The computation of the Bures-Wasserstein (BW) barycenter of an ensemble of positive definite matrices arises throughout machine learning, optimal transport, and quantum information. Riemannian gradient descent (RGD) at unit step size -- the fixed-point iteration used in practice -- converges rapidly, yet existing analyses present a dichotomy: unit-step guarantees carry worst-case exponential dependence on the dimension, while dimension-independent guarantees require small step sizes that forfeit the empirical speed. We resolve this dichotomy, not by improving the guarantees for unit-step RGD, but by proposing a Projected RGD algorithm that achieves dimension-independent linear convergence at unit step size. The achieved rate, $(1 - κ^{-3/2})$, where $κ$ is the condition number of the ensemble, also polynomially improves on the best small-step guarantee ($κ^{3/2}$ versus $κ^{5/2}$ iteration complexity). The crux is a novel Projection Lemma: clipping the eigenvalues of a positive matrix to an interval $[α, β]$ is the closed-form, non-expansive (1-Lipschitz) BW-metric projection onto the set $\{S : αI \leq S \leq βI\}$ -- a statement which, unlike its known one-sided counterpart, does not follow from convexity. The projection is moreover free: it reuses an eigendecomposition the next iteration must perform in any case, so the projected and unprojected iterations cost the same per step. The same analysis covers the invariant matrix projection problem of Brahmachari et al. (2025), whose fixed-point algorithm we identify as unit-step RGD on a totally geodesic submanifold, thereby extending the dimension-independent guarantee to that setting verbatim.
Infrared-visible object detection (IVOD) integrates complementary evidence from visible and infrared sensors for reliable perception in challenging scenes. In practice, sensors may fail or drop frames, leaving one modality unavailable or intermittent. Existing methods for IVOD assume both modalities are always present, and fixed fusion collapses when one stream is missing. Furthermore, it remains a critical challenge to reliably estimate semantic correlation across heterogeneous modalities, especially under spectral distribution discrepancy. We present FlexibleFusion, a unified and adaptive method that flexibly allocates integration pathways and fusion strength, operating seamlessly across complete and missing-modality regimes. At its core, the Modality-Aware Experts Collaboration (MAEC) mechanism selectively activates and aggregates cross-modal or intra-modal expert pathways. It allows cross-modal fusion when full modalities are available and falls back to self-fusion under missing conditions. Additionally, we design Residual Self-Paced Entropic Optimal Transport (RSPEOT) to align heterogeneous feature distributions from a transport perspective. Instead of relying on the fixed sparsity coefficient in standard entropic optimal transport (EOT), RSPEOT introduces a residual-driven self-paced update that prioritizes reliable matches and progressively refines harder ones. This design alleviates the additional optimization burden of standard EOT while preserving reliable semantic alignment. Comprehensive experiments under complete and missing-modality protocols show consistent performance across arbitrary modality configurations. Code will be released upon publication.
The performance of Flow Matching largely depends on the quality of the coupling between the source and target distributions. However, independent coupling often leads to path crossings and local velocity ambiguity, while OT-based couplings typically incur high construction costs. To address this challenge, we propose Quantile AlignTree Flow Matching (QAT-FM), an efficient structured coupling strategy that constructs a hierarchical coupling between a Gaussian prior and the target data distribution via a quantile-aligned tree structure. QAT-FM constructs the coupling in $\mathcal{O}(Nd\log N)$ time and supports per-pair source sampling with $\mathcal{O}(d)$ complexity, enabling scalable training for large-scale high-dimensional generative tasks. Theoretically, we prove that the QAT coupling satisfies marginal consistency, induces non-crossing linear interpolation paths, and consistently improves path separation at intermediate times compared with independent coupling, thereby alleviating local velocity ambiguity. QAT-FM further extends naturally to conditional generation, enabling structured conditional coupling while preserving global Gaussian alignment. Experiments across diverse benchmark datasets demonstrate that QAT-FM achieves competitive generative performance while substantially reducing coupling construction cost.
Gabriel Rioux, Joanna Marks, Riccardo Passeggeri +1math.ST cs.IT math.OC stat.ML
The Gromov-Wasserstein (GW) distance provides a principled framework for aligning metric measure (mm) spaces based solely on their intrinsic structure. Its ability to identify isomorphic representations of distributions across spaces renders it valuable for comparing data where equality up to isomorphism occurs naturally such as in graphs or, more generally, distributions on graphs. Recently, a type of dual form for the GW distance between Euclidean distributions with the squared Euclidean or inner product costs was derived, spurring the development of new statistical and algorithmic results for this setting. This work furnishes a novel duality result for GW distances with and without entropic regularization that is applicable to all finitely supported mm spaces. Leveraging this result, we derive the sample complexity of empirical GW distances between finite mm spaces, as well as limit distributions under proper centering and scaling. Furthermore, we propose new algorithms for solving the regularized GW problem which are subject to formal convergence guarantees. These statistical and algorithmic advancements give rise to a principled and efficient framework for testing whether two distributions on the set of graphs with a fixed number of nodes are isomorphic based on samples.
