Spectral Methods

Hessian spectral properties are a standard tool in analysing neural-network training, with eigenvalues linked to sharpness, generalization, and optimization dynamics. Eigenvalues quantify curvature magnitude, while eigenvectors identify which parameters generate that curvature. In this work, we study how the leading Hessian eigenvectors evolve during training and how they affect the learning trajectories. We track the training dynamics of multilayer perceptrons on a classification problem and measure eigenvector dynamics through two complementary statistics: (i) displacement over time, inspired by analyses of glassy systems, and (ii) localization via the inverse participation ratio. The metrics are compared against a random null model of the Hessian induced by the architecture. Our results reveal clear optimizer-dependent behaviour. SGD leads to progressively more stable leading curvature directions, while Adam exhibits substantially stronger reorganization of eigenvectors throughout training. We also observe a localization phenomenon under Adam, where a small subset of parameters contributes disproportionately to the leading curvature directions. These results suggest that Hessian eigenvector dynamics capture key differences in optimizer behaviour and the resulting training trajectories.

We show that for tall matrix parameters, like projection matrices in the MLP layers, the Muon update can have row norms that are arbitrarily non-uniform. This can lead to a self-reinforcing feedback loop whereby neurons receive persistently small updates and eventually do not contribute meaningfully to network outputs. This problem is effectively mitigated by an additional row normalization step, but current methods do this in a way that moves the Muon update geometry away from the polar factor of the momentum matrix, which we find is undesirable. We propose Aurora, an optimizer that enforces row-uniformity of matrix parameter updates while respecting Muon's polar factor geometry. Aurora outperforms Muon in our pre-training experiments and, when combined with existing methods, achieves state-of-the-art performance among spectral optimizers on the optimizer track of the modded-nanoGPT speedrun. Additionally, we find that Aurora's empirical gains over Muon scale with the MLP expansion factor, suggesting that Aurora may allow for effective training of very wide MLP layers.

Molecule generation methods that leverage generative models have been successfully applied to drug discovery. However, they often require extensive pre-training, suffer statistical biases in the training data, and might suffer from limited interpretability of generated chemical structures. In this work, we introduce SpectralMol, an algorithm based on evolutionary computation that processes chemical structures as a compact matrix of Fourier coefficients, projected onto a fixed basis to generate position-wise latent vectors for SELFIES decoding. The NSGA-II algorithm enforces diversity and enable separate objective functions rather than collapsed objectives into a scalar reward. The quality of the algorithm was tested against standardized benchmarks. The results show comparable aggregate benchmark performance with a task-dependent profile: SpectralMol is strongest on several multi-parameter optimization tasks. The same benchmark was used to perform an ablation study to demonstrate the advantages of a structured latent matrix. Finally, method was tested on a realistic ClpP-targeted drug-discovery benchmark, comparing it with the reinforcement-learning-based model under a fixed oracle-call budget. SpectralMol generates more docking hits and more diverse scaffolds while maintaining competitive physicochemical properties. The representation adopted in this work can cleanly separates scaffold-level modifications from localized substructure variations, as the former occur with perturbations of low-frequency Fourier modes and the latter with perturbations of high-frequency Fourier modes. The results support the evidence that frequency-controlled evolutionary dynamics provide an interpretable, efficient, and training-free route to multi-objective molecular design.

Transformer-based models have recently attracted increasing attention for Raman spectral classification. In this study, a transformer-based approach was systematically evaluated using a nested leave-one-replicate-out cross-validation framework and compared with conventional machine-learning pipelines combining PCA or ICA with LDA, SVM, and Random Forest classifiers. A bacterial Raman dataset comprising 5,417 single-cell spectra from six bacterial species and nine independent measurement replicates was used. The transformer consistently achieved the highest classification performance across independent test replicates and significantly outperformed all conventional approaches. Analysis of the learned latent feature space revealed improved class separation compared with PCA- and ICA-based representations. Furthermore, the transformer maintained superior performance when applied directly to raw Raman spectra without preprocessing, demonstrating robust behavior across measurement replicates. These findings highlight the potential of transformer-based models for robust Raman spectral classification and emphasize the importance of replicate-aware validation for realistic model evaluation.

