Conditional Flow Matching

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points as unpaired snapshot populations, leaving substantial temporal gaps. This motivates trajectory inference at unmeasured time points. Existing methods mainly follow two directions, optimal-transport (OT) alignment provides distribution-level matching between observed snapshots, while continuous-time generative models support forecasting via learned dynamics. However, two challenges remain: (i) unpaired snapshots render local transitions between adjacent time points ambiguous, leading to unstable supervision; and (ii) long-horizon prediction relies on repeated integration, where small modeling errors compound and cause distribution drift. To address these challenges, we propose single-cell Flow Matching (scFM), a latent generative framework based on coupling-conditioned flow matching. First, we compute entropically regularized OT couplings between adjacent snapshots and use them to construct soft, weighted flow-matching targets for learning time-dependent velocity fields. Second, we learn bidirectional velocity fields and leverage their consistency to refine couplings and improve temporal coherence under sparse supervision. Third, we introduce distribution-level alignment and latent dynamic regularization to anchor long rollouts and mitigate drift. Experiments on real-world time-series scRNA-seq datasets show that scFM consistently improves distributional prediction performance for both temporal interpolation and extrapolation. Moreover, scFM yields more accurate trajectory reconstruction and temporally coherent visualizations where intermediate time points are absent, indicating a more faithful recovery of underlying temporal gene expression dynamics.

Phylogenetic trees are hybrid objects: branch lengths vary continuously, while topologies change discretely through edge contractions and expansions. Billera-Holmes-Vogtmann (BHV) tree space provides a canonical geometry for this structure, representing each resolved topology as a Euclidean orthant and topological changes as motion across shared lower-dimensional boundaries. We introduce PhylaFlow, a hybrid flow-matching model that learns posterior-basin transport in BHV tree space. PhylaFlow is trained on BHV geodesic paths from random starting trees to short-run posterior samples, coupling continuous branch-length motion within orthants with learned boundary events and discrete topology transitions. We evaluate the learned geometry operationally: if the flow reaches posterior-relevant regions, finite-budget Bayesian refinement initialized from, or guided by, its terminal trees should recover posterior-supported topologies more efficiently. Across DS1-DS8 phylogenetic posterior benchmarks, PhylaFlow substantially reduces initial Tree-KL relative to classical initializers. After finite-budget MrBayes refinement, direct PhylaFlow improves early and intermediate topology-recovery trajectories on most datasets, while split-guided PhylaFlow-MCMC obtains the strongest hard-case results. The best PhylaFlow variant outperforms short-warmup on seven of eight datasets and PhyloGFN on five of eight under the same refinement budget. In a joint sequence-conditioned experiment, sequence embeddings steer posterior split recovery, although exact posterior topology recovery remains preliminary. These results show that hybrid flow matching can learn actionable transport in BHV tree space and provide a geometry-aware proposal mechanism for Bayesian phylogenetic inference.

Standard generative models struggle with heavy-tailed data: Lipschitz architectures cannot produce power-law tails from Gaussian noise, and interpolating between heavy-tailed data and Gaussians is ill-posed. We propose a simple fix: apply the soft-log transform $φ(x) = \mathrm{sign}(x) \cdot \log(1 + |x|)$ coordinate-wise to data before training, then exponentiate samples after generation. A Hill diagnostic decides per-coordinate whether to transform, leaving light-tailed margins untouched at no added complexity. This compresses heavy tails into a range where standard flow matching succeeds, without heavy-tailed base distributions or architectural modifications. We provide theoretical intuition for why this works: the log-transform maps Pareto tails to exponentials, and the induced dynamics implement a form of tail annealing via power transformations. On a 144-configuration multivariate benchmark (3 copulas, $d$ up to 100, 4 tail indices), Log-FM dominates specialized baselines on $W_1$, CVaR$_{99}$, and extreme-quantile metrics, and is the only method with zero severe divergences across 2{,}880 runs.

Digital twins (DTs) rely on continuous synchronization between physical systems and their virtual counterparts through online parameter estimation under uncertainty. In many practical settings, however, this task is challenged by low observability, weak excitation, nonlinear dynamics, and noisy or biased measurements. In this work, we develop a new mathematical framework that integrates Weighted Flow Matching (WFM) generative modeling with physics-informed nonlinear filtering to enhance parameter estimation in DTs. WFM relies on dynamic reweighting of training samples, which guides the generative model toward parameter regimes most informative of the evolving system state. This generative component is tightly coupled with a physics-informed filtering architecture based on the Unscented Kalman Filter (UKF), yielding a unified DT framework that combines data-driven probability transport with physically consistent state and parameter estimation. The effectiveness of the new integrated framework is demonstrated within a spacecraft DT architecture, where stable moment of inertia estimation is achieved under uncertain and noisy sensing, with significant performance improvements over established approaches such as Extended Kalman Filtering (EKF) and Ensemble Kalman Filtering (EnKF). These results highlight the potential of weighted generative modeling as a core mechanism for real-time DT synchronization in operational and mission-critical systems.

Learning permutations is fundamental to sorting, ranking, and matching, but existing differentiable methods based on entropy-regularized Sinkhorn produce a single softened solution and collapse under ambiguity. We present PermFlow, a conditional flow matching framework that operates directly on the affine subspace of matrices with unit row and column sums. A closed-form tangent-space projector preserves these constraints exactly along every trajectory, by construction rather than through iterative correction, and a nearest-target coupling routes distinct noisy initializations toward distinct valid permutations. The result is a model that captures multimodal permutation distributions rather than collapsing them to a single mode. On a visual sorting task with blended-digit ambiguity and a symmetric linear assignment problem, PermFlow achieves high accuracy on unambiguous inputs and recovers both valid permutations under ambiguity, where Sinkhorn-based baselines structurally fail.

