Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling

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, several challenges prevent the development of computational methods for designing diverse types of cyclic peptides. These challenges include the scarcity of 3D structural data on target proteins and associated cyclic peptide ligands, the geometric constraints that cyclization imposes, and the involvement of non-canonical amino acids in cyclization. To address the above challenges, we introduce CpSDE, which consists of two key components: AtomSDE, a generative structure prediction model based on harmonic SDE, and ResRouter, a residue type predictor. Utilizing a routed sampling algorithm that alternates between these two models to iteratively update sequences and structures, CpSDE facilitates the generation of cyclic peptides. By employing explicit all-atom and bond modeling, CpSDE overcomes existing data limitations and is proficient in designing a wide variety of cyclic peptides. Our experimental results demonstrate that the cyclic peptides designed by our method exhibit reliable stability and affinity.

Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression

Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep generative models to efficiently explore the conformational space of proteins. However, existing approaches either fail to explicitly capture the temporal dependencies between conformations or do not support direct generation of time-independent samples. To address these limitations, we introduce ConfRover, an autoregressive model that simultaneously learns protein conformation and dynamics from MD trajectories, supporting both time-dependent and time-independent sampling. At the core of our model is a modular architecture comprising: (i) an encoding layer, adapted from protein folding models, that embeds protein-specific information and conformation at each time frame into a latent space; (ii) a temporal module, a sequence model that captures conformational dynamics across frames; and (iii) an SE(3) diffusion model as the structure decoder, generating conformations in continuous space. Experiments on ATLAS, a large-scale protein MD dataset of diverse structures, demonstrate the effectiveness of our model in learning conformational dynamics and supporting a wide range of downstream tasks. ConfRover is the first model to sample both protein conformations and trajectories within a single framework, offering a novel and flexible approach for learning from protein MD data.

On the Design of KL-Regularized Policy Gradient Algorithms for LLM Reasoning

Policy gradient algorithms have been successfully applied to enhance the reasoning capabilities of large language models (LLMs). Despite the widespread use of Kullback-Leibler (KL) regularization in policy gradient algorithms to stabilize training, the systematic exploration of how different KL divergence formulations can be estimated and integrated into surrogate loss functions for online reinforcement learning (RL) presents a nuanced and systematically explorable design space. In this paper, we propose regularized policy gradient (RPG), a systematic framework for deriving and analyzing KL-regularized policy gradient methods in the online RL setting. We derive policy gradients and corresponding surrogate loss functions for objectives regularized by both forward and reverse KL divergences, considering both normalized and unnormalized policy distributions. Furthermore, we present derivations for fully differentiable loss functions as well as REINFORCE-style gradient estimators, accommodating diverse algorithmic needs. We conduct extensive experiments on RL for LLM reasoning using these methods, showing improved or competitive results in terms of training stability and performance compared to strong baselines such as GRPO, REINFORCE++, and DAPO. The code is available at https://github.com/complex-reasoning/RPG.

An All-Atom Generative Model for Designing Protein Complexes

Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in models like the series of ESM and AlphaFold. Despite these developments, the study and modeling of multi-chain proteins remain largely uncharted, though they are vital for understanding biological functions. Recognizing the importance of these interactions, we introduce APM (All-Atom Protein Generative Model), a model specifically designed for modeling multi-chain proteins. By integrating atom-level information and leveraging data on multi-chain proteins, APM is capable of precisely modeling inter-chain interactions and designing protein complexes with binding capabilities from scratch. It also performs folding and inverse-folding tasks for multi-chain proteins. Moreover, APM demonstrates versatility in downstream applications: it achieves enhanced performance through supervised fine-tuning (SFT) while also supporting zero-shot sampling in certain tasks, achieving state-of-the-art results. Code will be released at https://github.com/bytedance/apm.

Elucidating the Design Space of Multimodal Protein Language Models

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.

Variance-Dependent Regret Lower Bounds for Contextual Bandits

Variance-dependent regret bounds for linear contextual bandits, which improve upon the classical $\tilde{O}(d\sqrt{K})$ regret bound to $\tilde{O}(d\sqrt{\sum_{k=1}^K\sigma_k^2})$, where $d$ is the context dimension, $K$ is the number of rounds, and $\sigma^2_k$ is the noise variance in round $k$, has been widely studied in recent years. However, most existing works focus on the regret upper bounds instead of lower bounds. To our knowledge, the only lower bound is from Jia et al. (2024), which proved that for any eluder dimension $d_{\textbf{elu}}$ and total variance budget $\Lambda$, there exists an instance with $\sum_{k=1}^K\sigma_k^2\leq \Lambda$ for which any algorithm incurs a variance-dependent lower bound of $\Omega(\sqrt{d_{\textbf{elu}}\Lambda})$. However, this lower bound has a $\sqrt{d}$ gap with existing upper bounds. Moreover, it only considers a fixed total variance budget $\Lambda$ and does not apply to a general variance sequence $\{\sigma_1^2,\ldots,\sigma_K^2\}$. In this paper, to overcome the limitations of Jia et al. (2024), we consider the general variance sequence under two settings. For a prefixed sequence, where the entire variance sequence is revealed to the learner at the beginning of the learning process, we establish a variance-dependent lower bound of $\Omega(d \sqrt{\sum_{k=1}^K\sigma_k^2 }/\log K)$ for linear contextual bandits. For an adaptive sequence, where an adversary can generate the variance $\sigma_k^2$ in each round $k$ based on historical observations, we show that when the adversary must generate $\sigma_k^2$ before observing the decision set $\mathcal{D}_k$, a similar lower bound of $\Omega(d\sqrt{ \sum_{k=1}^K\sigma_k^2} /\log^6(dK))$ holds. In both settings, our results match the upper bounds of the SAVE algorithm (Zhao et al., 2023) up to logarithmic factors.