Fourier Neural Operators (FNO) learn solution operators of partial differential equations by parameterizing global convolutions in the complex Fourier domain. For real-valued PDE solutions, the complex FFT carries representational redundancy through conjugate symmetry. We introduce the Hartley Neural Operator (HNO), the exact real-valued mirror of FNO: it replaces the FFT with the purely real Discrete Hartley Transform and learns a single real multiplier per retained spectral mode, with no complex arithmetic. Because the real Hartley spectrum is not halved by conjugate symmetry, HNO retains twice as many frequency corners as FNO but one real weight where FNO carries a complex pair, so the two operators are iso-parametric at equal width and differ only in spectral basis. Our central thesis is that the best basis is a property of the operator. Self-adjoint elliptic operators (Poisson, biharmonic) have real, symmetric Green's functions that the real Hartley multiplier diagonalizes exactly, and HNO is favored there. Time-dependent operators carry phase, from oscillation in the wave equation to transport in advection, Burgers, and Navier-Stokes, which a real diagonal multiplier cannot represent, so FNO is favored there, and increasingly so with the operator's phase content, leaving the phaseless heat equation as the borderline case. Training both operators identically and benchmarking across PDE classes, initial-condition families, and boundary conditions, we find an elliptic-versus-time-dependent split that is monotone in operator phase content and matches the Green's-function theory we develop. Rather than a universal winner, our findings give a predictive rule: match the spectral basis to the symmetry of the solution operator.

Spectral filtering recently delivered substantial pruning for \emph{static} subgraph matching: Laplacian interlacing rejects candidates whose neighborhoods cannot host the query. We study whether such aggregate structural tests can accelerate \emph{continuous} subgraph matching (CSM) over dynamic graphs, and answer in three parts. First, lazily maintained spectral bounds are infeasible exactly where spectral pruning has value: we characterize the tightest safe rule over a formalized perturbation relaxation and show that even it loses essentially all pruning power within four touching updates. Second, exact maintenance is affordable when selective: pruning utility and recomputation cost are anti-correlated across vertices -- hubs provably never prune -- so recomputing small-neighborhood spectra on touch sustains exact local spectra at microseconds per update, complete by construction. Third, integrated into a decoupled CSM benchmark against an identical-minus-spectra control, the tests remove up to $51\%$ of candidates or safely skip up to $47\%$ of update enumerations, yet enumeration intermediates remain unchanged -- beyond the gates' skipped first-level bindings, typically zero -- across two engines, four real graphs, two stream types, and $77$ solved queries; a constructed radius-stratified workload confirms the instrument detects the exception when one exists ($-99.9\%$ intermediates, $748\times$ faster). Aggregate tests accelerate what scales with candidate sets -- construction, list scans -- never adjacency-guided exploration. We distill an intermediate-invariance methodology for evaluating CSM filters and release a reusable dynamic local-spectra index.

Spectral graph neural networks (GNNs) interpret message passing as frequency-selective filtering. While low-order spectral filters are efficient, their limited selectivity often leads to weak attenuation outside the passband, whereas high-order alternatives introduce optimization challenges. We propose DCQ-GNN, a spectral GNN based on a compact bank of adaptive convex--concave quadratic filters. By restricting the filter order to two while explicitly exploiting complementary curvature, DCQ-GNN improves spectral selectivity as quantified by Dirichlet energy and entropy measures without resorting to high-order polynomial expansions. The model fuses filter outputs through a node-adaptive gating mechanism to enable node-wise structure-aware spectral selection. We provide a formal spectral analysis grounded in Dirichlet energy attenuation, von Neumann entropy, and curvature polarity, and derive explicit characterizations of filter behavior across varying levels of homophily and structural perturbations. Extensive benchmarks on 10 datasets show that DCQ-GNN ties for the top average rank (3.0) on heterophilic graphs and obtains the second-best rank (4.2) on homophilic graphs, remaining competitive with representative high-order polynomial spectral filters. Furthermore, under strong structural perturbations, DCQ-GNN exhibits substantially smaller performance degradation compared to both first-order and high-order baselines. These results demonstrate that curvature-aware quadratic banks provide a robust and efficient alternative to high-order spectral models while preserving optimization stability and computational efficiency.

