Daily Papers

Despite recent advances in accuracy and efficiency, coarse matching remains an indispensable yet costly stage in existing semi-dense matchers due to dense token-level matching. We present UltraMatch, an ultra-efficient and scalable semi-dense matching framework that bypasses the quadratic computation and memory cost of dense token-level matching by routing only a small fraction of candidate matching paths. At its core, a lightweight Transport Path Router operates on coarse block representations to rank candidate target blocks for each source block and retain only a small set, restricting subsequent token-level matching to the selected paths and avoiding the construction of the full token-to-token matching matrix. We further design a sparse global Dual-Softmax that performs matching only over the routed block candidates while retaining global competition across the sparse matching space. Beyond matching acceleration, UltraMatch employs deployment-oriented structural reparameterization for feature extraction and a tiny fine matching head with shared parameters, further reducing inference cost and memory consumption. UltraMatch achieves competitive accuracy among semi-dense matchers, while running 1.67times faster than SuperPoint+LightGlue with only 0.44 GiB peak inference memory. Its scalability enables inference at up to 6K resolution on a single RTX 3090, whereas existing semi-dense matchers run out of memory before reaching 2K. Our routing strategy is also transferable, delivering about 2times end-to-end speedup in EDM and ELoFTR without accuracy loss. The project repository is available at https://github.com/JiajunLe/UltraMatch.

Effective image inversion in rectified flow models - mapping real images to editable latent representations - is crucial for practical image editing applications; however, achieving optimal balance between reconstruction fidelity and editing flexibility remains a fundamental challenge. In this work, we introduce the Optimal Transport Inversion Pipeline (OTIP), a zero-shot framework that leverages optimal transport theory to guide the inversion process in rectified flow models. Our underlying hypothesis is that incorporating transport-based guidance during the reverse diffusion process can effectively balance reconstruction accuracy and editing controllability through principled trajectory optimization. The method computes optimal transport paths between image and noise distributions while maintaining computational efficiency. Our approach achieves high-fidelity reconstruction with LPIPS scores of 0.001 and SSIM of 0.992 on face editing benchmarks, demonstrating superior preservation of fine-grained details compared to existing methods. We evaluate the framework across multiple editing tasks, observing 7.8% to 12.9% improvements in reconstruction loss over RF-Inversion on the LSUN-Bedroom and LSUN-Church datasets, respectively. For semantic face editing, our method achieves an 11.2% improvement in identity preservation and a 1.6% enhancement in perceptual quality, while maintaining computational efficiency comparable to baseline approaches. Qualitatively, our method produces visually compelling edits with superior semantic consistency and fine-grained detail preservation across diverse editing scenarios. Code is available at: https://github.com/marianlupascu/OT-Inversion

We present FlowDet, the first formulation of object detection using modern Conditional Flow Matching techniques. This work follows from DiffusionDet, which originally framed detection as a generative denoising problem in the bounding box space via diffusion. We revisit and generalise this formulation to a broader class of generative transport problems, while maintaining the ability to vary the number of boxes and inference steps without re-training. In contrast to the curved stochastic transport paths induced by diffusion, FlowDet learns simpler and straighter paths resulting in faster scaling of detection performance as the number of inference steps grows. We find that this reformulation enables us to outperform diffusion based detection systems (as well as non-generative baselines) across a wide range of experiments, including various precision/recall operating points using multiple feature backbones and datasets. In particular, when evaluating under recall-constrained settings, we can highlight the effects of the generative transport without over-compensating with large numbers of proposals. This provides gains of up to +3.6% AP and +4.2% AP_{rare} over DiffusionDet on the COCO and LVIS datasets, respectively.

Inferring cellular dynamics from unpaired single-cell snapshots requires modeling both state transitions and population growth or death. Unbalanced dynamic optimal transport (UDOT) addresses this by penalizing growth along transport paths, making the choice of growth penalty a key way to encode biological priors on proliferation and apoptosis. However, existing UDOT solvers either rely on computationally expensive NeuralODE simulations or depend on analytical solutions of conditional paths, restricting their efficiency solely to quadratic penalties, i.e. Wasserstein-Fisher-Rao (WFR) geodesics. To enable an efficient UDOT solver for general growth penalties, we first show that concave growth penalties lead to degenerate solutions where growth and transport are separated. We then introduce Simulation-free Unbalanced Dynamic Optimal transport (SUDO), a simulation-free framework for UDOT with general non-quadratic convex growth penalties. SUDO learns the conditional paths and transport costs, solves the induced semi-coupling problem, and subsequently leverages unbalanced flow matching to achieve a simulation-free solution. On WFR benchmarks, SUDO matches the accuracy of efficient, analytical solution-driven algorithms while outperforming simulation-based methods in computational speed. Beyond WFR, SUDO supports asymmetric penalties that encode proliferation-dominant priors and produce more plausible trajectories and growth estimates on synthetic and single-cell datasets.

Synthetic electrocardiogram generation serves medical AI applications requiring privacy-preserving data sharing and training dataset augmentation. Current diffusion-based methods achieve high generation quality but require hundreds of neural network evaluations during sampling, creating computational bottlenecks for clinical deployment. We propose FlowECG, a flow matching approach that adapts the SSSD-ECG architecture by replacing the iterative diffusion process with continuous flow dynamics. Flow matching learns direct transport paths from noise to data distributions through ordinary differential equation solving. We evaluate our method on the PTB-XL dataset using Dynamic Time Warping, Wasserstein distance, Maximum Mean Discrepancy, and spectral similarity metrics. FlowECG matches SSSD-ECG performance at 200 neural function evaluations, outperforming the baseline on three metrics. The key finding shows that FlowECG maintains generation quality with substantially fewer sampling steps, achieving comparable results with 10-25 evaluations compared to 200 for diffusion methods. This efficiency improvement reduces computational requirements by an order of magnitude while preserving physiologically realistic 12-lead ECG characteristics. The approach enables practical deployment in resource-limited clinical settings where real-time generation or large-scale synthetic data creation is needed.

Flow-based policies provide an expressive framework for continuous robot control, but their iterative ODE integration incurs substantial inference cost. Naively reducing the integration budget can severely degrade control, since policies optimized under full-step execution are not explicitly constrained to remain reliable under coarse numerical integration. We refer to this mismatch as the few-step discretization gap. To address this problem, we introduce RFPO, a flow-policy optimization framework for reliable few-step execution. Reward-aware online Reflow rectifies student-induced transport paths during on-policy learning, making the resulting policy more robust to coarse integration. A frozen Gaussian PPO controller supplies complementary action-space supervision at full and intermediate integration budgets, while the deployed policy remains a single flow student executed with one Euler step. Across Unitree Go2, Boston Dynamics Spot, Unitree H1, and Unitree G1, RFPO consistently preserves full-step control performance under one-step execution, with one-step returns remaining within 2.4% of their corresponding 64-step values across both zero and random initialization. On Unitree Go2, one-step execution retains 98.5% of the 64-step reward while reducing onboard mean inference latency from 4.39 ms to 0.08 ms, yielding a 54.9x speedup. Real-robot experiments further validate stable one-step locomotion. Code: https://github.com/AIGeeksGroup/RFPO. Website: https://aigeeksgroup.github.io/RFPO.

Generative modeling of peptide sequences requires navigating a discrete and highly constrained space in which many intermediate states are chemically implausible or unstable. Existing discrete diffusion and flow-based methods rely on reversing fixed corruption processes or following prescribed probability paths, which can force generation through low-likelihood regions and require countless sampling steps. We introduce Minimal-action discrete Schrödinger Bridge Matching (MadSBM), a rate-based generative framework for peptide design that formulates generation as a controlled continuous-time Markov process on the amino-acid edit graph. To yield probability trajectories that remain near high-likelihood sequence neighborhoods throughout generation, MadSBM 1) defines generation relative to a biologically informed reference process derived from pre-trained protein language model logits and 2) learns a time-dependent control field that biases transition rates to produce low-action transport paths from a masked prior to the data distribution. We finally introduce guidance to the MadSBM sampling procedure towards a specific functional objective, expanding the design space of therapeutic peptides; to our knowledge, this represents the first-ever application of discrete classifier guidance to Schrödinger bridge-based generative models.