The source distribution in conditional flow matching is a design parameter that can be calibrated to data, not a default isotropic prior. We exploit this in Multi-Fidelity Flow Matching (MFFM), a cascade refinement framework for parametric PDE solutions: the source is calibrated to the empirical low-to-high-fidelity residual scale with local Gaussian-blur correlation, and the velocity network is conditioned on the low-fidelity solution. Conditioning makes the residual refinement problem substantially easier than unconditional field generation, while residual-calibrated source noise improves the flow-matching training geometry. A multi-resolution cascade applies the same construction independently between adjacent fidelities. After level-wise flow-matching pretraining, we fine-tune the composed cascade end-to-end with a deterministic one-step rollout, which makes one velocity evaluation per cascade level the optimized operating point at inference. The result is a learned analog of multigrid refinement that reaches the finest grid in $L$ deterministic network evaluations per query. We validate MFFM on eight benchmarks: two super-resolution problems and six spatiotemporal forecasting tasks from PDEBench, The Well, and the FNO Navier--Stokes dataset.

Visuomotor policies aim to learn complex manipulation tasks from expert demonstrations. However, generating smooth and coherent trajectories remains challenging, as it requires balancing proximal precision with distal foresight. Existing approaches typically focus on optimizing intra-chunk action distributions, often neglecting the inter-chunk coherence. Consequently, inter-chunk discontinuities significantly impede the learning of coherent long-horizon actions. To overcome this limitation and achieve a synergetic balance between precision and foresight, we propose FocalPolicy, a foresight-aware visuomotor policy that combines Frequency-Optimized Chunking with Locally Anchored flow matching. We introduce a foresight composite objective that supervises time-domain alignment within the proximal actions while regularizing frequency-domain structure over multiple future action chunks to improve cross-chunk coherence. To efficiently learn complex action distributions, we design locally anchored sampling to enhance target signal propagation efficiency during consistency flow matching training. Extensive experiments demonstrate that FocalPolicy outperforms existing approaches and confirm the generalizability of our modules to other baselines. Project website: https://focalpolicy.github.io/

Flow matching trains a neural velocity field by regression against a target velocity associated with a prescribed probability path connecting a simple initial distribution to the data distribution. A central design choice is the path itself. Existing constructions, including rectified and optimal-transport-based paths, transport samples along straight lines between coupled endpoints and thus cover only a narrow class of dynamics. We observe that this corresponds to the simplest case of the least-action principle in classical mechanics, in which the kinetic Lagrangian yields free-particle straight-line trajectories. Building on this observation, we propose Lagrangian flow matching, a physics-based framework in which the probability path and velocity field are determined by minimizing the action of a general Lagrangian subject to the continuity equation and the prescribed endpoints. We show that this dynamic problem admits an equivalent static optimal transport (OT) formulation, yielding a family of simulation-free training objectives that recover OT-based flow matching as the kinetic special case and the trigonometric variance-preserving diffusion path as the harmonic-oscillator case. More general Lagrangians give rise to new probability paths and velocity fields, and numerical experiments show that they induce meaningful changes in the learned dynamics while remaining competitive with existing conditional flow matching models.

Flow Language Models (FLMs) are a recently introduced class of language models which adapt continuous flow matching for one-hot encoded token sequences. Their denoisers have a special structure absent from generic continuous diffusion models: each block of the denoising mean is a posterior marginal distribution over the clean token at that position. Standard DDPM-style samplers collapse these marginals to a single conditional-mean endpoint and bridge toward this simplex-valued point, which is generally not a valid one-hot sequence. We argue that the natural sampler for an FLM is instead posterior-predictive. At each reverse step, we sample a clean one-hot endpoint from the factorized posterior defined by the FLM token marginals, and then sample the next continuous state from the analytic Ornstein--Uhlenbeck bridge conditioned on that endpoint. The method is training-free, uses the same model evaluations as standard sampling, and gives a principled interface for token-level decoding controls such as temperature scaling and nucleus truncation. We show that, under exact posterior marginals, the endpoint approximation error is exactly the conditional multi-information among token positions. The induced one-step bridge kernel preserves all token-wise posterior-predictive marginals and loses only the residual cross-position dependence. Finally, we prove a Girsanov path-space comparison showing that the marginal-conditioned bridge has a no-larger denoising-error term than the frozen conditional-mean bridge, with strict improvement whenever intermediate coordinate-wise bridge observations reveal additional information about the clean token. Experiments with FLMs show that the sampler improves the quality--diversity tradeoff. Code is available at: github.com/imbirik/mcb.

Flow Matching is a powerful framework for learning transport maps between probability distributions. Yet its standard single-parameter formulation is not designed to capture multi-parameter variations where the resulting transport should be path-independent. Path independence is crucial because it ensures that transformations depend only on the initial and target distributions, not on the specific path. In this work, we introduce Path-independent Flow Matching (PiFM), a method for learning vector fields whose induced flows yield path-independent transport between distributions. We show that PiFM generalizes Flow Matching to higher-dimensional parameter domains while enforcing structural conditions that ensure consistency of composed transformations. In addition, we show that, under suitable assumptions, PiFM approximates the Wasserstein barycenter, linking the framework to a notion of distributional interpolation. To enable practical training, we propose a tractable, simulation-free objective that regresses onto multi-parameter conditional probability paths. We showcase empirically that PiFM outperforms other approaches on both synthetic and real world data in interpolating path-independent trajectories and generating desired out of distribution samples.

