Kernel Methods

Testing conditional independence is fundamental yet intrinsically difficult: without additional assumptions, Type I error control is impossible in general. The "Model-X'' paradigm addresses this difficulty by assuming exact knowledge of a relevant conditional distribution. While small deviations from this assumption can sometimes be tolerated in classical one-shot testing, existing sequential conditional independence tests typically require the Model-X conditional to be known exactly, making them fragile when it must instead be estimated. We propose a new approach that is substantially more robust to such estimation error. Our method applies testing-by-betting to an adaptively optimized Kernel Conditional Independence statistic, together with a normalization scheme and a truncate-and-shift calibration strategy. These modifications greatly reduce Type I error inflation while preserving high power across high-dimensional synthetic benchmarks and real-world fairness tasks, outperforming existing sequential Model-X approaches. Code is available at https://github.com/he-zh/SKCI.

A recent line of work has reframed individual decision trees as linear models on engineered features associated with their splits, opening routes for oracle inequalities and feature-importance reinterpretation, but leaving open the question of what unified geometric object a forest induces when one indexes its feature map by nodes rather than by splits. The present paper studies that object. KPP indexes the feature map by the nodes of the forest, weighted by a path metric that turns each coordinate into a component of a squared-Euclidean path-isometric embedding. KPP unifies four pillars under a single node-indexed representation whose Gram is non-diagonal and carries a metric: prediction, exact additive attribution, deterministic Lipschitz robust radius in the KPP metric, and uniform Rademacher risk bounds for regression and classification under fixed, honest, or cross-fit conditioning. All probabilistic guarantees are conditional on the representation and are stated under three explicit conditioning regimes; the robust-radius guarantee is deterministic in the KPP metric rather than in a norm on the raw input. Conjectured fast-rate refinements for both regression and classification are stated as open problems and are not claimed as theorems.

Pairwise learning is a specialized form of supervised learning that focuses on predicting outcomes for pairs of objects. In this work, we introduce SPaiK, a new scalable kernel learning method tailored for pairwise settings. Our approach preserves the expressive power of kernel methods while substantially reducing computational and memory requirements. The key innovation is the stochastic generalized vec trick (sGVT), a stochastic extension of the sparse Kronecker product multiplication algorithm, which enables efficient large-scale training with pairwise kernels. By incorporating sGVT, SPaiK makes it possible to apply kernel-based pairwise learning to datasets of a size previously out of reach. We evaluate the performance of SPaiK on seven real-world drug-target affinity datasets and compare the results with state-of-the-art methods in pairwise learning.

Do different LLM architectures encode high-level concepts in structurally compatible ways? We systematically characterize a geometric-functional universality dissociation: across multiple concept domains and architectural families, moderate geometric convergence coexists with near-perfect functional transfer. Using contrastive-difference CKA (CKA_Delta), a training-free diagnostic that computes kernel alignment on per-sample contrastive differences, we isolate concept-specific convergence from generic similarity -- achieving significant discrimination where standard CKA cannot. The dissociation replicates across all six concept domains we test (five with p <= 0.017 geometric discrimination and safety as a converging-functional trend, p = 0.08), including two non-instruction concepts (code-vs-NL, reasoning-vs-recall) validated without system prompts; a single 70B--70B pair provides an observational note that universality may strengthen with scale, requiring replication with additional >=70B models. We position CKA_Delta as a practical regime classifier and architectural outlier detector (Gemma: d = 1.08, AUC = 0.79) rather than an absolute transfer-accuracy predictor, providing a training-free diagnostic for cross-architecture concept monitoring.

Constructing mathematically tractable function spaces that capture hierarchical compositional representations remains a central challenge in statistical learning theory. We introduce Brownian kernel ladders (BKLs), a recursively defined hierarchy of integral reproducing kernel Hilbert spaces generated through Brownian-kernel integral constructions. Starting from linear functionals, each layer is obtained by integrating Brownian kernels over probability measures supported on subsets of the previous layer, yielding a recursive function-space model in which depth is encoded directly through the hierarchy. Based on this framework, we define canonical BKL spaces together with an associated complexity functional. We establish several analytical and statistical properties of these spaces. In particular, we show that BKL spaces form quasi-Banach spaces, satisfy depth-dependent Hölder regularity estimates, and exhibit strict monotonicity with respect to depth. We further prove existence results for regularized empirical risk minimization and derive Gaussian complexity bounds that remain uniformly controlled with respect to both the ambient dimension and the hierarchy depth. A key ingredient of the analysis is a combinatorial proof technique based on recursive subset decompositions and Brownian-kernel threshold representations. These estimates yield excess-risk guarantees of near-parametric order for regularized empirical risk minimization over BKL spaces. Our results provide a mathematically tractable hierarchical function-space framework for studying compositional representations in deep learning.

