Decomposed Direct Preference Optimization for Structure-Based Drug Design

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 the alignment of generative models such as large language models and diffusion models, providing greater flexibility and accuracy by directly aligning model outputs with human preferences. Building on this advancement, we introduce DPO to SBDD in this paper. We tailor diffusion models to pharmaceutical needs by aligning them with elaborately designed chemical score functions. We propose a new structure-based molecular optimization method called DecompDPO, which decomposes the molecule into arms and scaffolds and performs preference optimization at both local substructure and global molecule levels, allowing for more precise control with fine-grained preferences. 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 in both molecule generation and optimization, with up to 100% Median High Affinity and a 54.9% Success Rate.

Uncertainty-Aware Reward-Free Exploration with General Function Approximation

Mastering multiple tasks through exploration and learning in an environment poses a significant challenge in reinforcement learning (RL). Unsupervised RL has been introduced to address this challenge by training policies with intrinsic rewards rather than extrinsic rewards. However, current intrinsic reward designs and unsupervised RL algorithms often overlook the heterogeneous nature of collected samples, thereby diminishing their sample efficiency. To overcome this limitation, in this paper, we propose a reward-free RL algorithm called \alg. The key idea behind our algorithm is an uncertainty-aware intrinsic reward for exploring the environment and an uncertainty-weighted learning process to handle heterogeneous uncertainty in different samples. Theoretically, we show that in order to find an $\epsilon$-optimal policy, GFA-RFE needs to collect $\tilde{O} (H^2 \log N_{\mathcal F} (\epsilon) \mathrm{dim} (\mathcal F) / \epsilon^2 )$ number of episodes, where $\mathcal F$ is the value function class with covering number $N_{\mathcal F} (\epsilon)$ and generalized eluder dimension $\mathrm{dim} (\mathcal F)$. Such a result outperforms all existing reward-free RL algorithms. We further implement and evaluate GFA-RFE across various domains and tasks in the DeepMind Control Suite. Experiment results show that GFA-RFE outperforms or is comparable to the performance of state-of-the-art unsupervised RL algorithms.

Self-Play Preference Optimization for Language Model Alignment

Traditional reinforcement learning from human feedback (RLHF) approaches relying on parametric models like the Bradley-Terry model fall short in capturing the intransitivity and irrationality in human preferences. Recent advancements suggest that directly working with preference probabilities can yield a more accurate reflection of human preferences, enabling more flexible and accurate language model alignment. In this paper, we propose a self-play-based method for language model alignment, which treats the problem as a constant-sum two-player game aimed at identifying the Nash equilibrium policy. Our approach, dubbed \textit{Self-Play Preference Optimization} (SPPO), approximates the Nash equilibrium through iterative policy updates and enjoys theoretical convergence guarantee. Our method can effectively increase the log-likelihood of the chosen response and decrease that of the rejected response, which cannot be trivially achieved by symmetric pairwise loss such as Direct Preference Optimization (DPO) and Identity Preference Optimization (IPO). In our experiments, using only 60k prompts (without responses) from the UltraFeedback dataset and without any prompt augmentation, by leveraging a pre-trained preference model PairRM with only 0.4B parameters, SPPO can obtain a model from fine-tuning Mistral-7B-Instruct-v0.2 that achieves the state-of-the-art length-controlled win-rate of 28.53% against GPT-4-Turbo on AlpacaEval 2.0. It also outperforms the (iterative) DPO and IPO on MT-Bench and the Open LLM Leaderboard. Notably, the strong performance of SPPO is achieved without additional external supervision (e.g., responses, preferences, etc.) from GPT-4 or other stronger language models.

Matching the Statistical Query Lower Bound for k-sparse Parity Problems with Stochastic Gradient Descent

The $k$-parity problem is a classical problem in computational complexity and algorithmic theory, serving as a key benchmark for understanding computational classes. In this paper, we solve the $k$-parity problem with stochastic gradient descent (SGD) on two-layer fully-connected neural networks. We demonstrate that SGD can efficiently solve the $k$-sparse parity problem on a $d$-dimensional hypercube ($k\le O(\sqrt{d})$) with a sample complexity of $\tilde{O}(d^{k-1})$ using $2^{\Theta(k)}$ neurons, thus matching the established $\Omega(d^{k})$ lower bounds of Statistical Query (SQ) models. Our theoretical analysis begins by constructing a good neural network capable of correctly solving the $k$-parity problem. We then demonstrate how a trained neural network with SGD can effectively approximate this good network, solving the $k$-parity problem with small statistical errors. Our theoretical results and findings are supported by empirical evidence, showcasing the efficiency and efficacy of our approach.