Real-world Image Restoration (Real-IR) aims to recover high-quality (HQ) images from complex and unknown degradations. Although recent diffusion-based methods have substantially improved perceptual quality, their current designs leave two key challenges unresolved. Methods that start from Gaussian noise are slow and often less faithful to the degraded input. Residual-based methods usually train from scratch, which makes it hard to exploit modern pre-trained generative priors. In this paper, we present ScaleResfusion, a scalable diffusion framework for real-world image restoration built on pre-trained text-to-image rectified-flow models. The core of our method is Residual Rectified Flow, which introduces the residual term R into Standard Rectified Flow. Instead of starting from pure noise, it uses a residual transport path that starts from noisy low-quality (LQ) images and admits an exact acceleration point. By learning the residual vector field, Residual Rectified Flow keeps the output distribution and linear diffusion process consistent with the pre-trained rectified-flow models. This makes parameter-efficient fine-tuning possible at scale. We further introduce a knowledge-distillation pipeline to reduce sampling cost while maintaining restoration quality. Extensive experiments on multiple real-world restoration tasks show that ScaleResfusion achieves state-of-the-art performance with much higher efficiency. These results suggest a practical and scalable way to adapt large pre-trained diffusion models to real-world image restoration. Our code and models are available at https://github.com/YukinoshitaLove/ScaleResfusion.

Classifier-free guidance (CFG) is the workhorse for steering large diffusion models toward text-conditioned targets, yet its native application to rectified flow (RF) based models provokes severe off-manifold drift, yielding visual artifacts, text misalignment, and brittle behaviour. We present Rectified-CFG++, an adaptive predictor-corrector guidance that couples the deterministic efficiency of rectified flows with a geometry-aware conditioning rule. Each inference step first executes a conditional RF update that anchors the sample near the learned transport path, then applies a weighted conditional correction that interpolates between conditional and unconditional velocity fields. We prove that the resulting velocity field is marginally consistent and that its trajectories remain within a bounded tubular neighbourhood of the data manifold, ensuring stability across a wide range of guidance strengths. Extensive experiments on large-scale text-to-image models (Flux, Stable Diffusion 3/3.5, Lumina) show that Rectified-CFG++ consistently outperforms standard CFG on benchmark datasets such as MS-COCO, LAION-Aesthetic, and T2I-CompBench. Project page: https://rectified-cfgpp.github.io/

GPU-initiated communication lets GPU threads post RDMA operations directly to the NIC. It underpins NVSHMEM, NCCL GIN, and DeepEP, which serve the fine-grained, latency-critical communication of Mixture-of-Experts (MoE) models, yet its performance characteristics and optimizations remain scarcely documented beyond source code, and library comparisons fail to separate the costs of the hardware mechanism from those of the library around it. This paper dissects GPU-initiated communication at the GPU-NIC boundary. We first detail the GPU-side network path: queue placement, work-request construction, doorbell ordering, and completion semantics. We then introduce mini-gda and mini-proxy, minimal transports for the GPU and CPU-proxy submission paths, and measure them alongside NVSHMEM IBGDA, NCCL GIN, DeepEP, UCCL-EP, MSCCL++, and fabric-lib on NVIDIA H100, H200, B200, and GB200 platforms. A minimal GPU path issues an operation in 0.7 μs and completes in 4.0 μs; libraries add up to 4.6 μs of issue time through queue management, memory ordering, and completion scope, and issue time scales with the SM clock. A tuned CPU proxy matches or beats the GPU path at idle, at the cost of a dedicated core whose operating state sets its latency and throughput. On either path, sharing a queue with bulk traffic raises latency by one to three orders of magnitude. Reaching the 260 M msg/s ceiling of our InfiniBand platform requires doorbell batching and queue parallelism, and both have resource costs: communication code can reduce GPU block residency even when unused, and all-to-all traffic loses 59% of its NIC message rate at about 3,000 active connections. The submission path alone therefore does not predict communication performance. Our experiment code and results are available at https://github.com/ParCoreLab/Dissecting-GPU-Communication-Experiments.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Motion generation is essential for animating virtual characters and embodied agents. While recent text-driven methods have made significant strides, they often struggle with achieving precise alignment between linguistic descriptions and motion semantics, as well as with the inefficiencies of slow, multi-step inference. To address these issues, we introduce TMR++ Aligned Preference Optimization (TAPO), an innovative framework that aligns subtle motion variations with textual modifiers and incorporates iterative adjustments to reinforce semantic grounding. To further enable real-time synthesis, we propose MotionFLUX, a high-speed generation framework based on deterministic rectified flow matching. Unlike traditional diffusion models, which require hundreds of denoising steps, MotionFLUX constructs optimal transport paths between noise distributions and motion spaces, facilitating real-time synthesis. The linearized probability paths reduce the need for multi-step sampling typical of sequential methods, significantly accelerating inference time without sacrificing motion quality. Experimental results demonstrate that, together, TAPO and MotionFLUX form a unified system that outperforms state-of-the-art approaches in both semantic consistency and motion quality, while also accelerating generation speed. The code and pretrained models will be released.

While recent Flow Matching models avoid the reconstruction bottlenecks of latent autoencoders by operating directly in pixel space, the lack of semantic continuity in the pixel manifold severely intertwines optimal transport paths. This induces severe trajectory conflicts near intersections, yielding sub-optimal solutions. Rather than bypassing this issue via information-lossy latent representations, we directly untangle the pixel-space trajectories by proposing Waypoint Diffusion Transformers (WiT). WiT factorizes the continuous vector field via intermediate semantic waypoints projected from pre-trained vision models. It effectively disentangles the generation trajectories by breaking the optimal transport into prior-to-waypoint and waypoint-to-pixel segments. Specifically, during the iterative denoising process, a lightweight generator dynamically infers these intermediate waypoints from the current noisy state. They then continuously condition the primary diffusion transformer via the Just-Pixel AdaLN mechanism, steering the evolution towards the next state, ultimately yielding the final RGB pixels. Evaluated on ImageNet 256x256, WiT beats strong pixel-space baselines, accelerating JiT training convergence by 2.2x. Code will be publicly released at https://github.com/hainuo-wang/WiT.git.

High-dimensional count data arise in applications such as single-cell RNA sequencing and neural spike trains, where mappings between distributions across successive batches or time points form critical components of data analysis. The recent success of diffusion- and flow-based deep generative models for images, video, and text motivates extending these ideas to count-valued settings, but many existing methods either treat each count as a categorical state or transform counts into a continuous space, neither of which is natural or efficient when the count range is large. We propose count-FM, a flow-matching framework for count data based on a continuous-time birth-death process with local unit jumps. Count-FM learns marginal transitions efficiently in count space through simulation-free training of conditional transition rates, allowing transport between arbitrary count-distributed source and target populations. In simulation, count-FM variants achieve strong sample quality while using substantially fewer parameters. We further apply count-FM to scRNA-seq and neural spike-train data for unconditional generation, transport, and conditional generation. Across these tasks, count-FM yields improved sample quality, greater modeling efficiency, and interpretable transport paths.

Accurate uncertainty quantification is critical for many time series forecasting applications, and recent studies have increasingly adopted generative models to capture predictive uncertainty. Existing approaches often combine deterministic forecasting with generative modeling to improve predictive performance. However, their joint training is typically unstable because the deterministic model is embedded within the generative process, resulting in deep computational graphs and changing the probability transport path. In this work, we propose DV-Flow, a unified flow-matching formulation that incorporates the deterministic predictor as a parallel velocity component rather than as the endpoint of the transport path. This design enables stable end-to-end optimization while subsuming several existing formulations as special cases, allowing direct comparisons among them. Extensive experiments on six real-world datasets demonstrate that DV-Flow consistently improves probabilistic forecasting performance over strong baselines. Our code is available at https://github.com/tufts-ml/dv-flow-time-series.

We study a dynamical optimal transport problem on path-space with kinetic cost and nonlocal interaction. For a Gaussian interaction kernel, cyclical monotonicity and the regularity of the effective endpoint cost yield a conservative vector field associated with the initial momentum of the optimal trajectories. Separately, the Gaussian interaction potential W_{π_0} satisfies a uniform gradient estimate and, under a quantitative condition on the interaction strength, is a classical and hence viscosity subsolution of an eikonal equation. We also derive the Euler--Lagrange dynamics directly from path-space optimality by means of endpoint-preserving perturbations of the optimal path measure. The associated phase-space marginals satisfy a measure-valued Liouville-type, or nonlocal kinetic, equation driven by the smooth Gaussian self-consistent force. Conversely, a superposition principle lifts suitable measure-valued solutions of the phase-space continuity equation to measures on phase-space trajectories. Thus path-space optimal transport provides a variational connection between endpoint geometry, eikonal behavior of the Gaussian interaction potential, and kinetic mean-field dynamics.

