Conditional Flow Matching

Single-cell snapshot data can resolve a continuum of cellular states but do not uniquely determine the dynamics governing transitions between them. However, additional dynamical information can often be encoded in a cell-cell Markov transition kernel. Existing generative approaches for single cell trajectory inference either infer transport only from population marginals, impose a symmetric geometry on the state space, or incorporate directionality through a single velocity vector at each observed state. We introduce Finsler Flow Matching (FFM), a framework for learning continuous stochastic dynamics from discrete Markov transition graphs. We use the first and second local moments to construct a Finsler structure motivated by the Freidlin--Wentzell action, where the second moment determines anisotropic accessibility and the first moment introduces a preferred direction of motion. We learn neural approximations of the resulting directed geodesics, use their Finsler cost to construct source-target couplings, and define geometry-aware stochastic conditional paths that can be distilled into a continuous generative process through simulation-free score and flow matching. Across synthetic and single-cell trajectory inference benchmarks, FFM improves recovery of withheld intermediate populations, particularly when the transition dynamics are strongly directional or anisotropic. Our results provide a principled route from discrete transition probabilities to continuous generative dynamics while retaining both directional and diffusive structure.

Rapid and accurate prediction of urban wind and temperature fields is important for urban microclimate design and climate adaptation. Large-eddy simulation (LES) effectively resolves these instantaneous fields, but its application is limited in iterative design of urban microclimate applications due to high computational cost. Existing regressive data-driven models offers quick outputs, but they produce only deterministic point predictions that inherently fail to represent turbulent stochasticity. This paper adopts a novel generative framework of Conditional Flow Matching (CFM) that uses building geometry and mean flow as guidance to generate plausible three-dimensional instantaneous velocity and temperature fields for urban microclimate in seconds. To overcome the GPU memory bottleneck of pixel space 3D generation, the model operates in parallel on overlapping pixel space through a shared-noise initialization that preserves high spatial continuity of flow structure across the entire domain. Against reference LES data, the CFM surrogate can rapidly and accurately restore the first-order statistics with Normalized Root Mean Square Error (NRMSE) of 2.99% for wind and 1.77% for temperature, second-order turbulence metrics with NRMSE of 7.17% for wind and 8.84% for temperature, turbulent kinetic energy with NRMSE of 7%, probability density function and vertical profiles in representative locations. Wind engineering application of local gust prediction demonstrate that the speed and accuracy of CFM, supporting the use of generative AI for making turbulence-aware resilient urban design and climate adaptation more computationally feasible.

We introduce MUNITE, a latent-variable framework for flexible any-to-any multimodal generation that treats encoding and latent generation as the same inference problem under different amounts of observed evidence. Given any subset of modalities, MUNITE models the conditional distribution over the latent representation associated with the complete observation. Full observation recovers deterministic encoding, no observation recovers the latent marginal, and intermediate subsets define conditional latent inference, all within a single conditional flow model. A shared latent sample captures variation that must remain consistent across generated targets, while modality-specific generative decoders model the remaining uncertainty independently. To learn these conditional distributions from incomplete training examples, we extend conditional flow matching through self-distillation: predictions conditioned on richer available observations supervise the same model conditioned on smaller subsets at the same intermediate latent state. When the richer-evidence trajectory follows the exact conditional flow, this provides the same expected learning signal as full-target denoising. Across PolyMNIST-D-Q, FFHQ64, and image-text-audio, MUNITE achieves competitive or better generation quality and source-target alignment, with higher joint-generation coherence. In particular, it attains the highest coherence in all one-to-many and unconditional image-text-audio comparisons, showing the effectiveness of unified latent inference across diverse multimodal settings.