Generative models are often conditioned on a small set of examples via cross-attention. Under the Gaussian optimal-transport path, we show that the exact velocity field induced by a finite support set is a Nadaraya--Watson kernel smoother whose bandwidth decreases with flow time, from broad averaging at early steps to nearest-neighbor at late steps. A single Gaussian-kernel attention head exactly computes this field, connecting cross-attention conditioning to classical kernel theory. The theory predicts three failure regimes: nearest-neighbor collapse of the kernel at high dimension, mismatch between the isotropic kernel and the data geometry, and insufficient support for nonparametric estimation. Experiments on Gaussian mixtures, spherical shells, and DINOv2 ImageNet features confirm that learned conditioning improves in precisely these regimes, and that IP-Adapter's cross-attention implements approximate NW smoothing in practice.

Designing continuous trajectories whose time-averaged occupancy provably matches a prescribed spatial density (the \emph{ergodic coverage} problem) is central to UAV-assisted data collection and sensing, robotic exploration, and mobile monitoring. For flying agents in particular, this challenge is acute: trajectories must balance coverage fidelity against tight energy budgets, no-fly zones, and acceleration limits. Existing methods either re-optimize each trajectory online (with cost growing in the horizon and re-running for every target, agent, and realization) or rely on bespoke analytical constructions that must be re-derived for each new constraint. We propose a \emph{epushforward} framework that decouples ergodicity from density matching: an analytic latent trajectory provides exact uniform ergodicity on a simple annular domain, and a single map, learned offline by optimal-transport conditional flow matching, transports this latent occupancy onto the prescribed target density. The composed trajectory is then asymptotically ergodic with respect to the learned pushforward distribution, with deviation from the target controlled by the flow-matching training loss. Once trained for a given target density and constraint set, the map serves an unbounded number of trajectories and a multi-agent fleet without per-agent retraining, and many differentiable operational constraints (no-fly zones, acceleration ceilings, or fairness penalties) enter as additive soft penalties in the training loss without re-deriving the design. We prove three results (an acceleration-energy bound, an $O(1/\sqrt{K})$ ergodic convergence rate in the number of trajectory cycles $K$, and an approximation-error bound) that combine into an end-to-end coverage bound estimable from CFM training diagnostics (certified given an architectural Lipschitz bound on $v_θ$).

We propose Coreset-Induced Conditional Velocity Flow Matching (CCVFM), a generative model that augments hierarchical rectified flow with a data-informed source distribution. Hierarchical flow matching models the full conditional velocity law in velocity space, but its inner flow is asked to transport isotropic Gaussian noise to a multimodal target velocity distribution from scratch. Our key observation is that this inner source can be replaced by a closed-form surrogate built from a coreset of the target. CCVFM first compresses the target into weighted atoms using an entropic Sinkhorn coreset and lifts them to a Gaussian mixture. The induced conditional velocity law is then a closed-form Gaussian mixture that can be sampled without a learned neural sampler. A lightweight correction flow, trained from this exact surrogate source, then refines the remaining surrogate-to-target residual rather than learning an entire noise-to-data map. We prove that the surrogate transport cost equals the target--surrogate Wasserstein gap under an explicit compression assumption, whereas the noise-source analogue has a dimension-scale lower bound. We further characterize the conditional second moment of the direct surrogate-source training target and show that its source-dependent excess is small when the surrogate conditional law is close to the true conditional velocity law in mean and covariance. Empirically, on MNIST, CIFAR-10, ImageNet-32, and CelebA-HQ, the proposed method reaches competitive few-step generation under matched architectures.

Many reinforcement learning (RL) tasks have discrete action spaces, but most generative policy methods based on diffusion and flow matching are designed for continuous control. Meanwhile, generative policies usually rely heavily on offline datasets and offline-to-online RL is itself challenging, as the policy must improve from new interaction without losing useful behavior learned from static data. To address those challenges, we introduce DRIFT, an online fine-tuning method that updates an offline pretrained continuous-time Markov chain (CTMC) policy with an advantage-weighted discrete flow matching loss. To preserve useful pretrained knowledge, we add a path-space penalty that regularizes the full CTMC trajectory distribution, rather than only the final action distribution. For large discrete action spaces, we introduce a candidate-set approximation that updates the actor over a small subset of actions sampled from reference-policy rollouts and uniform exploration. Our theoretical analysis shows that the candidate-set error is controlled by missing target probability mass, and the induced CTMC generator error decreases as the candidate set covers more high-probability actions. Experiments on prevailing discrete action RL task show that our method provides stable offline-to-online improvement across all tasks, achieving the highest average score on Jericho with a simple GRU encoder while outperforming methods that use pretrained language models. Controlled experiments further confirm that the path-space penalty remains bounded during fine-tuning and that the CTMC generator adapts to shifted rewards faster than deterministic baselines. The candidate-set mechanism is supported by a stability analysis showing that the generator error decreases exponentially with candidate coverage.

Existing imitation learning methods enable robots to interact autonomously with the physical environment. However, contact-rich manipulation tasks remain a significant challenge due to complex contact dynamics that demand high-precision force feedback and control. Although recent efforts have attempted to integrate force/torque sensing into policies, how to build a simple yet effective framework that achieves robust generalization under multimodal observations remains an open question. In this paper, we propose ForceFlow, a force-aware reactive framework built upon flow matching. For contact-stage policy design, we investigate force signal fusion mechanisms and adopt an asymmetric multimodal fusion architecture that treats force as a global regulatory signal, combined with a joint prediction paradigm that enhances the policy's understanding of instantaneous force and historical information, thereby achieving deep coupling between force and motion. For task-level hierarchical decomposition, we divide manipulation into a vision-dominant approach stage (VLM-based pointing for target localization) and a touch-dominant interaction stage (force-driven contact execution), with a Vision-to-Force (V2F) handover mechanism that explicitly decouples spatial generalization from contact regulation. Experimental results across six real-world contact-rich tasks demonstrate that ForceFlow achieves a 37% success rate improvement over the strong baseline ForceVLA while maintaining significantly lower cost. Moreover, ForceFlow exhibits accurate force signal prediction and demonstrates superior performance in contact force self-regulation and zero-shot out-of-distribution (OOD) generalization.