A transformer carries each token's state from layer to layer, and the whole vocabulary carried together forms a cloud that moves with depth. We ask whether a trained network moves this cloud the way optimal transport would: at the cheapest cost, and along the map that pairs each token with its optimal destination. We measure both on Pythia-160m and Pythia-410m, with an exact assignment between consecutive layer clouds, a measured sampling floor, calibration on couplings known to be optimal, and a split of the cost into the common shift of the cloud and the token-specific moves. At the last layer, both models move their tokens where the optimal-transport map sends them, at the optimal cost for Pythia-410m and slightly above it for Pythia-160m. At the first layer they do not. In between, single layers can be judged on cost at only two of ten transitions, and blocks of several layers move the cloud at close to the optimal cost. The agreement at the last layer is much weaker at initialisation (0.64 against 0.86) and grows with training.
Modern explicit-time generative models, such as Flow Matching [Lipman et al., 2023] and Rectified Flow [Liu et al., 2023], are typically derived top-down via Optimal Transport and the continuity equation. This standard Eulerian approach focuses on the macroscopic transport of probability mass. In this paper, we present an alternative, bottom-up mechanical derivation grounded in a Lagrangian (particle-centric) perspective. By analyzing the local Taylor expansion of a continuous denoiser, we motivate a strict invariance condition required for optimal, singlestep generation: the conservation of target identity. Enforcing this condition yields a governing quasi-linear advection Partial Differential Equation (PDE). We demonstrate that solving this PDE via the Method of Characteristics analytically yields the straight-line trajectories of Flow Matching. This geometric perspective isolates the Jacobian of the denoiser as the primary source of trajectory curvature, providing a direct mathematical explanation for why straight-line flows enable massive step sizes, and why empirical models require distillation to flatten intersecting characteristics.
We study unsupervised hypergraph alignment, where the goal is to infer node correspondences between two hypergraphs using only structural information, without node features, labels, seed matches, or side information. Direct higher-order formulations can represent hyperedge interactions faithfully, but they can be computationally demanding and cumbersome for non-uniform hypergraphs. Graph-reduction approaches introduce a different challenge: clique expansions keep the alignment problem on the original node set but collapse all hyperedge evidence into one pairwise graph, whereas bipartite expansions preserve incidence structure but enlarge the problem from nodes to nodes plus hyperedges. We introduce FALCON (Filtration-based hypergrAph aLignment via Cross-scale Optimal traNsport), an unsupervised optimal-transport framework for hypergraph alignment. Instead of representing each hypergraph by a single collapsed clique graph, FALCON constructs a filtration-induced sequence of clique-based co-occurrence dissimilarity matrices and jointly aligns all levels through one shared multi-scale Gromov--Wasserstein (GW) objective. The shared transport plan enforces a globally consistent node correspondence across filtration levels while avoiding the auxiliary hyperedge nodes introduced by bipartite expansion. Experiments on perturbation benchmarks derived from real-world hypergraphs show that FALCON is robust to structural noise and in almost all cases outperforms strong graph- and hypergraph-alignment baselines.
Unsupervised action segmentation aims to discover latent action categories and their temporal organization without action annotations. Optimal transport-based methods provide structured frame-to-action assignments, however, their pseudo-label quality is fundamentally conditioned on the representation space used to construct the transport cost. We argue that reliable OT pseudo-labeling requires a representation geometry that is simultaneously sensitive to discriminative action changes and coherent along local temporal progressions. Based on this insight, we propose SpecT-OT, a spectral-temporal representation learning framework built upon an unbalanced optimal transport pseudo-labeling concept. SpecT-OT introduces a Spectral Reparameterization Projector (SRP), which parameterizes projector weights with fixed Fourier bases and learnable coefficients to improve the modeling of rapidly varying discriminative features, and Temporal Affinity Regularization (TAR), which imposes distance-aware, label-free constraints on pairwise frame affinities to stabilize local temporal structure. The two components jointly produce more discriminative and temporally stable transport costs, yielding more reliable pseudo-labels for iterative representation learning. Experiments on four benchmarks demonstrate strong performance compared with state-of-the-art methods. SpecT-OT achieves the best results on 13 of 15 metrics, including 4.1-point MoF and 7.4-point F1 gains over the baseline on Breakfast and Desktop Assembly, respectively.
