Latent Diffusion Models for Controllable RNA Sequence Generation

This paper presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences. RNA is a particularly dynamic and versatile molecule in biological processes. RNA sequences exhibit high variability and diversity, characterized by their variable lengths, flexible three-dimensional structures, and diverse functions. We utilize pretrained BERT-type models to encode raw RNAs into token-level biologically meaningful representations. A Q-Former is employed to compress these representations into a fixed-length set of latent vectors, with an autoregressive decoder trained to reconstruct RNA sequences from these latent variables. We then develop a continuous diffusion model within this latent space. To enable optimization, we train reward networks to estimate functional properties of RNA from the latent variables. We employ gradient-based guidance during the backward diffusion process, aiming to generate RNA sequences that are optimized for higher rewards. Empirical experiments confirm that RNAdiffusion generates non-coding RNAs that align with natural distributions across various biological indicators. We fine-tuned the diffusion model on untranslated regions (UTRs) of mRNA and optimize sample sequences for protein translation efficiencies. Our guided diffusion model effectively generates diverse UTR sequences with high Mean Ribosome Loading (MRL) and Translation Efficiency (TE), surpassing baselines. These results hold promise for studies on RNA sequence-function relationships, protein synthesis, and enhancing therapeutic RNA design.

Relative-Translation Invariant Wasserstein Distance

We introduce a new family of distances, relative-translation invariant Wasserstein distances ($RW_p$), for measuring the similarity of two probability distributions under distribution shift. Generalizing it from the classical optimal transport model, we show that $RW_p$ distances are also real distance metrics defined on the quotient set $\mathcal{P}_p(\mathbb{R}^n)/\sim$ and invariant to distribution translations. When $p=2$, the $RW_2$ distance enjoys more exciting properties, including decomposability of the optimal transport model, translation-invariance of the $RW_2$ distance, and a Pythagorean relationship between $RW_2$ and the classical quadratic Wasserstein distance ($W_2$). Based on these properties, we show that a distribution shift, measured by $W_2$ distance, can be explained in the bias-variance perspective. In addition, we propose a variant of the Sinkhorn algorithm, named $RW_2$ Sinkhorn algorithm, for efficiently calculating $RW_2$ distance, coupling solutions, as well as $W_2$ distance. We also provide the analysis of numerical stability and time complexity for the proposed algorithm. Finally, we validate the $RW_2$ distance metric and the algorithm performance with three experiments. We conduct one numerical validation for the $RW_2$ Sinkhorn algorithm and show two real-world applications demonstrating the effectiveness of using $RW_2$ under distribution shift: digits recognition and similar thunderstorm detection. The experimental results report that our proposed algorithm significantly improves the computational efficiency of Sinkhorn in certain practical applications, and the $RW_2$ distance is robust to distribution translations compared with baselines.

Conversational Dueling Bandits in Generalized Linear Models

Conversational recommendation systems elicit user preferences by interacting with users to obtain their feedback on recommended commodities. Such systems utilize a multi-armed bandit framework to learn user preferences in an online manner and have received great success in recent years. However, existing conversational bandit methods have several limitations. First, they only enable users to provide explicit binary feedback on the recommended items or categories, leading to ambiguity in interpretation. In practice, users are usually faced with more than one choice. Relative feedback, known for its informativeness, has gained increasing popularity in recommendation system design. Moreover, current contextual bandit methods mainly work under linear reward assumptions, ignoring practical non-linear reward structures in generalized linear models. Therefore, in this paper, we introduce relative feedback-based conversations into conversational recommendation systems through the integration of dueling bandits in generalized linear models (GLM) and propose a novel conversational dueling bandit algorithm called ConDuel. Theoretical analyses of regret upper bounds and empirical validations on synthetic and real-world data underscore ConDuel's efficacy. We also demonstrate the potential to extend our algorithm to multinomial logit bandits with theoretical and experimental guarantees, which further proves the applicability of the proposed framework.

Diffusion Transformer Captures Spatial-Temporal Dependencies: A Theory for Gaussian Process Data

Diffusion Transformer, the backbone of Sora for video generation, successfully scales the capacity of diffusion models, pioneering new avenues for high-fidelity sequential data generation. Unlike static data such as images, sequential data consists of consecutive data frames indexed by time, exhibiting rich spatial and temporal dependencies. These dependencies represent the underlying dynamic model and are critical to validate the generated data. In this paper, we make the first theoretical step towards bridging diffusion transformers for capturing spatial-temporal dependencies. Specifically, we establish score approximation and distribution estimation guarantees of diffusion transformers for learning Gaussian process data with covariance functions of various decay patterns. We highlight how the spatial-temporal dependencies are captured and affect learning efficiency. Our study proposes a novel transformer approximation theory, where the transformer acts to unroll an algorithm. We support our theoretical results by numerical experiments, providing strong evidence that spatial-temporal dependencies are captured within attention layers, aligning with our approximation theory.

Natural language is not enough: Benchmarking multi-modal generative AI for Verilog generation

Natural language interfaces have exhibited considerable potential in the automation of Verilog generation derived from high-level specifications through the utilization of large language models, garnering significant attention. Nevertheless, this paper elucidates that visual representations contribute essential contextual information critical to design intent for hardware architectures possessing spatial complexity, potentially surpassing the efficacy of natural-language-only inputs. Expanding upon this premise, our paper introduces an open-source benchmark for multi-modal generative models tailored for Verilog synthesis from visual-linguistic inputs, addressing both singular and complex modules. Additionally, we introduce an open-source visual and natural language Verilog query language framework to facilitate efficient and user-friendly multi-modal queries. To evaluate the performance of the proposed multi-modal hardware generative AI in Verilog generation tasks, we compare it with a popular method that relies solely on natural language. Our results demonstrate a significant accuracy improvement in the multi-modal generated Verilog compared to queries based solely on natural language. We hope to reveal a new approach to hardware design in the large-hardware-design-model era, thereby fostering a more diversified and productive approach to hardware design.