We develop a spectral theory for \emph{normalized corrected GNN propagation}. The object of study is the symmetric normalized adjacency with its degree-stationary component removed, matching the normalization used by standard GCN-style models while isolating the stationary direction most directly tied to oversmoothing. The central theoretical question is whether this corrected normalized operator preserves class-discriminative signal after many propagation layers. Our main result is a high-probability exact-recovery theorem for the binary Contextual Stochastic Block Model after $k=O(\log n)$ propagation steps in the dense polylogarithmic regime $p\ge C\log^B n/n$, for any fixed $B>4$, under explicit graph-signal and feature-SNR conditions. We also establish a multi-class partial recovery theorem showing contraction toward class centers for most nodes. Synthetic and real node-classification experiments are included as empirical checks of the theory's predicted dependence on depth, graph signal, and feature noise.

Higher-order structures are powerful relational modeling tools, yet existing spectral operators decompose the topology into separate ranks, leaving practitioners to fuse the information back to vertices through ad hoc choices. We introduce Collapsed Effective Operators, which condense higher-order degrees of freedom into a single vertex-level operator via Schur complementation of a graded Laplacian. This yields a (generally dense) operator that encodes long-range interactions mediated by topology and is applicable to arbitrary higher-order constructs. We show it preserves positive semi-definiteness with a spectral upper bound relative to the rank-0 Hodge Laplacian, effectively lowering system energy under higher-order connectivity. Empirically, our operator improves spectral clustering, signal smoothing, and enables the inclusion of topological features in neural network architectures via positional encoding. The project page can be found http://circle-group.github.io/research/CollapsedEffectiveOperators

Laser-induced breakdown spectroscopy (LIBS) faces challenges in high-accuracy quantitative measurement under few-shot scenarios due to spectral noise and data scarcity. Traditional preprocessing methods often fail to preserve subtle spectral features or capture nonlinear correlations. This work proposes a standardized processing pipeline integrating diffusion-based denoising, attention-based autoencoder for dimensionality reduction, group shuffling data augmentation, and ordinary least squares regression. The diffusion module employs a 3D UNet architecture to remove spectral noise while preserving essential emission features. The attention-autoencoder captures nonlinear spectral correlations, effectively reducing high-dimensional spectral data to compact latent representations. Group shuffling data augmentation enhances model robustness by creating synthetic samples through feature group permutation. Experimental results on multiple elemental concentrations demonstrate that our Diffusion-DA-AE pipeline achieves superior performance with a mean RMAE of 0.2847, representing 37.7% and 37.6% improvements over baseline autoencoder and traditional PCA-PLS regression, respectively. The framework's effectiveness validates its generalizability and establishes a new benchmark for few-shot LIBS regression.

Nondestructive detection methods, based on vibrational spectroscopy, are vitally important in a wide range of applications including industrial chemistry, pharmacy and national defense. Recently, deep learning has been introduced into vibrational spectroscopy showing great potential. Different from images, text, etc. that offer large labeled data sets, vibrational spectroscopic data is very limited, which requires novel concepts beyond transfer and meta learning. To tackle this, we propose a task-enhanced augmentation network (TeaNet). The key component of TeaNet is a reconstruction module that inputs randomly masked spectra and outputs reconstructed samples that are similar to the original ones, but include additional variations learned from the domain. These augmented samples are used to train the classification model. The reconstruction and prediction parts are trained simultaneously, end-to-end with back-propagation. Results on both synthetic and real-world datasets verified the superiority of the proposed method. In the most difficult synthetic scenarios TeaNet outperformed CNN by 17%. We visualized and analysed the neuron responses of TeaNet and CNN, and found that TeaNet's ability to identify discriminant wavenumbers was excellent compared to CNN. Our approach is general and can be easily adapted to other domains, offering a solution to more accurate and interpretable few-shot learning.