Motivated by sequence-to-sequence transport in the context time-series domain adaptation, we study the problem of transportation between trajectories of Markov processes. Given a limited number of trajectories from source distribution and the target distribution, we formulate a flow matching based algorithm which learns a transport map from the source to target trajectory distribution, while preserving the Markov structure. We show that this is consistent in the population limit and derive finite-sample error bounds under mixing time assumptions, following the analysis of classical statistical problems including regression (Nagaraj et al., 2020), principal component analysis (Kumar and Sarkar, 2023), and matrix concentration (Neeman et al., 2024) in the Markov setting. We complement that with a lower-bound construction showing that a mixing-time dependent sample complexity is unavoidable even with regular Gaussian conditional transitions. We evaluate on synthetic and real-world data. For image retrieval from electroencephalography (EEG) on THINGS-EEG2 (Gifford et al., 2022), the task is to identify the viewed image from EEG signals captured from human subjects, which suffers from high inter subject variability. We augment the ENIGMA decoder (Kneeland et al., 2026) with a conditional flow before its subject-specific temporal map. This improves mean top-5 retrieval accuracy from 43.87% to 49.05%, an 11.82% relative improvement.

Neurons of the brain exhibit a rich repertoire of electrophysiology dynamics with the same repeated stimulus eliciting very different voltage responses from the same cell. One common approach in biophysically detailed models is to capture this variability through ensembles of deterministic parametrizations, at a cost of hundreds of thousands of CPU hours. Existing machine learning surrogates inherit the same limitation, where a stimulus is mapped to a single voltage response. We address this challenge by learning a conditional generative model for single-neuron electrophysiology, using flow matching with a velocity field conditioned on the input current. On biophysically detailed models of two human cortical interneuron types, the generated responses closely reproduce the electrophysiological feature distributions, spike-time structure, and excitability profiles, even matching the experimental recordings from the corresponding human cortical neurons. Near the firing threshold, firing and non-firing responses coexist at the same stimulus amplitude, and at high amplitudes, ensembles may split into low- and high-firing modes near depolarization block. We show that our model recovers both modes in each case, while a neural operator baseline suppresses spiking near threshold and blurs the gap between modes at depolarization block.

Recent work has shown that probabilistic flow matching for time series forecasting benefits from a data-matched prior. The resulting prior introduces local correlations, which a sequential architecture usually absorbs: a recurrent neural network (RNN), a structured state-space model (S4), or a Transformer. However, such a backbone costs GPU memory and time per epoch. A cheaper alternative is MLP-based latent-space flow matching: embed the time series via an invertible map to a single latent vector and learn the flow there, so a tabular MLP can treat the series as a set of features. The relationship between the prior and the choice of linear latent map is understudied in conditional flow matching (CFM) forecasting, yet we found it strongly affects performance. Fixed transforms such as Fourier or discrete cosine (DCT) are only well-conditioned for Ornstein--Uhlenbeck priors, while a principal-component (PCA) map fit to the data is a strong but training-set-dependent reference sensitive to train--test shift. Instead, we propose to use the Mercer eigenbasis of the prior kernel: it diagonalises the centred covariance exactly, decouples from training data, and adapts to non-stationary and periodic priors. On five GluonTS benchmarks (ETTh1, ETTh2, Weather, Electricity, Traffic) under a shared protocol with TSFlow, the resulting MLP matches or beats it on CRPS at about $4.7\times$ less training memory and $3.5\times$--$4.4\times$ less time per epoch.

Deep generative networks have recently achieved unprecedented performance in precise image and video editing using sophisticated textual prompts. However, the effectiveness of such models heavily depends on access to very large supervised and annotated image datasets, which can be very difficult to obtain. This is particularly true for satellite instruments, which very rarely overlap with labelled data, and suffer from domain shifts in the rare occasions they do. In this paper, we investigate the potential of flow matching models for unsupervised domain adaptation of satellite radiometer images. Our main contribution is a novel unsupervised method that achieves precise domain alignment by leveraging parts of the deterministic ordinary differential equations in flow matching models, conditioned on different satellite instruments. A key strength of our approach is its ability to preserve essential information while adapting across any domains since the perturbations are in theory bijective. Extensive experiments conducted on the GPM-Core constellation show the benefit of our conditional domain adaptation, particularly in improving rain precipitation estimation from radiometer imagery.

Forecasting time-varying functional connectivity from electroencephalography (EEG) requires modeling both history-dependent trends and structured variability across channels. Conditional flow matching provides a framework for distributional forecasting, yet it remains unclear whether graph-informed source distributions offer practical advantages over isotropic noise and strong deterministic predictors. We introduce a graph-structured residual flow framework that separates conditional mean prediction from stochastic residual transport. A history-only predictor estimates the future connectivity graph, while a graph Gaussian source encodes dependencies derived from past connectivity through a Laplacian-based covariance. A conditional velocity field transports source samples to future graph residuals, with transport time explicitly distinguished from physical EEG time. Our study identifies the conditions and controls needed to distinguish useful residual transport from improvements attributable to deterministic prediction, learned representations, and sampling effects.

