Features in Backgrounds of Microscopy Images Introduce Biases in Machine Learning Analyses

Abstract

Subvisible particles may be encountered throughout the processing of therapeutic protein formulations. Flow imaging microscopy (FIM) and backgrounded membrane imaging (BMI) are techniques commonly used to record digital images of these particles, which may be analyzed to provide particle size distributions, concentrations, and identities. Although both techniques record digital images of particles within a sample, FIM analyzes particles suspended in flowing liquids, whereas BMI records images of dry particles after collection by filtration onto a membrane. This study compared the performance of convolutional neural networks (CNNs) in classifying images of subvisible particles recorded by both imaging techniques. Initially, CNNs trained on BMI images appeared to provide higher classification accuracies than those trained on FIM images. However, attribution analyses showed that classification predictions from CNNs trained on BMI images relied on features contributed by the membrane background, whereas predictions from CNNs trained on FIM features were based largely on features of the particles. Segmenting images to minimize the contributions from image backgrounds reduced the apparent accuracy of CNNs trained on BMI images but caused minimal reduction in the accuracy of CNNs trained on FIM images. Thus, the seemingly superior classification accuracy of CNNs trained on BMI images compared to FIM images was an artifact caused by subtle features in the backgrounds of BMI images. Our findings emphasize the importance of examining machine learning algorithms for image analysis with attribution methods to ensure the robustness of trained models and to mitigate potential influence of artifacts within training data sets.

Keywords: Image analysis; Machine learning; Monoclonal antibodies; Neural networks; Protein aggregation.