Generative models are powerful tools for sampling from a learned distribution $\mathcal{P}(Y \mid X)$, and inverse-design methods invert this map to find an input $x$ that produces a desired point output $y^*$. However, many design goals are naturally distributional rather than pointwise, incorporating the inherent uncertainty of $Y$ and targeting a specific form for it, a task not addressed by standard inverse design. To address this issue we introduce Conditional Distribution Matching (CDM), a new inverse-design problem class in generative modeling: given a joint distribution $\mathcal{P}(X, Y)$ and a target distribution $\mathcal{G}(Y)$, find an input $x^*$ whose induced conditional distribution $\mathcal{P}(Y \mid X = x^*)$ matches $\mathcal{G}$. We formally define two variants: Conditional Distribution Matching Sampling (CDMS) and Conditional Distribution Matching Optimization (CDMO). To solve these problems, we propose MLGD-F (Matching-Loss Guided Diffusion with a Fast inner sampler), a plug-and-play inference-time algorithm that combines a pretrained score-based diffusion model with a pretrained fast conditional sampler, requiring no additional training or fine-tuning. By leveraging single-step conditional sampling, MLGD-F enables tractable gradient computation, making the estimation of $\mathcal{P}(Y \mid X)$ both memory-efficient and computationally lightweight. We validate MLGD-F on synthetic benchmarks, structured image transformations, and generative editing optimization, demonstrating reliable recovery of inputs whose conditional distributions match diverse user-specified targets, including discrete mixtures and continuous low-rank supports.

Metric-induced discrete flow matching (MI-DFM) exploits token-latent geometry for discrete generation, but its practical use is limited by two issues: heuristic schedulers requiring hyperparameter search, and finite-step path-tracking error from its first-order continuous-time Markov chain (CTMC) solver. We address both issues. First, we derive a kinetic-optimal scheduler for prescribed scalar-parameterized probability paths, and instantiate it for MI-DFM as a training-free numerical schedule that traverses the path at constant Fisher-Rao speed. Second, we introduce a finite-step moment correction that adjusts the jump probability while preserving the CTMC jump destination distribution. We validate the resulting method, GibbsTTS, on codec-based zero-shot text-to-speech (TTS). Under controlled comparisons with a unified architecture and large-scale dataset, GibbsTTS achieves the best objective naturalness and is preferred in subjective evaluations over masked discrete generative baselines. Additionally, in comparison with the evaluated state-of-the-art TTS systems, GibbsTTS shows strong speaker similarity, achieving the highest similarity on three of four test sets and ranking second on the fourth. Project page: https://ydqmkkx.github.io/GibbsTTSProject

Flow Matching has recently emerged as a popular class of generative models for simulating a target distribution $μ_1$ from samples drawn from a source distribution $μ_0$. This framework relies on a fixed coupling between $μ_0$ and $μ_1$, and on a deterministic or stochastic bridge to define an interpolating process between the two distributions. The time marginals of this process can then be approximately sampled by estimating the transition rates, or more generally the generator, of its Markovian projection. This framework has recently been extended to the case of discrete source and target distributions, under the name Discrete Flow Matching (DFM). However, theoretical guarantees for such models remain scarce. In this paper, we study two DFM models on $\mathbb{Z}_m^d = \{0,\ldots,m-1\}^d$, sampled through time discretization, and derive non-asymptotic associated bounds for both of them. In contrast to previous work, we establish non-asymptotic bounds in Kullback--Leibler divergence for the early-stopped version of the target distribution. We also derive explicit convergence guarantees in total variation distance with respect to the true target distribution. Importantly, these bounds rely only on an approximation error assumption, relaxing standard score assumptions used in earlier works, while also yielding improved dependence on the vocabulary size $m$ and the dimension $d$.

Discrete flow matching generates text by iteratively transforming noise tokens into coherent language, but may require hundreds of forward passes. Distillation uses the multi-step trajectory to train a student to reproduce the process in a few steps. When the student underperforms, the usual explanation is insufficient capacity. We argue the opposite: the trajectory is the bottleneck, not the student. Each training trajectory is built through a chain of blind stochastic jumps with no evaluation of sequence quality; a single bad decision at an early midpoint propagates through subsequent steps, yet the student must imitate the result. Trajectory-Shaped Discrete Flow Matching (TS-DFM) replaces these blind jumps with guided navigation: a lightweight energy compass evaluates candidate continuations at each midpoint, selecting the most coherent. All shaping is training-only; inference cost is unchanged. On 170M-parameter language modeling, the shaped student at 8 steps achieves 32% lower perplexity than the 1,024-step teacher while being 128x faster, with gains consistent across source distributions and three evaluators of increasing scale. TS-DFM achieves the best perplexity of any discrete-generation baseline we compare against, including methods trained on 6x more data or using 5x larger models.

We study Flow Matching in a semi-discrete setting where a Gaussian source is transported toward a discrete target supported on finitely many points. This semi-discrete regime is the theoretical setting behind the use of Flow Matching for generative modeling, where the target distribution is represented by a finite dataset. In this semi-discrete regime, the exact Flow Matching velocity field is available in closed form, which makes it possible to analyze the geometry induced by the terminal flow map independently of optimization and approximation effects. We investigate the terminal assignment regions, namely the preimages of the target atoms under the terminal flow. We show that these regions are open, simply connected and, under an additional assumption, homeomorphic to the unit ball. At the same time, a planar four-point example shows that these cells can differ sharply from Laguerre cells arising in semi-discrete optimal transport: they may be non-convex, have curved boundaries, and exhibit different boundedness and adjacency patterns. These results clarify the geometry intrinsically induced by the exact semi-discrete Flow Matching objective before neural approximation enters the picture.

