Machine Learning (Statistics) · Cross-listed from cs.SI
Not All Nodes Are Created Equal: Homophily-Aware Stratification for Stable GNN Evaluation
Naga Venkata Sai Jitin Jami, Thomas Altstidl, Sebastian Hoefler et al. (+4 more)
Graph neural networks are widely used for transductive node classification, with accuracy typically measured on randomly drawn train/validation/test splits. Reported accuracy has been shown to shift substantially across different random splits of the same
dataset, making published comparisons between architectures unreliable. The classical remedy in non-graph settings is stratified $k$-fold cross-validation, which ensures each test fold reflects the full class distribution of the
dataset. We argue that class stratification alone is insufficient for graphs: nodes are not isolated but connected, and folds that differ in their distribution of local neighbourhood homophily expose the model to systematically different relational conditions that directly affect message-passing behaviour. The resulting cross-fold variation reflects the homophily composition of each split, inflating reported variance beyond what model behaviour alone would produce. To address this, we propose \hp{}, a
topology-aware stratification procedure that treats node homophily as the primary stratification axis, aligning folds with respect to local relational consistency alongside the class marginal that standard stratification already controls. Stratifying on homophily alone does not guarantee class balance, so \hp{} incorporates class label as a secondary axis, preserving class representativeness as a natural consequence of the procedure. We evaluate \hp{} on a broad
benchmark suite comprising 15 node-classification
datasets spanning the full homophily spectrum and 7 GNN architectures. \hp{} achieves a mean stability rank of 1.49 compared to 2.31 for random $k$-fold, achieving the lowest mean stability rank on 13 of 15
datasets while preserving class balance close to class-stratified splits and substantially better than random. We argue that homophily-aware split construction merits broader adoption for GNN evaluation.
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All authors Naga Venkata Sai Jitin Jami, Thomas Altstidl, Sebastian Hoefler, Jonas Mueller, Dario Zanca, Bjoern Eskofier, Heike Leutheuser
Machine Learning (Statistics)
Federated Soft Clustering via Generalized Total Variation Minimization
Shamsiiat Abdurakhmanova and Alexander Jung
We study
federated soft clustering over
federated learning (FL) networks of devices that each hold a private local
dataset and fit a personalized Gaussian mixture model (GMM). Generalized total variation minimization (GTVMin) couples the local maximum likelihood problems through a graph regularizer that penalizes a discrepancy between the models of connected nodes. The choice of discrepancy measure is a key design decision: we compare a squared Euclidean distance between model parameters, which requires component matching, with two measures that compare the local model distributions directly and hence need no matching: a Monte-Carlo approximated Kullback-Leibler (KL) divergence and a closed-form maximum mean discrepancy (MMD). All three resulting GTVMin instances are optimized by synchronous projected gradient updates; for the smooth MMD instance we provide a convergence guarantee to stationary points. We characterize their computational cost and evaluate their robustness to data heterogeneity.
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Machine Learning (Statistics) · Cross-listed from cs.CV
Training-Adaptive Convolutional Sparse Coding via Information Bottleneck for Robust Visual Representation
Meng'en Qin, Yinchen Liu, Mingxuan Cui et al. (+1 more)
Visual signals require compact yet sufficient representations for robust downstream prediction. Convolutional sparse coding (CSC) provides an explicit mechanism for suppressing redundant components while preserving signal content, but its sparsity coefficient is often manually selected during training. We propose a training-adaptive convolutional sparse coding framework for robust visual signal representation. Specifically, we unfold the CSC optimization with the Fast Iterative Shrinkage-Thresholding
Algorithm (FISTA) and treat the sparsity coefficient as a differentiable variable jointly learned with the network parameters. From the information bottleneck perspective, this coefficient controls the trade-off between information retention and compression: the sparsity term promotes compact representations, while the reconstruction term together with task loss preserves task-relevant signal content. We further introduce a label-free post-training strategy that adjusts the compression strength for corrupted inputs with the main network parameters fixed. Experiments on CIFAR and ImageNet demonstrate competitive clean-data recognition and greatly improved robustness under different input perturbations.