Despite its importance to applications in protein design, predicting protein properties like binding affinity and thermostability from sparse experimental data remains a significant challenge. Accordingly, we introduce a class of sequence kernels that exploit evolutionary substitution matrices as well as local linearity and demonstrate that the resulting Gaussian processes provide data-efficient models of protein property landscapes, frequently outperforming alternatives that rely on foundation model embeddings. Furthermore--by learning what are in effect structure-aware substitution matrices--we show that our kernels can readily incorporate structural information from foundation models. We demonstrate that these structure-conditioned kernels are well suited to multi-task learning across multiple protein property landscapes and can decisively outperform local supervised learning methods.

Bernstein--Schur kernels are products of a finite-feature kernel and a completely monotone shift-invariant kernel: nonstationary kernels falling between the shift-invariant and dot-product templates random features exploit, so neither Bochner sampling nor polynomial sketching applies to the full kernel directly. We give one random-feature construction for the whole class that randomizes both factors: it sketches the finite modulation and samples the radial factor's one-dimensional Bernstein--Widder scale before applying Gaussian random Fourier features, giving feature dimension $Dm$, free of the $O(d^2)$ size of the exact modulation feature. With the modulation kept exact (the $m\to\infty$ limit), we prove unbiasedness, an exact variance, and a matrix-Bernstein operator-norm bound controlled by the top kernel and modulation eigenvalues and an intrinsic dimension rather than the crude $N\max_{ij}$ route. Whitening this argument at the ridge makes the effective dimension $d_{\mathrm{eff}}(λ)$ the \emph{exact} intrinsic dimension of the matrix variance, so $O((1+\|P\|_{\mathrm{op}}/λ)\log(d_{\mathrm{eff}}/δ))$ radial draws preserve the kernel-ridge solution; tilting the draw by a closed-form whitened leverage improves this to the effective-dimension count $O((1+d_{\mathrm{eff}})\log(d_{\mathrm{eff}}/δ))$. Conditioning on the sketch carries every guarantee to the deployed doubly-randomized estimator up to one additive sketch term, and all hold for the whole class with the modulation Gram in place of the polynomial one. The flagship instance is the biased $yat$-kernel $k_{yat,b}(w,x)=(w^\top x+b)^2/(\|w-x\|^2+\varepsilon)$, whose family span contains the inverse-multiquadric kernel by finite differences in $b$.

We propose a fast and correspondence-free local point cloud registration method that leverages geometric surface structure and reproducing kernel Hilbert space (RKHS) embeddings. The method represents point clouds as continuous functions with point-wise anisotropic kernels that encode local geometry. This formulation improves alignment along surface normals while relaxing alignment along tangential directions. To solve the resulting registration problem, we propose a second-order on-manifold optimization scheme with approximate Riemannian Hessians, achieving a speedup of up to 10x over the first-order solvers used in prior correspondence-free RKHS-based methods. We demonstrate improved frame-to-frame LiDAR and RGB-D tracking accuracy across diverse indoor and outdoor datasets. On a LiDAR tracking registration task in the driving domain, we achieve a reduction of $>55\%$ in both translational and rotational drift in challenging feature-sparse environments. On object registration benchmarks, we show improved robustness over ICP-based methods and further gains when refining global initialization, particularly under moderate misalignment.

TorchKM is an open-source library for kernel machines, including support vector machines, kernel logistic regression, and kernel quantile regression, with GPU acceleration. The library features a scikit-learn-style API and is designed to exploit GPU-friendly linear algebra, accelerating the full training and model-selection pipeline through intelligent reuse of matrix operations. Benchmarks show competitive predictive performance with substantial speedups over standard baselines. The efficiency and programmable design also make TorchKM a kernel-learning component for AI-driven workflows. Code and documentation are available at https://github.com/YikaiZhang95/torchkm, and the package can be easily installed via PyPI.

