Constrained Generative Modeling

Generating samples from limited information is a fundamental problem across scientific domains. Classical maximum entropy methods provide principled uncertainty quantification from moment constraints but require sampling via MCMC or Langevin dynamics, which typically exhibit exponential slowdown in high dimensions. In contrast, generative models based on diffusion and flow matching efficiently transport noise to data but offer limited theoretical guarantees and can overfit when data is scarce. We introduce Moment Guided Diffusion (MGD), which combines elements of both approaches. Building on the stochastic interpolant framework, MGD samples maximum entropy distributions by solving a stochastic differential equation that guides moments toward prescribed values in finite time, thereby avoiding slow mixing in equilibrium-based methods. We formally obtain, in the large-volatility limit, convergence of MGD to the maximum entropy distribution and derive a tractable estimator of the resulting entropy computed directly from the dynamics. Applications to financial time series, turbulent flows, and cosmological fields using wavelet scattering moments yield estimates of negentropy for high-dimensional multiscale processes.

While deep generative models excel at capturing graph data distributions, they struggle to satisfy complex, hard constraints. In unconstrained settings, these models typically produce valid topologies; yet imposing strict compositional rules, like those in drug discovery, creates an out-of-distribution (OOD) setting where purely neural methods frequently fail. Because these neural approaches rely on soft conditioning and post-hoc filtering on such tasks, they cannot provide the formal guarantees needed for high-stakes domains. To address this, we introduce Neuro-Symbolic Graph Generative Modeling (NSGGM), a framework built on the principle of Neural Proposals, Symbolic Guarantees. NSGGM decouples generation: an autoregressive model proposes structural scaffolds, and a Satisfiability Modulo Theories (SMT) solver handles the final discrete assembly of the proposed substructures. Empirically, NSGGM is competitive with state-of-the-art methods on unconstrained tasks. To evaluate logical-constraint satisfaction inspired by real drug discovery workflows, we introduce MolSAT, a benchmark for hard compositional rules. On MolSAT, purely neural baselines completely fail OOD (0% satisfaction with zero training support), while NSGGM achieves >95% satisfaction in-distribution and 64-86% with zero training support.

Flow and diffusion models are typically pre-trained on limited available data (e.g., molecular samples), covering only a fraction of the valid design space (e.g., the full molecular space). As a consequence, they tend to generate samples from only a narrow portion of the feasible domain. This is a fundamental limitation for scientific discovery applications, where one typically aims to sample valid designs beyond the available data distribution. To this end, we address the challenge of leveraging access to a verifier (e.g., an atomic bonds checker), to adapt a pre-trained flow model so that its induced density expands beyond regions of high data availability, while preserving samples validity. We introduce formal notions of strong and weak verifiers and propose algorithmic frameworks for global and local flow expansion via probability-space optimization. Then, we present Flow Expander (FE), a scalable mirror descent scheme that provably tackles both problems by verifier-constrained entropy maximization over the flow process noised state space. Next, we provide a thorough theoretical analysis of the proposed method, and state convergence guarantees under both idealized and general assumptions. Ultimately, we empirically evaluate our method on both illustrative, yet visually interpretable settings, and on a molecular design task showcasing the ability of FE to expand a pre-trained flow model increasing conformer diversity while preserving validity.

Generating realistic synthetic populations is essential for agent-based models (ABM) in transportation and urban planning. Current methods face two major limitations. First, many rely on a single dataset or follow a sequential data fusion and generation process, which means they fail to capture the complex interplay between features. Second, these approaches struggle with sampling zeros (valid but unobserved attribute combinations) and structural zeros (infeasible combinations due to logical constraints), which reduce the diversity and feasibility of the generated data. This study proposes a novel method to simultaneously integrate and synthesize multi-source datasets using a Wasserstein Generative Adversarial Network (WGAN) with gradient penalty. This joint learning method improves both the diversity and feasibility of synthetic data by defining a regularization term (inverse gradient penalty) for the generator loss function. For the evaluation, we implement a unified evaluation metric for similarity, and place special emphasis on measuring diversity and feasibility through recall, precision, and the F1 score. Results show that the proposed joint approach outperforms the sequential baseline, with recall increasing by 7% and precision by 15%. Additionally, the regularization term further improves diversity and feasibility, reflected in a 10% increase in recall and 1% in precision. We assess similarity distributions using a five-metric score. The joint approach performs better overall, and reaches a score of 88.1 compared to 84.6 for the sequential method. Since synthetic populations serve as a key input for ABM, this multi-source generative approach has the potential to significantly enhance the accuracy and reliability of ABM.