Non-stationary partial differential equations (PDEs) arise throughout scientific computing, where the dominant frequency content and energy distribution can drift over time. While efficient in PDE solving, many spectral neural operators apply a shared spectral response across rollout stages, leading to mismatch with time-varying spectra in non-stationary systems. To address this issue, we propose Time-Frequency Gated Spectral Neural Operator (TF-SNO), a state-adaptive framework with learnable time-frequency gating inside spectral blocks. TF-SNO extracts compact frequency-domain and physical-space statistics from the current state to generate modulation coefficients, enabling the spectral response to evolve with the dynamics. TF-SNO learns temporal variation implicitly from the evolving state without introducing an explicit time dimension or time embedding, keeping the modeling complexity low. We further embed the adaptive operator blocks to accurately capture the multi-scale features, thereby improving long-horizon stability. Experiments on six non-stationary PDE benchmarks in 1D and 2D demonstrate that TF-SNO significantly reduces prediction errors and improves robustness compared to strong baselines, with particularly clear gains in long rollout, suggesting the effectiveness of state-dependent spectral adaptation in modeling non-stationary physical systems.

Singular learning theory characterises the complexity of a deep network through the geometry of its loss singularities. The local learning coefficient (LLC), the standard estimator of Watanabe's real log canonical threshold (RLCT, $λ$), reads this geometry as an integrated Bayesian scalar through SGLD, which needs per-task calibration and $10^4$-$10^6$ forward-backward passes per checkpoint. We introduce Dead-Direction Signatures (DDS), a family of cheap closed-form spectral readings of singular structure: each reads a network's activation matrix or per-sample-gradient Fisher-Gram at a chosen layer, replacing the SGLD posterior chain with spectral linear algebra. The readings rest on a dead-direction framework that predicts a structural correlation between activation- and Fisher-side spectra at any singular minimum, and a rank-multiplicative volume identity that single-eigenvalue monitors cannot produce: the active-volume $\log\det^{+}(G)$ slope counts the dead directions, tracking the rank-deficit $r$ across $r \in \{1,2,3,4\}$ (slope ratios $2.0, 3.1, 4.0$ at $r{=}2,3,4$ against the predicted $2,3,4$), where the smallest eigenvalue is rank-blind. On reduced-rank regression with closed-form $λ$, calibrated LLC recovers $λ$ at $99\%$ mean and the DDS observables rank-track it at the framework-predicted sign; on a non-linear modular-addition transformer DDS separates $d_{\mathrm{model}}$ across eighteen orders of magnitude where calibrated LLC at the protocol budget is rank-flat. Complementary to LLC's integrated posterior reading, DDS gives a directional, layer-local handle on a network's dead directions, read in closed form from its activation and gradient spectra.

Selecting a small, diverse, high-quality subset from a massive pool of candidates is a recurring primitive in modern machine learning -- data curation and coreset selection for training and fine-tuning large models, active-learning batch acquisition, prompt and exemplar selection for in-context learning, retrieval diversification, and experimental design. Determinantal Point Processes (\DPP s) give a principled, well-calibrated notion of diversity for this task, but their \emph{MAP} objective -- pick a size-$k$ subset $S$ maximizing $\logdet(L_S)$ -- is NP-hard, and the standard greedy and sampling algorithms scale superlinearly in the ground-set size $n$. This cost is prohibitive precisely in the data-centric regime where diversity matters most, where $n$ ranges over millions to billions of candidate examples, features, or embeddings. We recast \DPP-MAP as a continuous optimization problem over the Stiefel manifold, and show that its first-order optimality conditions form a \emph{Nonlinear Eigenvalue Problem with eigenvector dependency} (\NEPv) of a previously unstudied form. This \NEPv\ admits a self-consistent field (\SCF) iteration with a spectral-gap-based local contraction guarantee, giving a principled iterative solver where the diversity objective drives an eigenvector-dependent operator. The resulting algorithm, \OurMethod, requires only matrix-vector products with the kernel and runs in time $O\!\big((ndk+nk^2)\,t\big)$ for a small number of iterations $t$, scaling near-linearly in $n$ and integrating directly with low-rank and feature-map kernels common in ML. This paper focuses on the relaxation, solver, and scaling analysis; full real-data benchmarking is left to a planned empirical study.