Guided Discrete Diffusion for Electronic Health Record Generation

Electronic health records (EHRs) are a pivotal data source that enables numerous applications in computational medicine, e.g., disease progression prediction, clinical trial design, and health economics and outcomes research. Despite wide usability, their sensitive nature raises privacy and confidentially concerns, which limit potential use cases. To tackle these challenges, we explore the use of generative models to synthesize artificial, yet realistic EHRs. While diffusion-based methods have recently demonstrated state-of-the-art performance in generating other data modalities and overcome the training instability and mode collapse issues that plague previous GAN-based approaches, their applications in EHR generation remain underexplored. The discrete nature of tabular medical code data in EHRs poses challenges for high-quality data generation, especially for continuous diffusion models. To this end, we introduce a novel tabular EHR generation method, EHR-D3PM, which enables both unconditional and conditional generation using the discrete diffusion model. Our experiments demonstrate that EHR-D3PM significantly outperforms existing generative baselines on comprehensive fidelity and utility metrics while maintaining less membership vulnerability risks. Furthermore, we show EHR-D3PM is effective as a data augmentation method and enhances performance on downstream tasks when combined with real data.

Nearly Optimal Algorithms for Contextual Dueling Bandits from Adversarial Feedback

Learning from human feedback plays an important role in aligning generative models, such as large language models (LLM). However, the effectiveness of this approach can be influenced by adversaries, who may intentionally provide misleading preferences to manipulate the output in an undesirable or harmful direction. To tackle this challenge, we study a specific model within this problem domain--contextual dueling bandits with adversarial feedback, where the true preference label can be flipped by an adversary. We propose an algorithm namely robust contextual dueling bandit (\algo), which is based on uncertainty-weighted maximum likelihood estimation. Our algorithm achieves an $\tilde O(d\sqrt{T}+dC)$ regret bound, where $T$ is the number of rounds, $d$ is the dimension of the context, and $ 0 \le C \le T$ is the total number of adversarial feedback. We also prove a lower bound to show that our regret bound is nearly optimal, both in scenarios with and without ($C=0$) adversarial feedback. Additionally, we conduct experiments to evaluate our proposed algorithm against various types of adversarial feedback. Experimental results demonstrate its superiority over the state-of-the-art dueling bandit algorithms in the presence of adversarial feedback.

Settling Constant Regrets in Linear Markov Decision Processes

We study the constant regret guarantees in reinforcement learning (RL). Our objective is to design an algorithm that incurs only finite regret over infinite episodes with high probability. We introduce an algorithm, Cert-LSVI-UCB, for misspecified linear Markov decision processes (MDPs) where both the transition kernel and the reward function can be approximated by some linear function up to misspecification level $\zeta$. At the core of Cert-LSVI-UCB is an innovative certified estimator, which facilitates a fine-grained concentration analysis for multi-phase value-targeted regression, enabling us to establish an instance-dependent regret bound that is constant w.r.t. the number of episodes. Specifically, we demonstrate that for an MDP characterized by a minimal suboptimality gap $\Delta$, Cert-LSVI-UCB has a cumulative regret of $\tilde{\mathcal{O}}(d^3H^5/\Delta)$ with high probability, provided that the misspecification level $\zeta$ is below $\tilde{\mathcal{O}}(\Delta / (\sqrt{d}H^2))$. Remarkably, this regret bound remains constant relative to the number of episodes $K$. To the best of our knowledge, Cert-LSVI-UCB is the first algorithm to achieve a constant, instance-dependent, high-probability regret bound in RL with linear function approximation for infinite runs without relying on prior distribution assumptions. This not only highlights the robustness of Cert-LSVI-UCB to model misspecification but also introduces novel algorithmic designs and analytical techniques of independent interest.

Feel-Good Thompson Sampling for Contextual Dueling Bandits

Contextual dueling bandits, where a learner compares two options based on context and receives feedback indicating which was preferred, extends classic dueling bandits by incorporating contextual information for decision-making and preference learning. Several algorithms based on the upper confidence bound (UCB) have been proposed for linear contextual dueling bandits. However, no algorithm based on posterior sampling has been developed in this setting, despite the empirical success observed in traditional contextual bandits. In this paper, we propose a Thompson sampling algorithm, named FGTS.CDB, for linear contextual dueling bandits. At the core of our algorithm is a new Feel-Good exploration term specifically tailored for dueling bandits. This term leverages the independence of the two selected arms, thereby avoiding a cross term in the analysis. We show that our algorithm achieves nearly minimax-optimal regret, i.e., $\tilde{\mathcal{O}}(d\sqrt T)$, where $d$ is the model dimension and $T$ is the time horizon. Finally, we evaluate our algorithm on synthetic data and observe that FGTS.CDB outperforms existing algorithms by a large margin.

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization

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 design as a protein sequence-structure co-design problem, considering both rationality and functionality. Leveraging a pre-trained conditional diffusion model that jointly models sequences and structures of complementarity-determining regions (CDR) in 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, demonstrating the superiority of our approach.

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models

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.