Predicting cellular responses to perturbations is a central problem in cellular biology, with broad applications in systems biology and drug discovery. This task is challenging because cellular responses can be complex and cell-state dependent, intrinsic cell-to-cell variability can be confounded with perturbation effects, and destructive single-cell RNA sequencing precludes paired measurements of the same cell before and after treatment. Flow matching transports control cells to perturbed states flexibly, but acting on the full cell state can confound perturbation effects with pre-existing cell-to-cell variability. Disentangled approaches separate responsive from invariant components, but model perturbations through prescribed mechanisms, such as latent shifts or graph edits, limiting their flexibility. We address both limitations in a unified framework. A variational encoder disentangles each cell into an invariant block, capturing state unaffected by the perturbation, and a responsive block, capturing state it changes, through conditional priors and an information-theoretic invariance constraint. Conditional flow matching transports only the responsive block, conditioned on the perturbation and invariant state, yielding a flexible, data-driven model of perturbation effects without confounding pre-existing variability. Across several benchmarks, our method outperforms the strongest published method in settings involving combinatorial and unseen perturbation prediction.

Conditional Flow Matching (CFM) models for text-to-speech (TTS) suffer from incoherent frequency evolution during inference. While similar spectral imbalances are addressed in diffusion models for other domains, those generic solutions fail to generalize to the inherently uncoordinated acoustic dynamics of CFM. We demonstrate that this issue can be effectively mitigated by introducing a novel training-free frequency-selective boosting strategy. Using the Discrete Wavelet Transform (DWT), our method dynamically modulates mel-spectrogram sub-bands during ODE integration, synchronizing spectral development by penalizing aggressive low-frequency growth and boosting lagging high-frequency details. Validated across diverse architectures (Matcha-TTS, F5-TTS, IndicF5), our approach reduces the required Number of Function Evaluations (NFE) from 32 to 26 and improves Frechet Audio Distance (FAD) by up to 61%, all without compromising mean opinion scores, speaker similarity, and speech intelligibility.

Critical mineral discovery is a positive-only problem: deposits are observed as sparse locations, while unlabeled regions are not reliable negatives, and similar geophysical signatures can arise from different subsurface states. We therefore model mineral targeting as learning a conditional spatial distribution over occurrence locations, $π(p\mid d)$, given geo-images $d$, rather than predicting a deterministic per-pixel score map. We introduce GeoCFM, a conditional flow-matching model that generates mineral occurrence point sets conditioned on multi-channel geo-images; GeoCFM learns a point-wise transport field in $\mathbb{R}^2$, using UNet features with point-conditioned velocity prediction to bridge dense rasters and sparse supervision without pseudo-negatives. On a synthetic magnetics--geochemistry benchmark with latent activation and on USGS Earth MRI data with a spatially disjoint tile split, GeoCFM improves geometric agreement with observed occurrences over score-map and non-conditional baselines, while representing epistemic uncertainty through conditional sampling.

Stream-level flow matching replaces the linear interpolant of conditional flow matching (CFM) by a Gaussian-process (GP) stream connecting each source--target pair, and reports lower sample error than \icfm{} on 2-Gaussian, MNIST and CIFAR-10 benchmarks. We ask what such a stream model actually contributes. Three results answer the question. (i)\emph{Reduction.} The stream-level CFM objective depends on the stream law only through the per-time joint law of $(s_t,\sdot_t)$, so the conditional paths a Gaussian stream can reach are exactly the Gaussian conditional paths CFM already parametrises; in the coordinate-wise, shared-scalar-kernel construction gpcfm actually uses, the entire design space collapses to two scalar curves $(m_t,v_t)$, and cross-time covariance affects only estimator variance. (ii)\emph{The GP is a constrained chart of that space.} One kernel sets both $m_t$ and $v_t$, so the paper's own recipe for widening coverage-shrinking the SE length-scale---destroys the interpolant (the midpoint mean weight falls from $1.03$ to $0.00$). On the 2-Gaussian benchmark this makes the GP chart diverge on $15/200$ runs at high coverage against $0/200$ for a decoupled $(m_t,v_t)$ chart ($p=6.6\times10^{-5}$), and crossing the two curves shows the divergence tracks the mean, not the variance. On MNIST the same sweep does not diverge and the ordering reverses, so whether the coupling is harmful is benchmark-dependent; what holds on both is that the recipe buys nothing---no coverage level beats the paper's own, and past $\max_t\sqrt{v_t}\approx0.6$ both charts degrade. (iii)~\emph{Audit.} The released code does not implement the mechanism it describes: state and velocity are drawn independently ($\mathrm{corr}=0.00\pm0.01$ against an intended $\pm0.83$--$0.99$).

