Analyzing Cell Painting images using different CNNs and Conformal Prediction variations : Optimization of a Deep Learning model to predict the MoA of different drugs

Abstract: Microscopy imaging based techniques, such as the Cell Painting assay, could be used to generate images that visualize the Mechanism of Action (MoA) of a drug, which could be of great use in drug development. In order to extract information and predict the MoA of a new compound from these images we need powerful image analysis tools. The purpose with this project is to further develop a Deep Learning model to predict the MoA of different drugs from Cell Painting images using Convolutional Neural Networks (CNNs) and Conformal Prediction. The specific task was to compare the accuracy of different CNN architectures and to compare the efficiency of different nonconformity functions.  During the project the CNN architectures ResNet50, ResNet101 and DenseNet121 were compared as well as the nonconformity functions Inverse Probability, Margin and a combination of them both. No significant difference in accuracy between the CNNs and no difference in efficiency between the nonconformity functions was measured. The results showed that the model could predict the MoA of a compound with high accuracy when all compounds were used both in training, validation and test of the model, which validates the implementations. However, it is desirable for the model to be able to predict the MoA of a new compound if the model has been trained on other compounds with the same MoA. This could not be confirmed through this project and the model needs to be further investigated and tested with another dataset in order to be used for that purpose.