MARS: Unleashing the Power of Variance Reduction for Training Large Models

Training deep neural networks--and more recently, large models--demands efficient and scalable optimizers. Adaptive gradient algorithms like Adam, AdamW, and their variants have been central to this task. Despite the development of numerous variance reduction algorithms in the past decade aimed at accelerating stochastic optimization in both convex and nonconvex settings, variance reduction has not found widespread success in training deep neural networks or large language models. Consequently, it has remained a less favored approach in modern AI. In this paper, to unleash the power of variance reduction for efficient training of large models, we propose a unified optimization framework, MARS (Make vAriance Reduction Shine), which reconciles preconditioned gradient methods with variance reduction via a scaled stochastic recursive momentum technique. Within our framework, we introduce three instances of MARS that leverage preconditioned gradient updates based on AdamW, Lion, and Shampoo, respectively. We also draw a connection between our algorithms and existing optimizers. Experimental results on training GPT-2 models indicate that MARS consistently outperforms AdamW by a large margin.

ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design

Nature creates diverse proteins through a `divide and assembly' strategy. Inspired by this idea, we introduce ProteinWeaver, a two-stage framework for protein backbone design. Our method first generates individual protein domains and then employs an SE(3) diffusion model to flexibly assemble these domains. A key challenge lies in the assembling step, given the complex and rugged nature of the inter-domain interaction landscape. To address this challenge, we employ preference alignment to discern complex relationships between structure and interaction landscapes through comparative analysis of generated samples. Comprehensive experiments demonstrate that ProteinWeaver: (1) generates high-quality, novel protein backbones through versatile domain assembly; (2) outperforms RFdiffusion, the current state-of-the-art in backbone design, by 13\% and 39\% for long-chain proteins; (3) shows the potential for cooperative function design through illustrative case studies. To sum up, by introducing a `divide-and-assembly' paradigm, ProteinWeaver advances protein engineering and opens new avenues for functional protein design.

Sharp Analysis for KL-Regularized Contextual Bandits and RLHF

Reverse-Kullback-Leibler (KL) regularization has emerged to be a predominant technique used to enhance policy optimization in reinforcement learning (RL) and reinforcement learning from human feedback (RLHF), which forces the learned policy to stay close to a reference policy. While the effectiveness and necessity of KL-regularization have been empirically demonstrated in various practical scenarios, current theoretical analysis of KL-regularized RLHF still obtains the same $\mathcal{O}(1 / \epsilon^2)$ sample complexity as problems without KL-regularization. To understand the fundamental distinction between policy learning objectives with KL-regularization and ones without KL-regularization, we are the first to theoretically demonstrate the power of KL-regularization by providing a sharp analysis for KL-regularized contextual bandits and RLHF, revealing an $\mathcal{O}(1 / \epsilon)$ sample complexity when $\epsilon$ is sufficiently small. We further explore the role of data coverage in contextual bandits and RLHF. While the coverage assumption is commonly employed in offline RLHF to link the samples from the reference policy to the optimal policy, often at the cost of a multiplicative dependence on the coverage coefficient, its impact on the sample complexity of online RLHF remains unclear. Previous theoretical analyses of online RLHF typically require explicit exploration and additional structural assumptions on the reward function class. In contrast, we show that with sufficient coverage from the reference policy, a simple two-stage mixed sampling strategy can achieve a sample complexity with only an additive dependence on the coverage coefficient. Our results provide a comprehensive understanding of the roles of KL-regularization and data coverage in RLHF, shedding light on the design of more efficient RLHF algorithms.

CoPS: Empowering LLM Agents with Provable Cross-Task Experience Sharing

Sequential reasoning in agent systems has been significantly advanced by large language models (LLMs), yet existing approaches face limitations. Reflection-driven reasoning relies solely on knowledge in pretrained models, limiting performance in novel scenarios, while experience-assisted reasoning often depends on external experiences and lacks clear principles for selecting representative experiences. We address these limitations by proposing CoPS (Cross-Task Experience Sharing), a generalizable algorithm that enhances sequential reasoning by cross-task experience sharing and selection. In detail, CoPS leverages agents' experiences on previous tasks, selecting distribution-matched experiences via a provable pessimism-based strategy to maximize utility while minimizing risks from distribution shifts. Extensive experimental results on benchmarks like Alfworld, Webshop, and HotPotQA demonstrate that CoPS consistently outperforms state-of-the-art baselines, with superior sample efficiency suitable for resource-constrained scenarios. Theoretically, we show that the performance of our algorithm depends on both the quality of the pretrained LLM and the matching between the agent's task-dependent trial distribution and that generated by the LLM. Our work bridges the gap between existing sequential reasoning paradigms and validates the effectiveness of leveraging cross-task experiences, shedding light on the potential to improve agents' generalization and adaptability across diverse tasks. Our codes are available at $\href{https://github.com/uclaml/COPS}{\text{https://github.com/uclaml/COPS}}$.