Graph-based learning methods have become increasingly prominent due to their strong performance across diverse applications. Among these, recent frameworks grounded in diffusion processes provide a unifying perspective that extends traditional graph neural network formulations while addressing limitations of standard message-passing mechanisms. Despite these advances, concerns remain regarding the fairness of such models, as they may propagate or amplify biases present in the data. In this work, we introduce a fairness-aware adaptation of graph-based diffusion by modifying the underlying Laplacian operator. Our approach incorporates multiple complementary transformations, including subspace projections, spectral adjustments, and frequency-based filtering, to mitigate bias-related components. Leveraging the intrinsic smoothing properties of graph diffusion, we provide a principled analysis of the resulting behavior and establish theoretical insights into fairness properties. We evaluate the proposed framework on both synthetic and real-world datasets, demonstrating that it achieves competitive performance while improving fairness metrics with limited additional computational cost.

Laser-induced breakdown spectroscopy (LIBS) quantitative analysis faces critical challenges in wavelength selection due to high-dimensional spectral data and the fundamental trade-off between prediction accuracy and feature efficiency. This paper presents a novel Multi-Adapter PPO framework that transforms wavelength selection into a reinforcement learning problem, leveraging cross-attention mechanisms and multiple specialized adapters to capture complex spectral relationships. Our approach outperforms traditional Particle Swarm Optimization (PSO) by an average of 28.4% in comprehensive score and 45.2% in prediction accuracy across steel and coal datasets. The proposed method demonstrates superior performance in balancing prediction accuracy with feature efficiency, achieving state-of-the-art results in LIBS quantitative analysis while maintaining interpretability and computational efficiency. We released our code and dataset here: https://github.com/Hflying/MAPPO

When small transformers grok modular multiplication, prior work reports that the learned embedding has a "dense" Fourier spectrum requiring all frequencies. This contrasts with modular addition, where only a sparse set of key frequencies suffices. We show this density is an artifact of analyzing in the wrong basis. The natural Fourier transform for multiplication is not the standard additive DFT but the multiplicative character transform, which decomposes functions on the multiplicative group $(\mathbb{Z}/p\mathbb{Z})^*$ into its irreducible representations. Applying this transform to a grokked transformer trained on $a \cdot b \bmod 113$, we find the embedding spectrum becomes highly sparse (Gini coefficient 0.58 vs. 0.07 in the additive basis) with only 4 key frequencies carrying significant energy. Furthermore, 96.9% of MLP neurons are cleanly tuned to a single multiplicative frequency, and neuron activation heatmaps reveal 2D-periodic structure when reordered by the discrete logarithm. These results demonstrate the transformer reduces multiplication to addition in discrete-log space, implementing a "Discrete-Log Clock" algorithm analogous to Nanda et al.'s Clock algorithm for addition. The methodology generalizes: matching the analysis basis to the algebraic structure of the task reveals interpretable structure where standard tools see noise.

While persistent Laplacians (PL) offer a richer geometric representation of data than persistent homology, utilizing their full eigenspectrum for learning tasks is often hampered by high dimensionality and the ``varying length'' problem across different filtration scales. We propose a compact spectral representation that distills the persistent Laplacian into three mathematically grounded invariants: Betti numbers, the spectral gap, and analytic torsion. Across benchmark datasets including MNIST, QM-3D, and SKEMPI WT, we demonstrate that this reduced feature space captures the essential predictive signal of the full spectrum, and in some cases outperforms it, while significantly reducing computational overhead and preventing the noise introduced by higher-frequency eigenvalues. Our results suggest that these invariants provide a principled, fixed-length interface between spectral geometry and topological learning.