Minibatch optimal transport coupling straightens paths in unconditional flow matching. This leads to computationally less demanding inference as fewer integration steps and less complex numerical solvers can be employed when numerically solving an ordinary differential equation at test time. However, in the conditional setting, minibatch optimal transport falls short. This is because the default optimal transport mapping disregards conditions, resulting in a conditionally skewed prior distribution during training. In contrast, at test time, we have no access to the skewed prior, and instead sample from the full, unbiased prior distribution. This gap between training and testing leads to a subpar performance. To bridge this gap, we propose conditional optimal transport C^2OT that adds a conditional weighting term in the cost matrix when computing the optimal transport assignment. Experiments demonstrate that this simple fix works with both discrete and continuous conditions in 8gaussians-to-moons, CIFAR-10, ImageNet-32x32, and ImageNet-256x256. Our method performs better overall compared to the existing baselines across different function evaluation budgets. Code is available at https://hkchengrex.github.io/C2OT

Recent successful generative models are trained by fitting a neural network to an a-priori defined tractable probability density path taking noise to training examples. In this paper we investigate the space of Gaussian probability paths, which includes diffusion paths as an instance, and look for an optimal member in some useful sense. In particular, minimizing the Kinetic Energy (KE) of a path is known to make particles' trajectories simple, hence easier to sample, and empirically improve performance in terms of likelihood of unseen data and sample generation quality. We investigate Kinetic Optimal (KO) Gaussian paths and offer the following observations: (i) We show the KE takes a simplified form on the space of Gaussian paths, where the data is incorporated only through a single, one dimensional scalar function, called the data separation function. (ii) We characterize the KO solutions with a one dimensional ODE. (iii) We approximate data-dependent KO paths by approximating the data separation function and minimizing the KE. (iv) We prove that the data separation function converges to 1 in the general case of arbitrary normalized dataset consisting of n samples in d dimension as n/drightarrow 0. A consequence of this result is that the Conditional Optimal Transport (Cond-OT) path becomes kinetic optimal as n/drightarrow 0. We further support this theory with empirical experiments on ImageNet.

Unbounded 3D world generation is emerging as a foundational task for scene modeling in computer vision, graphics, and robotics. In this work, we present WorldFlow3D, a novel method capable of generating unbounded 3D worlds. Building upon a foundational property of flow matching - namely, defining a path of transport between two data distributions - we model 3D generation more generally as a problem of flowing through 3D data distributions, not limited to conditional denoising. We find that our latent-free flow approach generates causal and accurate 3D structure, and can use this as an intermediate distribution to guide the generation of more complex structure and high-quality texture - all while converging more rapidly than existing methods. We enable controllability over generated scenes with vectorized scene layout conditions for geometric structure control and visual texture control through scene attributes. We confirm the effectiveness of WorldFlow3D on both real outdoor driving scenes and synthetic indoor scenes, validating cross-domain generalizability and high-quality generation on real data distributions. We confirm favorable scene generation fidelity over approaches in all tested settings for unbounded scene generation. For more, see https://light.princeton.edu/worldflow3d.

We consider some classical optimization problems in path planning and network transport, and we introduce new auction-based algorithms for their optimal and suboptimal solution. The algorithms are based on mathematical ideas that are related to competitive bidding by persons for objects and the attendant market equilibrium, which underlie auction processes. However, the starting point of our algorithms is different, namely weighted and unweighted path construction in directed graphs, rather than assignment of persons to objects. The new algorithms have several potential advantages over existing methods: they are empirically faster in some important contexts, such as max-flow, they are well-suited for on-line replanning, and they can be adapted to distributed asynchronous operation. Moreover, they allow arbitrary initial prices, without complementary slackness restrictions, and thus are better-suited to take advantage of reinforcement learning methods that use off-line training with data, as well as on-line training during real-time operation. The new algorithms may also find use in reinforcement learning contexts involving approximation, such as multistep lookahead and tree search schemes, and/or rollout algorithms.

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

Model compression offers a promising path to reducing the cost and inaccessibility of large pre-trained models, without significantly compromising their impressive performance. Large Transformer models, including large language models (LLMs), often contain computational redundancy, which can serve as a target for new model compression methods. In this work, we specifically target neuron-level redundancies in model layers by combining groups of similar neurons into fewer neurons. We frame this width reduction as a Discrete Optimal Transport problem, and propose DOTResize, a novel Transformer compression method that uses optimal transport theory to transform and compress model weights. To ensure applicability within the Transformer architecture, we motivate and incorporate entropic regularization and matrix factorization into the transportation maps produced by our method. Unlike pruning-based approaches which discard neurons based on importance measures, DOTResize re-projects the entire neuron width, allowing the retention and redistribution of useful signal across the reduced layer. Empirical results show that compared to simple or state-of-the-art neuron width-pruning techniques, DOTResize can outperform these methods across multiple LLM families and sizes, while achieving measurable reductions in real-world computational cost.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

In an experiment on a turbulent jet, we detect interfacial turbulent layers in a frame that moves, on average, along with the \tnti. This significantly prolongs the observation time of scalar and velocity structures and enables the measurement of two types of Lagrangian coherent structures. One structure, the finite-time Lyapunov field (FTLE), quantifies advective transport barriers of fluid parcels while the other structure highlights barriers of diffusive momentum transport. These two complementary structures depend on large-scale and small-scale motion and are therefore associated with the growth of the turbulent region through engulfment or nibbling, respectively. We detect the \tnti\ from cluster analysis, where we divide the measured scalar field into four clusters. Not only the \tnti\ can be found this way, but also the next, internal, turbulent-turbulent interface. Conditional averages show that these interfaces are correlated with barriers of advective and diffusive transport when the Lagrangian integration time is smaller than the integral time scale. Diffusive structures decorrelate faster since they have a smaller timescale. Conditional averages of these structures at internal turbulent-turbulent interfaces show the same pattern with a more pronounced jump at the interface indicative of a shear layer. This is quite an unexpected outcome, as the internal interface is now defined not by the presence or absence of vorticity, but by conditional vorticity corresponding to two uniform concentration zones. The long-time diffusive momentum flux along Lagrangian paths represents the growth of the turbulent flow into the irrotational domain, a direct demonstration of nibbling. The diffusive flux parallel to the \tnti\ appears to be concentrated in a diffusive superlayer whose width is comparable with the Taylor microscale, which is relatively invariant in time.

Inverse path tracing has recently been applied to joint material and lighting estimation, given geometry and multi-view HDR observations of an indoor scene. However, it has two major limitations: path tracing is expensive to compute, and ambiguities exist between reflection and emission. Our Factorized Inverse Path Tracing (FIPT) addresses these challenges by using a factored light transport formulation and finds emitters driven by rendering errors. Our algorithm enables accurate material and lighting optimization faster than previous work, and is more effective at resolving ambiguities. The exhaustive experiments on synthetic scenes show that our method (1) outperforms state-of-the-art indoor inverse rendering and relighting methods particularly in the presence of complex illumination effects; (2) speeds up inverse path tracing optimization to less than an hour. We further demonstrate robustness to noisy inputs through material and lighting estimates that allow plausible relighting in a real scene. The source code is available at: https://github.com/lwwu2/fipt

Recent reconstruction methods based on radiance field such as NeRF and 3DGS reproduce indoor scenes with high visual fidelity, but break down under scene editing due to baked illumination and the lack of explicit light transport. In contrast, physically based inverse rendering relies on mesh representations and path tracing, which enforce correct light transport but place strong requirements on geometric fidelity, becoming a practical bottleneck for real indoor scenes. In this work, we propose Emission-Aware Gaussians and Path Tracing (EAG-PT), aiming for physically based light transport with a unified 2D Gaussian representation. Our design is based on three cores: (1) using 2D Gaussians as a unified scene representation and transport-friendly geometry proxy that avoids reconstructed mesh, (2) explicitly separating emissive and non-emissive components during reconstruction for further scene editing, and (3) decoupling reconstruction from final rendering by using efficient single-bounce optimization and high-quality multi-bounce path tracing after scene editing. Experiments on synthetic and real indoor scenes show that EAG-PT produces more natural and physically consistent renders after editing than radiant scene reconstructions, while preserving finer geometric detail and avoiding mesh-induced artifacts compared to mesh-based inverse path tracing. These results suggest promising directions for future use in interior design, XR content creation, and embodied AI.

