Advancements in AI for science unlocks capabilities for critical drug discovery tasks such as protein-ligand binding affinity prediction. However, current models overfit to existing oversimplified datasets that does not represent naturally occurring and biologically relevant proteins with modifications. In this work, we curate a complete and modification-aware version of the widely used DAVIS dataset by incorporating 4,032 kinase–ligand pairs involving substitutions, insertions, deletions, and phosphorylation events. This enriched dataset enables benchmarking of predictive models under biologically realistic conditions. Based on this new dataset, we propose three benchmark settings—Augmented Dataset Prediction, Wild-Type to Modification Generalization, and Few-Shot Modification Generalization—designed to assess model robustness in the presence of protein modifications. Through extensive evaluation of both docking-free and docking-based methods, we find that docking-based model generalize better in zero-shot settings. In contrast, docking-free models tend to overfit to wild-type proteins and struggle with unseen modifications but show notable improvement when fine-tuned on a small set of modified examples. We anticipate that the curated dataset and benchmarks offer a valuable foundation for developing models that better generalize to protein modifications, ultimately advancing precision medicine in drug discovery. The benchmark is available at: https://github.com/ZhiGroup/DAVIS-complete

Self-attention in vision transformers is often thought to perform perceptual grouping where tokens attend to other tokens with similar embeddings, which could correspond to semantically similar features of an object. However, attending to dissimilar tokens can be beneficial by providing contextual information. We propose to analyze the query-key interaction by the singular value decomposition of the interaction matrix (i.e. ${\textbf{W}_q}^\top\textbf{W}_k$). We find that in many ViTs, especially those with classification training objectives, early layers attend more to similar tokens, while late layers show increased attention to dissimilar tokens, providing evidence corresponding to perceptual grouping and contextualization, respectively. Many of these interactions between features represented by singular vectors are interpretable and semantic, such as attention between relevant objects, between parts of an object, or between the foreground and background. This offers a novel perspective on interpreting the attention mechanism, which contributes to understanding how transformer models utilize context and salient features when processing images.