A spectral analysis of the Koopman operator, which is an infinite dimensional linear operator on an observable, gives a (modal) description of the global behavior of a nonlinear dynamical system without any explicit prior knowledge of its governing equations. In this paper, we consider a spectral analysis of the Koopman operator in a reproducing kernel Hilbert space (RKHS). We propose a modal decomposition algorithm to perform the analysis using finite-length data sequences generated from a nonlinear system. The algorithm is in essence reduced to the calculation of a set of orthogonal bases for the Krylov matrix in RKHS and the eigendecomposition of the projection of the Koopman operator onto the subspace spanned by the bases. The algorithm returns a decomposition of the dynamics into a finite number of modes, and thus it can be thought of as a feature extraction procedure for a nonlinear dynamical system. Therefore, we further consider applications in machine learning using extracted features with the presented analysis. We illustrate the method on the applications using synthetic and real-world data.

Large language models have achieved remarkable success but remain largely black boxes with poorly understood internal mechanisms. To address this limitation, many researchers have proposed various interpretability methods including mechanistic analysis, probing classifiers, and activation visualization, each providing valuable insights from different perspectives. Building upon this rich landscape of complementary approaches, we introduce CAST (Compositional Analysis via Spectral Tracking), a probe-free framework that contributes a novel perspective by analyzing transformer layer functions through direct transformation matrix estimation and comprehensive spectral analysis. CAST offers complementary insights to existing methods by estimating the realized transformation matrices for each layer using Moore-Penrose pseudoinverse and applying spectral analysis with six interpretable metrics characterizing layer behavior. Our analysis reveals distinct behaviors between encoder-only and decoder-only models, with decoder models exhibiting compression-expansion cycles while encoder models maintain consistent high-rank processing. Kernel analysis further demonstrates functional relationship patterns between layers, with CKA similarity matrices clearly partitioning layers into three phases: feature extraction, compression, and specialization.

Understanding the spectral properties of kernels offers a principled perspective on generalization and representation quality. While deep models achieve state-of-the-art accuracy in molecular property prediction, kernel methods remain widely used for their robustness in low-data regimes and transparent theoretical grounding. Despite extensive studies of kernel spectra in machine learning, systematic spectral analyses of molecular kernels are scarce. In this work, we provide the first comprehensive spectral analysis of kernel ridge regression on the QM9 dataset, molecular fingerprint, pretrained transformer-based, global and local 3D representations across seven molecular properties. Surprisingly, richer spectral features, measured by four different spectral metrics, do not consistently improve accuracy. Pearson correlation tests further reveal that for transformer-based and local 3D representations, spectral richness can even have a negative correlation with performance. We also implement truncated kernels to probe the relationship between spectrum and predictive performance: in many kernels, retaining only the top 2% of eigenvalues recovers nearly all performance, indicating that the leading eigenvalues capture the most informative features. Our results challenge the common heuristic that "richer spectra yield better generalization" and highlight nuanced relationships between representation, kernel features, and predictive performance. Beyond molecular property prediction, these findings inform how kernel and self-supervised learning methods are evaluated in data-limited scientific and real-world tasks.

Self-attention layers have become fundamental building blocks of modern deep neural networks, yet their theoretical understanding remains limited, particularly from the perspective of random matrix theory. In this work, we provide a rigorous analysis of the singular value spectrum of the attention matrix and establish the first Gaussian equivalence result for attention. In a natural regime where the inverse temperature remains of constant order, we show that the singular value distribution of the attention matrix is asymptotically characterized by a tractable linear model. We further demonstrate that the distribution of squared singular values deviates from the Marchenko-Pastur law, which has been believed in previous work. Our proof relies on two key ingredients: precise control of fluctuations in the normalization term and a refined linearization that leverages favorable Taylor expansions of the exponential. This analysis also identifies a threshold for linearization and elucidates why attention, despite not being an entrywise operation, admits a rigorous Gaussian equivalence in this regime.

The Madden-Julian oscillation (MJO) is a planetary-scale, intraseasonal tropical rainfall phenomenon crucial for global weather and climate; however, its dynamics and predictability remain poorly understood. Here, we leverage deep learning (DL) to investigate the sources of MJO predictability, motivated by a central difference in MJO theories: which spatial scales are essential for driving the MJO? We first develop a deep convolutional neural network (DCNN) to forecast the MJO indices (RMM and ROMI). Our model predicts RMM and ROMI up to 21 and 33 days, respectively, achieving skills comparable to leading subseasonal-to-seasonal models such as NCEP. To identify the spatial scales most relevant for MJO forecasting, we conduct spectral analysis of the latent feature space and find that large-scale patterns dominate the learned signals. Additional experiments show that models using only large-scale signals as the input have the same skills as those using all the scales, supporting the large-scale view of the MJO. Meanwhile, we find that small-scale signals remain informative: surprisingly, models using only small-scale input can still produce skillful forecasts up to 1-2 weeks ahead. We show that this is achieved by reconstructing the large-scale envelope of the small-scale activities, which aligns with the multi-scale view of the MJO. Altogether, our findings support that large-scale patterns--whether directly included or reconstructed--may be the primary source of MJO predictability.