Advances in generative modeling have recently been extensively employed in robotics for policy learning. In particular, Conditional Flow Matching (CFM) trained with expert demonstrations has been shown to outperform existing methods on robot manipulation benchmarks. While prior work has mainly focused on single-task settings, we study the problem from a multi-task perspective, as training independent models for each task is computationally expensive. Multi-Task policy learning comes with its own set of challenges, as naively training on a concatenated dataset of demonstrations would either require increased model capacity to accommodate the added complexity or result in drops in performance. We propose to distill knowledge from single-task CFM experts into a shared multi-task policy by transferring their learned velocity fields. We combine this distillation signal with the original CFM objective to retain fidelity to the demonstrations. Experiments on RLBench show that our approach improves multi-task policy performance over naive training while maintaining a fixed model size.

Flow matching methods for imaging inverse problems typically incorporate measurements through network conditioning or guidance during sampling. Neither approach explicitly applies the forward operator within the learned conditional velocity field. We develop a principled measurement-conditional velocity parameterization that does. For a linear interpolation path, we express the optimal velocity through the posterior mean $E[x_1|x_t, y]$ and show that this mean is the unique minimizer of a variational objective with an explicit data-consistency term. The velocity defined by this minimizer provably transports the source distribution to the measurement-conditioned posterior. This result leads to a forward operator-aware velocity field that is trained end-to-end and requires no separate guidance during sampling. Across five imaging tasks, our method achieves leading reconstruction quality with up to $50\times$ fewer network evaluations than competitive flow-based methods. Varying the number of sampling steps also controls the distortion-perception trade-off without retraining.

Three-dimensional ultrasound (US) is a safe, radiation-free complementary modality to CT and X-rays for longitudinal monitoring, yet its segmentation-derived partial point clouds are extremely artifact-laden. Consequently, it is challenging to recover a clean and complete anatomical structure from such US point clouds. In this paper, we present UBone3D, a novel framework based on physics-rectified conditional flow matching (CFM) that performs point cloud completion directly from partial US observations. UBone3D models deterministic physics artifacts (e.g., surface thickening, streaking, dropouts) via a simulated physics proxy, and introduces test-time physics rectification to steer the shape completion. At inference, the completion is jointly steered by two decoupled forces: (1) anatomical plausibility enforced by a CT-trained generative shape prior, BoneFM, and (2) physics consistency enforced by USimNet in the ultrasound formation space. Extensive experiments on simulated and in-vivo data demonstrate significant improvements in reconstruction accuracy and anatomical fidelity over existing baselines.

Reliable matching between partially observed, deforming point clouds requires global context and fine geometric detail. Coarse candidate selection can exclude correct fine-level correspondences. We present \paper, a unified conditional transport framework with the matching matrix itself as the evolving state. Coarse diffusion establishes global matching hypotheses; hierarchy-preserving lifting expands them into a structured high-resolution source. Geometry-conditioned ODE and SDE bridges continue refinement in the complete fine-level candidate space, allowing coarse errors to be corrected. The deterministic endpoint-parameterized conditional flow matching (CFM) design improves matching through iteration, while the SDE forward drift enables effective few-step refinement. Experiments on 4DMatch and 4DLoMatch demonstrate competitive matching and non-rigid registration, with transfer to CAPE and DeepDeform without target-domain training.