We study the empirical Sinkhorn estimator of the entropic optimal transport potentials under the uniform loss. Since the potentials are only unique up to additive constants, we measure the error using the quotient supremum norm, defined as $d_\infty([u],[v]) = \inf_{a\in\mathbb{R}}\|u-v-a\|_\infty$. For a fixed regularization parameter $\varepsilon>0$, we establish a non-asymptotic statistical rate of $n^{-1/2}$. This is achieved by combining the Birkhoff-Hopf contraction theorem with entropy bounds on normalized kernel sections. However, the constant in this bound grows exponentially with $1/ε$. To improve this, we isolate geometric conditions under which the empirical estimator maintains the $n^{-1/2}$ rate but features polynomial dependence on $1/\varepsilon$. The key requirement is a polynomial residual-stability estimate for the population Sinkhorn map. We provide sufficient criteria for this, including a polynomial contraction property and a local inverse estimate. Furthermore, we introduce two rigorously verifiable model classes an $\varepsilon$-weak residual-interaction class obtained after separable centering and another based on connected tight-edge graphs for fixed discrete costs where the polynomial rate is guaranteed without relying on abstract resolvent assumptions. Finally, we establish matching minimax lower bounds demonstrating that the $\varepsilon n^{-1/2}$ rate cannot be uniformly improved in the bounded-interaction regime.
Ian Hsieh, Soumya Snigdha Kundu, Tom Vercauteren +1cs.LG
Entropic optimal transport (EOT) has been shown to offer a computationally tractable approximation to exact optimal transport. However, the standard Sinkhorn-Knopp algorithm has two main limitations. First, given discrete measures with $N$ points, each iteration requires $O(N^2)$ operations, which restricts its use on large-scale datasets (e.g. $N\geq10^4$). Second, it uses the independent coupling as a reference measure for regularisation. This assigns mass to high-cost transport edges at moderate regularisation strengths. We propose SinkSLOT, which addresses both limitations by putting forth the expected sliced lifted transport plan as a natural way to sparsify the Gibbs kernel with a non-independent prior coupling. We prove that: 1) SinkSLOT converges; 2) with $L$ slices, each resulting sparse Sinkhorn iteration costs $O(LN)$; and 3) the resulting objective is a divergence requiring no debiasing. Experiments on synthetic benchmarks show that SinkSLOT delivers substantial speedups over state-of-the-art dense and sparse EOT methods. We also demonstrate the applicability of the proposed divergence in a gradient flow experiment. The code is publicly available at https://github.com/cai4cai/SinkSLOT.
Linking the internal representations of deep neural networks (DNNs) to human mental representations is important for using DNNs as computational models of human vision. Existing DNN representations remain insufficiently similar to human mental representations, which are not directly observable and are therefore commonly measured through large-scale similarity judgments of object images. A natural approach to narrowing this gap is to directly transfer the relational structure of human representations into DNNs, and previous studies have reported improved human-DNN representational similarity. However, whether this improvement holds under stricter evaluation remains untested in two respects: fine-grained alignment at the individual-object level, and generalization to a human embedding derived from a dataset independent of the training data. Here, we employ an unsupervised comparison method, Gromov-Wasserstein optimal transport (GWOT), which estimates human-DNN correspondences from the internal distance structure alone and thereby tests fine-grained alignment. We further assess generalization on a curated test set of concepts non-overlapping with the training data. We show that fine-tuning pre-trained DNNs with Relational Knowledge Distillation (RKD), an established relational transfer method, brings DNNs close enough to humans to be aligned at the individual-object level on this test set. We also show that this improvement is driven by a more human-like global structure, as reflected in the ordering of distances among coarse categories, while the local human-DNN nearest-neighbor overlap rate remains largely unchanged. These findings indicate that relational transfer from humans brings the global structure of pre-trained DNNs close enough to the human structure to enable fine-grained human-DNN alignment without supervision.