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All authors Meng'en Qin, Yinchen Liu, Mingxuan Cui, Youlu Xing
Machine Learning (Statistics)
A General Kernel Framework for Non-CND Distance Measures Using |D|-Dimensional Sparse Landmark Embeddings
Marcus M. Noack, Maher B. Alghalayini and Mark D. Risser
Kernel methods, and Gaussian Processes (GPs) in particular, require a Hilbertian distance measure—one whose square is conditionally negative definite (CND)—to guarantee positive semi-definiteness (PSD) of the kernel
matrix; a condition that fails for many natural input spaces, including smooth
manifolds and spaces of probability distributions. We propose the Sparse Landmark
Embedding (SLE) kernel, which eliminates this requirement entirely. Each input is embedded into a sparse feature vector via compactly supported bump functions centered at all |D| training points; applying any standard PSD kernel in this
embedding space yields a kernel that is provably PSD for arbitrary distance measures. The compact support automatically controls
embedding sparsity, keeping kernel
matrices well-conditioned and computationally tractable despite the high ambient dimension. We provide theoretical guarantees on PSD, sparsity, stability, and universal approximation, and demonstrate, using geodesic and Wasserstein distances, that the SLE kernel matches or substantially exceeds domain-specific baselines in both predictive accuracy and uncertainty quantification.
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Machine Learning (Statistics)
Fast Learning Rates for Physics-Informed Kernel Methods
Luc Brogat-Motte, Joachim Bona-Pellissier, Giacomo Meanti et al. (+1 more)
In physics-informed machine learning, a target function $u^*$ is learned from noisy value observations $y_i=u^*(x_i)+ \varepsilon_i$, together with differential information, given either by noisy observations $d_j=(Du^*)(z_j)+\xi_j$ or by a known physical constraint $Du^*=v$. We consider the setting where $D$ is a linear differential operator and analyze a physics-informed kernel
estimator $\hat u$ combining $n$ value observations and $m$ differential observations. In this context, we ask how much can differential information improve predictions, and how does this improvement depend quantitatively on $n$, $m$, and $D$. We prove finite-sample bounds, supported by numerical simulations, revealing a two-regime structure for the prediction error. When $m$ is limited, the rate depends jointly on $n$ and $m$; when $m$ exceeds a problem-dependent threshold, the rate saturates and matches the oracle rate obtained when the perfect constraint $D \hat u = Du^*$ is imposed. Examples are discussed for Sobolev spaces which are reproducing kernel
Hilbert spaces and include partial
Laplacian constraints on the
torus and gradient observations on bounded domains. These examples illustrate the range of possible learning rate improvements — from the standard nonparametric $n^{-1/4}$ to the parametric rate $n^{-1/2}$. Finally, we derive physically consistent rates in a stronger norm that jointly controls the errors in $\hat u$ and $D\hat u$.
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All authors Luc Brogat-Motte, Joachim Bona-Pellissier, Giacomo Meanti, Lorenzo Rosasco
Machine Learning (Statistics) · Cross-listed from eess.SP
Stable Filters for Generative Modeling of Graph Signals
Martin Schmidt and Gonzalo Mateos
Generating signals on graphs requires permutation-equivariant models that exhibit stability with respect to relative structural perturbations. While recent graph-aware Schrödinger bridge models incorporate
topology information directly into their reference dynamics, it is unclear how perturbations of the graph propagate through these dynamics and affect the resulting generated distributions. In this paper, we analyze the structural stability of graph-aware continuous-time generative models whose drift combines a graph filter with a learned graph neural network. We derive explicit Wasserstein stability bounds that quantify the effect of relative graph perturbations on the generated distributions. Motivated by these bounds, we introduce a principled framework for designing stable graph filters that preserve the smoothing behavior of graph heat
diffusion, while boosting structural stability. Experiments on synthetic and fMRI signals show our stable filters enhance structural robustness while matching or exceeding the generative quality of the heat equation baseline.