Vision-language foundation models such as CLIP and SigLIP provide widely used representations for multimodal learning systems. While these models are typically compared through downstream performance, such evaluations often do not explain how their representations differ structurally. In this work, we study this problem through the task of Contrastive Embedding Clustering: identifying sample subsets that are weakly clustered under one representation but strongly clustered under another. We propose \emph{Kernel Optimization for Discrepancy Analysis (KODA)}, a kernel-based framework for contrastive representation comparison and alignment. KODA constructs unified multimodal kernels through modality-wise kernel composition and formulates discrepancy discovery as a constrained optimization problem that searches for coherent structures in one representation while suppressing coherence in a reference representation. This yields interpretable discrepancy directions associated with specific sample subsets and modality interactions. To scale KODA to large vision-language datasets, we develop randomized low-dimensional approximations of joint kernels using random projections, including Random Fourier Features for shift-invariant kernels. Empirically, KODA identifies consistent and interpretable discrepancy structures across vision-language representations and provides sample subsets for representation alignment. The code is available at https://github.com/yokiwuuu/KODA.

Machine learning interatomic potentials (MLIPs) enable efficient and accurate atomistic simulations but depend critically on the quality and diversity of the training data. We introduce Stein kernelized molecular dynamics (SKMD), an enhanced sampling method that uses interacting particle dynamics to acquire informative training configurations for the active learning and fine-tuning of MLIPs. SKMD corresponds to a stochastic variant of Stein variational gradient descent that is adapted for molecular dynamics by incorporating asynchronous particle updates and a kernel of global atomic descriptors, which provides a symmetry-aware measure of configurational similarity. Unlike other enhanced samplers used in molecular dynamics, SKMD preserves the Boltzmann distribution as the asymptotic distribution of the dynamics. This property enforces a balance between the exploration of diverse configurations and attraction toward high-probability regions of the energy landscape. We further propose an approach to efficient online data acquisition using an adaptive stopping criterion that selects non-redundant training data over the course of simulation. We demonstrate SKMD for the active learning of a neural network model of the Müller-Brown potential and the fine-tuning of a MACE interatomic potential for alanine dipeptide. Compared to active learning baselines, our method achieves higher model accuracy in fewer training iterations with the same number of acquired training samples.

For nonconvex optimization problems whose objective is the prediction function of a trained Support Vector Regression (SVR) model with the Gaussian radial basis function (RBF) kernel (RBF-SVR), we present a framework that applies the difference of convex functions (DC) algorithm (DCA) by exploiting the analytical structure of the RBF kernel to construct an explicit DC decomposition. Specifically, we derive in closed form both the lower bound $μ$ of the strong convexity parameter of the DC components and the upper bound $L$ of the gradient Lipschitz constant of the subproblem. Both $μ$ and $L$ are determined solely by the post-training dual-coefficient sum $C_α$ and the RBF kernel parameter $γ$, together with the DC decomposition parameter $ρ$, and they share a common leading term $C_αρ$. Through numerical experiments on six benchmark functions, we show that $C_αρ$ is the primary single quantity characterizing both the convergence properties and the initial-point dependence of DCA, and further demonstrate that it decomposes into two independent pathways, $C \to C_α$ and $γ\to ρ$, with its primary variation governed by the SVR hyperparameters $(C, γ)$. Together, these results allow the convergence properties of DCA on RBF-SVR to be assessed in advance through the single scalar quantity $C_αρ$: approximately from $(C, γ)$ before training, and exactly in closed form after training.

Modeling spatial dependencies is central to spatiotemporal data analysis using Graph Neural Networks (GNNs). Traditional methods rely on distance-based kernels with predefined parameters, which restricts model capacity. Although generic adaptive mechanisms (e.g., Graph Attention Networks) offer flexibility, they often fail to capture the underlying geometric structure, performing worse than distance-based models in data-sparse scenarios. Addressing this, we revisit the kernel parameterization problem and theoretically prove that misspecified kernel parameters introduce unavoidable approximation errors in GNNs. To overcome this, we propose AdaKernel, a simple yet effective approach that learns adaptive kernel parameters within the neural network. Unlike methods that learn graph structures from scratch, AdaKernel adopts a structure-preserving strategy that optimizes the scale of physical interactions rather than discarding them. Extensive experiments on Kriging, Imputation, and Forecasting demonstrate that AdaKernel consistently improves various GNN architectures and outperforms model-agnostic adaptive baselines, validating that accurately learned kernel parameters are superior to both fixed priors and fully latent graph structures.

