Deep Low-Shot Learning for Biological Image Classification and Visualization From Limited Training Samples

Predictive modeling is useful but very challenging in biological image analysis due to the high cost of obtaining and labeling training data. For example, in the study of gene interaction and regulation in Drosophila embryogenesis, the analysis is most biologically meaningful when in situ hybridization (ISH) gene expression pattern images from the same developmental stage are compared. However, labeling training data with precise stages is very time-consuming even for developmental biologists. Thus, a critical challenge is how to build accurate computational models for precise developmental stage classification from limited training samples. In addition, identification and visualization of developmental landmarks are required to enable biologists to interpret prediction results and calibrate models. To address these challenges, we propose a deep two-step low-shot learning framework to accurately classify ISH images using limited training images. Specifically, to enable accurate model training on limited training samples, we formulate the task as a deep low-shot learning problem and develop a novel two-step learning approach, including data-level learning and feature-level learning. We use a deep residual network as our base model and achieve improved performance in the precise stage prediction task of ISH images. Furthermore, the deep model can be interpreted by computing saliency maps, which consists of pixel-wise contributions of an image to its prediction result. In our task, saliency maps are used to assist the identification and visualization of developmental landmarks. Our experimental results show that the proposed model can not only make accurate predictions but also yield biologically meaningful interpretations. We anticipate our methods to be easily generalizable to other biological image classification tasks with small training datasets. Our open-source code is available at https://github.com/divelab/lsl-fly.