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General Machine Learning · Unsupervised and Semi-supervised Learning

Leonardo Hernandez Cano, Maxine Perroni-Scharf, Neil Dhir, Arun Ramamurthy, Armando Solar-Lezama

We present Structured World Modeling for Policy Optimization (SWMPO), a framework for unsupervised learning of neurosymbolic Finite State Machines (FSM) that capture environmental structure for policy optimization. Traditional unsupervised world modeling methods rely on unstructured representations, such as neural networks, that do not explicitly represent high-level patterns within the system (e.g., patterns in the dynamics of regions such as \emph{water} and \emph{land}).Instead, SWMPO models the environment as a finite state machine (FSM), where each state corresponds to a specific region with distinct dynamics. This structured representation can then be leveraged for tasks like policy optimization. Previous works that synthesize FSMs for this purpose have been limited to discrete spaces, not continuous spaces. Instead, our proposed FSM synthesis algorithm operates in an unsupervised manner, leveraging low-level features from unprocessed, non-visual data, making it adaptable across various domains. The synthesized FSM models are expressive enough to be used in a model-based Reinforcement Learning scheme that leverages offline data to efficiently synthesize environment-specific world models.We demonstrate the advantages of SWMPO by benchmarking its environment modeling capabilities in simulated environments.

Optimization · Discrete and Combinatorial Optimization

Fabian Spaeh, Atsushi Miyauchi

Maximizing a single submodular set function subject to a cardinality constraint is a well-studied and central topic in combinatorial optimization. However, finding a set that maximizes multiple functions at the same time is much less understood, even though it is a formulation which naturally occurs in robust maximization or problems with fairness considerations such as fair influence maximization or fair allocation. In this work, we consider the problem of maximizing the minimum over many submodular functions subject to a cardinality constraint, which is known as multiobjective submodular maximization. All known polynomial-time approximation algorithms either obtain a weak approximation guarantee or rely on the evaluation of the multilinear extension. The latter is expensive to evaluate and renders such algorithms impractical. We bridge this gap and introduce the first scalable and practical algorithm that obtains the best-known approximation guarantee. We furthermore introduce a novel application fair centrality maximization and show how it can be addressed via multiobjective submodular maximization. In our experimental evaluation, we show that our algorithm outperforms known algorithms in terms of objective value and running time.

Applications · Chemistry, Physics, and Earth Sciences

Jiahe Du, Kaixiong Zhou, Xinyu Hong, Zhaozhuo Xu, Jinbo Xu, Xiao Huang

Generating novel enzymes for target molecules in zero-shot scenarios is a fundamental challenge in biomaterial synthesis and chemical production. Without known enzymes for a target molecule, training generative models becomes difficult due to the lack of direct supervision. To address this, we propose a retrieval-augmented generation method that uses existing enzyme-substrate data to guide enzyme design. Our method retrieves enzymes with substrates that share structural similarities with the target molecule, leveraging functional similarities in catalytic activity. Since none of the retrieved enzymes directly catalyze the target molecule, we use a conditioned discrete diffusion model to generate new enzymes based on the retrieved examples. An enzyme-substrate relationship classifier guides the generation process to ensure optimal protein sequence distributions. We evaluate our model on enzyme design tasks with diverse real-world substrates and show that it outperforms existing protein generation methods in catalytic capability, foldability, and docking accuracy. Additionally, we define the zero-shot substrate-specified enzyme generation task and introduce a dataset with evaluation benchmarks.

Optimization · Discrete and Combinatorial Optimization

Dan-Xuan Liu, Chao Qian

The subset selection problem with a monotone and submodular objective function under a linear cost constraint has wide applications, such as maximum coverage, influence maximization, and feature selection, just to name a few. Various greedy algorithms have been proposed with good performance both theoretically and empirically. Recently, evolutionary algorithms (EAs), inspired by Darwin's evolution theory, have emerged as a prominent methodology, offering both empirical advantages and theoretical guarantees. Among these, the multi-objective EA, POMC, has demonstrated the best empirical performance to date, achieving an approximation guarantee of $(1/2)(1-1/e)$. However, there remains a gap in the approximation bounds of EAs compared to greedy algorithms, and their full theoretical potential is yet to be realized. In this paper, we re-analyze the approximation performance of POMC theoretically, and derive an improved guarantee of $1/2$, which thus provides theoretical justification for its encouraging empirical performance. Furthermore, we propose a novel multi-objective EA, EPOL, which not only achieves the best-known practical approximation guarantee of $0.6174$, but also delivers superior empirical performance in applications of maximum coverage and influence maximization. We hope this work can help better solving the subset selection problem, but also enhance our theoretical understanding of EAs.

