EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Accurate prediction of compound-protein interactions (CPI) remains a cornerstone challenge in computational drug discovery. While existing sequence-based approaches leverage molecular fingerprints or graph representations, they critically overlook three-dimensional (3D) structural determinants of binding affinity. To bridge this gap, we present EquiCPI, an end-to-end geometric deep learning framework that synergizes first-principles structural modeling with SE(3)-equivariant neural networks. Our pipeline transforms raw sequences into 3D atomic coordinates via ESMFold for proteins and DiffDock-L for ligands, followed by physics-guided conformer re-ranking and equivariant feature learning. At its core, EquiCPI employs SE(3)-equivariant message passing over atomic point clouds, preserving symmetry under rotations, translations, and reflections, while hierarchically encoding local interaction patterns through tensor products of spherical harmonics. The proposed model is evaluated on BindingDB (affinity prediction) and DUD-E (virtual screening), EquiCPI achieves performance on par with or exceeding the state-of-the-art deep learning competitors.

MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints

Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts inmolecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios. Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates. The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA

ISIC 2017 Skin Lesion Segmentation Using Deep Encoder-Decoder Network

This paper summarizes our method and validation results for part 1 of the ISBI Challenge 2018. Our algorithm makes use of deep encoder-decoder network and novel skin lesion data augmentation to segment the challenge objective. Besides, we also propose an effective testing strategy by applying multi-model comparison.