Clément Soubrier, Geoffrey Woollard, Andrew Warren +1math.OC cs.LG
Efficiently and robustly analyzing shape data is critical across many scientific disciplines. While chirality is a fundamental property in numerous applications - most notably in molecular science - existing shape analysis metrics fail to distinguish between a shape and its mirror image. To address this gap, we introduce a multilinear generalization of the Gromov-Wasserstein objective. Under mild assumptions, this objective yields a distance between shapes, represented as probability distributions quotiented by a symmetry group $G$. In particular, for $G = SO(d)$, we introduce the Chiral Gromov-Wasserstein ($\mathrm{CGW}$) distance, sensitive to chirality. We establish robustness properties for the multilinear Gromov-Wasserstein distances and develop efficient algorithms to compute them, reformulating the underlying optimization problem by projecting couplings onto a low-dimensional space. We derive algorithms for both local and approximate global solutions, yielding a fully polynomial-time approximation scheme for these problems. We validate the framework through numerical experiments that demonstrate the effectiveness of $\mathrm{CGW}$ as a shape metric for chiral objects.
Nguyen Xuan-Vu, Octavian Susanu, Daniel Armstrong +1cs.AI
Chemical reactions are fundamentally transformations in electron space, yet most machine learning approaches model them either through \textit{de novo} generation of product molecules or through heuristic graph edits that operate directly on molecular topology. We introduce MAELLE (\textbf{M}ech\textbf{A}nistic \textbf{E}dit f\textbf{L}ow-matching on e\textbf{L}ectron r\textbf{E}arrangements), which instead models reactions as discrete flow matching over electron occupation vectors. Concretely, we formulate the reactant-to-product mapping as a Continuous-time Markov Chain (CTMC) over the graph-structured integer-valued electron occupation space defined on all bonding, non-bonding, and hydrogen sites. To construct the intermediate edit trajectories, we generalize the discrete flow matching mixture path to discrete electron rearrangements using Optimal Transport, yielding a sequence of mechanistically interpretable edit moves without requiring elementary step annotations. MAELLE achieves competitive performance on the USPTO-480K benchmark compared with leading reaction prediction models. Beyond in-distribution accuracy, we evaluate robustness across two out-of-distribution settings - structural complexity and reaction type - and find that MAELLE maintains strong performance where existing methods degrade. Finally, because the learned flow operates over the full electron redistribution, MAELLE naturally recovers mechanistic trajectories that align with known chemistry and can predict side products of a reaction.
In this paper, we explore a novel task of Multimodal Unsupervised Continual Post-Training (MU-CPT), enabling deployed MLLMs to continually evolve from streaming unlabeled data. Existing unsupervised post-training methods for MLLMs typically optimize target tokens uniformly, overlooking their heterogeneous visual dependence (VD). However, we reveal that token-level VD is crucial for MU-CPT. Specifically, its structural distortion serves as an indicator of cross-modal catastrophic forgetting, and its inherent heterogeneity acts as a compass to guide new-task learning. Leveraging this property, we propose a Visual Dependence-Aware (VDA) framework with two main components. First, Visually Constrained Optimal Transport (VC-OT) formulates the VD structural distortion of old-task VD during new-task learning as an optimal transport problem to mitigate cross-modal forgetting. By designing a region-aware ground cost and a dependence-stratified transport penalty, it prevents global shifts in visual focus while strictly prohibiting visual reliance from degenerating into language bias. Second, Visually Modulated Adaptation (VMA) exploits VD heterogeneity to emphasize visually grounded new-task learning, promoting new-task plasticity. Together, our method simultaneously maintains old-task stability and new-task plasticity during challenging MU-CPT. Extensive experiments under our MU-CPT setting validate the effectiveness of VDA.
Gromov-Wasserstein (GW) compares distributions through relations within each space. This pointwise comparison can be too sensitive in one-to-many settings, where several target outcomes refine one source state and their mean carries the geometry of interest. We introduce a weak GW framework that compares source relations with relations between the target conditional laws induced by a coupling. For inner-product relations, we retain the conditional means $m_π(x)=\mathbb{E}_π[Y\mid X=x]$. The resulting barycentric weak inner-product GW (wIGW) satisfies $\mathrm{wIGW}_{\mathrm{bar}}^2(μ,ν)=\inf_{η\preceq_{\mathrm{cx}}ν}\mathrm{IGW}^2(μ,η)$. Here $η\preceq_{\mathrm{cx}}ν$ means that $ν$ is a mean-preserving spread of $η$. Thus wIGW searches for an intermediate target geometry that can be refined into the prescribed target law without changing conditional means. Under finite second moments, minimizers exist and martingale gluing recovers an optimal coupling. With ridge regularization, moment duality gives an $A$-$B$ min-max problem whose inner step is weak optimal transport with a quadratic cost parameterized by $A$ and $B$; the outer problem optimizes these matrices. For finitely supported measures, we give an iterative algorithm. Under a quantitative ridge condition, the reduced problem is convex--concave, and the projected outer iteration satisfies an explicit contraction bound for inexact inner solves. Point cloud and graph feature refinement experiments illustrate how mean-preserving target refinements can have zero cost. A paired peripheral blood mononuclear cell (PBMC) multiome study evaluates atlas based cell type transfer through RNA/ATAC alignment in cell to cell and prototype to cell settings, with the prototype to cell setting representing the one-to-many case.