Optimization · Discrete and Combinatorial Optimization

Liangliang Shi, Shenhui Zhang, Xingbo Du, Nianzu Yang, Junchi Yan

Global routing (GR) is a fundamental task in modern chip design and various learning techniques have been devised. However, a persistent challenge is the inherent lack of a mechanism to guarantee the routing connectivity in network's prediction results, necessitating post-processing search or reinforcement learning (RL) to enforce the connectivity. In this paper, we propose a neural GR solver called DSBRouter, leveraging the Diffusion Schr\"{o}dinger Bridge (DSB) model for GR. During training, unlike previous works that learn the mapping from noise to routes, we establish a bridge between the initial pins and the routing via DSB, which learns the forward and backward mapping between them. For inference, based on the evaluation metric (e.g. low overflow), we further introduce a sampling scheme with evaluation-based guidance to enhance the routing predictions. Note that DSBRouter is an end-to-end model that does not require a post-step to ensure connectivity. Empirical results show that it achieves SOTA performance on the overflow reduction in ISPD98 and part of ISPD07. In some cases, DSBRouter can even generate routes with zero overflow.

Optimization

Yeqing Qiu, Ye XUE, Akang Wang, Yiheng Wang, Qingjiang Shi, Zhiquan Luo

The Max-$k$-Cut problem is a fundamental combinatorial optimization challenge that generalizes the classic $\mathcal{NP}$-complete Max-Cut problem. While relaxation techniques are commonly employed to tackle Max-$k$-Cut, they often lack guarantees of equivalence between the solutions of the original problem and its relaxation. To address this issue, we introduce the Relax-Optimize-and-Sample (ROS) framework. In particular, we begin by relaxing the discrete constraints to the continuous probability simplex form. Next, we pre-train and fine-tune a graph neural network model to efficiently optimize the relaxed problem. Subsequently, we propose a sampling-based construction algorithm to map the continuous solution back to a high-quality Max-$k$-Cut solution. By integrating geometric landscape analysis with statistical theory, we establish the consistency of function values between the continuous solution and its mapped counterpart. Extensive experimental results on random regular graphs and the Gset benchmark demonstrate that the proposed ROS framework effectively scales to large instances with up to $20,000$ nodes in just a few seconds, outperforming state-of-the-art algorithms. Furthermore, ROS exhibits strong generalization capabilities across both in-distribution and out-of-distribution instances, underscoring its effectiveness for large-scale optimization tasks.

Reinforcement Learning

Hanyang Zhao, Haoxian Chen, Ji Zhang, David Yao, Wenpin Tang

Reinforcement learning from human feedback (RLHF), which aligns a diffusion model with input prompt, has become a crucial step in building reliable generative AI models. Most works in this area uses a *discrete-time* formulation, which is prone to induced errors, and often not applicable to models with higher-order/black-box solvers. The objective of this study is to develop a disciplined approach to fine-tuning diffusion models using *continuous-time* RL, formulated as a stochastic control problem with a reward function that aligns the end result (terminal state) with input prompt. The key idea is to treat score matching as controls or actions, and thereby connecting to policy optimization and regularization in continuous-time RL. To carry out this idea, we lay out a new policy optimization framework for continuous-time RL, and illustrate its potential in enhancing the value networks design space via leveraging the structural property of diffusion models. We validate the advantages of our method by experiments in downstream tasks of fine-tuning large-scale Text2Image models, Stable Diffusion v1.5.

