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.
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