Destructive single-cell measurements provide unpaired population snapshots rather than observations of the same cells across conditions. Local cell states and transition requests may also be insufficient to distinguish responses across source populations. We introduce TempoBridge, a common source-conditioned transport formulation for temporal, genetic, and chemical population transitions. Source cells initialize latent transport and provide a fixed empirical population summary. The velocity field receives this summary alongside the evolving cell state, flow time, and a structured transition descriptor. Minibatch optimal transport (OT) supplies couplings only for conditional flow-matching training paths; inference requires neither target expression nor OT computation. On held-out donors, TempoBridge achieves an Energy distance of 0.129 versus 0.144 for scGen. Genetic mean-expression L_2 error is 2.261 versus 3.156 for scGPT-scratch under Seen 2/2. On held-out compounds, condition-averaged drug-effect correlation is 0.598 versus 0.561 for the CellFlow adapter. Temporal ablations show higher mean distributional error after removing source context, replacing optimal transport with random pairing, or replacing flow matching with static residual regression. Together, these results demonstrate the predictive utility of a common source-conditioned transport formulation across held-out donors, gene combinations, and compounds.

Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the Controlled Monte Carlo Diffusion sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{\"o}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.

We introduce COT-FM, a general framework that reshapes the probability path in Flow Matching (FM) to achieve faster and more reliable generation. FM models often produce curved trajectories due to random or batchwise couplings, which increase discretization error and reduce sample quality. COT-FM fixes this by clustering target samples and assigning each cluster a dedicated source distribution obtained by reversing pretrained FM models. This divide-and-conquer strategy yields more accurate local transport and significantly straighter vector fields, all without changing the model architecture. As a plug-and-play approach, COT-FM consistently accelerates sampling and improves generation quality across 2D datasets, image generation benchmarks, and robotic manipulation tasks.

Diffusion and flow-matching schedules control the signal and noise coefficients that mix data and noise along affine probability paths. Minimizing a kinetic action defined on coefficient paths, motivated by optimal transport, helps explain strong baselines but remains model-agnostic and ignores prediction error. Here we introduce a model-aware schedule construction based on fiberwise optimal transport. At a fixed time and state on the probability path, compatible signal/noise decompositions form an affine fiber. We define a fiberwise prediction risk by averaging optimal-transport costs between the true and predictor-induced decompositions within these fibers. On a fixed coefficient curve, combining this risk with coefficient-path kinetic action yields a closed-form optimal time allocation. This construction extends to general linear prediction targets, and the risk profile can be estimated from an early baseline checkpoint. We evaluate DDPMs and flow matching across prediction targets, training configurations, risk-estimation checkpoints, datasets, and architectures. Our model-aware schedules consistently outperform strong baselines, including a 38.6% relative FID reduction for flow matching on CIFAR-10 at 16 function evaluations. Each model-agnostic kinetic baseline determines its own kinetic reference coordinate. In these coordinates, fiberwise-risk profiles from independently trained models in different settings align closely after normalization to unit area. The resulting schedule deformations used in training also align, suggesting empirical universality across the evaluated models and settings. Pretrained-checkpoint diagnostics extend this normalized-risk agreement to larger conditional latent diffusion and 2-RF models. A frozen analytic allocation template retains most of the model-aware improvement without further risk estimation or model-specific fitting.

Large language models (LLMs) have demonstrated strong capabilities in biological reasoning; however, genomic disease inference remains largely dependent on memorized gene-disease associations rather than understanding biological pathways. This shortcut learning undermines robustness and generalization, and breaks down when molecular identifiers are unavailable. We present GenoMorph, a multimodal genomic reasoning framework that shifts disease prediction from associative gene-disease mapping toward pathway-grounded reasoning. GenoMorph couples a frozen DNA foundation model with question-conditioned cross-attention fusion, self-adaptive latent reasoning (LatentSp), a residual reasoning gate for iterative genomic evidence reinjection, and rejection sampling fine-tuning regularized by hierarchical optimal transport (OT). Rather than learning direct gene-disease mappings, GenoMorph aligns genomic sequence representations with latent pathway dynamics, enabling reasoning trajectories that follow molecular interactions before producing disease predictions. LatentSp dynamically allocates computation according to reasoning confidence, reducing unnecessary reasoning steps and improving inference efficiency. We further construct an anonymized benchmark from the Kyoto Encyclopedia of Genes and Genomes (KEGG), replacing every gene and molecular identifier with anonymous symbols while preserving sequences and pathway topology, thereby removing memorization shortcuts. GenoMorph raises the weighted F1 from 0.7863 (BioReason) to 0.9412, and rejection sampling fine-tuning with self-adaptive latent reasoning pushes it to 0.9725 while cutting latency nearly 60%. On the anonymized benchmark it reaches 0.9465 F1, substantially outperforming prior systems and confirming that accurate disease prediction can arise from pathway reasoning rather than memorized gene-disease associations.

It is increasingly common to encounter data from dynamic processes captured by static cross-sectional measurements over time, particularly in biomedical settings. Recent attempts to model individual trajectories from this data use optimal transport to create pairwise matchings between time points. However, these methods cannot model continuous dynamics and non-linear paths that entities can take in these systems. To address this issue, we establish a link between continuous normalizing flows and dynamic optimal transport, that allows us to model the expected paths of points over time. Continuous normalizing flows are generally under constrained, as they are allowed to take an arbitrary path from the source to the target distribution. We present TrajectoryNet, which controls the continuous paths taken between distributions to produce dynamic optimal transport. We show how this is particularly applicable for studying cellular dynamics in data from single-cell RNA sequencing (scRNA-seq) technologies, and that TrajectoryNet improves upon recently proposed static optimal transport-based models that can be used for interpolating cellular distributions.

Developing a face anti-spoofing model that meets the security requirements of clients worldwide is challenging due to the domain gap between training datasets and diverse end-user test data. Moreover, for security and privacy reasons, it is undesirable for clients to share a large amount of their face data with service providers. In this work, we introduce a novel method in which the face anti-spoofing model can be adapted by the client itself to a target domain at test time using only a small sample of data while keeping model parameters and training data inaccessible to the client. Specifically, we develop a prototype-based base model and an optimal transport-guided adaptor that enables adaptation in either a lightweight training or training-free fashion, without updating base model's parameters. Furthermore, we propose geodesic mixup, an optimal transport-based synthesis method that generates augmented training data along the geodesic path between source prototypes and target data distribution. This allows training a lightweight classifier to effectively adapt to target-specific characteristics while retaining essential knowledge learned from the source domain. In cross-domain and cross-attack settings, compared with recent methods, our method achieves average relative improvements of 19.17% in HTER and 8.58% in AUC, respectively.

The generation of 3D molecules requires simultaneously deciding the categorical features~(atom types) and continuous features~(atom coordinates). Deep generative models, especially Diffusion Models (DMs), have demonstrated effectiveness in generating feature-rich geometries. However, existing DMs typically suffer from unstable probability dynamics with inefficient sampling speed. In this paper, we introduce geometric flow matching, which enjoys the advantages of both equivariant modeling and stabilized probability dynamics. More specifically, we propose a hybrid probability path where the coordinates probability path is regularized by an equivariant optimal transport, and the information between different modalities is aligned. Experimentally, the proposed method could consistently achieve better performance on multiple molecule generation benchmarks with 4.75times speed up of sampling on average.

Unsupervised anomaly detection (UAD) in brain imaging is crucial for identifying pathologies without the need for labeled data. However, accurately localizing anomalies remains challenging due to the intricate structure of brain anatomy and the scarcity of abnormal examples. In this work, we introduce REFLECT, a novel framework that leverages rectified flows to establish a direct, linear trajectory for correcting abnormal MR images toward a normal distribution. By learning a straight, one-step correction transport map, our method efficiently corrects brain anomalies and can precisely localize anomalies by detecting discrepancies between anomalous input and corrected counterpart. In contrast to the diffusion-based UAD models, which require iterative stochastic sampling, rectified flows provide a direct transport map, enabling single-step inference. Extensive experiments on popular UAD brain segmentation benchmarks demonstrate that REFLECT significantly outperforms state-of-the-art unsupervised anomaly detection methods. The code is available at https://github.com/farzad-bz/REFLECT.