Crystal generators can now propose periodic structures, but their control interfaces remain poorly matched to the mixed descriptors used in materials design. Text provides a compact way to combine composition, symmetry, prototype and property cues, yet it has not been clear whether such information can steer flow-based crystal generation. Here we introduce TFMat, a text-conditioned flow-matching framework that uses structured materials language as a semantic prior for a CrystalFlow generator. Across Perov-5, Carbon-24 and MP-20 crystal structure prediction benchmarks, TFMat improves one-candidate match rates over CrystalFlow and reaches a 92.04% MP-20 match rate with 20 candidates; in de novo generation, it improves element-count and density distribution alignment while retaining coarse property consistency in composition-selected outputs. These results position structured text as an inspectable control layer for translating human-readable materials intent into candidate crystals for downstream simulation and validation.

Magnetic resonance images of the same subject look markedly different across field strengths, which complicates the comparison and pooling of data across sites. We address cross-field brain-MRI translation for the MRIxFields2026 challenge, and in particular its Task~3: a single model that translates between any directed pair of the five field strengths and across three contrasts. We phrase the problem as a conditional flow matching path: because the source and target volumes are spatially registered, we learn a velocity field that carries the source slice directly to the target slice, rather than starting from noise. To learn this mapping from only three paired subjects, the unified model is trained in three stages: a degradation-bridge pretraining that distills a restoration prior from the abundant unpaired retrospective cohort, a cross-field finetuning over all directed pairs on the paired cohort, and an adversarial refinement that sharpens the output. At inference, we integrate the learned velocity with a second-order Heun solver in a handful of steps. A restoration prior learned without any paired data already reaches a mean SSIM of 0.837, and each subsequent training stage improves on it. A single 6.3M-parameter model thereby covers all 60 field-pair and contrast combinations, with inference in five solver steps per slice. On the challenge evaluation set the model reaches a mean SSIM of 0.909, averaged over the three contrasts, outperforming regression and diffusion baselines built on the identical network on all three challenge metrics.

Engineering inverse design is often limited by the high computational cost of iterative solvers for optimization problems constrained by partial differential equations (PDEs) and by their sensitivity to initialization. Deep generative models can produce candidate designs without rerunning the simulator at inference time. Generative adversarial networks (GANs) sample in one forward pass, whereas diffusion models require iterative reverse-time integration. In this work, we add conditional flow matching (CFM) to EngiOpt and compare it with a conditional diffusion model and a conditional generative adversarial network (cGAN) on structural (beams2d) and thermal (heatconduction2d) benchmarks from EngiBench using the same downstream optimization protocol. We use cumulative optimality gap (COG) and final optimality gap (FOG) as the primary metrics for evaluating the generated designs as warm starts for gradient-based refinement. On the evaluated EngiOpt implementations and two EngiBench tasks, CFM achieves the lowest measured COG, FOG, maximum mean discrepancy (MMD), and volume-fraction deviation on both tasks. CFM has mean volume-fraction deviations of 0.4% and 1.0% on beams2d and heatconduction2d, respectively, compared with 3.8% and 11.2% for diffusion. At Euler s = 16, CFM achieves 53.2 samples/s on beams2d, about 66 times the measured throughput of the evaluated diffusion baseline using 1000 network evaluations under the same timing protocol, with COG 1.182 +/- 3.126, compared with 1.173 +/- 3.100 for Euler s = 32. Across the two tasks, CFM produces warm starts with lower measured COG than both baselines and uses fewer network evaluations than diffusion.

In this work we demonstrate that a single transformer-based generative model can capture Standard Model structure spanning five decades of invariant mass, from the sub-GeV regime to the TeV continuum, a range that no single Monte Carlo sample covers. To achieve this we design \textsc{ShellFlow}, a Riemannian conditional flow matching model that, given the recorded event composition, generates each particle on its on-shell manifold. Its only physics priors are the on-shell condition and the invariant-mass formula. The model is trained on $\sim 10^{9}$ real $pp$ collision events from the ATLAS Open Data 13~TeV release and told nothing else. From a single training run, the model learns to reproduce all of the following: intra-particle kinematics, the dilepton resonances ($J/ψ$, $Υ$, $Z$) at their PDG positions, the leptonic Weinberg angle, the $W$ and top-quark masses, and inter-particle correlations that enter no training objective. A substantial fraction of the Standard Model is thus learnable directly from recorded collision data.