Conformal prediction gives prediction intervals with finite-sample coverage when the data are exchangeable. Many time-indexed datasets are not exchangeable. They have seasons, recurring regimes, changing frequencies, or other forms of structured dependence. This paper studies a simple way to use that structure. We propose spectral adaptive conformal prediction, a method that forms weighted conformal quantiles using local spectral similarity and then updates the target miscoverage level online. The spectral weights choose calibration residuals that look relevant to the current test point. The adaptive update corrects the long-run miss rate when uncertainty changes over time. We give an approximate coverage result for the fixed spectral weighted quantile and a deterministic long-run calibration result for the adaptive update. Simulations with recurring regimes and slowly changing frequencies, together with three U.S. real-data examples, show that the hybrid method can improve on fixed spectral weighting, while also showing that spectral weighting must be monitored through effective sample size diagnostics.

Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

Muon is an increasingly widely used optimizer that replaces a gradient $G=USV^\top$ with its polar factor $UV^\top$, thereby flattening the singular spectrum. However, full flattening discards singular-value information that may matter for adaptation. We introduce Muon$^p$, a Muon-style optimizer that instead uses fractional spectral-power updates $US^pV^\top$ for rational $p\in(0,1)$, interpolating between Muon and gradient descent. To make it practical, we prove that fractional spectral powers cannot be computed by any fixed univariate polynomial iteration, and furthermore derive low-degree odd bivariate recurrences that approximate $US^pV^\top$ using only matrix multiplications, preserving Muon's matrix-multiplication-only structure and compute complexity. We show that Muon$^p$ maximizes the linear improvement in loss under the Schatten $q$-norm for $q=1+\frac{1}{p}$. Empirically, Muon$^p$ is especially effective for finetuning: on billion-scale models, Muon$^p$ improves validation perplexity and downstream task performance. We further analyze when Muon$^p$ is less suitable, through the lens of spectral geometry. Our results reveal important insights on when preserving the singular spectrum can bring significant gains, and introduce a principled way to achieve them.

Frequency Modulated Continuous Wave (FMCW) radar systems traditionally rely on Fourier-based methods, such as the Fast Fourier Transform (FFT), to estimate target range and velocity. While computationally efficient, these approaches require storing and processing large blocks of data, which can become a bottleneck in memory-constrained or low-latency applications. In this work, we propose a neuromorphic-inspired signal processing method based on adaptive resonate-and-fire (ARF) neurons formulated as a discrete-time dynamical system. Each neuron dynamically adjusts its internal frequency to match dominant frequency components of the input radar signal, enabling direct estimation of target ranges and velocities without computing the full frequency spectrum. The proposed model operates in a sample-by-sample fashion, resulting in memory requirements that scale with the number of tracked targets rather than the signal length. A feedback mechanism is also introduced to enable multiple neurons to lock on distinct frequency components in multi-target cases. Results on simulated and experimental data demonstrate that the method can successfully track multiple targets. Compared to conventional FFT-based approaches, the proposed method offers reduced memory usage proportional only to the number of tracked targets, making it suitable for resource-constrained and edge-based radar applications.

Learning functional relationships from noisy data is a central problem in scientific inference. Spectral methods approximate unknown functions by expanding them in a basis and estimating the corresponding coefficients from data, but the stability of these coefficients under noise remains poorly understood. Here we study supervised regression with additive label noise using sparse spectral representations across multiple bases and dimensions. We show that noise induces a predictable drift in the learned coefficient vector whose magnitude depends on the effective number of active spectral modes. After whitening the empirical feature geometry, we derive a closed-form expression for the overlap between noisy and noiseless coefficient vectors, revealing a universal degradation curve governed by a single intrinsic noise scale. Numerical experiments across Fourier, Legendre, Bessel, and Haar bases confirm the theoretical prediction. The results demonstrate that spectral learning exhibits a fundamental noise threshold beyond which coefficient estimates become unstable, placing intrinsic limits on recovering functional structure from noisy data.