Recent work in random matrix theory (RMT) has developed the notion of deterministic equivalents: typically linear surrogate models that approximate the spectral behavior of large nonlinear random matrices, such as nonlinear feature maps in neural networks (NNs). Such equivalents make theoretical predictions tractable by reducing a complex model to a simpler one with properties that fall under the umbrella of classical RMT tools. However, this leaves open the question of whether this idealized linear equivalence remains meaningful for classification of high-dimensional nonlinearly separable data. Motivated by this, we consider the conjugate kernel (CK), which is the nonlinear feature map of a one-layer feedforward NN, under a canonical nonlinearly separable dataset for the XOR problem; and we use the study of informative outlier eigenvalues in the CK and whether their corresponding eigenvectors asymptotically align with XOR labels as a proxy for nonlinear learnability. We develop a robust quadratic equivalent of the CK matrix that enables a precise analysis of emergent informative spikes, as one modifies various knobs common in ML practice: sample complexity, signal-to-noise ratio (SNR), nonlinear activation choice, and pretrained features. We identify regimes in which these knobs move the CK beyond the linear equivalent and produce BBP-type transitions to label-aligned outlier eigenspaces. Our analysis helps bring deterministic-equivalence tools from RMT to bear on problems of practical relevance in ML.

Learning representations that capture both intrinsic data geometry and target-relevant structure remains a fundamental challenge, particularly in settings where data reduction must balance compression with predictive fidelity. While distributional reduction-encompassing joint clustering and dimensionality reduction-offers a principled way to summarize data, its supervised variants remain relatively under-explored, despite the importance of retaining task-relevant signal for downstream prediction and decision-making. We propose Supervised Distributional Reduction (SDR), an algorithm for learning target-aware representations by combining optimal transport with explicit dependence maximization. SDR builds on the Fused Gromov-Wasserstein (FGW) objective to align the relational structure of the input distribution with a set of representative points, while augmenting it with a direct dependence term that encourages the learned embeddings to capture predictive signal more explicitly. This results in compact representations that reflect both geometric structure and supervision. Beyond representation learning, SDR naturally induces a data-dependent, non-stationary geometry that can be leveraged for settings such as Gaussian Process (GP) modelling. By redefining distances through target-aware distributional alignment, SDR enables the construction of adaptive kernels that respond to local variations in both data geometry and supervision, offering an optimal transport-based perspective on non-stationary kernel design.

We develop semiparametrically efficient inference for kernel measures of noise heterogeneity in additive noise models. In many applications, the regression function is estimated using flexible machine learning methods. Downstream procedures based on the resulting residuals can then inherit first-stage bias: regression error may induce spurious dependence between covariates and residuals, invalidating the assumptions needed for standard analysis. We construct a novel Hilbert-valued one-step estimator of the kernel covariance operator between covariates and residuals. Our estimator yields bootstrap-calibrated tests for residual independence and goodness of fit in additive noise models, while also providing asymptotically efficient confidence intervals for the kernel dependence measure under noise heterogeneity. The framework extends to settings with additional covariates, enabling inference on distributional heterogeneity of residual noise across treatment groups. Simulations show improved calibration and power relative to naive plug-in residual methods.

Collaborative analysis of decentralized confidential datasets is important, but direct sharing of original datasets is often restricted by privacy and institutional constraints. Data collaboration (DC) analysis transforms each dataset into privacy-preserving intermediate representations via party-specific obfuscation functions and integrates them into common collaboration representations using an anchor dataset. However, many existing DC analysis methods rely on linear transformations for data obfuscation and integration, which may increase reconstruction risk. Although nonlinear dimensionality reduction can mitigate this risk, conventional linear integration methods cannot accurately align intermediate representations produced by nonlinear transformations. Moreover, existing integration methods mainly minimize discrepancies among parties and do not explicitly incorporate geometric or target-variable information useful for downstream analysis. To overcome these limitations, we first formulate linear kernel integration (LKI) as a linear integration method and then kernelize it to obtain nonlinear kernel integration (NKI). NKI admits a globally optimal solution via kernel ridge regression and an eigenvalue problem. We also introduce graph regularization and a centering constraint so that the target representation can capture geometric and target-variable information useful for downstream analysis. Experiments on image classification tasks demonstrate that NKI improves classification accuracy over existing linear integration methods under nonlinear dimensionality reduction, with further gains from target-variable-aware graph regularization and centering. The results also show that dimensionality reduction choices substantially affect both classification accuracy and reconstruction risk.

