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Mar 2

AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design

We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural sequences with metrics such as amino acid recovery rate or structural RMSD, AbBiBench instead treats the antibody-antigen (Ab-Ag) complex as the fundamental unit. It evaluates an antibody design's binding potential by measuring how well a protein model scores the full Ab-Ag complex. We first curate, standardize, and share more than 184,500 experimental measurements of antibody mutants across 14 antibodies and 9 antigens-including influenza, lysozyme, HER2, VEGF, integrin, Ang2, and SARS-CoV-2-covering both heavy-chain and light-chain mutations. Using these datasets, we systematically compare 15 protein models including masked language models, autoregressive language models, inverse folding models, diffusion-based generative models, and geometric graph models by comparing the correlation between model likelihood and experimental affinity values. Additionally, to demonstrate AbBiBench's generative utility, we apply it to antibody F045-092 in order to introduce binding to influenza H1N1. We sample new antibody variants with the top-performing models, rank them by the structural integrity and biophysical properties of the Ab-Ag complex, and assess them with in vitro ELISA binding assays. Our findings show that structure-conditioned inverse folding models outperform others in both affinity correlation and generation tasks. Overall, AbBiBench provides a unified, biologically grounded evaluation framework to facilitate the development of more effective, function-aware antibody design models.

  • 12 authors
·
May 23, 2025

GI-GS: Global Illumination Decomposition on Gaussian Splatting for Inverse Rendering

We present GI-GS, a novel inverse rendering framework that leverages 3D Gaussian Splatting (3DGS) and deferred shading to achieve photo-realistic novel view synthesis and relighting. In inverse rendering, accurately modeling the shading processes of objects is essential for achieving high-fidelity results. Therefore, it is critical to incorporate global illumination to account for indirect lighting that reaches an object after multiple bounces across the scene. Previous 3DGS-based methods have attempted to model indirect lighting by characterizing indirect illumination as learnable lighting volumes or additional attributes of each Gaussian, while using baked occlusion to represent shadow effects. These methods, however, fail to accurately model the complex physical interactions between light and objects, making it impossible to construct realistic indirect illumination during relighting. To address this limitation, we propose to calculate indirect lighting using efficient path tracing with deferred shading. In our framework, we first render a G-buffer to capture the detailed geometry and material properties of the scene. Then, we perform physically-based rendering (PBR) only for direct lighting. With the G-buffer and previous rendering results, the indirect lighting can be calculated through a lightweight path tracing. Our method effectively models indirect lighting under any given lighting conditions, thereby achieving better novel view synthesis and relighting. Quantitative and qualitative results show that our GI-GS outperforms existing baselines in both rendering quality and efficiency.

  • 3 authors
·
Oct 3, 2024