Giries Abu Ayoub, Loay Mualem, Simon Kormancs.SD cs.AI
Fully few-shot class-incremental audio classification (FFCAC) requires recognizing new sound classes from only a handful of labeled examples per session, without forgetting previously learned classes and without any large base dataset. Existing methods typically freeze a pre-trained audio--language encoder and classify with point prototypes, but they suffer from significant performance degradation throughout the sessions due to generic feature representations. We propose SPECTRA, a framework built on a frozen encoder which adds three components. (i) a lightweight trainable adapter that calibrates the generic embeddings to the task; (ii) subspace feature replay, an exemplar-free anti-forgetting scheme that replays old classes by sampling from the low-rank subspace of their stored features; and (iii) a transductive optimal-transport refinement of prototypes at test time. Our central finding is that the subspace structure of the replay diminishes forgetting and outperforms naive Gaussian replay of equal variance. On three FFCAC benchmarks (NSynth-100, FSC-89, LS-100), SPECTRA improves average accuracy and reduces forgetting over current state-of-the-art methods, and our ablations statistically validate each component.
Partial optimal transport compares two measures while leaving part of the mass unmatched, which is what makes it robust to outliers, occlusion, and clutter. The quantity of interest is usually the whole profile - the optimal cost at every transported cardinality - because the right amount to transport is rarely known in advance, and on the real line the PAWL algorithm returns that profile in $O(N\log N)$. Much data is periodic rather than linear: angles, phases, orientations, time of day, hue, and every direction obtained by projecting onto a great circle. On the circle the same problem acquires a global circulation, or equivalently an optimized cut, which the naive exact method handles by running the line algorithm once per support gap, at $O(N^{2}\log N)$. We show that this factor $N$ is unnecessary. The line structure survives in cut-free form, and a free-gap invariant supplies, at every step, a cut at which all previous local updates remain valid line updates. This yields PAWC: an exact $O(N\log N)$ time, $O(N)$ memory algorithm returning all $K+1$ costs, nested active sets and plans in one run, together with a single gap that is simultaneously optimal for every cardinality. Slicing over great circles extends it to $\mathbb{S}^{d-1}$. Empirically the whole profile costs $0.56$ms at $N=4096$ against $1.5$s for a single transported fraction from a general solver; on occluded, cluttered mpeg-7 shapes, holding the descriptor fixed and varying only the cost, it retains $66\%$ of the clean-data retrieval score against $16\%$ for balanced circular OT, and on $\mathbb{S}^{2}$ it halves the fitting error of spherical sliced Wasserstein against contaminated targets, synthetic and real. Code is available at https://github.com/mint-vu/Partial_Wasserstein_on_Circles.
Estimating heterogeneous single and interaction treatment effects from observational data under multiple simultaneous treatments is crucial for decision-making. To mitigate estimation variance, previous studies balance representation distributions between every pair of treatment patterns. However, such pairwise balancing scales quadratically with the number of treatment patterns and fails to preserve consistent local proximity structures across patterns, which degrades counterfactual estimation. To address these challenges, we propose the Causal Inference for Heterogeneous Single and Interaction Treatment Effects Network (CIHSI-Net), a deep learning framework built on a novel Barycentric Fused Gromov-Wasserstein Balancing (BFG-WB) objective. BFG-WB aligns the representation distribution of each treatment pattern with a shared Wasserstein barycenter, achieving global alignment while reducing the computational complexity from quadratic to linear, and its Fused Gromov-Wasserstein discrepancy preserves the local proximity structures essential for reliable heterogeneous effect estimation. Simulation studies show that CIHSI-Net consistently outperforms state-of-the-art baselines, and an application to real-world marketing data demonstrates its practical utility in complex multi-treatment scenarios.
Inferring continuous system evolution from sparse temporal snapshots is a key challenge in generative modeling and single-cell omics. While Optimal Transport (OT) is popular, existing frameworks are largely restricted to first-order dynamics, assuming memoryless velocity fields. This limits expressiveness, as first-order systems fail to account for regulatory momentum and time-delayed responses inherent in processes like cell differentiation. Here, we introduce TracingFlow, a simulation-free Flow Matching framework generalizing to second-order dynamics. By using neural networks to regress the acceleration field, TracingFlow provides an exact, efficient solution to the Dynamical Optimal Acceleration Transport (DOAT) problem. Unlike first-order methods yielding over-smoothed trajectories, our second-order formulation captures high-curvature transitions and nonlinear evolutions by learning the underlying force fields. Evaluated on complex synthetic and large-scale scRNA-seq datasets, TracingFlow achieves superior accuracy in distributional reconstruction and trajectory faithfulness. Moreover, by integrating lineage tracing priors, it recovers dynamical structures that are both mathematically optimal and biologically plausible.
