13 accepted papers
Whole-slide images (WSIs) in computational pathology contain billions of pixels, making end-to-end training of feature extractors and multi-instance learning (MIL) networks infeasible on a single commodity GPU.Existing methods often freeze the feature extractor and train MIL networks on the resultin
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative models have achieved great success in linear peptide design…
Although multi-instance learning (MIL) has succeeded in pathological image classification, it faces the challenge of high inference costs due to processing numerous patches from gigapixel whole slide images (WSIs).To address this, we propose HDMIL, a hierarchical distillation multi-instance learning…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding…
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective pepti…
We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the results from information geometry. We demonstrate the effectiveness of our method on the discrete generation problem by inst…
Predicting the effects of protein mutations is crucial for analyzing protein functions and understanding genetic diseases. However, existing models struggle to effectively extract mutation-related local structure motifs from protein databases, which hinders their predictive accuracy and robustness.…
Despite the striking success of general protein folding models such as AlphaFold2 (AF2), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise…
Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present *PepFlow*, the first multi-modal deep generative model grounded in the flow-matchin…
End-to-end autonomous driving recently emerged as a promising research direction to target autonomy from a full-stack perspective. Along this line many of the latest works follow an open-loop evaluation setting on nuScenes to study the planning behavior. In this paper we delve deeper into the proble…
Recently virtual staining technology has greatly promoted the advancement of histopathology. Despite the practical successes achieved the outstanding performance of most virtual staining methods relies on hard-to-obtain paired images in training. In this paper we propose a method for virtual immunoh…
Equivariance has been a long-standing concern in various fields ranging from computer vision to physical modeling. Most previous methods struggle with generality, simplicity, and expressiveness --- some are designed ad hoc for specific data types, some are too complex to be accessible, and some sacr…
Designing protein sequences with a particular biological function is a long-lasting challenge for protein engineering. Recent advances in machine-learning-guided approaches focus on building a surrogate sequence-function model to reduce the burden of expensive in-lab experiments. In this paper, we s…