We study the adversarial kernel bandit problem, in which the loss at each round is induced by an arbitrary bounded element of a reproducing kernel Hilbert space (RKHS). We propose an exponential-weights algorithm built on a regularized importance-weighted loss estimator, together with an explicit correction term that cancels the bias introduced by the regularization. Our main result bounds the regret by $\widetilde{O}\big(\sqrt{T\, d_*(λ)\,\log|{X}|}\big)$, where $d_*(λ)$ is a widely-adopted notion of effective dimension that captures the complexity of the kernel. Up to logarithmic factors, this matches the known rate achieved in the related stochastic kernel bandit problem. A notable application is the Matérn$(ν,d)$ kernel with smoothness parameter $ν$ on $\mathbb{R}^d$, for which our bound specializes to $\widetilde{O}\big(T^{(ν+d)/(2ν+d)}\big)$, improving over the best-known prior rate of Chatterji et al. [2019] while simultaneously removing the rank-one adversary assumption required by their analysis. Moreover, this rate is the same as the known optimal rate for stochastic kernel bandits, and also matches a lower bound from concurrent work up to a $\log T$ factor.

Conditionally positive definite (CPD) kernels are defined with respect to a function class $\mathcal{F}$. It is well known that such a kernel $K$ is associated with its native space (defined analogously to an RKHS), which in turn gives rise to a learning method -- called conditional kernel ridge regression (conditional KRR) due to its analogy with KRR -- where the estimated regression function is penalized by the square of its native space norm. This method is of interest because it can be viewed as classical linear regression, with features specified by $\mathcal{F}$, followed by the application of standard KRR to the residual (unexplained) component of the target variable. Methods of this type have recently attracted increasing attention. We study the statistical properties of this method by reducing its behavior to that of KRR with another fixed kernel, called the residual kernel. Our main theoretical result shows that such a reduction is indeed possible, at the cost of an additional term in the expected test risk, bounded by $\mathcal{O}(1/\sqrt{N})$, where $N$ is the sample size and the hidden constant depends on the class $\mathcal{F}$ and the input distribution. This reduction enables us to analyze conditional KRR in the case where $K$ is positive definite and $\mathcal{F}$ is given by the first $k$ principal eigenfunctions in the Mercer decomposition of $K$. We also consider the setting where $\mathcal{F}$ consists of $k$ random features from a random feature representation of $K$. It turns out that these two settings are closely related. Both our theoretical analysis and experiments confirm that conditional KRR outperforms standard KRR in these cases whenever the $\mathcal{F}$-component of the regression function is more pronounced than the residual part.

We develop a branched signature kernel solver for linear and nonlinear ordinary differential equations driven by a \emph{single observed trajectory} of a possibly rough forcing signal--a setting common within earthquake engineering, finance, biology, and structural health monitoring, where only one forcing realization is available, and the solver must respect the underlying physical law without an ensemble of realizations. We first introduce a count-sampling construction method to turn the single observation into a hierarchical family of $N+1$ nested training paths on which the branched signature kernel can be evaluated; this allows the signature kernel machinery, originally designed for multi-realization regression problems, to operate on a single-trajectory observation. Then we build a kernel-collocation framework, which places the ansatz either on the highest-order derivative of the solution or on the solution itself. We prove a universal approximation theorem for the branched signature kernel, leveraging the Hairer--Kelly morphism to express branched signature evaluations through geometric signatures of time-extended paths. The offline solver is extended to a streaming Test/Train/Retrain protocol with optional closed-form online updates in both linear and nonlinear cases. Numerical experiments on six benchmarks show accurate, stable predictions across all regimes.