Airin Akter Tania, Md Raihan Khan, Mohiuddin Ahmadcs.CV
Single-shot exposure correction aims to map an arbitrarily degraded image---whether under-exposed, over-exposed, or a spatial mixture of both---to a well-exposed output from a single capture. We present AutoLumNet, a framework that decomposes this task into a global monotone tone curve and a bounded local residual, making the global component the locus of formal guarantees. The tone curve is parameterized as the normalized cumulative integral of a strictly positive density, ensuring strict monotonicity by construction rather than by penalty. We prove that this parameterization (i)~preserves the pairwise luminance ordering of all pixels and all spatial extrema unconditionally, and (ii)~is dense in the space of valid tone corrections, containing the one-dimensional optimal-transport map from the input to any target luminance distribution. A differentiable sorted-sample Wasserstein-2 objective drives the learned curve toward the OT optimum during training. Spatially varying effects that the global map provably cannot address---local shading, chrominance shifts, and clipped-region restoration---are handled by a bounded residual decoder with dual-branch convex fusion, for which we provide an explicit sufficient condition for local order preservation. Experiments on five benchmarks (MSEC, SICE, LCDP, LOL-v1, LOL-v2-real) show that AutoLumNet achieves state-of-the-art PSNR and SSIM across both under- and over-exposure regimes at 11.2\,ms per frame, and generalizes zero-shot to pure low-light benchmarks without retraining. To our knowledge, AutoLumNet is the first exposure-correction method to unite structural monotonicity, optimal-transport optimality, and bounded local adaptivity within a single trainable architecture. Code is available at https://github.com/kraihan/Autolumnet.
Existing optimal transport (OT) models primarily seek an OT map or plan between distributions by minimizing a prescribed transport cost or distortion. However, minimizing transport cost or distortion alone may fail to identify a geometrically meaningful transformation between the two distributions. To address this limitation, this paper proposes a novel coupled OT framework that leverages a small number of annotated landmarks to guide the recovery of an underlying deformation governing the distribution transformation. The coupled OT framework integrates the optimization of the transport plan and the deformation field into a unified model, where the landmark-guided deformation field and the cost-driven transport plan are coupled through a mutual-consistency constraint. As a result, the deformation is jointly determined by the annotated landmarks and cost-driven distribution matching. The proposed framework provides a principled connection between landmark-based registration and transport-based distribution matching, enabling the recovery of transport maps from sparse geometric supervision. We establish the well-definedness of the proposed model in a general variational setting and develop a finite-element-based numerical algorithm for computation whose convergence properties are systematically analyzed. The practical effectiveness of the proposed approach is verified in shape matching.
Deep Kumar Ganguly, Jan Křetínskýcs.AI cs.LG stat.ML
An agent still learning its environment should be cautious while ignorant and bold once confident. The entropic value-at-risk captures this through a robust-optimization identity---a confidence level fixes the radius of a relative-entropy ball of alternative models---but that ball cannot reach catastrophes the nominal deems impossible, precisely what a safe agent must hedge. We instead use an optimal-transport ball and study the coherent risk measure it induces, the Wasserstein entropic value-at-risk. It has a variational dual mirroring the entropic formula (an inverse temperature becomes a transport price), occupies a definite place in the risk hierarchy, and provably accounts for the reachable catastrophes the entropic measure ignores; we verify both dualities numerically. Driving the transport radius by belief entropy then yields a closed-form robust dynamic-programming operator whose caution contracts as the belief sharpens, with a certified safety sandwich and a sharp safety switch.
Generative models promise a route to explainable clinical AI: rather than probe a classifier, model the distributions of healthy and diseased patients and read explanations off the geometry between them. We build such a system - an optimal-transport rectified flow trained between two clinical distributions - and use it to ask a pointed question the field too rarely tests: do the resulting explanation heatmaps actually localize disease? On tabular tumour biomarkers (Breast Cancer Wisconsin) a single flow yields per-patient counterfactuals, an unsupervised malignancy score (AUROC 0.91; 0.93 +/- 0.01 across five seeds), and a label-free attribution that agrees with a supervised classifier (r ~ 0.5) - a compact, honest interpretability engine, though it never out-predicts logistic regression. Moving to chest X-rays, we show the transport heatmap is a population-level signal, not a localiser; a reconstruction-based, identity-preserving variant does localize synthetic lesions (pointing game 0.52), yet on real RSNA radiologist boxes it collapses to chance while only supervised Grad-CAM stays above it. The central result is a synthetic-to-real gap: label-free heatmaps that look compelling on planted lesions are not evidence of real localisation. We contribute a reusable optimal-transport recipe for generative explanations and a controlled benchmark for stress-testing whether they localize.
