Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

Diffusion bridge models and stochastic interpolants enable high-quality image-to-image (I2I) translation by creating paths between distributions in pixel space. However, recent diffusion bridge models excel in image translation but suffer from restricted design flexibility and complicated hyperparameter tuning, whereas Stochastic Interpolants offer greater flexibility but lack essential refinements. We show that these complementary strengths can be unified by interpreting all existing methods within a single SI-based framework. In this work, we unify and expand the space of bridge models by extending Stochastic Interpolants (SIs) with preconditioning, endpoint conditioning, and an optimized sampling algorithm. These enhancements expand the design space of diffusion bridge models, leading to state-of-the-art performance in both image quality and sampling efficiency across diverse I2I tasks. Furthermore, we identify and address a previously overlooked issue of low sample diversity under fixed conditions. We introduce a quantitative analysis for output diversity and demonstrate how we can modify the base distribution for further improvements.

Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

Recent advances in diffusion bridge models leverage Doob's $h$-transform to establish fixed endpoints between distributions, demonstrating promising results in image translation and restoration tasks. However, these approaches frequently produce blurred or excessively smoothed image details and lack a comprehensive theoretical foundation to explain these shortcomings. To address these limitations, we propose UniDB, a unified framework for diffusion bridges based on Stochastic Optimal Control (SOC). UniDB formulates the problem through an SOC-based optimization and derives a closed-form solution for the optimal controller, thereby unifying and generalizing existing diffusion bridge models. We demonstrate that existing diffusion bridges employing Doob's $h$-transform constitute a special case of our framework, emerging when the terminal penalty coefficient in the SOC cost function tends to infinity. By incorporating a tunable terminal penalty coefficient, UniDB achieves an optimal balance between control costs and terminal penalties, substantially improving detail preservation and output quality. Notably, UniDB seamlessly integrates with existing diffusion bridge models, requiring only minimal code modifications. Extensive experiments across diverse image restoration tasks validate the superiority and adaptability of the proposed framework. Our code is available at https://github.com/UniDB-SOC/UniDB/.

Diffusion bridge models have demonstrated promising performance in conditional image generation tasks, such as image restoration and translation, by initializing the generative process from corrupted images instead of pure Gaussian noise. However, existing diffusion bridge models often rely on Stochastic Differential Equation (SDE) samplers, which result in slower inference speed compared to diffusion models that employ high-order Ordinary Differential Equation (ODE) solvers for acceleration. To mitigate this gap, we propose a high-order ODE sampler with a stochastic start for diffusion bridge models. To overcome the singular behavior of the probability flow ODE (PF-ODE) at the beginning of the reverse process, a posterior sampling approach was introduced at the first reverse step. The sampling was designed to ensure a smooth transition from corrupted images to the generative trajectory while reducing discretization errors. Following this stochastic start, Heun's second-order solver is applied to solve the PF-ODE, achieving high perceptual quality with significantly reduced neural function evaluations (NFEs). Our method is fully compatible with pretrained diffusion bridge models and requires no additional training. Extensive experiments on image restoration and translation tasks, including super-resolution, JPEG restoration, Edges-to-Handbags, and DIODE-Outdoor, demonstrated that our sampler outperforms state-of-the-art methods in both visual quality and Frechet Inception Distance (FID).

The Feynman-Kac Operator Expectation Estimator (FKEE) is an innovative method for estimating the target Mathematical Expectation $\mathbb{E}_{X\sim P}[f(X)]$ without relying on a large number of samples, in contrast to the commonly used Markov Chain Monte Carlo (MCMC) Expectation Estimator. FKEE comprises diffusion bridge models and approximation of the Feynman-Kac operator. The key idea is to use the solution to the Feynmann-Kac equation at the initial time $u(x_0,0)=\mathbb{E}[f(X_T)|X_0=x_0]$. We use Physically Informed Neural Networks (PINN) to approximate the Feynman-Kac operator, which enables the incorporation of diffusion bridge models into the expectation estimator and significantly improves the efficiency of using data while substantially reducing the variance. Diffusion Bridge Model is a more general MCMC method. In order to incorporate extensive MCMC algorithms, we propose a new diffusion bridge model based on the Minimum Wasserstein distance. This diffusion bridge model is universal and reduces the training time of the PINN. FKEE also reduces the adverse impact of the curse of dimensionality and weakens the assumptions on the distribution of $X$ and performance function $f$ in the general MCMC expectation estimator. The theoretical properties of this universal diffusion bridge model are also shown. Finally, we demonstrate the advantages and potential applications of this method through various concrete experiments, including the challenging task of approximating the partition function in the random graph model such as the Ising model.