Fast linear algebra in deep learning usually comes with a choice: fixed geometry and exact computation, as in the Fourier transform, or adaptive geometry paid for by dense parameters, random features, or low-rank surrogates. To move beyond this trade-off, we introduce LAPLEX, a class of exact, trainable (phased) Laplace-kernel operators. A LAPLEX layer is a typically full-rank dense matrix, implicitly defined by learnable coordinate anchors, with FFT-like scaling. Consequently, it supports trainable matrix--vector operations at vector dimensions up to $10^9$ on modern GPUs. As a neural layer, it yields compact projections and classification heads interpretable as soft, trainable routing models. The same primitive also serves as an efficient Gram operator, enabling high-dimensional covariance models on flattened images of dimension $3 \cdot 10^6$ that preserve visible spatial structure without imposing convolutional bias. These applications reflect a single principle: dense geometry can be learned without storing a dense matrix, which enables data-adaptive global interactions in regimes where ordinary dense layers are out of reach. In this sense, LAPLEX separates expressivity from storage cost: it behaves like a dense trainable matrix, but is represented and applied through a small structured set of parameters.

The Hilbert-Schmidt Independence Criterion (HSIC) and its joint-independence extension $d\mathrm{HSIC}$ are degenerate $V$-statistics whose data-dependent weighted-$χ^2$ null limits force a permutation calibration that multiplies the per-test cost by the number of permutations, in practice two orders of magnitude. Adapting the recent martingale MMD construction for two-sample testing to the (joint) independence problem, we introduce two studentised statistics whose null distributions are standard normal regardless of the data law, so that a single normal-quantile lookup replaces the permutation step entirely. The first, $m\mathrm{HSIC}$, is a self-normalised lower-triangular sum of the Hadamard product of two empirically centred Gram matrices. Under independence and bounded-fourth-moment kernels it converges to a standard normal. It is consistent against every fixed alternative, and runs at quadratic cost in the sample size without any sample split, matching the biased HSIC $V$-statistic. Our second statistic, $md\mathrm{HSIC}$, achieves finite-sample consistency with a single half-sample split: the centring is estimated on one half and the lower-triangular self-normalised martingale is run on the other, shrinking the conditional-mean residual to a quantity that is exponentially small in $d$, so the statistic is asymptotically standard normal at every fixed number of jointly tested variables, with a per-test cost that grows only linearly in $d$. On synthetic data with per-variable input dimension from $1$ to $500$ and between $2$ and $10$ jointly tested variables, both statistics match the empirical type-I error rate and test power of permutation-calibrated baselines while running $25$ to $60\times$ faster.

Kernel methods are typically formulated under the assumption of exact, noise-free access to the Gram matrix. However, in emerging settings such as quantum machine learning, each kernel entry must be inferred from noisy observations, and its accuracy depends on how a limited measurement budget is allocated. Despite this, existing approaches overwhelmingly rely on uniform allocation, which equalizes estimator variance but ignores the highly non-uniform dependence of kernelized classifiers on the Gram matrix. In this work, we introduce an adaptive measurement-allocation strategy for learning kernelized Support Vector Machines (SVMs) from noisy Bernoulli observations. Our approach combines two complementary principles: (i) geometric sensitivity, capturing how perturbations of individual kernel entries affect the classifier margin, and (ii) active-set instability, quantifying the probability of discrete changes in support-vector membership induced by measurement noise. These signals define a task-aware allocation scheme that concentrates measurements on the most decision-critical regions of the kernel matrix. We provide a theoretical analysis showing that the benefit of adaptive allocation is governed by the heterogeneity of the induced kernel importance structure, leading to distinct regimes in which adaptive or uniform strategies are preferable. Empirical evaluations on synthetic datasets demonstrate that adaptive allocation significantly improves support-vector recovery, margin estimation, and decision-function accuracy under fixed measurement budgets. A dual-coefficient stability criterion further enables early stopping, achieving near-optimal performance while using only a fraction of the measurement cost. Additional experiments on quantum kernels derived from real-world data reveal a regime-dependent behavior aligned with known phenomena such as kernel concentration. Together...