Keyi Li, Yuval Kluger, Boris Landastat.ML cs.LG stat.AP stat.ME
Dataset alignment is a central step in data analysis across science and engineering, where the goal is to match observations between datasets. Entropic Optimal Transport (EOT) offers a computationally tractable framework for this task by encoding cross-dataset affinities in a transport plan. However, when two datasets are sampled from geometrically similar low-dimensional structures with substantially different sampling densities, the EOT plan may match points by relative sampling density rather than geometric proximity, yielding geometrically misleading correspondences. To address this issue, we propose a density-reweighted EOT framework in which the influence of sampling density on the transport plan can be discounted to a desired degree, ranging from standard EOT to alignment driven purely by underlying geometry. Under suitable regularity conditions, we establish convergence of the reweighted EOT plan to a family of population-level plans whose dependence on sampling density is made explicit. Through simulations, we show that our approach recovers geometrically faithful correspondences, improving over related EOT-based frameworks when datasets exhibit substantial sampling density disparity.
Coresets distill large datasets into small, representative subsets for efficient downstream learning. Yet Optimal Transport (OT)-based selection typically requires intensive computation of transport plans, limiting scalability. We introduce a scalable Sinkhorn coreset method that permits closed-form updates of the entropically regularized OT coupling by allowing non-uniform coreset weights. This produces centroids that generalize k-means via soft assignments. We establish asymptotic consistency of the selected measure and Lipschitz stability to data perturbations, providing accuracy and robustness guarantees. Across synthetic and real-world benchmarks, the proposed method achieves competitive or improved approximation quality while substantially reducing runtime compared to Wasserstein- and standard Sinkhorn-based coreset selection, especially at large scale.
High-throughput single-cell and spatial transcriptomic technologies provide high-resolution snapshots of heterogeneous cellular states, but their destructive nature prevents repeated measurements of the same cells over time. Consequently, temporal and spatial dynamics must be inferred from independently sampled, unaligned cell populations, making it challenging to reconstruct developmental trajectories. Optimal transport (OT) offers a geometric framework for aligning cell populations and inferring developmental trajectories, but many existing approaches focus on modeling the evolution of distributions of cells in gene expression space rather than the relational structure encoded by gene expression networks. To address this limitation, we introduce a geometric framework for analyzing the spatiotemporal evolution of gene expression networks through embeddings in Gromov--Wasserstein (GW) space. By representing each developmental stage as a graph combining gene expression and spatial proximity, our approach enables comparisons of network structure across time, continuous interpolation between developmental stages via GW geodesics, and quantification of network-level changes using Ollivier-Ricci curvature. We evaluate our framework on a spatiotemporal transcriptomic \textit{Drosophila} dataset and show that GW geodesic interpolations reproduce main trends in curvature dynamics observed in empirical gene expression networks. Agreement with higher-order Co-Optimal Transport (COOT) distances, which jointly represent spatial and temporal information, further validates the framework and suggests that hypernetwork representations successfully record salient biological changes across time. In general, our approach provides a unified geometric approach to study dynamically evolving biological networks.
Gauthier Avité, Maxime Sanchez-Renauld, Nicolas Bourriez +1cs.CV cs.LG
High-content microscopy enables systematic profiling of cellular responses to chemical perturbations, but the scale of the chemical space makes exhaustive phenotypic characterization experimentally infeasible. This motivates computational models that can predict image-derived phenotypes without acquiring the corresponding treated cells. We formulate molecule-induced phenotype prediction as an inductive conditional transport problem in image representation space. Given a negative-control phenotype and the structure of a molecule, we aim to predict the phenotype induced by the corresponding molecule. We first evaluate classical optimal transport baselines and show that static couplings do not yield useful predictions on large-scale phenotypic image datasets. We then introduce a molecule-conditioned Neural Optimal Transport (NOT) model with a Monge-Gap regularization training objective that learns to transport negative-control unperturbed phenotypes toward perturbed phenotypes using molecular structure as conditioning information. NOT recovers molecule-specific phenotypic effects while reducing microscopy-associated technical variation, thereby facilitating comparisons across experimental batches. On unseen active molecules, the model outperforms baseline approaches, demonstrating that chemically conditioned transport can generalize beyond the molecules observed during training. We identified the molecular encoder as the main limitation to this generalization, while transport in a compressed representation space improves performance and scalability. These results establish NOT as a promising framework for predicting cellular phenotypes from molecular structure and negative-control phenotypes, while highlighting the development of more informative molecular representations as a key direction for improving out-of-distribution performance.