Multi-path speculative decoding accelerates lossless sampling from a target model by using a cheaper draft model to generate a draft tree of tokens, and then applies a verification algorithm that accepts a subset of these. While prior work has proposed various verification algorithms for i.i.d rollouts, their relative performance under matched settings remains unclear. In this work, we firstly present a systematic evaluation of verification strategies across model families, tasks, and sampling regimes, and find that Traversal Verification dominates consistently, with OT-based methods lagging far behind. Our analysis uncovers that this occurs because OT-based methods achieve high multi-token acceptance near the root of the draft tree, while multi-token gains are most impactful deeper in the draft tree, where draft and target distributions diverge. Based on this insight, we propose delayed tree expansion, which drafts a partial single path, delaying the i.i.d. branching point. We show that delayed tree expansion preserves the target distribution and improves on root-node i.i.d rollouts. Further, we develop a dynamic neural selector that estimates the expected block efficiency of optimal-transport-based verification methods from draft and target features, enabling context-dependent expansion decisions. Our neural selector allows OT-based methods like SpecInfer to outperform Traversal Verification for the first time, achieving 5% higher average throughput across a wide range of models, datasets, and sampling settings.

Recent diffusion- and flow-based VTON methods achieve strong results with pretrained generative models, but their reliance on multi-step sampling incurs high inference cost, while existing acceleration methods largely overlook the intrinsic structure of the try-on task. In this paper, we highlight a key observation: VTON outputs are highly constrained by the conditional inputs, suggesting that the conditional sampling trajectory can be much straighter than that in general image generation, making one-step generation a natural solution. However, limited task-specific data makes training from scratch impractical, forcing existing methods to fine-tune pretrained models whose objectives do not encourage such straight conditional trajectories. Thus, the deviation from an ideal straight path mainly comes from the mismatch between pretrained base models and the conditional nature of try-on generation, rather than from the task itself. Motivated by this insight, we encourage straighter VTON sampling trajectories through three targeted modifications: pure conditional transport, a garment preservation loss, and a self consistency loss. We further introduce a one-step distillation stage. Extensive experiments show that our method achieves state-of-the-art performance with one-step sampling, establishing a new standard for efficient and high-quality VTON.

This article presents an in-depth review of the topic of path following for autonomous robotic vehicles, with a specific focus on vehicle motion in two dimensional space (2D). From a control system standpoint, path following can be formulated as the problem of stabilizing a path following error system that describes the dynamics of position and possibly orientation errors of a vehicle with respect to a path, with the errors defined in an appropriate reference frame. In spite of the large variety of path following methods described in the literature we show that, in principle, most of them can be categorized in two groups: stabilization of the path following error system expressed either in the vehicle's body frame or in a frame attached to a "reference point" moving along the path, such as a Frenet-Serret (F-S) frame or a Parallel Transport (P-T) frame. With this observation, we provide a unified formulation that is simple but general enough to cover many methods available in the literature. We then discuss the advantages and disadvantages of each method, comparing them from the design and implementation standpoint. We further show experimental results of the path following methods obtained from field trials testing with under-actuated and fully-actuated autonomous marine vehicles. In addition, we introduce open-source Matlab and Gazebo/ROS simulation toolboxes that are helpful in testing path following methods prior to their integration in the combined guidance, navigation, and control systems of autonomous vehicles.

LLM coding agents issue Bash commands through interfaces that may serialize, wrap, and reparse model output. Matched execution scores alone cannot distinguish command-generation errors from failures introduced after generation. QuoteBench measures this boundary with exact final-state validation on 56 one-shot tasks from 14 incident-derived families, crossing the generation contract with the execution transport around one deliberately unescaped added parser. Escaping at the interpolation point reproduces each replayed reply's raw-path outcome, so any recovery under a disclosed boundary must come from the model changing its generation. Across eight same-window configurations, replaying the same reply through the added parser lowers success by 55.4 to 73.2 percentage points; disclosure recovers 30.4 to 60.7 points for six configurations, and zero or slightly negative for the other two. Raw generation is nearly saturated at the frontier; boundary adaptation is what still separates models. GPT-5.6-sol's matched gap of -3.6 points hides -64.3 points of damage and +60.7 points of compensation. The deployment configuration reorders models: one reversal among 26 comparable pairs is unambiguous and four more sit on single-task margins. Evaluations of command-issuing agents should report the model configuration, generation contract, execution path, operating point, and final-state validator rather than treat a matched score as an intrinsic model property.

Missing modality imputation aims to synthesize unobserved modalities from observed ones. Existing methods treat each modality as living on its own latent manifold, forcing the generator to learn a long, unstructured jump between them. We present SphereFlow, which takes a fundamentally different view: by projecting all modalities into a shared hyperspherical latent space via a frozen self-supervised encoder, cross-modal imputation reduces to short-range geometric transport between nearby points on the sphere. Realizing this idea with flow matching, however, exposes two geometric conflicts: the standard Gaussian noise source is catastrophically mismatched with the unit-norm data manifold, and the linear interpolation path departs the sphere surface into a region where the decoder has no training signal. We resolve both with simple, geometry-aware modifications: replacing the noise source with the observed-modality latent so that the velocity field learns only the cross-modal displacement, and training the decoder with a time-weighted loss that extends its domain to the near-surface region traversed by the flow. We prove that this data-as-source formulation reduces the worst-case off-manifold deviation from a quantity that grows with the latent dimension to a small, dimension-independent bound governed by inter-modality similarity. Experiments on BraTS multi-modal MRI imputation and CT-MRI translation demonstrate state-of-the-art generation fidelity across all settings, while downstream brain tumor segmentation with our imputed data closes roughly eighty percent of the gap to the full-modality oracle. Code is available at https://github.com/WTHH031230/SphereFlow.

Adapting pre-trained continuous-time generative models to sequentially incoming data without forgetting earlier tasks is a central challenge in lifelong learning. A leading strategy, generative replay, uses a generative model trained on historical tasks to augment its own continual update with synthetic samples from experience. However, it requires full trajectory simulations at every training step, which accumulate discretization errors and can degrade the replayed historical distribution. Here, we propose trajectory replay, which bypasses sample generation by training an updated velocity field to match both a frozen historical velocity along its trajectories and the incoming task's velocity field, weighted by a stability-plasticity coefficient. Through the lens of continuous-time transport, we show the resulting optimum averages the two task velocities by their respective densities and generates the mixture of their probability paths. Combined with mean velocity distillation, trajectory replay accesses historical trajectories using only a few network evaluations per continual update. Empirically, it outperforms generative replay and distillation baselines on class-incremental image generation. In two biological case studies, trajectory replay extends generative perturbation models to new contexts and experimental batches across two data modalities while preserving treatment-effect prediction.

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

One of the distinguishing aspects of CP2K is its seamless integration of diverse structural and transition-state optimization techniques with advanced sampling approaches including Monte Carlo, molecular dynamics, and metadynamics, enabling the efficient exploration of complex potential- and free-energy landscapes, including rare events. These capabilities are combined with a broad hierarchy of energy and force evaluation methods, ranging from classical and machine-learned interaction potentials and mixed quantum-classical multiscale and semiempirical schemes, to highly accurate quantum-mechanical electronic-structure approaches. At the heart of the latter lies the Gaussian and plane-wave framework, along with its augmented all-electron generalization, which have been described in detail in our previous code review [T. D. Kühne et al., J. Chem. Phys. 152, 194103 (2020)]. Building on this foundation, the present work revisits the methods within CP2K that turn electronic structure into dynamics, transport, and spectroscopic response. Particular emphasis is placed on the coupling between static response calculations and nuclear motion: spectra may be evaluated at optimized structures, averaged over thermally sampled configurations, obtained from time-correlation functions along ab-initio or path integral molecular trajectories, or followed in real time together with electronic and nuclear dynamics. The same modular structure also enables equilibrium and biased transport simulations, from Kubo-type linear response to open-boundary approaches under external potentials, highlighting CP2K's unique capability to unify quantum chemistry with quantum and statistical mechanics within a versatile, holistic simulation environment.

