Quanquan Gu

Xiwei Cheng, Xiangxin Zhou, Yuwei Yang et al.

Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which hinders the models' generation capabilities. Recently, Direct Preference Optimization (DPO) has emerged as a pivotal tool for aligning generative models with human preferences. In this paper, we propose DecompDPO, a structure-based optimization method aligns diffusion models with pharmaceutical needs using multi-granularity preference pairs. DecompDPO introduces decomposition into the optimization objectives and obtains preference pairs at the molecule or decomposed substructure level based on each objective's decomposability. Additionally, DecompDPO introduces a physics-informed energy term to ensure reasonable molecular conformations in the optimization results. Notably, DecompDPO can be effectively used for two main purposes: (1) fine-tuning pretrained diffusion models for molecule generation across various protein families, and (2) molecular optimization given a specific protein subpocket after generation. Extensive experiments on the CrossDocked2020 benchmark show that DecompDPO significantly improves model performance, achieving up to 95.2% Med. High Affinity and a 36.2% success rate for molecule generation, and 100% Med. High Affinity and a 52.1% success rate for molecular optimization. Code is available at https://github.com/laviaf/DecompDPO.

Xiangxin Zhou, Dongyu Xue, Ruizhe Chen et al.

Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nature. In this paper, we tackle antigen-specific antibody sequence-structure co-design as an optimization problem towards specific preferences, considering both rationality and functionality. Leveraging a pre-trained conditional diffusion model that jointly models sequences and structures of antibodies with equivariant neural networks, we propose direct energy-based preference optimization to guide the generation of antibodies with both rational structures and considerable binding affinities to given antigens. Our method involves fine-tuning the pre-trained diffusion model using a residue-level decomposed energy preference. Additionally, we employ gradient surgery to address conflicts between various types of energy, such as attraction and repulsion. Experiments on RAbD benchmark show that our approach effectively optimizes the energy of generated antibodies and achieves state-of-the-art performance in designing high-quality antibodies with low total energy and high binding affinity simultaneously, demonstrating the superiority of our approach.

Xiangxin Zhou, Mingyu Li, Yi Xiao et al.

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.

Yuanzhe Tao, Huizhuo Yuan, Xun Zhou et al.

Optimization algorithms such as AdaGrad and Adam have significantly advanced the training of deep models by dynamically adjusting the learning rate during the optimization process. However, adhoc tuning of learning rates poses a challenge, leading to inefficiencies in practice. To address this issue, recent research has focused on developing "learning-rate-free" or "parameter-free" algorithms that operate effectively without the need for learning rate tuning. Despite these efforts, existing parameter-free variants of AdaGrad and Adam tend to be overly complex and/or lack formal convergence guarantees. In this paper, we present AdaGrad++ and Adam++, novel and simple parameter-free variants of AdaGrad and Adam with convergence guarantees. We prove that AdaGrad++ achieves comparable convergence rates to AdaGrad in convex optimization without predefined learning rate assumptions. Similarly, Adam++ matches the convergence rate of Adam without relying on any conditions on the learning rates. Experimental results across various deep learning tasks validate the competitive performance of AdaGrad++ and Adam++.

Yuning Shen, Lihao Wang, Huizhuo Yuan et al.

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.

Qiwei Di, Kaixuan Ji, Xuheng Li et al.

LLM inference often generates a batch of candidates for a prompt and selects one via strategies like majority voting or Best-of- N (BoN). For difficult tasks, this single-shot selection often underperforms. Consequently, evaluations commonly report Pass@$k$: the agent may submit up to $k$ responses, and only the best of them is used when computing regret. Motivated by this, we study inference scaling in the more general Pass@$k$ inference setting, and prove that neither majority voting nor BoN exhibits the desirable scaling with $k$ and the sampling budget $N$. Combining the advantages of majority voting and BoN, we propose a new inference strategy called Best-of-Majority (BoM), with a pivotal step that restricts the candidates to the responses with high frequency in the $N$ samples before selecting the top-$k$ rewards. We prove that when the sampling budget is $N=\tildeΩ(C^*)$, the regret of BoM is $O(ε_{\mathrm{opt}}+\sqrt{ε_{\mathrm{RM}}^2C^*/k})$, where $C^*$ is the coverage coefficient, $ε_{\mathrm{RM}}$ is the estimation error of the reward model, and $ε_{\mathrm{opt}}$ is the estimation error of reward at the optimal response. We further establish a matching lower bound, certifying that our algorithm is minimax optimal. Beyond optimality, BoM has a key advantage: unlike majority voting and BoN, its performance does not degrade when increasing $N$. Experimental results of inference on math problems show BoM outperforming both majority voting and BoN.