Large Language Models (LLMs) have demonstrated remarkable capabilities in orchestrating tools for reasoning tasks. However, existing methods rely on a step-wise paradigm that lacks a global perspective, which causes error accumulation over long horizons and restricts generalization to unseen tools. To overcome these limitations, we propose Tools as Continuous Flow for Evolving Agentic Reasoning (FlowAgent), which reconceptualizes tool chaining as continuous trajectory generation within a semantic space. To systematically evaluate this paradigm, we introduce the first plan-level closed-loop benchmark dedicated to plan-level agentic reasoning in dynamic real-world environments. Specifically, the proposed FlowAgent leverages conditional flow matching to generate continuous latent trajectories, providing a global planning perspective to ensure coherent and robust tool execution. Theoretically, we establish formal bounds on utility convergence and prove that our continuous formulation fundamentally guarantees robust generalization and error attenuation. Empirical evaluations show that FlowAgent achieves superior robustness and adaptability in long-horizon reasoning tasks.

Designing photonic integrated circuits requires accurate electromagnetic field simulations, which remain computationally expensive even for simple device geometries. We present PIC-Flow, a generative neural surrogate that predicts electromagnetic field distributions for photonic devices given their geometry and operating wavelength as an alternative to costly finite-difference time-domain (FDTD) simulations. Our approach combines three key ideas: (i) conditional flow matching as the generative framework, learning a velocity field that transports Gaussian noise to physically valid field solutions; (ii) a real-valued U-Net operating on split real and imaginary field channels; and (iii) physics-constrained training through a Helmholtz residual loss enforcing $\nabla^2 E_z + k_0^2 \varepsilon E_z = 0$. We introduce an interface-aware masking scheme for the Helmholtz residual that excludes dielectric boundary pixels where finite-difference stencil errors dominate, yielding a physically meaningful compliance metric. The data set consists of 22,500 ground-truth FDTD simulations split evenly between multimode interferometers, Y-branches, and directional couplers at $λ=1.55\,μ$m in an 80/10/10 split between training, validation, and test sets. We evaluate ablations on the network against the held out test devices and also show that the model generalizes to held out device classes such as S-bends, tapers, and cascaded Y-branches. Rather than a drop-in replacement for FDTD, this work establishes a foundation that, with broader data coverage, more compute, and further training optimization, could scale toward broadband, device-agnostic field prediction with dramatically improved runtime for rapid design-space exploration of complex photonic devices and circuits.

We introduce a new generative modeling framework, \textbf{Flow Matching with Arbitrary Auxiliary Paths (AuxPath-FM)}, which generalizes conditional flow matching by incorporating an auxiliary variable drawn from an arbitrary distribution into the probability path. Unlike prior methods that restrict auxiliary components to Gaussian noise, AuxPath-FM allows the variable $η$ to follow any distribution, producing trajectories of the form $X_t = a(t)X_1 + b(t)X_0 + c(t)η$. We theoretically demonstrate that this construction preserves the continuity equation and maintains a training objective consistent with the marginal formulation. This flexibility enables the design of diverse probability paths using various priors, including Gaussian, Uniform, Laplace, and discrete Rademacher distributions, each offering unique geometric properties for generative flows. Furthermore, our framework allows for specialized tasks such as label-guided generation by encoding structured semantic information into the auxiliary distribution. Overall, AuxPath-FM provides a principled and general foundation for probability path design, offering both theoretical generality and practical flexibility for diverse generative modeling tasks.

Vector quantization (VQ) with autoregressive (AR) token modeling is a widely adopted and highly competitive paradigm for time-series generation. However, such models are fundamentally limited by exposure bias: during inference, errors can accumulate across sequential predictions, leading to pronounced quality degradation in long-horizon generation. To address this, we propose SDFlow ($\textbf{S}$imilarity-$\textbf{D}$riven $\textbf{Flow}$ Matching), a non-autoregressive framework that operates entirely in the frozen VQ latent space and enables parallel sequence generation via flow matching. We tackle three key challenges in making this transition: (1) eliminating exposure bias by replacing step-wise token prediction with a global transport map; (2) mitigating the high-dimensionality of VQ token spaces via a low-rank manifold decomposition with a learned anchor prior over the latent manifold; and (3) incorporating discrete supervision into continuous transport dynamics by introducing a categorical posterior over codebook indices within a variational flow-matching formulation. Extensive experiments show that SDFlow achieves state-of-the-art performance, improving Discriminative Score and substantially reducing Context-FID, particularly for challenging long-sequence generation. Moreover, SDFlow provides significant inference speedups over autoregressive baselines, offering both high fidelity and computational efficiency. Code is available at https://anonymous.4open.science/r/SDFlow-D6F3/

Recent flow matching (FM) methods improve the few-shot adaptation of vision-language models, by modeling cross-modal alignment as a continuous multi-step flow. In this paper, we argue that existing FM methods are inherently constrained by incompatible geometric priors on pre-trained cross-modal features, resulting in suboptimal adaptation performance. We first analyze these methods from a polar decomposition perspective (i.e., radial and angular sub-manifolds). Under this new geometric view, we identify three overlooked limitations in them: 1) Angular dynamics distortion: The radial-angular coupling induces non-uniform speed on the angular sub-manifold, leading to regression training difficulty and extra truncation errors. 2) Radial dynamics neglect: Feature normalization discards modality confidence, failing to distinguish out-of-distribution and in-distribution data, and abandoning crucial radial dynamics. 3) Context-agnostic unconditional flow: Dataset-specific information loss during pre-trained cross-modal feature extraction remains unrecovered. To resolve these issues, we propose warped product flow matching (WP-FM), a unified Riemannian framework that reformulates alignment on a warped product manifold. Within this framework, we derive direct product flow matching (DP-FM) by introducing a constant-warping metric, which yields a decoupled cylindrical manifold (i.e., direct product manifold). DP-FM enables independent radial evolution and constant-speed angular geodesic transport, effectively eliminating angular dynamics distortion while preserving radial consistency. Meanwhile, we incorporate classifier-free guidance by conditioning the flow on the pre-trained VLMs' hidden states to inject missing dataset-specific information. Extensive results across 11 benchmarks have demonstrated that DP-FM achieves a new state-of-the-art for multi-step few-shot adaptation.