Reinforcement Learning · Deep RL

Jijia Liu, Feng Gao, Qingmin Liao, Chao Yu, Yu Wang

Reinforcement learning (RL) for continuous control often requires large amounts of online interaction data. Value-based RL methods can mitigate this burden by offering relatively high sample efficiency. Some studies further enhance sample efficiency by incorporating offline demonstration data to “kick-start” training, achieving promising results in continuous control. However, they typically compute the Q-function independently for each action dimension, neglecting interdependencies and making it harder to identify optimal actions when learning from suboptimal data, such as non-expert demonstration and online-collected data during the training process.To address these issues, we propose Auto-Regressive Soft Q-learning (ARSQ), a value-based RL algorithm that models Q-values in a coarse-to-fine, auto-regressive manner.First, ARSQ decomposes the continuous action space into discrete spaces in a coarse-to-fine hierarchy, enhancing sample efficiency for fine-grained continuous control tasks. Next, it auto-regressively predicts dimensional action advantages within each decision step, enabling more effective decision-making in continuous control tasks. We evaluate ARSQ on two continuous control benchmarks, RLBench and D4RL, integrating demonstration data into online training. On D4RL, which includes non-expert demonstrations, ARSQ achieves an average 1.62× performance improvement over SOTA value-based baseline. On RLBench, which incorporates expert demonstrations, ARSQ surpasses various baselines, demonstrating its effectiveness in learning from suboptimal online-collected data.

Optimization · Discrete and Combinatorial Optimization

Sijia Zhang, Shuli Zeng, Shaoang Li, Feng Wu, Shaojie Tang, Xiangyang Li

Many real-world applications, such as logistics, routing, scheduling, and production planning, involve dynamic systems that require continuous updates to solutions for new Mixed Integer Linear Programming (MILP) problems. These systems often require rapid updates to their solutions to accommodate slight modifications in constraints or objectives introduced by evolving conditions.While reoptimization techniques have been explored for Linear Programming (LP) and certain specific MILP problems, their effectiveness in addressing general MILP is limited. In this work, we propose a two-stage reoptimization framework for efficiently identifying high-quality feasible solutions. Specifically, we first utilize the historical solving process information to predict a high confidence solution space for modified MILPs, which is likely to contain high-quality solutions. Building on the prediction results, we fix a part of variables within the predicted intervals and apply the Thompson Sampling algorithm to determine which variables to fix. This is done by updating the Beta distributions based on the solutions obtained from the solver. Extensive experiments across nine reoptimization datasets show that our VP-OR outperforms the state-of-the-art methods, achieving higher-quality solutions under strict time limits.

Applications · Chemistry, Physics, and Earth Sciences

Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities—continuous 3D positions and discrete 2D topologies—which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9\% on CrossDock, more than 10\% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Optimization · Discrete and Combinatorial Optimization

Nathaniel Lahn, Sharath Raghvendra, Emma Saarinen, Pouyan Shirzadian

The $p$-Wasserstein distance measures the cost of optimally transporting one distribution to another, where the cost of moving a unit mass from $a$ to $b$ is the $p^{th}$ power of the ground distance $\mathrm{d}(a,b)$ between them. Despite its strong theoretical properties, its use in practice -- especially for $p \ge 2$ -- is limited due to two key challenges: sensitivity to noise and a lack of scalable algorithms.We identify noise sensitivity as a key reason why some existing approximation algorithms for $p=1$ fail to generalize to $p \ge 2$ and then present new algorithms for approximating the $p$-Wasserstein distance and its variant. First, when $\mathrm{d}(\cdot,\cdot)$ is a metric, for any constant $p \ge 2$, we present a novel relative $O(\log n)$-approximation algorithm to compute the $p$-Wasserstein distance between any two discrete distributions of size $n$. The algorithm runs in $O(n^2 \log U\log \Delta\log n)$ time, where $\log U$ is the bit-length of the input probabilities and $\Delta$ is the ratio of the largest to the smallest pairwise distance. We use $p$ hierarchically well-separated trees to define a distance that approximates the $p$-Wasserstein cost within a factor of $O(\log n)$ and then present a simple primal-dual algorithm to compute the $p$-Wasserstein cost with respect to this distance. Second, due to the noise sensitivity of the $p$-Wasserstein distance, we show that existing combinatorial approaches require $\Omega(n^2/\delta^p)$ time to approximate the $p$-Wasserstein distance within an additive error of $\delta$. In contrast, we show that, for any arbitrary distance $\mathrm{d}(\cdot,\cdot)$, a recent noise-resistant variant of the $p$-Wasserstein distance, called the $p$-RPW distance, can be approximated in $O(n^2/\delta^3)$ time.