We analyze a weighted Frobenius loss for approximating symmetric positive definite matrices in the context of preconditioning iterative solvers. Unlike the standard Frobenius norm, the weighted loss penalizes error components associated with small eigenvalues of the system matrix more strongly. Our analysis reveals that each eigenmode is scaled by the corresponding square of its eigenvalue, and that, under a fixed error budget, the loss is minimized only when the error is confined to the direction of the largest eigenvalue. This provides a rigorous explanation of why minimizing the weighted loss naturally suppresses low-frequency components, which can be a desirable strategy for the conjugate gradient method. The analysis is independent of the specific approximation scheme or sparsity pattern, and applies equally to incomplete factorizations, algebraic updates, and learning-based constructions. Numerical experiments confirm the predictions of the theory, including an illustration where sparse factors are trained by a direct gradient updates to IC(0) factor entries, i.e., no trained neural network model is used.

As machine learning models are increasingly considered for high-stakes domains, effective explanation methods are crucial to ensure that their prediction strategies are transparent to the user. Over the years, numerous metrics have been proposed to assess quality of explanations. However, their practical applicability remains unclear, in particular due to a limited understanding of which specific aspects each metric rewards. In this paper we propose a new framework based on spectral analysis of explanation outcomes to systematically capture the multifaceted properties of different explanation techniques. Our analysis uncovers two distinct factors of explanation quality-stability and target sensitivity-that can be directly observed through spectral decomposition. Experiments on both MNIST and ImageNet show that popular evaluation techniques (e.g., pixel-flipping, entropy) partially capture the trade-offs between these factors. Overall, our framework provides a foundational basis for understanding explanation quality, guiding the development of more reliable techniques for evaluating explanations.

We are interested in the estimation of a rank-one tensor signal when only a portion $\varepsilon$ of its noisy observation is available. We show that the study of this problem can be reduced to that of a random matrix model whose spectral analysis gives access to the reconstruction performance. These results shed light on and specify the loss of performance induced by an artificial reduction of the memory cost of a tensor via the deletion of a random part of its entries.

Delineating the superconducting order parameters is a pivotal task in investigating superconductivity for probing pairing mechanisms, as well as their symmetry and topology. Point-contact Andreev reflection (PCAR) measurement is a simple yet powerful tool for identifying the order parameters. The PCAR spectra exhibit significant variations depending on the type of the order parameter in a superconductor, including its magnitude ($\mathit{\Delta}$), as well as temperature, interfacial quality, Fermi velocity mismatch, and other factors. The information on the order parameter can be obtained by finding the combination of these parameters, generating a theoretical spectrum that fits a measured experimental spectrum. However, due to the complexity of the spectra and the high dimensionality of parameters, extracting the fitting parameters is often time-consuming and labor-intensive. In this study, we employ a convolutional neural network (CNN) algorithm to create models for rapid and automated analysis of PCAR spectra of various superconductors with different pairing symmetries (conventional $s$-wave, chiral $p_x+ip_y$-wave, and $d_{x^2-y^2}$-wave). The training datasets are generated based on the Blonder-Tinkham-Klapwijk (BTK) theory and further modified and augmented by selectively incorporating noise and peaks according to the bias voltages. This approach not only replicates the experimental spectra but also brings the model's attention to important features within the spectra. The optimized models provide fitting parameters for experimentally measured spectra in less than 100 ms per spectrum. Our approaches and findings pave the way for rapid and automated spectral analysis which will help accelerate research on superconductors with complex order parameters.

Measuring representational similarity between neural recordings and computational models is challenging due to constraints on the number of neurons that can be recorded simultaneously. In this work, we investigate how such limitations affect similarity measures, focusing on Canonical Correlation Analysis (CCA) and Centered Kernel Alignment (CKA). Leveraging tools from Random Matrix Theory, we develop a predictive spectral framework for these measures and demonstrate that finite neuron sampling systematically underestimates similarity due to eigenvector delocalization. To overcome this, we introduce a denoising method to infer population-level similarity, enabling accurate analysis even with small neuron samples. Our theory is validated on synthetic and real datasets, offering practical strategies for interpreting neural data under finite sampling constraints.