Unified Convergence Analysis for Score-Based Diffusion Models with Deterministic Samplers

Score-based diffusion models have emerged as powerful techniques for generating samples from high-dimensional data distributions. These models involve a two-phase process: first, injecting noise to transform the data distribution into a known prior distribution, and second, sampling to recover the original data distribution from noise. Among the various sampling methods, deterministic samplers stand out for their enhanced efficiency. However, analyzing these deterministic samplers presents unique challenges, as they preclude the use of established techniques such as Girsanov's theorem, which are only applicable to stochastic samplers. Furthermore, existing analysis for deterministic samplers usually focuses on specific examples, lacking a generalized approach for general forward processes and various deterministic samplers. Our paper addresses these limitations by introducing a unified convergence analysis framework. To demonstrate the power of our framework, we analyze the variance-preserving (VP) forward process with the exponential integrator (EI) scheme, achieving iteration complexity of $\tilde O(d^2/\epsilon)$. Additionally, we provide a detailed analysis of Denoising Diffusion Implicit Models (DDIM)-type samplers, which have been underexplored in previous research, achieving polynomial iteration complexity.

DPLM-2: A Multimodal Diffusion Protein Language Model

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Enhancing Multi-Step Reasoning Abilities of Language Models through Direct Q-Function Optimization

Reinforcement Learning (RL) plays a crucial role in aligning large language models (LLMs) with human preferences and improving their ability to perform complex tasks. However, current approaches either require significant computational resources due to the use of multiple models and extensive online sampling for training (e.g., PPO) or are framed as bandit problems (e.g., DPO, DRO), which often struggle with multi-step reasoning tasks, such as math problem-solving and complex reasoning that involve long chains of thought. To overcome these limitations, we introduce Direct Q-function Optimization (DQO), which formulates the response generation process as a Markov Decision Process (MDP) and utilizes the soft actor-critic (SAC) framework to optimize a Q-function directly parameterized by the language model. The MDP formulation of DQO offers structural advantages over bandit-based methods, enabling more effective process supervision. Experimental results on two math problem-solving datasets, GSM8K and MATH, demonstrate that DQO outperforms previous methods, establishing it as a promising offline reinforcement learning approach for aligning language models.

CryoFM: A Flow-based Foundation Model for Cryo-EM Densities

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CRYOFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

Accelerated Preference Optimization for Large Language Model Alignment

Reinforcement Learning from Human Feedback (RLHF) has emerged as a pivotal tool for aligning large language models (LLMs) with human preferences. Direct Preference Optimization (DPO), one of the most popular approaches, formulates RLHF as a policy optimization problem without explicitly estimating the reward function. It overcomes the stability and efficiency issues of two-step approaches, which typically involve first estimating the reward function and then optimizing the policy via proximal policy optimization (PPO). Since RLHF is essentially an optimization problem, and it is well-known that momentum techniques can accelerate optimization both theoretically and empirically, a natural question arises: Can RLHF be accelerated by momentum? This paper answers this question in the affirmative. In detail, we first show that the iterative preference optimization method can be viewed as a proximal point method. Based on this observation, we propose a general Accelerated Preference Optimization (APO) framework, which unifies many existing preference optimization algorithms and employs Nesterov's momentum technique to speed up the alignment of LLMs. Theoretically, we demonstrate that APO can achieve a faster convergence rate than the standard iterative preference optimization methods, including DPO and Self-Play Preference Optimization (SPPO). Empirically, we show the superiority of APO over DPO, iterative DPO, and other strong baselines for RLHF on the AlpacaEval 2.0 benchmark.

Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis

Diffusion models have achieved great success in generating high-dimensional samples across various applications. While the theoretical guarantees for continuous-state diffusion models have been extensively studied, the convergence analysis of the discrete-state counterparts remains under-explored. In this paper, we study the theoretical aspects of score-based discrete diffusion models under the Continuous Time Markov Chain (CTMC) framework. We introduce a discrete-time sampling algorithm in the general state space $[S]^d$ that utilizes score estimators at predefined time points. We derive convergence bounds for the Kullback-Leibler (KL) divergence and total variation (TV) distance between the generated sample distribution and the data distribution, considering both scenarios with and without early stopping under specific assumptions. Notably, our KL divergence bounds are nearly linear in dimension $d$, aligning with state-of-the-art results for diffusion models. Our convergence analysis employs a Girsanov-based method and establishes key properties of the discrete score function, which are essential for characterizing the discrete-time sampling process.