Macrocycles are ring-shaped molecules that offer a promising alternative to small-molecule drugs due to their enhanced selectivity and binding affinity against difficult targets. Despite their chemical value, they remain underexplored in generative modeling, likely owing to their scarcity in public datasets and the challenges of enforcing topological constraints in standard deep generative models. We introduce MacroGuide: Topological Guidance for Macrocycle Generation, a diffusion guidance mechanism that uses Persistent Homology to steer the sampling of pretrained molecular generative models toward the generation of macrocycles, in both unconditional and conditional (protein pocket) settings. At each denoising step, MacroGuide constructs a Vietoris-Rips complex from atomic positions and promotes ring formation by optimizing persistent homology features. Empirically, applying MacroGuide to pretrained diffusion models increases macrocycle generation rates from 1% to 99%, while matching or exceeding state-of-the-art performance on key quality metrics such as chemical validity, diversity, and PoseBusters checks.

Large language models (LLMs) are increasingly used to generate executable outputs, JSON objects, and API calls, where a single syntax error can make the output unusable. Constrained decoding enforces validity token-by-token via masking and renormalization, but it can distort generation when the model assigns low probability mass to valid continuations, pushing decoding toward locally valid yet semantically incorrect trajectories. We propose Draft-Conditioned Constrained Decoding (DCCD), a simple two-step, training-free inference procedure that decouples semantic planning from structural enforcement: an unconstrained draft is generated first, and constrained decoding is then applied, conditioned on this draft, to guarantee validity. We analyze DCCD through a KL-projection view, showing that draft conditioning increases feasible mass and reduces the cumulative "projection tax" induced by hard constraints, with an optional best-of-$K$ draft selection. Across structured reasoning benchmarks, DCCD improves strict structured accuracy by up to +24 percentage points over standard constrained decoding (e.g., 15.2% to 39.0% on GSM8K with a 1B model), and enables smaller model pairs to match or exceed much larger constrained baselines, yielding substantial gains in parameter efficiency.

Generative models have enjoyed widespread success in a variety of applications. However, they encounter inherent mathematical limitations in modeling distributions where samples are constrained by equalities, as is frequently the setting in scientific domains. In this work, we develop a computationally cheap, mathematically justified, and highly flexible distributional modification for combating known pitfalls in equality-constrained generative models. We propose perturbing the data distribution in a constraint-aware way such that the new distribution has support matching the ambient space dimension while still implicitly incorporating underlying manifold geometry. Through theoretical analyses and empirical evidence on several representative tasks, we illustrate that our approach consistently enables data distribution recovery and stable sampling with both diffusion models and normalizing flows.

Generating property-optimized mRNA sequences is central to applications such as vaccine design and protein replacement therapy, but remains challenging due to limited data, complex sequence-function relationships, and the narrow space of biologically viable sequences. Generative methods that drift away from the data manifold can yield sequences that fail to fold, translate poorly, or are otherwise nonfunctional. We present RNAGenScape, a property-guided manifold Langevin dynamics framework for mRNA sequence generation that operates on a learned manifold of real data. By performing iterative local optimization constrained to this manifold, RNAGenScape preserves favorable computational viability proxies, accesses reliable guidance, and discourages excursions into regions poorly supported by the training data. The framework integrates three components: (1) an autoencoder jointly trained with a property predictor to learn a property-organized latent manifold, (2) a denoising autoencoder that projects updates back onto the manifold, and (3) a property-guided Langevin dynamics procedure that performs optimization along the manifold. Across three real-world mRNA datasets spanning two orders of magnitude in size, RNAGenScape increases median oracle-predicted property gain by up to 267% and success rate by up to 31%, while maintaining good biological viability proxy measures and achieving competitive inference efficiency compared to existing generative approaches.