We propose a spectral-based, unsupervised representation learning framework to derive low-dimensional embeddings for clinical concepts and patients in rare disease cohorts from electronic health records, where data are high-dimensional but sample sizes are limited. To overcome this challenge, we incorporate a knowledge matrix extracted from a broader population that shares a partially overlapping subspace with the rare-disease cohort. Our method departs from existing approaches by relaxing restrictive one-to-one signal-alignment assumptions between the latent data matrix and knowledge matrix, allowing more flexible and realistic forms of structured sharing. We introduce a novel two-step spectral embedding procedure: first, we identify and remove irrelevant components from the knowledge matrix; then, we apply a projection-based method to separately recover shared and heterogeneous components. Simulations and an analysis of a real-world multiple sclerosis cohort show that the proposed method outperforms competing approaches, particularly in challenging scenarios where shared signals are weak and only partially aligned, as is common in rare-disease data.

Spectral methods rely fundamentally on the stability of principal eigenspaces under random perturbations. Classically, this stability is quantified by the Davis-Kahan and Wedin theorems, which bound the eigenspace error using the operator norm of the noise and the relevant spectral gaps. While these worst-case bounds are sharp for arbitrary deterministic perturbations, they can be wasteful in the low-rank signal-plus-random-noise setting, as they fail to capture the fine-grained interaction between the signal geometry and the noise distribution. In this paper, we study the spectral perturbation of signal-plus-noise matrices corrupted by sparse, random noise with an arbitrary, inhomogeneous variance profile. We demonstrate that under heterogeneous noise variances, the empirical eigenvectors suffer a systematic, deterministic geometric bias that is entirely invisible to classical perturbation bounds. By leveraging the Quadratic Vector Equation (QVE) and establishing fine-grained isotropic local laws, we derive near-optimal, non-asymptotic perturbation bounds for the leading eigenspaces in the operator and $2\to\infty$ norms. The bounds separate the usual signal-to-noise contribution, stochastic fluctuations, and structured geometric bias terms determined by the alignment between the signal eigenspaces and the row-wise variance profile.

Muon replaces a matrix gradient $G=UΣV^\top$ by its polar factor $UV^\top$. This keeps the singular directions selected by the gradient, but makes the update spectrum flat. We study the optimization bias created by this operation. Under explicit alignment assumptions, we prove that the polar update is the one-step entropy-maximizing choice among bounded updates that use the gradient singular directions and do not adapt to the current weight spectrum. In an underdetermined regression model, we derive exact singular-value dynamics for continuous-time Muon and identify a measurement-dependent condition under which the normalized spectrum moves toward equal nonzero singular values. This geometry also rules out a common low-rank interpretation: at fixed Frobenius norm, Muon's distinguished state has a flat spectrum, whereas nuclear-norm minimization favors spectral concentration. Controlled matrix-sensing experiments separate the effect from simple gradient rescaling, show that norm-matched gradient descent does not reproduce Muon, and recover the predicted flattening trend across broad ablations. In small NanoGPT pretraining, Muon preserves stable rank, has a broad learning-rate plateau, and improves validation loss relative to AdamW; in a matched small-ViT control, the ranking reverses. The resulting picture is regime-dependent: Muon is not universally superior, but its flat-spectrum bias can help when many spectral directions need to remain active.

We introduce CHIAR-Former (CHIAroscuro Attention-based tRansFormer), an efficient transformer that routes each token to either DCT spectral mixing (O(d log d), sub-quadratic) or full self-attention (O(n^2 d), quadratic in sequence length n) based on per-token spectral entropy H(x) in [0,1], which measures the frequency-domain complexity of each token embedding x. We make three contributions: (1) we discover routing collapse -- a three-operator system collapses to DCT+Attention, revealing the optimal operator subset; (2) we propose a learned task-level MetaRouter g = sigma(Linear(x-bar)) in [0,1], where x-bar is the batch-mean embedding and g soft-blends spectral and identity paths end-to-end; and (3) we demonstrate 35-40% FLOP reduction at 400M parameters with a 3.93 PPL cost on WikiText-103 (Test PPL 27.51 vs. 23.58). Under mixed-dataset training, CHIAR-Former dramatically outperforms full attention on small corpora, confirming the regularisation value of spectral mixing. The MetaRouter stabilises at g ~ 0.22, indicating that at scale the model reaches a robust compute-quality equilibrium: attention layers absorb representational complexity while spectral preprocessing efficiently anchors low-frequency structure.

