Diagonal Multi-omics Integration of Heterogeneous Datasets

In this paper, we consider methods for the diagonal multi-omics integration of heterogeneous datasets. Several approaches to the nature of biological heterogeneity are analyzed and developed to comprehend more clearly the generated differences. Specifically, the extremal trace problems for the coupled Laplacian on sets homeomorphic to the Stiefel manifold embedded in the complex Euclidean space are investigated. The gradient ascent method for the maximization problem is elaborated in the classical terms of functional analysis, which is of significant interest in itself. On this basis, we introduce a novel characteristic of dataset heterogeneity by employing the norm of the difference between the maximum and minimum points.

Newton-Schulz Retraction-Based Inference Enables Hidden Quantum Markov Models to Outperform Classical HMMs

Hidden Markov models (HMMs) are widely used probabilistic models for discrete sequential data but can be limited when hidden dynamics are complex. Hidden quantum Markov models (HQMMs) generalize HMMs by replacing probability vectors with density matrices and stochastic transitions with quantum operations, enabling richer latent representations. However, existing HQMM learning methods have not consistently outperformed Expectation--Maximization (EM)-trained HMMs on data not generated by quantum processes, limiting their practical applicability. We introduce NS-RIS, Newton--Schulz Retraction-based Inference on the Stiefel manifold, a scalable algorithm for learning trace-preserving HQMMs. NS-RIS uses Newton--Schulz orthogonalization to compute a polar-factor search direction while preserving Stiefel-manifold feasibility, avoiding costly matrix decompositions. We further establish a finite-time stationarity guarantee under standard assumptions on smoothness, stochastic gradients, and finite Newton--Schulz accuracy. Empirically, NS-RIS provides the first benchmark evidence that an HQMM can significantly outperform an EM-trained HMM on data not generated by a quantum model. On synthetic HMM-generated benchmarks, NS-RIS outperforms both EM and the state-of-the-art HQMM method COSM, improving the evaluation metric by an average of 38.5% and by up to 50.6%. On a synthetic HQMM benchmark, it improves the test metric over COSM by 18.9% while reducing runtime by 12.0%. On the real-world Splice classification benchmark, NS-RIS also surpasses both EM and COSM in higher-dimensional latent regimes, reducing mean classification error by 17.9% for latent dimension 6 and 14.9% for latent dimension 8 relative to COSM. These results move HQMMs beyond a theoretical generalization of HMMs and establish them as practical and expressive models for scientific sequence data.

Muon on the Stiefel Manifold Admits an Exact Closed-Form Update

We study Muon, a recently proposed matrix-aware optimization method, in the context of the Stiefel manifold. This manifold consists of matrices with orthonormal columns and is ubiquitous in machine learning and scientific computing. Existing extensions of Muon to this manifold rely on heuristic, approximate, or iterative updates with varying computational efficiency. We show that the corresponding Stiefel Muon update admits an exact closed-form solution and use this result to develop Skewon, a practical algorithm for orthogonality-constrained optimization with an efficient implementation. We further establish first-order convergence guarantees for Skewon in the smooth non-convex setting.

Retraction-Free Optimization over the Stiefel Manifold for the LoRA Fine-Tuning

Optimization over the Stiefel manifold plays a significant role in various machine learning tasks. Existing methods either use the retraction operators, requiring costly orthonormalization for large-scale matrices, or employ landing methods that rely on careful step size selection and penalty parameter tuning. To address these challenges, we propose a retraction-free and penalty parameter-free algorithm that directly lands on the manifold. By leveraging the strongly-convex-like property of the quadratic penalty function and the proximal smoothness of the Stiefel manifold, we establish global convergence guarantees with the best-known iteration complexities under both constant and diminishing step sizes. Then, we reformulate the low-rank adaptation (LoRA) fine-tuning problem for large language models as a manifold optimization problem, introducing Manifold-LoRA for geometry-accelerated adaptation. This approach employs the proposed landing technique and a carefully designed step size strategy to accelerate the training process. Numerical experiments on benchmark datasets demonstrate the efficiency and strong downstream performance of the proposed method.

Projection Pursuit CPCANet for Domain Generalization

Domain Generalization (DG) aims to learn representations robust to distribution shifts. Recent geometric alignment methods, such as CPCANet, extract domain-invariant structures through batch-wise Common Principal Component Analysis (CPCA). However, CPCANet suffers from rank-deficient covariance estimation due to the small-sample-size issue in mini-batch training. To address this limitation, we propose Projection Pursuit CPCANet (PP-CPCANet), a covariance-free framework that learns a global orthogonal basis on the Stiefel manifold and jointly optimizes it with network parameters via the Cayley transform. We further introduce a symmetry-breaking detached-median PP dispersion objective to extract common principal components (CPCs) with dense and robust optimization signals. Experiments on four DG benchmarks show that PP-CPCANet achieves SOTA performance while maintaining stable training.