Optimization · Discrete and Combinatorial Optimization

Chengrui Gao, Haopu Shang, Ke Xue, Chao Qian

Machine learning has increasingly been employed to solve NP-hard combinatorial optimization problems, resulting in the emergence of neural solvers that demonstrate remarkable performance, even with minimal domain-specific knowledge. To date, the community has created numerous open-source neural solvers with distinct motivations and inductive biases. While considerable efforts are devoted to designing powerful single solvers, our findings reveal that existing solvers typically demonstrate complementary performance across different problem instances. This suggests that significant improvements could be achieved through effective coordination of neural solvers at the instance level. In this work, we propose the first general framework to coordinate the neural solvers, which involves feature extraction, selection model, and selection strategy, aiming to allocate each instance to the most suitable solvers. To instantiate, we collect several typical neural solvers with state-of-the-art performance as alternatives, and explore various methods for each component of the framework. We evaluated our framework on two typical problems, Traveling Salesman Problem (TSP) and Capacitated Vehicle Routing Problem (CVRP). Experimental results show that our framework can effectively distribute instances and the resulting composite solver can achieve significantly better performance (e.g., reduce the optimality gap by 0.88% on TSPLIB and 0.71% on CVRPLIB) than the best individual neural solver with little extra time cost.

Applications · Health / Medicine

Lea Bogensperger, Dominik Narnhofer, Ahmed Allam, Konrad Schindler, Michael Krauthammer

The goal of protein fitness optimization is to discover new protein variants with enhanced fitness for a given use. The vast search space and the sparsely populated fitness landscape, along with the discrete nature of protein sequences, pose significant challenges when trying to determine the gradient towards configurations with higher fitness. We introduce *Variational Latent Generative Protein Optimization* (VLGPO), a variational perspective on fitness optimization. Our method embeds protein sequences in a continuous latent space to enable efficient sampling from the fitness distribution and combines a (learned) flow matching prior over sequence mutations with a fitness predictor to guide optimization towards sequences with high fitness. VLGPO achieves state-of-the-art results on two different protein benchmarks of varying complexity. Moreover, the variational design with explicit prior and likelihood functions offers a flexible plug-and-play framework that can be easily customized to suit various protein design tasks.

Theory · Reinforcement Learning and Planning

Kaiwen Wang, Dawen Liang, Nathan Kallus, Wen Sun

We study risk-sensitive RL where the goal is learn a history-dependent policy that optimizes some risk measure of cumulative rewards.We consider a family of risks called the optimized certainty equivalents (OCE), which captures important risk measures such as conditional value-at-risk (CVaR), entropic risk and Markowitz's mean-variance. In this setting, we propose two meta-algorithms: one grounded in optimism and another based on policy gradients, both of which can leverage the broad suite of risk-neutral RL algorithms in an augmented Markov Decision Process (MDP). Via a reductions approach, we leverage theory for risk-neutral RL to establish novel OCE bounds in complex, rich-observation MDPs. For the optimism-based algorithm, we prove bounds that generalize prior results in CVaR RL and that provide the first risk-sensitive bounds for exogenous block MDPs. For the gradient-based algorithm, we establish both monotone improvement and global convergence guarantees under a discrete reward assumption. Finally, we empirically show that our algorithms learn the optimal history-dependent policy in a proof-of-concept MDP, where all Markovian policies provably fail.

Applications · Health / Medicine

Xinyu Yuan, Zichen Wang, Marcus Collins, Huzefa Rangwala

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce **StructTokenBench**, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop **AminoAseed**, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31\% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83\% and 124.03\%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench.

Social Aspects · Privacy

Clément Lalanne, Franck Iutzeler, Loubes Jean-Michel, Julien Chhor

Estimating optimal transport maps between two distributions from respective samples is an important element for many machine learning methods. To do so, rather than extending discrete transport maps, it has been shown that estimating the Brenier potential of the transport problem and obtaining a transport map through its gradient is near minimax optimal for smooth problems. In this paper, we investigate the private estimation of such potentials and transport maps with respect to the distribution samples.We propose a differentially private transport map estimator with $L^2$ error at most $n^{-1} \vee n^{-\frac{2 \alpha}{2 \alpha - 2 + d}} \vee (n\epsilon)^{-\frac{2 \alpha}{2 \alpha + d}} $ up do polylog terms where $n$ is the sample size, $\epsilon$ is the desired level of privacy, $\alpha$ is the smoothness of the true transport map, and $d$ is the dimension of the feature space. We also provide a lower bound for the problem.