Video-to-audio (V2A) generation aims to synthesize content-matching audio from silent video, and it remains challenging to build V2A models with high generation quality, efficiency, and visual-audio temporal synchrony. We propose Frieren, a V2A model based on rectified flow matching. Frieren regresses the conditional transport vector field from noise to spectrogram latent with straight paths and conducts sampling by solving ODE, outperforming autoregressive and score-based models in terms of audio quality. By employing a non-autoregressive vector field estimator based on a feed-forward transformer and channel-level cross-modal feature fusion with strong temporal alignment, our model generates audio that is highly synchronized with the input video. Furthermore, through reflow and one-step distillation with guided vector field, our model can generate decent audio in a few, or even only one sampling step. Experiments indicate that Frieren achieves state-of-the-art performance in both generation quality and temporal alignment on VGGSound, with alignment accuracy reaching 97.22%, and 6.2% improvement in inception score over the strong diffusion-based baseline. Audio samples are available at http://frieren-v2a.github.io.

Large language models have achieved remarkable success under the autoregressive paradigm, yet high-quality text generation need not be tied to a fixed left-to-right order. Existing alternatives still struggle to jointly achieve generation efficiency, scalable representation learning, and effective global semantic modeling. We propose Cola DLM, a hierarchical latent diffusion language model that frames text generation through hierarchical information decomposition. Cola DLM first learns a stable text-to-latent mapping with a Text VAE, then models a global semantic prior in continuous latent space with a block-causal DiT, and finally generates text through conditional decoding. From a unified Markov-path perspective, its diffusion process performs latent prior transport rather than token-level observation recovery, thereby separating global semantic organization from local textual realization. This design yields a more flexible non-autoregressive inductive bias, supports semantic compression and prior fitting in continuous space, and naturally extends to other continuous modalities. Through experiments spanning 4 research questions, 8 benchmarks, strictly matched ~2B-parameter autoregressive and LLaDA baselines, and scaling curves up to about 2000 EFLOPs, we identify an effective overall configuration of Cola DLM and verify its strong scaling behavior for text generation. Taken together, the results establish hierarchical continuous latent prior modeling as a principled alternative to strictly token-level language modeling, where generation quality and scaling behavior may better reflect model capability than likelihood, while also suggesting a concrete path toward unified modeling across discrete text and continuous modalities.

Shortcut models represent a promising, non-adversarial paradigm for generative modeling, uniquely supporting one-step, few-step, and multi-step sampling from a single trained network. However, their widespread adoption has been stymied by critical performance bottlenecks. This paper tackles the five core issues that held shortcut models back: (1) the hidden flaw of compounding guidance, which we are the first to formalize, causing severe image artifacts; (2) inflexible fixed guidance that restricts inference-time control; (3) a pervasive frequency bias driven by a reliance on low-level distances in the direct domain, which biases reconstructions toward low frequencies; (4) divergent self-consistency arising from a conflict with EMA training; and (5) curvy flow trajectories that impede convergence. To address these challenges, we introduce iSM, a unified training framework that systematically resolves each limitation. Our framework is built on four key improvements: Intrinsic Guidance provides explicit, dynamic control over guidance strength, resolving both compounding guidance and inflexibility. A Multi-Level Wavelet Loss mitigates frequency bias to restore high-frequency details. Scaling Optimal Transport (sOT) reduces training variance and learns straighter, more stable generative paths. Finally, a Twin EMA strategy reconciles training stability with self-consistency. Extensive experiments on ImageNet 256 x 256 demonstrate that our approach yields substantial FID improvements over baseline shortcut models across one-step, few-step, and multi-step generation, making shortcut models a viable and competitive class of generative models.

Generative policies based on diffusion and flow matching have become a dominant paradigm for visuomotor robotic control. We show that replacing the standard Gaussian source distribution with WarmPrior, a simple temporally grounded prior constructed from readily available recent action history, consistently improves success rates on robotic manipulation tasks. We trace this gain to markedly straighter probability paths, echoing the effect of optimal-transport couplings in Rectified Flow. Beyond standard behavior cloning, WarmPrior also reshapes the exploration distribution in prior-space reinforcement learning, improving both sample efficiency and final performance. Collectively, these results identify the source distribution as an important and underexplored design axis in generative robot control.

We introduce a new paradigm for generative modeling built on Continuous Normalizing Flows (CNFs), allowing us to train CNFs at unprecedented scale. Specifically, we present the notion of Flow Matching (FM), a simulation-free approach for training CNFs based on regressing vector fields of fixed conditional probability paths. Flow Matching is compatible with a general family of Gaussian probability paths for transforming between noise and data samples -- which subsumes existing diffusion paths as specific instances. Interestingly, we find that employing FM with diffusion paths results in a more robust and stable alternative for training diffusion models. Furthermore, Flow Matching opens the door to training CNFs with other, non-diffusion probability paths. An instance of particular interest is using Optimal Transport (OT) displacement interpolation to define the conditional probability paths. These paths are more efficient than diffusion paths, provide faster training and sampling, and result in better generalization. Training CNFs using Flow Matching on ImageNet leads to consistently better performance than alternative diffusion-based methods in terms of both likelihood and sample quality, and allows fast and reliable sample generation using off-the-shelf numerical ODE solvers.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

Direct Preference Optimization (DPO) is a principled, scalable alternative to RLHF for aligning large language models from pairwise preferences, but its internal geometric footprint remains undercharacterized, limiting audits, checkpoint comparisons, and failure prediction. We introduce SPINAL (Scaling-law and Preference Integration in Neural Alignment Layers), a diagnostic that measures how alignment reshapes representations across depth by tracing localized structural change layer by layer. Across model families, DPO produces a layerwise calibration effect concentrated in the final decoder blocks (often layers 21-30), where preference gradients most directly affect the next-token distribution. SPINAL encodes each checkpoint as a depth trace over (layer index, contraction score, transport score). The contraction score summarizes how quickly the tail of a layer's spectrum decays (how fast small modes vanish); higher values indicate stronger contraction into fewer effective directions. The transport score summarizes how much the token distribution shifts between adjacent layers using a bounded overlap measure; lower values indicate shorter, smoother steps through representation space. Aligned checkpoints show a late-layer ramp-up in contraction and a smooth reduction in transport, consistent with tightened and stabilized policy mass, while unaligned models trace higher-curvature, more entropic, and geometrically incoherent depth paths. Overall, alignment is geometrically localized: the final layers encode the dominant preference-induced corrections. SPINAL turns this localization into a practical audit signal, quantifying where alignment concentrates, how strongly it manifests, and when it begins to destabilize during training.

Many scientific datasets, such as molecular conformational ensembles or single-cell tissue measurements, are naturally modeled as meta-distributions: distributions over probability measures on non-Euclidean domains. Existing generative methods largely assume Euclidean geometry and fail to capture this structure. We introduce Riemannian Wasserstein Entropic Flow Matching (RWEFM), a generative framework on the Wasserstein space P_2(M) of a Riemannian manifold (M,g). RWEFM is trained by regressing a neural vector field onto Riemannian optimal transport velocities, using McCann displacement interpolations as conditional paths. We confirm theoretically that this construction leads to a valid flow matching approach on P_2(M) and introduce the Riemannian Entropic Map, a GPU-efficient approximation of the optimal transport map on manifolds. Our experiments show that by respecting the intrinsic geometry of the data, RWEFM can generate whole single-cell samples in hyperspherical latent spaces and protein conformational ensembles on the torus. As RWEFM requires only a geodesic distance and a projection operator, it is not restricted to manifolds with closed-form geometry, which we demonstrate by generating distributions on a general triangulated mesh.

At the core of modern generative modeling frameworks, including diffusion models, score-based models, and flow matching, is the task of transforming a simple prior distribution into a complex target distribution through stochastic paths in probability space. Schrödinger bridges provide a unifying principle underlying these approaches, framing the problem as determining an optimal stochastic bridge between marginal distribution constraints with minimal-entropy deviations from a pre-defined reference process. This guide develops the mathematical foundations of the Schrödinger bridge problem, drawing on optimal transport, stochastic control, and path-space optimization, and focuses on its dynamic formulation with direct connections to modern generative modeling. We build a comprehensive toolkit for constructing Schrödinger bridges from first principles, and show how these constructions give rise to generalized and task-specific computational methods.