Ground-to-space astronomical super-resolution requires recovering space-quality images from ground-based observations that are simultaneously limited by pixel sampling resolution and atmospheric seeing, which imposes a stochastic, spatially varying PSF that cannot be resolved through upsampling alone. Existing methods rely on synthetic training pairs that fail to capture real atmospheric statistics and are prone to either over-smoothed reconstructions or hallucination sources with no physical counterpart in the observed sky. We propose FluxFlow, a conservative pixel-space flow-matching framework that incorporates observation uncertainty and source-region importance weights during training, and a training-free Wiener-regularized test-time correction to suppress hallucination sources while preserving recovered detail. We further construct the DESI--HST Dataset, the large-scale real-world benchmark comprising 19,500 real co-registered ground-to-space image pairs with real atmospheric PSF variation. Experiments demonstrate that FluxFlow consistently outperforms existing baseline methods in both photometric and scientific accuracy.

Open-set supervised anomaly detection (OSAD) aims to identify unseen anomalies using limited anomalous supervision. However, existing prototype-based methods typically model normal data via a unimodal Gaussian prior, failing to capture inherent multi-modality and resulting in blurred decision boundaries. To address this, we propose Mixture Prototype Flow Matching (MPFM), a framework that learns a continuous transformation from normal feature distributions to a structured Gaussian mixture prototype space. Departing from traditional flow-based approaches that rely on a single velocity vector, MPFM explicitly models the velocity field as a Gaussian mixture prior where each component corresponds to a distinct normal class. This design facilitates mode-aware and semantically coherent distribution transport. Furthermore, we introduce a Mutual Information Maximization Regularizer (MIMR) to prevent prototype collapse and maximize normal-anomaly separability. Extensive experiments demonstrate that MPFM achieves state-of-the-art performance across diverse benchmarks under both single- and multi-anomaly settings.

Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional methods for free energy surface sampling involve simulation in high-dimensional configuration space and projecting the resulting configurations onto the CV space. To reduce the computational costs of such sampling, we propose FES-FM, a reduced flow matching (FM) method for free energy sampling (FES). We train a dynamical transport map in the CV space, thereby enabling direct sampling of the free energy surface. For many-particle systems, we construct a prior distribution based on the Hessian at a local minimum of the potential, which ensures both rotation-translation invariance and physically meaningful configurations. We evaluate the proposed method across a variety of potential functions and collective variables. Comparative experiments demonstrate that our approach drastically reduces computational costs while delivering superior accuracy per unit sampling time.

Precipitation in complex terrain is governed by orographic processes operating at scales of a few kilometers, yet climate models typically run at resolutions of 50--100km where this topographic detail is absent. Dynamical downscaling with high-resolution regional models such as WRF can resolve these processes, but the computational cost -- months of wall-clock time per scenario -- precludes the large ensembles needed for uncertainty quantification. We present WxFlow, a conditional generative model based on flow matching that learns to map coarse-resolution climate model output and high-resolution topography to calibrated probabilistic ensembles of fine-scale precipitation fields. Applied to 4km WRF simulations of maximum 3-day snowfall over southeast Alaska, WxFlow achieves 87.8% improvement in spectral fidelity and dramatically lower Continuous Ranked Probability Scores relative to conventional lapse-rate-corrected bicubic downscaling, while generating 50-member ensembles in seconds on a laptop. Ensemble spread is spatially coherent and governed by topography, reflecting physically plausible uncertainty structure. All code is available at https://github.com/glide-ism/wrf-flow.

Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although single-cell RNA sequencing provides quantitative snapshots of the transcriptome, current methods for inferring gene-regulatory dynamics often lack mechanistic interpretability and fail to generalize to unseen conditions. Here we introduce Probability Flow Matching (PFM), a scalable framework for learning biophysically consistent stochastic processes directly from time-resolved single-cell measurements. Applying PFM to three hematopoiesis datasets, we show that models with similar interpolation accuracy can encode fundamentally different dynamics, with only biophysically consistent formulations accurately capturing mechanisms of lineage transitions, fate specification, and gene perturbation responses. We further demonstrate that PFM accommodates unbalanced populations, enabling simultaneous inference of cellular proliferation and death dynamics. Together, these results establish PFM as a flexible, scalable framework for integrating mechanistic modeling with single-cell omics.

Accurate yet low-latency channel state information (CSI) acquisition is essential for multiple-input multiple-output (MIMO) communication systems. While advanced deep generative models, such as score-based and diffusion models, enable high-fidelity CSI reconstruction from limited pilot observations, they often suffer from high inference latency. To achieve accurate CSI estimation under stringent latency constraints, this paper proposes a null-space flow matching (FM) framework that decomposes pilot-limited MIMO channel estimation into a range-space reconstruction problem and a null-space generation problem. Specifically, the range-space component of the channel is directly recovered from noisy pilot observations, while only the ambiguous null-space component is iteratively refined using an FM-based generative prior. To further improve the robustness of the proposed framework, we introduce a power-law time schedule to better allocate the limited number of refinement steps, along with a noise-aware adaptive correction strategy to suppress channel noise on the refinement trajectory. Experimental results demonstrate that our method achieves a competitive normalized mean square error (NMSE) even under a strict latency budget of around 3 ms, while delivering superior estimation accuracy and faster inference than both model-based and generative baselines.