Self-driving laboratories or autonomous experimentation are emerging as transformative platforms for accelerating scientific discovery. Bayesian optimization (BO) is among the most widely used machine learning frameworks for these purposes, but these BO-based frameworks rely on predefined scalar descriptors to guide experimentation. In many situations, the determination of an appropriate scalar descriptor can be challenging, and may fail to capture subtle yet scientifically important phenomena apparent to experts with interdisciplinary insight. To overcome this limitation, here we develop deep-kernel pairwise learning (DKPL), an approach for autonomous microscopy experiments which incorporates human expertise and interdisciplinary scientific knowledge into an active learning loop. Instead of relying on explicit scalar objectives, DKPL enables experts to directly evaluate which experimental output is more promising using interdisciplinary knowledge. DKPL then learns a latent utility function from these expert judgements to guide subsequent autonomous microscopy experiments. We demonstrate DKPL's performance in learning physically meaningful nanoscale structures while effectively prioritizing high-information measurement regions using an experimental model dataset with known ground truth. We further apply DKPL to analyze the character of ferroelectric domain walls, where we find DKPL capable of distinguishing between high and low characteristic domain-wall angles in bismuth ferrite, and able to discover both head-to-head and tail-to-tail domain-wall character in erbium manganite. This development establishes an approach to integrate expert knowledge into autonomous microscopy experiments and demonstrates a pathway toward expert-guided self-driving laboratories capable of addressing scientific problems beyond the limits of scalar-metrics-driven learning.

Kolmogorov-Arnold Networks (KANs) approximate multivariate functions using learnable univariate edge functions, typically parameterized by B-spline bases. Although effective, spline-based implementations can be computationally expensive. A modified version of KANs, called FastKAN, improves efficiency by replacing splines with Gaussian radial basis functions (RBFs), but it relies on a fixed kernel and shape parameter. In this work, we extend the RBF-based KAN framework by introducing a broader family of radial basis kernels and by initializing the kernel shape parameter using leave-one-out cross-validation (LOOCV). To the best of our knowledge, this is the first study that integrates LOOCV-based kernel scale estimation with deep KAN training. We also introduce Matérn and Wendland kernels into the KAN framework for the first time, enabling more flexible basis representations beyond the Gaussian kernel used in FastKAN. The LOOCV estimate provides a data-driven initialization of the kernel scale, which is subsequently refined during network training. The proposed adaptive RBF-KAN is evaluated on several two-dimensional benchmark functions. The results highlight the importance of kernel selection and adaptive shape parameters, with different kernels showing advantages for smooth functions, discontinuities, and oscillatory patterns. Overall, combining LOOCV-based initialization with adaptive kernel learning provides a practical strategy for improving RBF-based KAN models.

Optimal transport provides a powerful framework for comparing measures while respecting the geometry of their support, but comes with an expensive computational cost, hindering its potential application to real world use cases. On manifolds, convolutional algorithms based on the heat kernel have been proposed to alleviate this cost, but their theoretical properties remain largely unexplored. We establish that the heat kernel cost converges to the optimal transport cost as time vanishes in the balanced and unbalanced cases. In the specific case of the 2-sphere $\mathbb{S}^2$, we ensure that the associated Sinkhorn divergences retains the desirable geometric and analytic properties of classical optimal transport discrepancies. Moreover, we leverage the harmonic structure of the sphere to derive a fast Sinkhorn algorithm, requiring only $\mathcal{O}(n)$ memory and $\mathcal{O}(n^{3/2})$ time per iteration, with fully dense GPU-friendly operations. We validate its computational efficiency on synthetic data, and discuss its potential use in the evaluation of global climate models, providing both spatial and seasonal insights into models performances.

Gaussian Process (GP) kernels are central to Bayesian optimization (BO), yet designing effective kernels for high-dimensional problems still relies on extensive manual engineering. Existing automated approaches struggle in high dimensions for two bottlenecks: their kernel search space is limited to additions and multiplications of base kernels, and LLM-based approaches require conditioning on raw observations, which becomes infeasible due to context-length limits and the difficulty of extracting meaningful patterns. We introduce \textbf{Kernel Discovery}, a LLM-driven evolutionary framework for high-dimensional BO that searches a broader kernel space beyond predefined composition rules and does not require conditioning on observations. Motivated by the observation that directly prompting an LLM to generate kernel code yields syntactically varied but functionally identical kernels, we adopt a two-stage approach: an LLM first proposes novel mathematical forms, then a second LLM call converts each form into validated, executable code. We also propose a leave-one-out continuous ranked probability score (LOO-CRPS) as a selection criterion that penalizes overfitted kernels. On five high-dimensional BO benchmarks, our method achieves an average rank of \textbf{1.2 out of 17}, outperforming competitive baselines. We further analyze the discovered kernels to identify which kernels lead to improvements in high-dimensional BO.