ManifoldFlow: SPD-Relaxed Stiefel Layers with Learnable Singular Spectrum

Orthogonal and Stiefel layers give neural weights exact spectral control, but they also impose a strong modeling constraint: all represented singular values are fixed at one. Many settings that benefit from an orthonormal basis still need direction-dependent attenuation or amplification. We introduce ManifoldFlow, a minimal relaxation of a fixed-spectrum Stiefel layer that keeps the basis on the Stiefel manifold while learning a bounded positive spectrum through W = Q S^{1/2}, with Q^T Q = I and S positive definite. Since W^T W = S, the eigenvalues of S are exactly the squared singular values of the realized weight, making eigenvalue clipping a direct singular-value control mechanism. Across paired sequence, tabular, and image experiments, the learnable SPD spectrum improves the fixed-spectrum Stiefel counterpart in the reported settings where the Stiefel prior is useful, with the largest gains in recurrent language-model projections. Boundary cases in convolutional classifier heads clarify the intended scope: ManifoldFlow is not a universal dense-layer replacement, but a spectrum-learnable Stiefel relaxation for settings where an orthonormal basis is a useful prior. When the basis should be orthonormal, its spectrum need not be frozen. Code available at https://github.com/Hik289/manifold_flow

Directed Graph Topology Inference via Graph Filter Identification

We address the problem of inferring a directed network from nodal measurements generated by linear diffusion dynamics on the sought graph. Observations are modeled as the outputs of a graph convolutional filter, i.e., a polynomial (with unknown coefficients) of a local diffusion graph-shift operator encoding the latent graph topology, excited with an ensemble of independent graph signals with arbitrarily-correlated nodal components. Unlike prior efforts that considered undirected graphs and white signal excitations, here the graph-shift operator and the observations' covariance matrix are not simultaneously diagonalizable. In this challenging context, we first rely on measurements of the output signals along with prior statistical information on the inputs to identify the diffusion filter. Such system identification problem involves solving a system of quadratic matrix equations, which we show is identifiable under spectral-diversity assumptions on the input covariances. For algorithmic purposes we recast it as a smooth quadratic minimization subject to Stiefel manifold constraints. Subsequent identification of the network topology given the graph filter estimate boils down to finding a sparse and structurally admissible shift that commutes with the given filter, thus, forcing the latter to be a polynomial in the sought graph-shift operator. A joint graph filter and topology identification algorithm is also proposed, which alternates between the aforementioned steps in a mutually reinforcing fashion to offer improved sample complexity. Numerical tests corroborate the effectiveness of the proposed algorithms in recovering synthetic digraphs and real-data case studies, and illustrate their potential utility on urban mobility analyses as well as portfolio optimization.

Learned Subspace Compression for Communication-Efficient Pipeline Parallelism

Pipeline parallelism enables training of large language models that exceed single-device memory, yet inter-stage activation communication becomes the dominant bottleneck when trained on low-bandwidth networks. Recent work in this area has proposed using fixed orthogonal projections to compress activations. However, this still results in a significant performance degradation and requires a number of non-standard adaptations to constrain the optimization. A natural alternative is to learn a low rank projection for each pipeline stage, however maintaining the necessary orthogonality of these projectors during training remains a challenge. We present Manifold Aware Projection Learning (MAPL), a method that treats inter-stage compression as a learnable orthogonal projection under explicit Stiefel manifold (orthogonal matrices) constraints. Rather than prescribing a fixed global subspace, MAPL lets each pipeline stage discover and continuously adapt its own task-optimal compression subspace via manifold-constrained steepest descent. To recover token-specific signals at stage boundaries, we introduce per-stage factorized anchor embeddings that allow for full-rank activation reconstruction with negligible communication overhead. We further show that we can incorporate residual vector quantization after projection with a streaming codebook synchronization protocol that amortizes dictionary communication. Across LLaMA models from 150M to 1B parameters we show that MAPL can be easily applied to the existing pipeline and can achieve high compression with neglibile performance degradation with a drastically improved tradeoffs in performance vs. compression compared to Subspace Networks.

A second-order method on the Stiefel manifold via Newton$\unicode{x2013}$Schulz

Retraction-free approaches offer attractive low-cost alternatives to Riemannian methods on the Stiefel manifold, but they are often first-order, which may limit the efficiency under high-accuracy requirements. To this end, we propose a second-order method landing on the Stiefel manifold without invoking retractions, which is proved to enjoy local quadratic (or superlinear for its inexact variant) convergence. The update consists of the sum of (i) a component tangent to the level set of the constraint-defining function that aims to reduce the objective and (ii) a component normal to the same level set that reduces the infeasibility. Specifically, we construct the normal component via Newton$\unicode{x2013}$Schulz, a fixed-point iteration for orthogonalization. Moreover, we establish a geometric connection between the Newton$\unicode{x2013}$Schulz iteration and Stiefel manifolds, in which Newton$\unicode{x2013}$Schulz moves along the normal space. For the tangent component, we formulate a modified Newton equation that incorporates Newton$\unicode{x2013}$Schulz. Numerical experiments on the orthogonal Procrustes problem, principal component analysis, and real-data independent component analysis illustrate that the proposed method performs better than the existing methods.