Diffusion and flow matching models have recently emerged as promising approaches for peptide binder design. Despite their progress, these models still face two major challenges. First, categorical sampling of discrete residue types collapses their continuous parameters into onehot assignments, while continuous variables (e.g., atom positions) evolve smoothly throughout the generation process. This mismatch disrupts the update dynamics and results in suboptimal performance. Second, current models assume unimodal distributions for side-chain torsion angles, which conflicts with the inherently multimodal nature of side chain rotameric states and limits prediction accuracy. To address these limitations, we introduce PepBFN, the first Bayesian flow network for full atom peptide design that directly models parameter distributions in fully continuous space. Specifically, PepBFN models discrete residue types by learning their continuous parameter distributions, enabling joint and smooth Bayesian updates with other continuous structural parameters. It further employs a novel Gaussian mixture based Bayesian flow to capture the multimodal side chain rotameric states and a Matrix Fisher based Riemannian flow to directly model residue orientations on the $\mathrm{SO}(3)$ manifold. Together, these parameter distributions are progressively refined via Bayesian updates, yielding smooth and coherent peptide generation. Experiments on side chain packing, reverse folding, and binder design tasks demonstrate the strong potential of PepBFN in computational peptide design.

Inverse problems lie at the heart of modern imaging science, with broad applications in areas such as medical imaging, remote sensing, and microscopy. Recent years have witnessed a paradigm shift in solving imaging inverse problems, where data-driven regularizers are used increasingly, leading to remarkably high-fidelity reconstruction. A particularly notable approach for data-driven regularization is to use learned image denoisers as implicit priors in iterative image reconstruction algorithms. This chapter presents a comprehensive overview of this powerful and emerging class of algorithms, commonly referred to as plug-and-play (PnP) methods. We begin by providing a brief background on image denoising and inverse problems, followed by a short review of traditional regularization strategies. We then explore how proximal splitting algorithms, such as the alternating direction method of multipliers (ADMM) and proximal gradient descent (PGD), can naturally accommodate learned denoisers in place of proximal operators, and under what conditions such replacements preserve convergence. The role of Tweedie's formula in connecting optimal Gaussian denoisers and score estimation is discussed, which lays the foundation for regularization-by-denoising (RED) and more recent diffusion-based posterior sampling methods. We discuss theoretical advances regarding the convergence of PnP algorithms, both within the RED and proximal settings, emphasizing the structural assumptions that the denoiser must satisfy for convergence, such as non-expansiveness, Lipschitz continuity, and local homogeneity. We also address practical considerations in algorithm design, including choices of denoiser architecture and acceleration strategies.

Reliable uncertainty quantification is critical for trustworthy AI. Conformal Prediction (CP) provides prediction sets with distribution-free coverage guarantees, but its two main variants face complementary limitations. Split CP (SCP) suffers from data inefficiency due to dataset partitioning, while full CP (FCP) improves data efficiency at the cost of prohibitive retraining complexity. Recent approaches based on meta-learning or in-context learning (ICL) partially mitigate these drawbacks. However, they rely on training procedures not specifically tailored to CP, which may yield large prediction sets. We introduce an efficient FCP framework, termed enhanced ICL-based FCP (E-ICL+FCP), which employs a permutation-invariant Transformer-based ICL model trained with a CP-aware loss. By simulating the multiple retrained models required by FCP without actual retraining, E-ICL+FCP preserves coverage while markedly reducing both inefficiency and computational overhead. Experiments on synthetic and real tasks demonstrate that E-ICL+FCP attains superior efficiency-coverage trade-offs compared to existing SCP and FCP baselines.

We propose Energy-based generator matching (EGM), a modality-agnostic approach to train generative models from energy functions in the absence of data. Extending the recently proposed generator matching, EGM enables training of arbitrary continuous-time Markov processes, e.g., diffusion, flow, and jump, and can generate data from continuous, discrete, and a mixture of two modalities. To this end, we propose estimating the generator matching loss using self-normalized importance sampling with an additional bootstrapping trick to reduce variance in the importance weight. We validate EGM on both discrete and multimodal tasks up to 100 and 20 dimensions, respectively.

Bayesian Optimization is critically vulnerable to extreme outliers. Existing provably robust methods typically assume a bounded cumulative corruption budget, which makes them defenseless against even a single corruption of sufficient magnitude. To address this, we introduce a new adversary whose budget is only bounded in the frequency of corruptions, not in their magnitude. We then derive RCGP-UCB, an algorithm coupling the famous upper confidence bound (UCB) approach with a Robust Conjugate Gaussian Process (RCGP). We present stable and adaptive versions of RCGP-UCB, and prove that they achieve sublinear regret in the presence of up to $O(T^{1/2})$ and $O(T^{1/3})$ corruptions with possibly infinite magnitude. This robustness comes at near zero cost: without outliers, RCGP-UCB's regret bounds match those of the standard GP-UCB algorithm.

Approaches based on point processes provide a principled statistical framework for modeling neural spiking activity.

However, training EBMs on data in discrete or mixed state spaces poses significant challenges due to the lack of robust and fast sampling methods. In this work, we propose to train discrete EBMs with Energy Discrepancy, a loss function which only requires the evaluation of the energy function at data points and their perturbed counterparts, thus eliminating the need for Markov chain Monte Carlo.

The fundamental building block for drug discovery is molecule geometry and thus, the molecule's geometrical

Specifically, we lay the foundation within the Bayesian framework.

Recent work [Ma et al., 2019] shows that in the non-convex case, sampling