Deep hedging learns trading policies from historical or simulated market trajectories, yet under nonstationarity these training paths may not represent future market conditions. We propose WRAP (Wasserstein-Reweighting Adversarial Perturbation), a drift-aware adversarial training framework derived from a two-budget distributionally robust optimization (DRO) formulation. The formulation is anchored to a weighted empirical reference distribution whose fixed baseline weights are chosen to balance sampling uncertainty against temporal drift. Around this reference distribution, the ambiguity set addresses two complementary forms of distributional misspecification by allowing an adversary to reweight the observed trajectories subject to a ϕ-divergence constraint and perturb their paths subject to an optimal-transport (OT) constraint. We derive a joint first-order expansion in which the leading-order increase over the nominal expected loss decomposes into a reweighting contribution determined by the dispersion of hedging losses across trajectories and a transport contribution determined by the sensitivity of the loss to path perturbations. This expansion yields an explicit finite-dimensional adversarial attack that replaces the distributional inner supremum with a tractable first-order approximation. Across stationary and nonstationary Heston dynamics and a generalized affine diffusion (GAD), the experiments show complementary benefits from reweighting and transport, with joint adversarial training providing the largest gains under nonstationarity.

Earlier, in the CINT program at Los Alamos National Laboratory, we focused ultrafast mode-locked lasers on the tip-sample junction of a scanning tunneling microscope to generate currents at hundreds of harmonics of the laser pulse repetition frequency. Each harmonic has a signal-to-noise ratio of 20 dB with a 10-dB linewidth of only 3 Hz. Now we model closed quantum nanocircuits with rectangular, triangular, or delta-function barrier, shunted by a beryllium filament for quasi-coherent electron transport over mean-free paths as great as 68 nm. The time-independent Schrödinger equation is solved with the boundary conditions that the wavefunction and its derivative are continuous at both connections. These four boundary conditions are used to form a four-by-four complex matrix equation with only zeros in the right-hand column vector which is required to have a non-trivial solution with each of the closed nanocircuits. Each model has four parameters: (1) the barrier length, (2) the height and shape of the barrier, (3) the length of the pre-barrier, and (4) the electron energy. Any three of these may be specified and then the fourth is varied to bring the determinant to zero to find the solutions on lines or surfaces in the space defined by the four parameters. First, we use a simplistic model having a rectangular barrier. The second model has a triangular barrier as a first approximation to field emission, and we are considering applying this approach for a self-contained nanoscale extension of our earlier effort to generate the harmonics at Los Alamos. The third model has a delta-function barrier, and the fourth model is an extension of the first one where the width of the rectangular barrier is varied inversely with its height.

The Model Context Protocol (MCP), introduced by Anthropic in November 2024, defines a standardized interface for connecting large language models (LLMs) to external tools, data sources, and services. Within months of release, hundreds of community-built MCP servers appeared on GitHub, but no software-maintenance literature has yet described how the ecosystem is being structured in production. This industry experience paper catalogues five recurring MCP server architectural patterns observed across an enumerated corpus of fifteen independently developed servers (five production servers from the ANSYR voice AI platform plus ten public servers from the official MCP registry): Resource Gateway, Tool Orchestrator, Stateful Session Server, Proxy Aggregator, and Domain-Specific Adapter. Each pattern is described in the structured form of Gamma et al.: context, problem, solution, and consequences. We also document four anti-patterns and a set of cross-cutting concerns around authentication, versioning, and observability. The quantitative evaluation contributes three measurements: inter-rater reliability of the taxonomy across two independent LLM raters on 54 held-out servers (Cohen's kappa = 0.76), which also localizes three pattern-boundary ambiguities; transport overhead measured end-to-end on loopback and modeled for cross-host paths; and a tool-count study showing tool-selection accuracy drops below 90% between 10 and 15 tools per context for Claude Haiku 4.5 and between 20 and 30 tools for Sonnet 4. Code, corpus, and prompts are released as a replication package.

Inferring the full transportation network, including sidewalks and cycleways, is crucial for many automated systems, including autonomous driving, multi-modal navigation, trip planning, mobility simulations, and freight management. Many transportation decisions can be informed based on an accurate pedestrian network, its interactions, and connectivity with the road networks of other modes of travel. A connected pedestrian path network is vital to transportation activities, as sidewalks and crossings connect pedestrians to other modes of transportation. However, information about these paths' location and connectivity is often missing or inaccurate in city planning systems and wayfinding applications, causing severe information gaps and errors for planners and pedestrians. This work begins to address this problem at scale by introducing a novel dataset of aerial satellite imagery, street map imagery, and rasterized annotations of sidewalks, crossings, and corner bulbs in urban cities. The dataset spans 2,700 km^2 land area, covering select regions from 6 different cities. It can be used for various learning tasks related to segmenting and understanding pedestrian environments. We also present an end-to-end process for inferring a connected pedestrian path network map using street network information and our proposed dataset. The process features the use of a multi-input segmentation network trained on our dataset to predict important classes in the pedestrian environment and then generate a connected pedestrian path network. Our results demonstrate that the dataset is sufficiently large to train common segmentation models yielding accurate, robust pedestrian path networks.

Optimal Transport (OT) problem aims to find a transport plan that bridges two distributions while minimizing a given cost function. OT theory has been widely utilized in generative modeling. In the beginning, OT distance has been used as a measure for assessing the distance between data and generated distributions. Recently, OT transport map between data and prior distributions has been utilized as a generative model. These OT-based generative models share a similar adversarial training objective. In this paper, we begin by unifying these OT-based adversarial methods within a single framework. Then, we elucidate the role of each component in training dynamics through a comprehensive analysis of this unified framework. Moreover, we suggest a simple but novel method that improves the previously best-performing OT-based model. Intuitively, our approach conducts a gradual refinement of the generated distribution, progressively aligning it with the data distribution. Our approach achieves a FID score of 2.51 on CIFAR-10 and 5.99 on CelebA-HQ-256, outperforming unified OT-based adversarial approaches.

We present a fast algorithm for the design of smooth paths (or trajectories) that are constrained to lie in a collection of axis-aligned boxes. We consider the case where the number of these safe boxes is large, and basic preprocessing of them (such as finding their intersections) can be done offline. At runtime we quickly generate a smooth path between given initial and terminal positions. Our algorithm designs trajectories that are guaranteed to be safe at all times, and detects infeasibility whenever such a trajectory does not exist. Our algorithm is based on two subproblems that we can solve very efficiently: finding a shortest path in a weighted graph, and solving (multiple) convex optimal-control problems. We demonstrate the proposed path planner on large-scale numerical examples, and we provide an efficient open-source software implementation, fastpathplanning.

Existing industrial-scale navigation applications contend with massive road networks, typically employing two main categories of approaches for route planning. The first relies on precomputed road costs for optimal routing and heuristic algorithms for generating alternatives, while the second, generative methods, has recently gained significant attention. However, the former struggles with personalization and route diversity, while the latter fails to meet the efficiency requirements of large-scale real-time scenarios. To address these limitations, we propose GenMRP, a generative framework for multi-route planning. To ensure generation efficiency, GenMRP first introduces a skeleton-to-capillary approach that dynamically constructs a relevant sub-network significantly smaller than the full road network. Within this sub-network, routes are generated iteratively. The first iteration identifies the optimal route, while the subsequent ones generate alternatives that balance quality and diversity using the newly proposed correctional boosting approach. Each iteration incorporates road features, user historical sequences, and previously generated routes into a Link Cost Model to update road costs, followed by route generation using the Dijkstra algorithm. Extensive experiments show that GenMRP achieves state-of-the-art performance with high efficiency in both offline and online environments. To facilitate further research, we have publicly released the training and evaluation dataset. GenMRP has been fully deployed in a real-world navigation app, demonstrating its effectiveness and benefits.

Public transit route planning traditionally depends on structured map infrastructure and complex routing engines, and no existing dataset supports training models to bypass this dependency. We present TransitLM, a large-scale dataset of over 13 million transit route planning records from four Chinese cities covering 120,845 stations and 13,666 lines, released as a continual pre-training corpus and benchmark data for three evaluation tasks with complementary metrics. Experiments show that an LLM trained on TransitLM produces structurally valid routes at high accuracy and implicitly grounds arbitrary GPS coordinates to appropriate stations without any explicit mapping. These results demonstrate that transit route planning can be learned entirely from data, enabling end-to-end, map-free route generation directly from origin-destination information. The dataset and benchmark are available at https://huggingface.co/datasets/GD-ML/TransitLM, with evaluation code at https://github.com/HotTricker/TransitLM.