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Machine Learning (Statistics) · Cross-listed from cs.LG
When Edit Flows are Edit Jumps: replicating Edit Flows and EvoFlows
Gabriel Bénédict, Melanie Buechler, Gerard Riera-Solà et al. (+3 more)
Antibody lead optimization calls for a small, bounded set of edits to an existing candidate: substitutions, but also insertions and deletions. Edit-based generative models are the only ones that allocate such an edit budget without fixing the edit positions, the edit count, or the output length in advance. However, the existing approaches Edit Flows and EvoFlows did not release code or complete training specifications. Here, we show that both methods follow the same underlying process – edits firing one at a time, at learned rates, in continuous time – the pure-jump case of generator matching over finite sequences. With EditJumps we introduce the first open implementation of this framework, with a single generalist antibody editor trained on 1.66M Observed Antibody Space homolog pairs to propose homolog-like variants of a seed sequence, editing unseen leads zero-shot, without the per-family retraining original approaches require. Replicating this system from scratch exposes why open code is essential for generative biology: reconciling published edit distributions required reverse-engineering an undocumented rate-scaling hyperparameter that dictates realized mutation counts. Moreover, we show that published evaluation metrics are highly sensitive to reference sample size, frequently flipping method rankings. We release our full codebase, automated test suite, and configurations at: https://github.com/VisiumCH/editjumps
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All authors Gabriel Bénédict, Melanie Buechler, Gerard Riera-Solà, Chloé de Ancos, Yves Gaetan Nana Teukam, Moritz Freidank
Machine Learning (Statistics)
Rank and computation of the pathlifting Jacobian of a DAG ReLU network
Manon Verbockhaven
This paper provides a self-contained proof of the rank of the pathlifting Jacobian of a DAG ReLU network by performing an induction on the network's number of hidden nodes. In fact, the induction is elementary, and the key recipe is to consider the skeleton
matrix of the network, a sparse
matrix encoding the network paths, and transform the representation of one of its hidden
neurons into an output node. The proof relies on intermediate propositions which link the pathlifting, its Jacobian, the network parameters, and its skeleton
matrix, which, on top of permitting to conclude on the rank of the pathlifting Jacobian, also provide a way to compute it without backpropagation and whose computation cost is super efficient in practice compare to usual backpropagation. The paper is provided with a Python module that implements the different propositions of the paper for feed forward networks and is used to experimentally quantifies the computational gain of computing the pathlifting Jacobian with the proposed theory.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Revisiting Distributed Sign-Based Variance Reduction
Wei Jiang, Zechao Li and Lijun Zhang
Sign-based methods reduce communication costs in distributed environments, but aggregating local signs can introduce bias when data are heterogeneous. As a result, existing sign-based variance reduction methods fail to obtain the optimal convergence rates. In this paper, we solve this problem and obtain optimal rates for both nonconvex
stochastic and finite-sum optimization. We first give a counterexample showing that majority voting can fail to approach stationary points even with exact local gradients. Motivated by this limitation, we propose tracking the global gradient at the server through unbiased compression of recursive gradient increments. As a result, we can obtain the convergence rates of $O(\sqrt{d/K}+\sqrt d (a/(nK))^{1/3})$ for the $\ell_1$-norm and $O(\sqrt{a/K}+\sqrt a/(nK)^{1/3})$ for the $\ell_2$-norm. Here, $K$ is the iteration number, $n$ is the number of workers, $d$ is the dimension, and $a=1+\omega$, with $\omega$ denoting the compressor's relative variance. For finite-sum problems with $M$ components, we combine periodic exact gradient refreshes with compressed component-gradient differences. The resulting total sample complexities are $O(M+d\sqrt{aM}\epsilon^{-2})$ and $O(M+a\sqrt M\ epsilon^{-2})$ for $\ell_1$ and $\ell_2$ gradient norms at most $\epsilon$, matching the corresponding bounds in centralized settings.
