Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques can make use of the increasing amounts of structural data that are becoming publicly available. Convolutional neural network (CNN) scoring functions in particular have shown promise in pose selection and affinity prediction for protein-ligand complexes. Neural networks are known for being difficult to interpret. Understanding the decisions of a particular network can help tune parameters and training data to maximize performance. Visualization of neural networks helps decompose complex scoring functions into pictures that are more easily parsed by humans. Here we present three methods for visualizing how individual protein-ligand complexes are interpreted by 3D convolutional neural networks. We also present a visualization of the convolutional filters and their weights. We describe how the intuition provided by these visualizations aids in network design.

Isolating and controlling specific features in the outputs of generative models in a user-friendly way is a difficult and open-ended problem. We develop techniques that allow an oracle user to generate an image they are envisioning in their head by answering a sequence of relative queries of the form "do you prefer image a or image b?" Our framework consists of a Conditional VAE that uses the collected relative queries to partition the latent space into preference-relevant features and non-preference-relevant features. We then use the user's responses to relative queries to determine the preference-relevant features that correspond to their envisioned output image. Additionally, we develop techniques for modeling the uncertainty in images' predicted preference-relevant features, allowing our framework to generalize to scenarios in which the relative query training set contains noise. 1