The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event sampling and long equilibration time problems, hindering their applications in general protein systems. Recently, deep generative modeling techniques, especially diffusion models, have been employed to generate novel protein conformations. However, existing score-based diffusion methods cannot properly incorporate important physical prior knowledge to guide the generation process, causing large deviations in the sampled protein conformations from the equilibrium distribution. In this paper, to overcome these limitations, we propose a force-guided SE(3) diffusion model, ConfDiff, for protein conformation generation. By incorporating a force-guided network with a mixture of data-based score models, ConfDiff can can generate protein conformations with rich diversity while preserving high fidelity. Experiments on a variety of protein conformation prediction tasks, including 12 fast-folding proteins and the Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our method surpasses the state-of-the-art method.
Real-world multi-agent systems are often dynamic and continuous, where the agents co-evolve and undergo changes in their trajectories and interactions over time. For example, the COVID-19 transmission in the U.S. can be viewed as a multi-agent system, where states act as agents and daily population movements between them are interactions. Estimating the counterfactual outcomes in such systems enables accurate future predictions and effective decision-making, such as formulating COVID-19 policies. However, existing methods fail to model the continuous dynamic effects of treatments on the outcome, especially when multiple treatments (e.g., "stay-at-home" and "get-vaccine" policies) are applied simultaneously. To tackle this challenge, we propose Causal Graph Ordinary Differential Equations (CAG-ODE), a novel model that captures the continuous interaction among agents using a Graph Neural Network (GNN) as the ODE function. The key innovation of our model is to learn time-dependent representations of treatments and incorporate them into the ODE function, enabling precise predictions of potential outcomes. To mitigate confounding bias, we further propose two domain adversarial learning-based objectives, which enable our model to learn balanced continuous representations that are not affected by treatments or interference. Experiments on two datasets (i.e., COVID-19 and tumor growth) demonstrate the superior performance of our proposed model.
This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance.
Fine-tuning Diffusion Models remains an underexplored frontier in generative artificial intelligence (GenAI), especially when compared with the remarkable progress made in fine-tuning Large Language Models (LLMs). While cutting-edge diffusion models such as Stable Diffusion (SD) and SDXL rely on supervised fine-tuning, their performance inevitably plateaus after seeing a certain volume of data. Recently, reinforcement learning (RL) has been employed to fine-tune diffusion models with human preference data, but it requires at least two images ("winner" and "loser" images) for each text prompt. In this paper, we introduce an innovative technique called self-play fine-tuning for diffusion models (SPIN-Diffusion), where the diffusion model engages in competition with its earlier versions, facilitating an iterative self-improvement process. Our approach offers an alternative to conventional supervised fine-tuning and RL strategies, significantly improving both model performance and alignment. Our experiments on the Pick-a-Pic dataset reveal that SPIN-Diffusion outperforms the existing supervised fine-tuning method in aspects of human preference alignment and visual appeal right from its first iteration. By the second iteration, it exceeds the performance of RLHF-based methods across all metrics, achieving these results with less data.
This study tackles the challenges of adversarial corruption in model-based reinforcement learning (RL), where the transition dynamics can be corrupted by an adversary. Existing studies on corruption-robust RL mostly focus on the setting of model-free RL, where robust least-square regression is often employed for value function estimation. However, these techniques cannot be directly applied to model-based RL. In this paper, we focus on model-based RL and take the maximum likelihood estimation (MLE) approach to learn transition model. Our work encompasses both online and offline settings. In the online setting, we introduce an algorithm called corruption-robust optimistic MLE (CR-OMLE), which leverages total-variation (TV)-based information ratios as uncertainty weights for MLE. We prove that CR-OMLE achieves a regret of $\tilde{\mathcal{O}}(\sqrt{T} + C)$, where $C$ denotes the cumulative corruption level after $T$ episodes. We also prove a lower bound to show that the additive dependence on $C$ is optimal. We extend our weighting technique to the offline setting, and propose an algorithm named corruption-robust pessimistic MLE (CR-PMLE). Under a uniform coverage condition, CR-PMLE exhibits suboptimality worsened by $\mathcal{O}(C/n)$, nearly matching the lower bound. To the best of our knowledge, this is the first work on corruption-robust model-based RL algorithms with provable guarantees.
Aligning large language models (LLM) with human preference plays a key role in building modern generative models and can be achieved by reinforcement learning from human feedback (RLHF). Despite their superior performance, current RLHF approaches often require a large amount of human-labelled preference data, which is expensive to collect. In this paper, inspired by the success of active learning, we address this problem by proposing query-efficient RLHF methods. We first formalize the alignment problem as a contextual dueling bandit problem and design an active-query-based proximal policy optimization (APPO) algorithm with an $\tilde{O}(d^2/\Delta)$ regret bound and an $\tilde{O}(d^2/\Delta^2)$ query complexity, where $d$ is the dimension of feature space and $\Delta$ is the sub-optimality gap over all the contexts. We then propose ADPO, a practical version of our algorithm based on direct preference optimization (DPO) and apply it to fine-tuning LLMs. Our experiments show that ADPO, while only making about half of queries for human preference, matches the performance of the state-of-the-art DPO method.
We study the Stochastic Shortest Path (SSP) problem with a linear mixture transition kernel, where an agent repeatedly interacts with a stochastic environment and seeks to reach certain goal state while minimizing the cumulative cost. Existing works often assume a strictly positive lower bound of the cost function or an upper bound of the expected length for the optimal policy. In this paper, we propose a new algorithm to eliminate these restrictive assumptions. Our algorithm is based on extended value iteration with a fine-grained variance-aware confidence set, where the variance is estimated recursively from high-order moments. Our algorithm achieves an $\tilde{\mathcal O}(dB_*\sqrt{K})$ regret bound, where $d$ is the dimension of the feature mapping in the linear transition kernel, $B_*$ is the upper bound of the total cumulative cost for the optimal policy, and $K$ is the number of episodes. Our regret upper bound matches the $\Omega(dB_*\sqrt{K})$ lower bound of linear mixture SSPs in Min et al. (2022), which suggests that our algorithm is nearly minimax optimal.
The advancement of Large Vision-Language Models (LVLMs) has increasingly highlighted the critical issue of their tendency to hallucinate non-existing objects in the images. To address this issue, previous works focused on using specially curated datasets or powerful LLMs (e.g., GPT-3.5) to rectify the outputs of LVLMs. However, these approaches require either expensive training/fine-tuning or API access to advanced LLMs to correct the model's output post-generation. In this paper, we tackle this challenge by introducing a framework called Mitigating hallucinAtion via classifieR-Free guIdaNcE (MARINE), which is both training-free and API-free, and can effectively and efficiently reduce object hallucinations during the generation process. Specifically, MARINE enriches the visual context of LVLMs by integrating existing open-source vision models, and employs classifier-free guidance to incorporate the additional object grounding features to improve the precision of LVLMs' generations. Through comprehensive evaluations across $6$ popular LVLMs with diverse evaluation metrics, we demonstrate the effectiveness of MARINE, which even outperforms existing fine-tuning-based methods. Remarkably, it not only reduces hallucinations but also improves the detailedness of LVLMs' generations, as assessed by GPT-4V.
Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.