Flow matching trains a neural network to regress the conditional velocity along a linear interpolant between noise and data, and the number of network evaluations~(NFE) sets the cost of sampling. The straight-line interpolant carries an implicit choice: the sample moves at constant speed throughout the trajectory. We relax this choice and introduce Velocity Scheduled Flow Matching~(VSFM), which replaces the conditional target $x_1 - x_0$ with $v(t)(x_1 - x_0)$ for any nonnegative profile $v:[0,1]\to\mathbb{R}_{\geq 0}$ satisfying $\int_0^1 v\,dt = 1$. We study six polynomial profiles drawn from motion planning. The first use of VSFM is at inference time: a pretrained linear flow-matching model can be sampled under any admissible profile by integrating its ODE on a non-uniform $τ$-schedule, with no retraining and no additional computation; on CIFAR-10 this lowers FID by up to $19.8\%$. Training from scratch under a braking profile gives a further reduction of $17.4\%$ at $4$~NFE. Both gains follow from the local truncation error of the Euler integrator on the induced grid.

Representation alignment (REPA) has been investigated to accelerate diffusion training, but we observe that regularizing intermediate representations in diffusion Transformers (DiT) may implicitly entangle latents and limit generative capacity. To address this issue, we propose ReGen, a hierarchical multi-prompt representation generation framework that jointly estimates multiple vector fields for both representations and data within a single diffusion model. We further introduce generalized flow matching (GFM) to improve the generalization of conditional flow matching (CFM). We validate ReGen on single-stage waveform diffusion models including neural audio codec and Wave-VAE. ReGen significantly improves waveform generation quality from highly compressed latent representations at 12.5 Hz. We also present ReGenVoice, a latent diffusion model (LDM)-based text-to-speech model that achieves strong speech intelligibility (WER) and speaker similarity (SIM) with a small dataset. Moreover, operating the LDM at 6.25 Hz with rich semantic and acoustic latent representation enables efficient training and sampling, requiring only 1 day of training on 4 GPUs and fast inference with an RTF of 0.08. Audio samples are available at https://regenvoice.github.io/demo/.

While prior work has explored emotion control in hybrid text-to-speech systems, the geometric properties of these modules, and their implications for steerability, remain poorly understood. We present the first comparative study of speech language model (SLM) and conditional flow-matching (CFM) modules as activation steering sites for mixed emotion speech synthesis. We first characterize emotion representations using linear probing and local intrinsic dimensionality (LID), and then evaluate single-site and joint steering for mixed-emotion synthesis. Our results show that SLM offers a clean, low-dimensional emotion-specific subspace with strong speaker--emotion disentanglement, while CFM exhibitspoor cross-speaker generalization due to speaker--emotion entanglement. Joint steering increases emotion intensity but degrades proportional control and speech quality on in-distribution data. These findings provide practical guidance for multi-site activation steering in hybrid TTS systems and highlight the importance of representation geometry in controllable speech generation.

Modeling chaotic systems is crucial yet challenging. Inverse problems in chaotic dynamics, namely inferring initial conditions from final states, remain largely unsolved because of ill-posedness, non-uniqueness, instability, and potentially chaotic time-reverse dynamics. We address this open problem with Bidirectional Conditional Flow Matching (Bi-CFM), which learns bidirectional mappings between distributions of initial and final states to capture the stochasticity of chaotic evolution and mitigate exponential error accumulation over time. Furthermore, for systems with conservation laws, we extend it to Conservation-constrained Bi-CFM (CBi-CFM). Across the classic Lorenz, Circuit, and high-dimensional Lorenz 96 systems, Bi-CFM improves five distribution-level metrics over baselines while achieving a speedup of more than two orders of magnitude. In the three-body planet-planet scattering problem in planetary dynamics, CBi-CFM better respects conservation laws, with conservation errors comparable to those of the ground truth. Finally, on real observations of globular clusters, collisional million-body systems shaped by $\sim 10^{10}$ years (10 Gyr) of evolution, our method represents an advance in accuracy, establishing a scalable route to solving inverse problems of long-timescale real-world chaotic dynamics.