Generative models have become increasingly powerful tools for robot motion generation, enabling flexible and multimodal trajectory generation across various tasks. Yet, most existing approaches remain limited in handling multiple types of constraints, such as collision avoidance, actuation limits, and dynamic consistency, which are typically addressed individually or heuristically. In this work, we propose UniConFlow, a unified constrained flow matching-based framework for trajectory generation that systematically incorporates both equality and inequality constraints. Moreover, UniConFlow introduces a novel prescribed-time zeroing function that shapes a time-varying guidance field during inference, allowing the generation process to adapt to varying system models and task requirements. Furthermore, to further address the computational challenges of long-horizon and high-dimensional trajectory generation, we propose two practical strategies for the terminal constraint enforcement and inference process: a violation-segment extraction protocol that precisely localizes and refines only the constraint-violating portions of trajectories, and a trajectory compression method that accelerates optimization in a reduced-dimensional space while preserving high-fidelity reconstruction after decoding. Empirical validation across three experiments, including a double inverted pendulum, a real-to-sim car racing task, and a sim-to-real manipulation task, demonstrates that UniConFlow outperforms state-of-the-art generative planners and conventional optimization baselines, achieving superior performance on certified motion planning metrics such as safety, kinodynamic consistency, and action feasibility. Project page is available at: https://uniconflow.github.io.

While text-to-motion generation is mainstream, integrating explicit spatial constraints has become a standard solution for precise animation. Existing state-of-the-art models are tailored for professional workflows, effectively processing high-quality, pre-aligned 3D inputs via unified conditioning mechanisms. However, this strictly aligned setting restricts accessibility for general users who rely on unaligned, in-the-wild 2D reference images. This accessible scenario introduces a fundamental conflict: heterogeneous geometric constraints, where user-defined global trajectories clash with local image-derived poses. To resolve this coordinate mismatch, we propose TPMDM, a diffusion model featuring a decoupled parallel control strategy that explicitly isolates and aligns these divergent signals. Furthermore, we introduce IKMo, a holistic framework that synergizes TPMDM with a VLM-powered multi-agent system. By bridging the semantic-geometric gap, IKMo translates user-friendly inputs into explicit motion constraints to drive the diffusion backbone. Experiments on HumanML3D and KIT-ML demonstrate that our method establishes a new state-of-the-art in the task of generating motions under heterogeneous trajectory and keyframe pose constraints.

De novo 3D molecular design with multiple properties and fragment-retention constraints is formulated as a constrained multi-objective optimization problem. Existing 3D diffusion models provide strong capabilities for generating novel molecules, but adapting them to new conditions and multi-objective optimization tasks remains difficult. We present Diffusion-based Evolutionary Molecular Optimization (DEMO), a framework that draws solely on the unconditional molecular prior of a frozen pretrained diffusion model to generate chemically valid 3D candidates, while evolutionary search handles conditional generation and constrained multi-objective optimization, without retraining or fine-tuning. DEMO performs crossover and mutation on intermediate diffusion states through an Evolutionary-Guided Diffusion (EGD) operator, combines 2D topology and 3D geometry in Structure-Aware Environmental Selection (SAES) to preserve structural diversity, and uses three cooperating populations to coordinate structural exploration, fragment-constraint satisfaction, and property optimization. Experimental results demonstrate that EGD outperforms task-specific conditional generators in property targeting; SAES preserves structural diversity while retaining competitive hypervolume in multi-objective optimization; and DEMO improves objective convergence and generates diverse feasible molecules under fragment constraints. These results show how evolutionary search can reuse existing diffusion models for diverse molecular design requirements.

Large Language Models (LLMs) struggle with reliably generating highly structured outputs, such as program code, mathematical formulas, or well-formed markup. Constrained decoding approaches mitigate this problem by greedily restricting what tokens an LLM can output at each step to guarantee that the output matches a given constraint. Specifically, in grammar-constrained decoding (GCD), the LLM's output must follow a given grammar. In this paper, we demonstrate that GCD techniques (and in general constrained decoding techniques) can distort the LLM's distribution, leading to outputs that are grammatical but appear with likelihoods that are not proportional to the ones given by the LLM, and so ultimately are low-quality. We call the problem of aligning sampling with a grammar constraint, grammar-aligned decoding (GAD), and propose adaptive sampling with approximate expected futures (ASAp), a decoding algorithm that guarantees the output to be grammatical while provably producing outputs that match the conditional probability of the LLM's distribution conditioned on the given grammar constraint. Our algorithm uses prior sample outputs to soundly overapproximate the future grammaticality of different output prefixes. Our evaluation on code generation and structured NLP tasks shows how ASAp often produces outputs with higher likelihood (according to the LLM's distribution) than existing GCD techniques, while still enforcing the desired grammatical constraints.