Trajectory planning is commonly used as part of a local planner in autonomous driving. This paper considers the problem of planning a continuous-curvature-rate trajectory between fixed start and goal states that minimizes a tunable trade-off between passenger comfort and travel time. The problem is an instance of infinite dimensional optimization over two continuous functions: a path, and a velocity profile. We propose a simplification of this problem that facilitates the discretization of both functions. This paper also proposes a method to quickly generate minimal-length paths between start and goal states based on a single tuning parameter: the second derivative of curvature. Furthermore, we discretize the set of velocity profiles along a given path into a selection of acceleration way-points along the path. Gradient-descent is then employed to minimize cost over feasible choices of the second derivative of curvature, and acceleration way-points, resulting in a method that repeatedly solves the path and velocity profiles in an iterative fashion. Numerical examples are provided to illustrate the benefits of the proposed methods.

Designing a transit network requires many sequential route extension decisions, but their quality is often visible only after the full network is assembled. This delayed-feedback challenge lies at the heart of the Transit Route Network Design Problem (TRNDP), where route interactions can be deceptive: an extension that appears useful locally can create transfer bottlenecks, produce redundant overlap, or reduce overall throughput. To guide route construction under delayed simulator feedback, we introduce AlphaTransit, a search-based planning framework for cityscale bus network design. AlphaTransit couples Monte Carlo Tree Search (MCTS) with a neural policy-value network: the policy proposes route extensions, the value estimates downstream design quality, and search uses these predictions to refine each decision. This provides decision-time lookahead during route construction without running simulator rollouts inside the search tree. We evaluate AlphaTransit on a new Bloomington TRNDP benchmark with realistic road topology and censusderived demand, under mixed and full transit demand settings. In the Bloomington network, AlphaTransit attains the highest service rate in both demand settings, reaching 54.6% and 82.1%, respectively. Relative to reinforcement learning without search, these correspond to 9.9% and 11.4% service rate gains; relative to MCTS without learned guidance, they correspond to 2.5% and 11.2% gains. These results suggest that coupling learned guidance with MCTS is more effective than using either approach alone for transit network design. Our code and data are publicly available in https://github.com/poudel-bibek/AlphaTransit.

Large-scale distributed training in production datacenters constitutes a challenging workload bottlenecked by network communication. In response, both major industry players (e.g., Ultra Ethernet Consortium) and parts of academia have surprisingly, and almost unanimously, agreed that packet spraying is necessary to improve the performance of large-scale distributed training workloads. In this paper, we challenge this prevailing belief and pose the question: How close can a singlepath transport approach an optimal multipath transport? We demonstrate that singlepath transport (from a NIC's perspective) is sufficient and can perform nearly as well as an ideal multipath transport with packet spraying, particularly in the context of distributed training in leaf-spine topologies. Our assertion is based on four key observations about workloads driven by collective communication patterns: (i) flows within a collective start almost simultaneously, (ii) flow sizes are nearly equal, (iii) the completion time of a collective is more crucial than individual flow completion times, and (iv) flows can be split upon arrival. We analytically prove that singlepath transport, using minimal flow splitting (at the application layer), is equivalent to an ideal multipath transport with packet spraying in terms of maximum congestion. Our preliminary evaluations support our claims. This paper suggests an alternative agenda for developing next-generation transport protocols tailored for large-scale distributed training.

Traffic congestion in dense urban centers presents an economical and environmental burden. In recent years, the availability of vehicle-to-anything communication allows for the transmission of detailed vehicle states to the infrastructure that can be used for intelligent traffic light control. The other way around, the infrastructure can provide vehicles with advice on driving behavior, such as appropriate velocities, which can improve the efficacy of the traffic system. Several research works applied deep reinforcement learning to either traffic light control or vehicle speed advice. In this work, we propose a first attempt to jointly learn the control of both. We show this to improve the efficacy of traffic systems. In our experiments, the joint control approach reduces average vehicle trip delays, w.r.t. controlling only traffic lights, in eight out of eleven benchmark scenarios. Analyzing the qualitative behavior of the vehicle speed advice policy, we observe that this is achieved by smoothing out the velocity profile of vehicles nearby a traffic light. Learning joint control of traffic signaling and speed advice in the real world could help to reduce congestion and mitigate the economical and environmental repercussions of today's traffic systems.

Invasive species in water bodies pose a major threat to the environment and biodiversity globally. Due to increased transportation and trade, non-native species have been introduced to new environments, causing damage to ecosystems and leading to economic losses in agriculture, forestry, and fisheries. Therefore, there is a pressing need for risk assessment and management techniques to mitigate the impact of these invasions. This study aims to develop a new physics-inspired model to forecast maritime shipping traffic and thus inform risk assessment of invasive species spread through global transportation networks. Inspired by the gravity model for international trades, our model considers various factors that influence the likelihood and impact of vessel activities, such as shipping flux density, distance between ports, trade flow, and centrality measures of transportation hubs. Additionally, by analyzing the risk network of invasive species, we provide a comprehensive framework for assessing the invasion threat level given a pair of origin and destination. Accordingly, this paper introduces transformers to gravity models to rebuild the short- and long-term dependencies that make the risk analysis feasible. Thus, we introduce a physics-inspired framework that achieves an 89% segmentation accuracy for existing and non-existing trajectories and an 84.8% accuracy for the number of vessels flowing between key port areas, representing more than 10% improvement over the traditional deep-gravity model. Along these lines, this research contributes to a better understanding of invasive species risk assessment. It allows policymakers, conservationists, and stakeholders to prioritize management actions by identifying high-risk invasion pathways. Besides, our model is versatile and can include new data sources, making it suitable for assessing species invasion risks in a changing global landscape.

We introduce SF-LIFE, a large-scale simulated movement dataset designed to accelerate research in transportation, mobility, and machine learning. The dataset contains 3,024,000,000,000 location records capturing complete, noise-free, multi-modality trajectories of 500,000 simulated agents observed at a 1Hz frequency navigating the San Francisco Bay Area network over a 70-day period. The data captures (1) needs-driven daily agendas of individual agents generated by an agent-based simulation of human patterns of life and (2) detailed kinematic trajectories moving agents across the OpenStreetMap representation of San Francisco using data from 40+ transit agencies across 9 counties. SF-LIFE provides unprecedented scale and detail as trajectories are based on real transit infrastructure using San Francisco General Transit Feed Specification (GTFS) data, having agent movements across multiple modalities, including bus, rail, bike, automobile, and walking. For this high-fidelity simulated representation of San Francisco, we provide (1) the full trajectory data annotated with transportation mode labels, (2) reduced-size versions of the trajectory data with reduced temporal frequency, (3) agent activity information describing the causal activity why an agent visits a place, (4) agent demographic data, and (5) the underlying OSM road network and building data. As the first dataset of its scale and level of detail, SF-LIFE overcomes the privacy, noise, and completeness limitations inherent in real-world tracking data, providing a robust and ethically sourced resource for research in transit optimization, human mobility analysis, and urban computing.

Generating trajectory data is among promising solutions to addressing privacy concerns, collection costs, and proprietary restrictions usually associated with human mobility analyses. However, existing trajectory generation methods are still in their infancy due to the inherent diversity and unpredictability of human activities, grappling with issues such as fidelity, flexibility, and generalizability. To overcome these obstacles, we propose ControlTraj, a Controllable Trajectory generation framework with the topology-constrained diffusion model. Distinct from prior approaches, ControlTraj utilizes a diffusion model to generate high-fidelity trajectories while integrating the structural constraints of road network topology to guide the geographical outcomes. Specifically, we develop a novel road segment autoencoder to extract fine-grained road segment embedding. The encoded features, along with trip attributes, are subsequently merged into the proposed geographic denoising UNet architecture, named GeoUNet, to synthesize geographic trajectories from white noise. Through experimentation across three real-world data settings, ControlTraj demonstrates its ability to produce human-directed, high-fidelity trajectory generation with adaptability to unexplored geographical contexts.