High-fidelity simulations and complex inverse problems, such as detector modeling and unfolding, are computationally intensive bottlenecks across subatomic physics, yet essential for accurate physical interpretation. While Conditional Flow Matching (CFM) offers a robust acceleration approach, we demonstrate its standard training loss is fundamentally misleading. Specifically, utilizing a Jefferson Lab Nuclear Physics (NP) kinematic dataset ($γp \to ρ^0 p \to π^+π^- p$), we expose that CFM loss plateaus prematurely, obscuring ongoing physical refinement. To verify this disconnect is a dataset-agnostic pathology, we introduce ScatterPrism, an efficient generative surrogate evaluated against both the NP data and synthetic stress tests modeling challenging 1D distribution topologies. Coupling these benchmarks, we establish that physics-informed metrics continue improving long after standard loss converges. Consequently, we propose a multi-metric diagnostic protocol to ensure true kinematic fidelity without data memorization. Driven by NP challenges relevant to the forthcoming Electron-Ion Collider (EIC), this unified machinery has strong potential to extend to High-Energy Physics (HEP) applications, such as jet modeling. Furthermore, the framework holds promise for broader domains requiring rigorous generative reliability, including medical imaging, astrophysics, and quantitative finance.

Generative models, particularly Diffusion Models (DM), have shown strong potential for Computed Tomography (CT) reconstruction serving as expressive priors for solving ill-posed inverse problems. However, diffusion-based reconstruction relies on Stochastic Differential Equations (SDEs) for forward diffusion and reverse denoising, where such stochasticity can interfere with repeated data consistency corrections in CT reconstruction. Since CT reconstruction is often time-critical in clinical and interventional scenarios, improving reconstruction efficiency is essential. In contrast, Flow Matching (FM) models sampling as a deterministic Ordinary Differential Equation (ODE), yielding smooth trajectories without stochastic noise injection. This deterministic formulation is naturally compatible with repeated data consistency operations. Furthermore, we observe that FM-predicted velocity fields exhibit strong correlations across adjacent steps. Motivated by this, we propose an FM-based CT reconstruction framework (FMCT) and an efficient variant (EFMCT) that reuses previously predicted velocity fields over consecutive steps to substantially reduce the number of Neural network Function Evaluations (NFEs), thereby improving inference efficiency. We provide theoretical analysis showing that the error introduced by velocity reuse is bounded when combined with data consistency operations. Extensive experiments demonstrate that FMCT/EFMCT achieve competitive reconstruction quality while significantly improving computational efficiency compared with diffusion-based methods. The codebase is open-sourced at https://github.com/EFMCT/EFMCT.

Modern vision generators transport a base distribution to data through time-indexed measures, implemented as deterministic flows (ODEs) or stochastic diffusions (SDEs). Despite strong empirical performance, standard flow-matching objectives do not directly control the information geometry of the trajectory, allowing low-entropy bottlenecks that can transiently deplete semantic modes. We propose Entropy-Controlled Flow Matching (ECFM): a constrained variational principle over continuity-equation paths enforcing a global entropy-rate budget d/dt H(mu_t) >= -lambda. ECFM is a convex optimization in Wasserstein space with a KKT/Pontryagin system, and admits a stochastic-control representation equivalent to a Schrodinger bridge with an explicit entropy multiplier. In the pure transport regime, ECFM recovers entropic OT geodesics and Gamma-converges to classical OT as lambda -> 0. We further obtain certificate-style mode-coverage and density-floor guarantees with Lipschitz stability, and construct near-optimal collapse counterexamples for unconstrained flow matching.

Visually-guided acoustic highlighting seeks to rebalance audio in alignment with the accompanying video, creating a coherent audio-visual experience. While visual saliency and enhancement have been widely studied, acoustic highlighting remains underexplored, often leading to misalignment between visual and auditory focus. Existing approaches use discriminative models, which struggle with the inherent ambiguity in audio remixing, where no natural one-to-one mapping exists between poorly-balanced and well-balanced audio mixes. To address this limitation, we reframe this task as a generative problem and introduce a Conditional Flow Matching (CFM) framework. A key challenge in iterative flow-based generation is that early prediction errors -- in selecting the correct source to enhance -- compound over steps and push trajectories off-manifold. To address this, we introduce a rollout loss that penalizes drift at the final step, encouraging self-correcting trajectories and stabilizing long-range flow integration. We further propose a conditioning module that fuses audio and visual cues before vector field regression, enabling explicit cross-modal source selection. Extensive quantitative and qualitative evaluations show that our method consistently surpasses the previous state-of-the-art discriminative approach, establishing that visually-guided audio remixing is best addressed through generative modeling.

Developing efficient and accurate visuomotor policies poses a central challenge in robotic imitation learning. While recent rectified flow approaches have advanced visuomotor policy learning, they suffer from a key limitation: After iterative distillation, generated actions may deviate from the ground-truth actions corresponding to the current visual observation, leading to accumulated error as the reflow process repeats and unstable task execution. We present Selective Flow Alignment (SeFA), an efficient and accurate visuomotor policy learning framework. SeFA resolves this challenge by a selective flow alignment strategy, which leverages expert demonstrations to selectively correct generated actions and restore consistency with observations, while preserving multimodality. This design introduces a consistency correction mechanism that ensures generated actions remain observation-aligned without sacrificing the efficiency of one-step flow inference. Extensive experiments across both simulated and real-world manipulation tasks show that SeFA Policy surpasses state-of-the-art diffusion-based and flow-based policies, achieving superior accuracy and robustness while reducing inference latency by over 98%. By unifying rectified flow efficiency with observation-consistent action generation, SeFA provides a scalable and dependable solution for real-time visuomotor policy learning. Code is available on https://github.com/RongXueZoe/SeFA.