Feature learning is widely regarded as the key mechanism distinguishing neural networks from fixed-kernel methods, yet its impact on the induced function space remains poorly understood. In this work, we precisely characterize how the function space spanned by the features of a two-layer neural network evolves during gradient descent training. We prove that, in the high-dimensional proportional regime, after a large gradient step the post-update feature distribution is well approximated by a target-dependent spiked Gaussian covariance. This induces a data-adaptive kernel that reshapes the function space and modifies its spectral structure. Our analysis reveals that feature learning can be interpreted as a distributional transformation in either parameter space or input space, equivalently as the introduction of a target-dependent kernel. In particular, it selectively amplifies eigenvalues aligned with the target direction and mixes leading eigenfunctions, coupling the top radial mode with a target-aligned quadratic harmonic. Overall, our results provide a precise function-space perspective on early-stage feature learning: rather than just rescaling a fixed kernel, gradient descent induces a data-adaptive deformation that preferentially enhances directions aligned with the signal in the data.

Diffusion geometry is a manifold learning framework that uses random walks defined by Markov transition matrices to characterize the geometry of a dataset at multiple scales. We use diffusion geometry for neural representations, incorporating tools from multi-view learning into this field for the first time. Our key technical observation is that a broad class of similarity measures based on representational similarity matrices (RSMs) admits a closed-form equivalent formulation in terms of row-stochastic Markov matrices, opening the door to manipulations from diffusion geometry. As a first application, we develop multi-scale variants of Centered Kernel Alignment and Distance Correlation, which utilise the $t^{th}$ power of the underlying transition matrix to probe the data geometry at adjustable diffusion scales. Going further, we introduce variants of these measures which fuse the Markov matrices of several layers via alternating diffusion into a single operator that captures the network's joint sample geometry, allowing similarity to be computed across multiple layers and shifting the comparison from layer-to-layer to network-to-network. We perform extensive numerical experiments, evaluating our measures on the Representational Similarity (ReSi) benchmark comprising 14 architectures trained on 7 datasets across three different domains. Our methods achieve SoTA results in accuracy and output correlation for both language and vision tasks across different models. We furthermore show SoTA performance on an additional benchmark evaluating on out-of-distribution data.

Estimating an $N \times N$ quantum kernel from circuit fidelities requires $Θ(N^2 S)$ measurement shots, the dominant bottleneck for deployment on near-term hardware. Existing budget-saving methods (Nyström-QKE, ShoFaR, kernel-target alignment) sub-sample \emph{which} entries to measure but allocate shots \emph{uniformly} within their chosen subset, ignoring how much each entry drives the downstream classifier. We close this gap with two contributions. \textbf{First, a complete regime decomposition} for shot-budgeted quantum kernel learning: a principled menu of when each allocator wins. Our method, \emph{AQKA}, dominates the budget-limited regime ($B \lesssim 16 n_{\mathrm{pairs}}$) on sparse-sensitivity KRR, with the gap \emph{growing} from $+8$ to $+25$ pts over uniform as $N$ scales $225{\to}1000$ and reaching $+26$--$32$ pts on an \texttt{ibm_pittsburgh} (156-qubit Heron) hardware kernel; Nyström-QKE wins at saturating budgets on planted-sparse via low-rank reconstruction; ShoFaR is competitive only at extreme low budgets. \textbf{Second, a closed-form pair-level acquisition theory}: $s_{ij}^{\star} \propto |g_{ij}|\sqrt{K_{ij}(1-K_{ij})}$ with explicit gradient $g_{ij}$ for KRR (Lemma1, $|β_iα_j+β_jα_i|\sqrt{K_{ij}(1-K_{ij})}$) and SVM via the envelope theorem ($|η_i^*η_j^*|\sqrt{K_{ij}(1-K_{ij})}$); a \emph{corrected} sparsity-aware Cauchy--Schwarz rate $ρ\le 2m/N$ matching empirics (vs.\ the naive $m^2/N^2$); an explicit-constant plug-in regret bound (Theorem2); and a tighter SVM ceiling $ρ^{\mathrm{SVM}} \le m_{\mathrm{sv}}^2/N^2$. We close with the first multi-seed live online adaptive shot allocation on quantum hardware: $+17.0 \pm 4.8$ pts at $N{=}20$ on \texttt{ibm_aachen} ($3.5σ$, 5 seeds), with the advantage holding at $N{=}30$ at higher budget on \texttt{ibm_berlin} ($+14.0 \pm 8.5$ pts, 5 seeds).