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Machine Learning (Statistics) · Cross-listed from cs.LG
How Many Labels Does Model Choice Need? Certificates and Budgets for Selective Prediction
Tetsuji Kuboyama
Classifiers can make identical predictions yet require labels to compare their selective performance: confidence ranks weight the same errors differently. We quantify this requirement for the area under the generalized risk-coverage curve (AUGRC). A prelabel lower bound rules out insufficient budgets. With all labels known, a covering linear program bounds the minimum number of labels sufficient to fix the winner (the certificate size) within $K-1$ labels for $K$ candidates. For fixed $K$, independent uniform orders and identical predictions, the prelabel bound approaches one quarter of the pool. With iid Bernoulli errors independent of the orders, every exact acquisition policy reads almost all labels asymptotically, although a two-candidate certificate needs only half. Across 108 feature-panel comparisons on nine
datasets, disagreement labels settle every accuracy choice but no AUGRC choice. A 20% budget is ruled out in 96 conditions; certificates need 56-57% on average. On ten conditions with pretrained image classifiers, confidence-score choice reads 68-91% of 10,000 labels for exact selection and 50-67% with AUGRC tolerance $5\times10^{-4}$. An exact stopping test works with any acquisition order. Together, these results link confidence ranks to label budgets and certified model comparison.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Provable Guarantees and Efficient Learning of Structural Equation Models with Latent Confounders
Weijian Yu and Jean Honorio
Causal discovery aims to recover causal relationships from observed data. In various fields, exploring causal relationships among variables remains an important topic, but this task becomes challenging due to the existence of latent confounders. Ignoring such confounders can lead to false associations and incorrect edge directions. In this paper, we study the linear structural equation model with latent confounders. We propose an
algorithm that iteratively identifies terminal (observed) nodes and reconstructs the directed acyclic graph of the observed variables. To do this, we recover the precision
matrix of the observed variables as a sparse plus low-rank
matrix: a sparse
matrix captures the conditional dependencies among observed variables, while a low-rank
matrix captures the combined influence of a few latent confounders. We establish that for $p$ observed variables, $r$ latent confounders and $s$ edges, our procedure correctly identifies the directed causal relationship among observed variables, for $n \gtrsim \max\{s\log p,\ r p\}$ samples. Experimental results validate our theoretical contributions.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Spatially Adaptive Noise Injection
Frantzeska Lavda, Maciej Falkiewicz, Van Khoa Nguyen et al. (+1 more)
Diffusion samplers reverse a learned noising process using either
stochastic (DDPM) or deterministic (DDIM) updates, which represent endpoints of a single family controlled by a scalar noise-injection variance that is applied identically at every spatial location. This uniform approach neglects the geometry of natural images: high-
curvature regions such as edges and textures, where the denoiser is uncertain, benefit from
stochastic correction, whereas smooth regions, where the score is precise, are degraded by injected noise. This work investigates whether each pixel requires
stochastic correction at a given timestep and introduces Spatially Adaptive Noise Injection (SANI), a novel sampling framework that dynamically adjusts noise application on a per-pixel basis. SANI integrates a probabilistic gating mechanism with a derived spatially adaptive variance, ensuring that noise is injected precisely where needed to refine complex features while preserving well-formed structures. Experimental results and decoupling ablations demonstrate that SANI consistently improves Fréchet Inception Distance (FID) over the vanilla DDPM and DDIM endpoint samplers across diverse sampling timesteps, while remaining competitive with variance-learning baselines, highlighting the importance of spatial adaptivity in
diffusion sampling.