Vision-Language-Action (VLA) models such as OpenVLA, Octo, and $π_0$ have shown strong generalization by leveraging large-scale demonstrations, yet their performance is still fundamentally constrained by the quality and coverage of supervised data. Reinforcement learning (RL) provides a promising path for improving and fine-tuning VLAs through online interaction. However, conventional policy gradient methods are computationally infeasible in the context of flow-matching based models due to the intractability of the importance sampling process, which requires explicit computation of policy ratios. To overcome this limitation, we propose Flow Policy Optimization (FPO) algorithm, which reformulates importance sampling by leveraging per-sample changes in the conditional flow-matching objective. Furthermore, FPO achieves stable and scalable online reinforcement fine-tuning of the $π_0$ model by integrating structure-aware credit assignment to enhance gradient efficiency, clipped surrogate objectives to stabilize optimization, multi-step latent exploration to encourage diverse policy updates, and a Q-ensemble mechanism to provide robust value estimation. We evaluate FPO on the LIBERO benchmark and the ALOHA simulation task against supervised, preference-aligned, diffusion-based, autoregressive online RL, and $π_0$-FAST baselines, observing consistent improvements over the imitation prior and strong alternatives with stable learning under sparse rewards. In addition, ablation studies and analyses of the latent space dynamics further highlight the contributions of individual components within FPO, validating the effectiveness of the proposed computational modules and the stable convergence of the conditional flow-matching objective during online RL.

Reconstructing a three-dimensional hyperspectral cube from a two-dimensional compressed measurement is a severely ill-posed inverse problem. Existing deep unfolding networks (DUNs) retain fidelity to the imaging model, but regression-trained denoisers can suppress spatial detail and smooth spectral structure under strong modulation. This paper proposes \emph{FMU}, a deep unfolding framework that couples a measurement-conditioned flow-matching prior with a sensing-model-guided measurement update. A two-phase scheme first learns a compact clean-HSI latent target and then trains a conditional velocity field to generate this target from Gaussian noise. A mean-velocity regularizer additionally penalizes the first-moment error of the learned field. On the KAIST 10-scene benchmark under the optical-filter setting, FMU obtains 42.13,dB PSNR and 0.9900 SSIM, outperforming LADE-DUN by 1.16,dB in PSNR under the same training data, sensing mask, and evaluation protocol. Under the same optical-filter operator, FMU is further evaluated on held-out KAIST and ICVL scenes without fine-tuning. We also report quantitative simulated-CASSI results and qualitative reconstructions of real CASSI measurements.

Learning the dynamics of a process given sampled observations at several time points is an important but difficult task in many scientific applications. When no ground-truth trajectories are available, but one has only snapshots of data taken at discrete time steps, the problem of modelling the dynamics, and thus inferring the underlying trajectories, can be solved by multi-marginal generalisations of flow matching algorithms. This paper proposes a novel flow matching method that overcomes the limitations of existing multi-marginal trajectory inference algorithms. Our proposed method, ALI-CFM, uses a GAN-inspired adversarial loss to fit neurally parametrised interpolant curves between source and target points such that the marginal distributions at intermediate time points are close to the observed distributions. The resulting interpolants are smooth trajectories that, as we show, are unique under mild assumptions. These interpolants are subsequently marginalised by a flow matching algorithm, yielding a trained vector field for the underlying dynamics. We showcase the versatility and scalability of our method by outperforming the existing baselines on spatial transcriptomics and cell tracking datasets, while performing on par with them on single-cell trajectory prediction. Code: https://github.com/mmacosha/adversarially-learned-interpolants.

We present a framework for fine-tuning flow-matching generative models to enforce physical constraints and solve inverse problems in scientific systems. Starting from a model trained on low-fidelity or observational data, we apply a differentiable post-training procedure that minimizes weak-form residuals of governing partial differential equations (PDEs), promoting physical consistency and adherence to boundary conditions without distorting the underlying learned distribution. To infer unknown physical inputs, such as source terms, material parameters, or boundary data, we augment the generative process with a learnable latent parameter predictor and propose a joint optimization strategy. The resulting model produces physically valid field solutions alongside plausible estimates of hidden parameters, effectively addressing ill-posed inverse problems in a data-driven yet physicsaware manner. We validate our method on canonical PDE benchmarks, demonstrating improved satisfaction of PDE constraints and accurate recovery of latent coefficients. Our approach bridges generative modelling and scientific inference, opening new avenues for simulation-augmented discovery and data-efficient modelling of physical systems.

Flow Matching (FM) is a simulation-free method for learning a continuous, invertible flow that interpolates between two distributions, and in particular generates data from noise. Inspired by the variational nature of the diffusion process as a gradient flow, we introduce a stepwise FM model, Local Flow Matching (LFM), which sequentially learns a sequence of FM submodels, each matching a diffusion process up to the time-step size in the data-to-noise direction. In each step, the two distributions to be interpolated by the sub-flow model are closer than those in the full-flow matching model, which interpolates data to noise distributions, enabling smaller models with more efficient training. This variational perspective also allows us to prove a theoretical generation guarantee for the proposed flow model in terms of the $χ^2$-divergence between the generated and true data distributions, leveraging the contraction property of the diffusion process. In practice, the stepwise structure of LFM is naturally amenable to model distillation, and various distillation techniques can be applied to accelerate generation. We empirically demonstrate that LFM achieves competitive generative performance compared to FM on unconditional generation of tabular and image datasets, and on conditional generation of robotic manipulation policies.