Contractual Reinforcement Learning: Pulling Arms with Invisible Hands

The agency problem emerges in today's large scale machine learning tasks, where the learners are unable to direct content creation or enforce data collection. In this work, we propose a theoretical framework for aligning economic interests of different stakeholders in the online learning problems through contract design. The problem, termed \emph{contractual reinforcement learning}, naturally arises from the classic model of Markov decision processes, where a learning principal seeks to optimally influence the agent's action policy for their common interests through a set of payment rules contingent on the realization of next state. For the planning problem, we design an efficient dynamic programming algorithm to determine the optimal contracts against the far-sighted agent. For the learning problem, we introduce a generic design of no-regret learning algorithms to untangle the challenges from robust design of contracts to the balance of exploration and exploitation, reducing the complexity analysis to the construction of efficient search algorithms. For several natural classes of problems, we design tailored search algorithms that provably achieve $\tilde{O}(\sqrt{T})$ regret. We also present an algorithm with $\tilde{O}(T^{2/3})$ for the general problem that improves the existing analysis in online contract design with mild technical assumptions.

Provable Statistical Rates for Consistency Diffusion Models

Diffusion models have revolutionized various application domains, including computer vision and audio generation. Despite the state-of-the-art performance, diffusion models are known for their slow sample generation due to the extensive number of steps involved. In response, consistency models have been developed to merge multiple steps in the sampling process, thereby significantly boosting the speed of sample generation without compromising quality. This paper contributes towards the first statistical theory for consistency models, formulating their training as a distribution discrepancy minimization problem. Our analysis yields statistical estimation rates based on the Wasserstein distance for consistency models, matching those of vanilla diffusion models. Additionally, our results encompass the training of consistency models through both distillation and isolation methods, demystifying their underlying advantage.

SAIL: Self-Improving Efficient Online Alignment of Large Language Models

Reinforcement Learning from Human Feedback (RLHF) is a key method for aligning large language models (LLMs) with human preferences. However, current offline alignment approaches like DPO, IPO, and SLiC rely heavily on fixed preference datasets, which can lead to sub-optimal performance. On the other hand, recent literature has focused on designing online RLHF methods but still lacks a unified conceptual formulation and suffers from distribution shift issues. To address this, we establish that online LLM alignment is underpinned by bilevel optimization. By reducing this formulation to an efficient single-level first-order method (using the reward-policy equivalence), our approach generates new samples and iteratively refines model alignment by exploring responses and regulating preference labels. In doing so, we permit alignment methods to operate in an online and self-improving manner, as well as generalize prior online RLHF methods as special cases. Compared to state-of-the-art iterative RLHF methods, our approach significantly improves alignment performance on open-sourced datasets with minimal computational overhead.

Self-Play with Adversarial Critic: Provable and Scalable Offline Alignment for Language Models

This work studies the challenge of aligning large language models (LLMs) with offline preference data. We focus on alignment by Reinforcement Learning from Human Feedback (RLHF) in particular. While popular preference optimization methods exhibit good empirical performance in practice, they are not theoretically guaranteed to converge to the optimal policy and can provably fail when the data coverage is sparse by classical offline reinforcement learning (RL) results. On the other hand, a recent line of work has focused on theoretically motivated preference optimization methods with provable guarantees, but these are not computationally efficient for large-scale applications like LLM alignment. To bridge this gap, we propose SPAC, a new offline preference optimization method with self-play, inspired by the on-average pessimism technique from the offline RL literature, to be the first provable and scalable approach to LLM alignment. We both provide theoretical analysis for its convergence under single-policy concentrability for the general function approximation setting and demonstrate its competitive empirical performance for LLM alignment on a 7B Mistral model with Open LLM Leaderboard evaluations.

SpecDec++: Boosting Speculative Decoding via Adaptive Candidate Lengths

Speculative decoding reduces the inference latency of a target large language model via utilizing a smaller and faster draft model. Its performance depends on a hyperparameter K -- the candidate length, i.e., the number of candidate tokens for the target model to verify in each round. However, previous methods often use simple heuristics to choose K, which may result in sub-optimal performance. We study the choice of the candidate length K and formulate it as a Markov Decision Process. We theoretically show that the optimal policy of this Markov decision process takes the form of a threshold policy, i.e., the current speculation should stop and be verified when the probability of getting a rejection exceeds a threshold value. Motivated by this theory, we propose SpecDec++, an enhanced version of speculative decoding that adaptively determines the candidate length on the fly. We augment the draft model with a trained acceptance prediction head to predict the conditional acceptance probability of the candidate tokens. SpecDec++ will stop the current speculation when the predicted probability that at least one token gets rejected exceeds a threshold. We implement SpecDec++ and apply it to the llama-2-chat 7B & 70B model pair. Our adaptive method achieves a 2.04x speedup on the Alpaca dataset (an additional 7.2% improvement over the baseline speculative decoding). On the GSM8K and HumanEval datasets, our method achieves a 2.26x speedup (9.4% improvement) and 2.23x speedup (11.1% improvement), respectively.