Given a dataset where a portion of the samples are contaminated, our goal is to recover the underlying clean population distribution. To this end, we propose Wasserstein Filtering (WF), a novel sample selection framework that discards a fraction of suspicious samples and estimates the target distribution using the empirical measure of the remaining data. The core insight is to select a subset of samples whose empirical distribution maximizes its Wasserstein distance to the fully contaminated empirical distribution, thereby preferentially isolating and removing geometrically influential outliers. To render this optimization computationally tractable, we introduce three algorithms: a marginal screening scheme, SinkMarg, and two joint optimization algorithms, SinkWF and SlicedWF, leveraging entropic optimal transport and sliced Wasserstein approximations, respectively. On the theoretical front, we introduce the Far Exclusion and Local Projection (FELP) contamination model, which characterizes corruptions consisting of well-separated outliers and locally indistinguishable perturbations. Under this model, we prove that the WF estimator achieves minimax optimality over distribution families with bounded covariance. Extensive numerical experiments on synthetic datasets, benchmark anomaly detection suites, and robust generative learning with diffusion models demonstrate that WF serves as a highly practical, model-agnostic preprocessing tool. It delivers competitive outlier detection performance and provides substantial downstream benefits for generative modeling under heavy contamination.
Han Dong, Jiaming Li, Yongqiang Gong +2stat.ML cs.LG math.OC math.ST
We develop the statistical and algorithmic theory of inverse optimal transport (IOT) under the feature-parameterized cost C_theta(i,j) = -theta^T phi(i,j). The core technical contribution is the Sinkhorn linearization -- the implicit-function sensitivity of the entropic OT plan to the cost -- together with its spectral proxy, a formula that is spectrally exact yet geometrically transparent. The restricted Hessian on the tangent space satisfies the spectral sandwich (pi_min/epsilon) I <= H_T^{-1} <= (pi_max/epsilon) I, yielding the single core bound sigma_min >= (pi_min/(a_max epsilon)) sqrt(lambda_min(Sigma)) that drives the entire theory. On this core we establish four theorems and one observation. T1 (identifiability): theta is globally injective on the quotient of the gauge kernel, with dimension bound F <= (K-1)^2. T2 (sparsistency): the l1-penalized estimator recovers the true support under irrepresentability and score concentration, with exponential failure probability. T3 (well-posedness): the feature-moment map M(theta) = Phi^T x_theta is strongly monotone, and the inverse is Lipschitz with constant L <= epsilon ||Phi^T S_a||_op / (pi_min lambda_min(Sigma)). T4 (convergence): local strong convexity with mu >= pi_min^2 lambda_min(Sigma) / epsilon^2 guarantees monotone gradient descent convergence. O5 (misspecification): the estimator converges to the OT-model projection of the truth; the Holder continuity of the projection map is assessed numerically, yielding setting-dependent empirical exponents alpha_eff in (0,1).
Carlos Cardoso-Perelló, Alberto González-Sanzstat.ME math.PR stat.ML
We propose a robust barycenter for distribution-valued data by incorporating the Huber loss directly into the optimal transport cost. In contrast to metric-space Huber means, which apply the Huber loss to the Wasserstein distance after optimization, our construction acts on individual transport displacements, preserving quadratic behavior locally while limiting the influence of large displacements. The resulting Huber-Wasserstein barycenters form a natural interpolation between Wasserstein means and $L^1$-type Wasserstein medians. We establish the analytical and statistical foundations of this construction. For optimal transport with Huber loss, we prove regularity and uniqueness properties of dual potentials, existence of optimal transport maps, and stability as the Huber parameter varies. For the associated barycenter problem, we prove existence and characterization results, consistency of empirical plug-in estimators, and a finite-sample breakdown point essentially equal to $1/2$. In dimension one, we further derive the pointwise influence function and asymptotic distribution, quantify the associated robustness-efficiency trade-off, and show that displacement-wise Huberization can retain first-order information that is lost by distance-based Huberization under localized shape contamination. Numerical experiments on contaminated distribution-valued data demonstrate the robustness of the proposed barycenters and illustrate their interpolation between mean- and median-like behavior.