Classical spectral descriptors such as the Heat Kernel Signature and Wave Kernel Signature are widely used for non-rigid 3D shape retrieval, yet their failure modes remain poorly understood. We present a frequency-scale saliency framework that audits these descriptors by quantifying the retrieval-level contribution of each descriptor scale interval through ablation. We introduce class spectral fingerprints to characterize category-level scale dependence, and show that descriptor similarity between class pairs is substantially correlated with retrieval failure, with a Spearman correlation of 0.479. Experiments on SHREC'11 demonstrate that short scales dominate retrieval performance while long scales are harmful, that HKS and WKS exhibit distinct scale dependence patterns, and that saliency-weighted retrieval improves mAP on hard categories by 0.156, with cross-fold and random-weight controls confirming that the gain is stable and not due to arbitrary reweighting.

Model merging combines several independently fine-tuned experts into a single multi-task model without any training data, reducing the storage, serving, and decentralized-development costs of large foundation models. State-of-the-art merging methods formulate merging as a layer-wise quadratic interference minimization problem. Although this problem admits an exact closed-form pseudoinverse solution, that solution underperforms hundreds of iterations of gradient descent in practice. The iterative loop dominates the cost of the pipeline, yet its effectiveness has remained unexplained. We revisit this regime and show that the iterative solver does not primarily act as an optimizer; rather, it serves as an implicit spectral regularizer for an ill-posed normal equation, where small-eigenvalue directions of the per-layer interference operator amplify proxy noise. Building on this finding, we formalize multi-task model merging as a noisy linear inverse problem and propose a spectral filtering estimator parameterized by a per-direction filter. We instantiate this estimator with SWUDI, a closed-form method that combines a soft exponential filter, which matches the gradient-flow trajectory of iterative descent, with a hard top-K truncation that suppresses noise-amplifying small-eigenvalue directions. Furthermore, we propose SWUDI-A, an adaptive variant that replaces the global rank hyperparameter with per-layer rank rules, further improving robustness across architectures. Both variants share a single symmetric eigendecomposition per linear layer and require no training data or optimizer state. Across four general benchmarks and a multimodal merging benchmark spanning VQA, Geometry, Chart, OCR, Grounding, and modality merging, our proposed spectral solvers match or outperform state-of-the-art merging methods. Crucially, they reduce wall-clock time by 28-72x and peak GPU memory by up to 50%.

Intrinsic methods fill the default toolbox for geometry processing on meshes. Intrinsic operators, in particular the Laplacian, underlie methods that require invariance to isometry and have hence been employed in many algorithms for shape analysis, learning, and editing. However, intrinsic methods are predicated on assumptions that quickly become brittle when working with in-the-wild geometry, where (i) mesh quality is not guaranteed, and (ii) many meshes are modeled with multiple connected components. In such settings, volumetric constructions are better-defined, since restrictions on surface topology can be relaxed. This paper presents a Monte Carlo method for estimating the Dirichlet-to-Neumann (DtN) operator -- a boundary-to-boundary volumetric operator -- and its associated Steklov eigenmodes. We build on recent developments in Monte Carlo geometry processing by casting this boundary operator itself as the subject of estimation. The DtN operator, defined through a volumetric stochastic process, is then generalized to the exterior domain, where it couples disconnected components through the surrounding ambient space. We show that our method is orders of magnitude faster than existing boundary-element approaches for computing Steklov spectra while remaining robust to poor triangulations, high-resolution meshes, and multi-component geometry. To demonstrate this scalability, we compute interior and exterior Steklov eigenspectra for approximately 450,000 shapes from the uncurated Objaverse dataset. We incorporate these operators into Steklov-CLIP, a mesh-based neural network that uses volumetric spectral operators for large-scale contrastive 3D representation learning. The resulting network learns semantically meaningful global and dense shape representations, illustrating that geometrically-principled volumetric operators can be made practical at the scale of modern 3D datasets.