Reconstructing continuous speech from scalp electroencephalography (EEG) remains fundamentally challenging. EEG provides a weak, spatially diffuse, and highly variable measurement of distributed cortical activity, whereas speech is organized as a coherent acoustic trajectory with strong harmonic and temporal structure. The resulting mismatch makes waveform regression unstable and causes stochastic multi-step generation to be sensitive to artifact-dependent conditioning and subject variability. We introduce NeuroSonic, a conditional flow-matching framework for EEG-to-speech reconstruction. Instead of predicting waveforms directly or refining them through stochastic denoising, NeuroSonic learns a deterministic probability-flow velocity field that transports a noise-corrupted acoustic state toward clean speech under EEG conditioning. EEG and audio are embedded into a shared token space and processed by a time-conditioned gated Transformer that parameterizes the transport ordinary differential equation. This formulation models trajectory evolution explicitly while avoiding iterative stochastic sampling. We evaluate NeuroSonic on the CineBrain and EAV benchmarks under cross-subject evaluation. Across both datasets, the proposed method improves distributional realism, spectral fidelity, and perceptual quality over representative GAN-, diffusion-, and mean-flow baselines, with up to a 26.3% gain in overall perceptual quality. The performance gap is most evident in artifact-heavy segments, where conditioning variability is strongest. These findings indicate that deterministic conditional transport provides a stable and effective formulation for EEG-driven speech reconstruction. Code is available at https://github.com/Y-Research-SBU/NeuroSonic/ .

Conditional generative models are increasingly used as scenario generators for stochastic optimization, but standard training objectives emphasize uniform distributional fit rather than the downstream decisions induced by generated scenarios. This creates an objective mismatch: errors in statistically common regions may have little effect on decision regret, whereas errors in decision-sensitive regions can substantially change the optimal action. We propose Decision-Weighted Flow Matching (DW-FM), a regret-aligned training framework that preserves the simplicity of standard flow matching while reweighting its velocity-regression objective using decision-sensitive endpoint information. Theoretically, we connect downstream regret to pathwise velocity mismatch through a loss-induced decision discrepancy and an adjoint transport argument, yielding an ideal regret-aligned surrogate and practical endpoint-weighted objectives with regret guarantees. Empirically, we demonstrate the effectiveness of DW-FM on three CVaR-based contextual stochastic optimization benchmarks spanning synthetic portfolio, semi-real financial, and traffic-CVaR tasks, where DW-FM improves downstream regret over standard baselines.

Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model. Current all-atom generators inherit expensive architectures from structure prediction, leading to high training costs and limited sample diversity. We argue that much of this complexity is unnecessary for generators, which condition on sparse geometric constraints rather than rich co-evolutionary signals. Emyx is a 140M-parameter conditional flow matching model that concentrates capacity within standard transformer blocks, replacing heavy embedding stacks with lightweight conditional representations and sparse connectivity. We additionally derive an exact reparametrisation of the flow matching interpolant into the EDM noise-level framework, bridging flow matching training efficiency with state-of-the-art sampling methods designed for diffusion models without retraining. Despite being the smallest model, Emyx outperforms both Proteína-Complexa and RFdiffusion3 against the AME enzyme design benchmark across success rate under strict evaluation requiring both global fold recovery and catalytic geometry accuracy, structural novelty, scaffold diversity, and geometric validity, while training in just $682$ GPU-hours, roughly $4\times$ less than RFdiffusion3.

Generative machine learning is an increasingly important complement to dynamical downscaling for producing high-resolution precipitation projections, with diffusion models currently the leading approach. Flow matching is a related generative framework that has recently achieved strong results across image, video and other domains, and shown early promise for downscaling. We train a flow matching model to map daily precipitation from 8 km to 2 km over a convective-scale domain centred on Singapore, and benchmark it against CPMGEM, a score-based diffusion model. Flow matching achieves consistently better spatial skill: higher fractions skill score at every precipitation threshold and neighbourhood scale tested, and tighter structure and amplitude components of the SAL score with comparable location skill. However, flow matching underestimates the upper tail of the precipitation distribution, resulting in a dry bias in the climatological mean. These results suggest that flow matching is a competitive generative framework for convective-scale precipitation downscaling, particularly well suited to capturing spatial structure.

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.

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.