Global Convergence and Rich Feature Learning in $L$-Layer Infinite-Width Neural Networks under $μ$P Parametrization

Despite deep neural networks' powerful representation learning capabilities, theoretical understanding of how networks can simultaneously achieve meaningful feature learning and global convergence remains elusive. Existing approaches like the neural tangent kernel (NTK) are limited because features stay close to their initialization in this parametrization, leaving open questions about feature properties during substantial evolution. In this paper, we investigate the training dynamics of infinitely wide, $L$-layer neural networks using the tensor program (TP) framework. Specifically, we show that, when trained with stochastic gradient descent (SGD) under the Maximal Update parametrization ($\mu$P) and mild conditions on the activation function, SGD enables these networks to learn linearly independent features that substantially deviate from their initial values. This rich feature space captures relevant data information and ensures that any convergent point of the training process is a global minimum. Our analysis leverages both the interactions among features across layers and the properties of Gaussian random variables, providing new insights into deep representation learning. We further validate our theoretical findings through experiments on real-world datasets.

Energy-Weighted Flow Matching for Offline Reinforcement Learning

This paper investigates energy guidance in generative modeling, where the target distribution is defined as $q(\mathbf x) \propto p(\mathbf x)\exp(-\beta \mathcal E(\mathbf x))$, with $p(\mathbf x)$ being the data distribution and $\mathcal E(\mathcal x)$ as the energy function. To comply with energy guidance, existing methods often require auxiliary procedures to learn intermediate guidance during the diffusion process. To overcome this limitation, we explore energy-guided flow matching, a generalized form of the diffusion process. We introduce energy-weighted flow matching (EFM), a method that directly learns the energy-guided flow without the need for auxiliary models. Theoretical analysis shows that energy-weighted flow matching accurately captures the guided flow. Additionally, we extend this methodology to energy-weighted diffusion models and apply it to offline reinforcement learning (RL) by proposing the Q-weighted Iterative Policy Optimization (QIPO). Empirically, we demonstrate that the proposed QIPO algorithm improves performance in offline RL tasks. Notably, our algorithm is the first energy-guided diffusion model that operates independently of auxiliary models and the first exact energy-guided flow matching model in the literature.

Understanding SGD with Exponential Moving Average: A Case Study in Linear Regression

Exponential moving average (EMA) has recently gained significant popularity in training modern deep learning models, especially diffusion-based generative models. However, there have been few theoretical results explaining the effectiveness of EMA. In this paper, to better understand EMA, we establish the risk bound of online SGD with EMA for high-dimensional linear regression, one of the simplest overparameterized learning tasks that shares similarities with neural networks. Our results indicate that (i) the variance error of SGD with EMA is always smaller than that of SGD without averaging, and (ii) unlike SGD with iterate averaging from the beginning, the bias error of SGD with EMA decays exponentially in every eigen-subspace of the data covariance matrix. Additionally, we develop proof techniques applicable to the analysis of a broad class of averaging schemes.

Multi-Step Alignment as Markov Games: An Optimistic Online Gradient Descent Approach with Convergence Guarantees

Reinforcement Learning from Human Feedback (RLHF) has been highly successful in aligning large language models with human preferences. While prevalent methods like DPO have demonstrated strong performance, they frame interactions with the language model as a bandit problem, which limits their applicability in real-world scenarios where multi-turn conversations are common. Additionally, DPO relies on the Bradley-Terry model assumption, which does not adequately capture the non-transitive nature of human preferences. In this paper, we address these challenges by modeling the alignment problem as a two-player constant-sum Markov game, where each player seeks to maximize their winning rate against the other across all steps of the conversation. Our approach Multi-step Preference Optimization (MPO) is built upon the natural actor-critic framework~\citep{peters2008natural}. We further develop OMPO based on the optimistic online gradient descent algorithm~\citep{rakhlin2013online,joulani17a}. Theoretically, we provide a rigorous analysis for both algorithms on convergence and show that OMPO requires $\mathcal{O}(\epsilon^{-1})$ policy updates to converge to an $\epsilon$-approximate Nash equilibrium. We also validate the effectiveness of our method on multi-turn conversations dataset and math reasoning dataset.