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All authors Frantzeska Lavda, Maciej Falkiewicz, Van Khoa Nguyen, Alexandros Kalousis
Machine Learning (Statistics) · Cross-listed from math.OC
Gradient Descent with Stochastic Subspaces via Persistence of Memory
Subhroshekhar Ghosh, Clement Z. Q. Ng, Pierre-Louis Poirion et al. (+1 more)
Stochastic subspace methods have gained popularity as gradient descent based techniques for large scale optimisation problems, especially in distributed settings. In this paper, we introduce the technique of "persistence of
memory" to greatly extend and improve the random subspace methods. To this end, we leverage a vector that is only weakly correlated with the gradient in order to provide a guiding structure to the generative process of the random subspace along which the descent is going to take place. This guidance vector may be fixed for a large number of iterations, only to be refreshed at wide intervals (on whose size we can provide guarantees in terms of problem parameters). In important machine learning settings, such as optimisation problems embodying sparsity or a minibatch structure, we show that the guidance vector can be obtained in an effective and computationally inexpensive manner by leveraging the structured properties of the problem. En route, we establish to our knowledge the first theoretical analysis of classical SSD methods for sparse functions. In a local neighbourhood of the optimum, we demonstrate an
alignment phenomenon of our gradient estimates with a low-lying eigenvector of the Hessian, allowing a once-for-all computation of the guidance vector which renders the method computationally favourable even in scenarios with unstructured objectives.
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All authors Subhroshekhar Ghosh, Clement Z. Q. Ng, Pierre-Louis Poirion, Akiko Takeda
Machine Learning (Statistics) · Cross-listed from cs.AI
Bad Genius: Counterfactual-Guided Harness Evolution Beyond Task-Specific Shortcuts
Guojun Zhu, Xunheng Huang, Peng Yin et al. (+3 more)
Reliable
agent evaluation is complicated by automatic harness optimization, which repeatedly uses a released
benchmark $B_{\mathrm{rel}}$ to guide a Proposer that edits
prompts,
memory,
retrieval, tools, and control code around a fixed foundation model. Task holdout is commonly used to guard against harness overfitting. It varies semantic tasks but leaves the
benchmark protocol fixed, so a bad genius Proposer can produce a cheating harness whose improvement over the initial harness on $B_{\mathrm{rel}}$ depends on a
benchmark-wide shortcut. We introduce Counterfactual Harness Search and
Evolution (CHASE), which casts harness
evolution as constraint generation over valid counterfactual
benchmarks. After each Proposer update, a Challenger searches for an executable protocol transformation with large gain destruction. A validity firewall checks that task semantics are preserved, while a held-out confirmation set determines whether the counterfactual enters a finite archive. We formalize an ideal shortcut-neutralized
benchmark $B_0$ and establish theoretical guarantees linking finite counterfactual archives to $B_0$ and characterizing sequential Challenger search. We evaluate CHASE on Syn-Ledger and OfficeQA, where CHASE retains strong released-
benchmark gains while substantially reducing gain destruction under valid protocol transformations.
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All authors Guojun Zhu, Xunheng Huang, Peng Yin, Jiahui Xie, Sanguo Zhang, Doudou Zhou
Machine Learning (Statistics) · Cross-listed from cs.LG
Beyond Quadratic Loss: The Stability Phase Diagram of Adam
Gaoxiang Tang, Huanran Chen and Ziming Liu
Loss spikes are recurrent instabilities in neural-network training and can arise from multiple mechanisms. For Adam in particular, macroscopic loss spikes have been linked to optimizer dynamics, yet how its two momentum timescales govern them remains unclear. We investigate this dependence by mapping training dynamics across the $(\beta_1,\beta_2)$ plane. Across a range of model–task settings, an approximately linear boundary, $1-\beta_2=C(1-\beta_1)$, separates spiky from non-spiky dynamics, whereas a one-dimensional quadratic loss produces approximately cubic slope. A one-dimensional superquadratic loss $L(x)\propto|x|^n$ recovers the near-linear scaling and links the boundary coefficient to the effective loss exponent $n$. We further show that confident cross-
entropy losses develop a core–wall landscape comprising a narrow quadratic core followed by a steep wall, which produces effective superquadratic behavior at the scale of an optimizer update. Together, these results connect Adam loss spikes to both the mismatch between momentum timescales and finite-scale superquadratic loss geometry beyond the Hessian.
