28% accuracy improvement in time series data

5-15% accuracy improvement in medical images

Significant F1 score enhancements over baseline methods

Abstract

Large Deep Neural Networks (DNNs) are often data hungry and need high-quality labeled data in copious amounts for learning to converge. This is a challenge in the field of medicine since high quality labeled data is often scarce. Data programming has been the ray of hope in this regard, since it allows us to label unlabeled data using multiple weak labeling functions. Such functions are often supplied by a domain expert. Data-programming can combine multiple weak labeling functions and suggest labels better than simple majority voting over the different functions. However, it is not straightforward to express such weak labeling functions, especially in high-dimensional settings such as images and time-series data. What we propose in this paper is a way to bypass this issue, using distance functions. In high-dimensional spaces, it is easier to find meaningful distance metrics which can generalize across different labeling tasks. We propose an algorithm that queries an expert for labels of a few representative samples of the dataset. These samples are carefully chosen by the algorithm to capture the distribution of the dataset. The labels assigned by the expert on the representative subset induce a labeling on the full dataset, thereby generating weak labels to be used in the data programming pipeline. In our medical time series case study, labeling a subset of 50 to 130 out of 3,265 samples showed 17-28% improvement in accuracy and 13-28% improvement in F1 over the baseline using clinician-defined labeling functions. In our medical image case study, labeling a subset of about 50 to 120 images from 6,293 unlabeled medical images using our approach showed significant improvement over the baseline method, Snuba, with an increase of approximately 5-15% in accuracy and 12-19% in F1 score.