Optimization · Discrete and Combinatorial Optimization

Jourdain Lamperski, Haeseong Yang, Oleg Prokopyev

We consider the *max-min eigenvalue augmentation* problem: given $n \times n$ symmetric positive semidefinite matrices $M,A_1,\ldots, A_m$ and a positive integer $k < m$, the goal is to choose a subset $I \subset \{1,\ldots,m\}$ of cardinality at most $k$ that maximizes the minimum eigenvalue of the matrix $M + \sum_{i \in I} A_i$. The problem captures both the *Bayesian E-optimal design* and *maximum algebraic connectivity augmentation* problems. In contrast to the existing work, we do not assume that the *augmentation matrices* are rank-one matrices, and we focus on the setting in which $k < n$. We show that a *simple* randomized rounding method provides a constant-factor approximation if the *optimal increase* is sufficiently large, specifically, if $\mathrm{OPT} - \lambda_{\mathrm{min}}(M) = \Omega(R \ln k)$, where $\mathrm{OPT}$ is the optimal value, and $R$ is the maximum trace of an augmentation matrix. To establish the guarantee, we derive a matrix concentration inequality that is of independent interest. The inequality can be interpreted as an *intrinsic dimension* analog of the matrix Chernoff inequality for the minimum eigenvalue of a sum of independent random positive semidefinite matrices; such an inequality has already been established for the maximum eigenvalue, but not for the minimum eigenvalue.

Optimization

Michael Sander, Vincent Roulet, Tianlin Liu, Mathieu Blondel

Energy-based models (EBMs) offer a flexible framework for parameterizing probability distributions using neural networks.However, learning EBMs by exact maximum likelihood estimation (MLE) is generally intractable, due to the need to compute the partition function.In this paper, we propose a novel min-min formulation for approximately learning probabilistic EBMs in combinatorially-large discrete spaces, such as sets or permutations. Our key idea is to jointly learn both an energy model and its log-partition, parameterized as a neural network. Our approach not only provides a novel tractable objective criterion to learn EBMs by stochastic gradient descent (without relying on MCMC), but also a novel means to estimate the log-partition function on unseen data points.On the theoretical side, we show that our approach recovers the optimal MLE solution when optimizing in the space of continuous functions.Furthermore, we show that our approach naturally extends to the broader family of Fenchel-Young losses, allowing us to obtainthe first tractable method for optimizing the sparsemax loss in combinatorially-large spaces.We demonstrate our approach on multilabel classification and label ranking.

Optimization · Non-Convex

Zhangyi Liu, Feng Liu, Rui Gao, Shuang Li

We study convergence properties of the discrete-time Mean-Field Langevin Stochastic Descent-Ascent (MFL-SDA) algorithm for solving distributional minimax optimization. These problems arise in various applications, such as zero-sum games, generative adversarial networks and distributionally robust learning. Despite the significance of MFL-SDA in these contexts, the discrete-time convergence rate remains underexplored.To address this gap, we establish a last-iterate convergence rate of $O(\frac{1}{\epsilon}\log\frac{1}{\epsilon})$ for MFL-SDA. This rate is nearly optimal when compared to the complexity lower bound of its Euclidean counterpart. This rate also matches the complexity of mean-field Langevin stochastic gradient descent for distributional minimization and the outer-loop iteration complexity of an existing double-loop algorithm for distributional minimax problems.By leveraging an elementary analysis framework that avoids PDE-based techniques, we overcome previous limitations and achieve a faster convergence rate.

Deep Learning · Attention Mechanisms

Binchi Zhang, Zaiyi Zheng, Zhengzhang Chen, Jundong Li

Symmetry in the parameter space of deep neural networks (DNNs) has proven beneficial for various deep learning applications. A well-known example is the permutation symmetry in Multi-Layer Perceptrons (MLPs), where permuting the rows of weight matrices in one layer and applying the inverse permutation to adjacent layers yields a functionally equivalent model. While permutation symmetry fully characterizes the equivalence set for MLPs, its discrete nature limits its utility for transformers. In this paper, we introduce rotation symmetry, a novel form of parameter space symmetry for transformers that generalizes permutation symmetry by rotating parameter matrices in self-attention layers. Unlike permutation symmetry, rotation symmetry operates in a continuous domain, thereby significantly expanding the equivalence set for transformers. Based on this property, we propose a theoretically optimal parameter matching algorithm as a plug-and-play module to enhance model fusion. We evaluate our approach using pre-trained transformers across diverse natural language and vision tasks. Experimental results demonstrate that our rotation symmetry-based matching algorithm substantially improves model fusion, highlighting the potential of parameter space symmetry to facilitate model fusion. Our code is available on https://github.com/zhengzaiyi/RotationSymmetry