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Machine Learning (Statistics)
Preservation of Log-Concavity and Convergence of Wasserstein-Fisher-Rao Gradient Flows
Francesca Romana Crucinio and Sahani Pathiraja
We study the convergence of Wasserstein-Fisher-Rao (WFR) gradient flows for sampling from probability distributions known up to a normalisation constant. By combining Wasserstein transport with Fisher-Rao birth-death dynamics, WFR flows balance exploration and selection. These flows have been recognised as a promising mechanism to accelerate convergence beyond Langevin dynamics. We show that for a class of strongly log-concave target distributions satisfying additional
curvature conditions, WFR flows preserve strong log-concavity, in contrast to Wasserstein flows which enjoy this property only in the Gaussian setting. Exploiting this result, we derive explicit non-asymptotic convergence rates for the symmetrised Kullback-Leibler divergence, without requiring a warm-start as required in current estimates. In particular, we show that the convergence rate decomposes additively into Wasserstein and Fisher-Rao contributions, thereby confirming a recent
conjecture within this setting. These results provide refined convergence guarantees and further develop the theoretical foundations of WFR gradient flows for sampling and
Bayesian inference.
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Machine Learning (Statistics) · Cross-listed from math.OC
Matching Multi-Loop Complexities with a Single Loop: Optimal Optimization Stationarity and Best-Known Game Stationarity in Nonconvex–Concave Minimax Optimization
Minghao Zhang and Zi Xu
We introduce a new single-loop algorithmic framework for smooth nonconvex–concave minimax optimization. The resulting projected damped extragradient method combines projected extragradient updates, dual momentum, and a moving proximal center. Under both the optimization-stationarity and game-stationarity criteria, our method achieves the best-known complexity among single-loop first-order methods. For optimization stationarity, our method achieves a gradient complexity of $O(L^2D_Y\bar\Delta_0\varepsilon^{-3})$, where $L$ is the gradient Lipschitz constant, $D_Y$ bounds the diameter of the dual feasible set, and $\bar\Delta_0$ is an initialization quantity involving the value-function gap and the initial gradients. Moreover, by incorporating a fixed-center warm-up phase, the complexity can be improved to $O(L^2D_Y\Delta_\phi\varepsilon^{-3})$, up to an additive lower-order cost, where $\Delta_\phi:=\phi(x_0)-\inf_x\phi(x)$. We further establish a lower bound of $\Omega(L^2D_Y\Delta_\phi\varepsilon^{-3})$ for optimization stationarity over projected zero-respecting first-order methods. This lower bound proves that the warm-started version of our
algorithm is optimal up to a constant factor for optimization stationarity within this oracle class. For game stationarity, our method achieves $\mathcal{O}\!(L^{3/2}D_Y^{1/2}\Delta_\phi\varepsilon^{-5/2})$ gradient complexity. This matches the best-known complexity of multi-loop first-order methods, thereby establishing the same complexity with a single-loop algorithmic structure. Under dual strong concavity, the proposed framework achieves $O\!(\sqrt{\kappa}\,L\Delta_\phi\varepsilon^{-2})$ leading complexity for both stationarity criteria, where $\kappa=L/\mu$ is the dual condition number, up to an additive initialization cost. The $\varepsilon^{-2}$ accuracy dependence is optimal under fixed regularity and initialization bounds.
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Machine Learning (Statistics) · Cross-listed from cs.LG
On the Identifiability of Mixed Ordinal and Exponential Family Causal DAGs under Linear Parametric Models
Sambit Mishra and Urbashi Mitra
The problem of identifiability in linear parametric models (LPMs) whose nodes follow either an ordered logit model or a regular one-parameter exponential family is evaluated. The results go beyond classical structural equation models as well as results for nodes with observations from a homogeneous family of distributions. The main result establishes that the orientation of every edge joining an ordinal node to an exponential-family node is identifiable from the joint distribution alone at every parameter value, provided the ordinal node has at least three categories and the exponential-family node at least three points of support, with no restriction on the sufficient statistic. Converses show that both requirements are necessary: the three-category requirement is binding only for affine sufficient statistics, and the three-point requirement is binding under the canonical link. The guarantee extends to orienting every such mixed ordinal-exponential family edge of a given $d$-node undirected skeleton. Numerical experiments illustrate the theoretical results by successfully separating orientations within a Markov equivalence class, which are indistinguishable by conditional independence alone.
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