Deep State Space Models (SSMs) reignite physics-grounded compute paradigms, as RNNs could natively be embodied into dynamical systems. This calls for dedicated learning algorithms obeying to core physical principles, with efficient techniques to simulate these systems and guide their design. We propose Recurrent Hamiltonian Echo Learning (RHEL), an algorithm which provably computes loss gradients as finite differences of physical trajectories of non-dissipative, Hamiltonian systems. In ML terms, RHEL only requires three "forward passes" irrespective of model size, without explicit Jacobian computation, nor incurring any variance in the gradient estimation. Motivated by the potential to implement our algorithm in non-digital physical systems, we first introduce RHEL in continuous time and demonstrate its formal equivalence with the continuous adjoint state method.

Variational quantum algorithms (VQAs) are leading strategies to reach practical utilities of near-term quantum devices. However, the no-cloning theorem in quantum mechanics precludes standard backpropagation, leading to prohibitive quantum resource costs when applying VQAs to large-scale tasks. To address this challenge, we reformulate the training dynamics of VQAs as a nonlinear partial differential equation and propose a novel protocol that leverages physics-informed neural networks (PINNs) to model this dynamical system efficiently. Given a small amount of training trajectory data collected from quantum devices, our protocol predicts the parameter updates of VQAs over multiple iterations on the classical side, dramatically reducing quantum resource costs. Through systematic numerical experiments, we demonstrate that our method achieves up to a 30x speedup compared to conventional methods and reduces quantum resource costs by as much as 90% for tasks involving up to 40 qubits, including ground state preparation of different quantum systems, while maintaining competitive accuracy. Our approach complements existing techniques aimed at improving the efficiency of VQAs and further strengthens their potential for practical applications.

In recent years, nonlinear dynamic system identification using artificial neural networks has garnered attention due to its broad potential applications across science and engineering. However, purely data-driven approaches often struggle with extrapolation and may yield physically implausible forecasts. Furthermore, the learned dynamics can exhibit instabilities, making it difficult to apply such models safely and robustly. This article introduces stable port-Hamiltonian neural networks, a machine learning architecture that incorporates physical biases of energy conservation and dissipation while ensuring global Lyapunov stability of the learned dynamics. Through illustrative and real-world examples, we demonstrate that these strong inductive biases facilitate robust learning of stable dynamics from sparse data, while avoiding instability and surpassing purely data-driven approaches in accuracy and physically meaningful generalization. Furthermore, the model's applicability and potential for data-driven surrogate modeling are showcased on multiphysics simulation data.

Variational quantum Eigensolver (VQE) is a leading candidate for harnessing quantum computers to advance quantum chemistry and materials simulations, yet its training efficiency deteriorates rapidly for large Hamiltonians. Two issues underlie this bottleneck: (i) the no-cloning theorem imposes a linear growth in circuit evaluations with the number of parameters per gradient step; and (ii) deeper circuits encounter barren plateaus (BPs), leading to exponentially increasing measurement overheads. To address these challenges, here we propose a deep learning framework, dubbed Titan, which identifies and freezes inactive parameters of a given ansätze at initialization for a specific class of Hamiltonians, reducing the optimization overhead without sacrificing accuracy. The motivation of Titan starts with our empirical findings that a subset of parameters consistently has negligible influence on training dynamics. Its design combines a theoretically grounded data construction strategy, ensuring each training example is informative and BP-resilient, with an adaptive neural architecture that generalizes across ansätze of varying sizes. Across benchmark transverse-field Ising models, Heisenberg models, and multiple molecule systems up to $30$ qubits, Titan achieves up to $3\times$ faster convergence and $40$-$60\%$ fewer circuit evaluations than state-of-the-art baselines, while matching or surpassing their estimation accuracy. By proactively trimming parameter space, Titan lowers hardware demands and offers a scalable path toward utilizing VQE to advance practical quantum chemistry and materials science.

Designing neural networks within a Hamiltonian framework offers a principled way to ensure that conservation laws are respected in physical systems. While promising, these capabilities have been largely limited to discrete, analytically solvable systems. In contrast, many physical phenomena are governed by PDEs, which govern infinite-dimensional fields through Hamiltonian functionals and their functional derivatives. Building on prior work, we represent the Hamiltonian functional as a kernel integral parameterized by a neural field, enabling learnable function-to-scalar mappings and the use of automatic differentiation to calculate functional derivatives. This allows for an extension of Hamiltonian mechanics to neural PDE solvers by predicting a functional and learning in the gradient domain. We show that the resulting Hamiltonian Neural Solver (HNS) can be an effective surrogate model through improved stability and conserving energy-like quantities across 1D and 2DPDEs. This ability to respect conservation laws also allows HNS models to better generalize to longer time horizons or unseen initial conditions.

Density functional theory (DFT) is a fundamental method for simulating quantum chemical properties, but it remains expensive due to the iterative self-consistent field (SCF) process required to solve the Kohn-Sham equations. Recently, deep learning methods are gaining attention as a way to bypass this step by directly predicting the Hamiltonian. However, they rely on deterministic regression and do not consider the highly structured nature of Hamiltonians. In this work, we propose QHFLOW, a high-order equivariant flow matching framework that generates Hamiltonian matrices conditioned on molecular geometry. Flow matching models continuous-time trajectories between simple priors and complex targets, learning the structured distributions over Hamiltonians instead of direct regression. To further incorporate symmetry, we use a neural architecture that predicts SE(3)-equivariant vector fields, improving accuracy and generalization across diverse geometries. To further enhance physical fidelity, we additionally introduce a fine-tuning scheme to align predicted orbital energies with the target. QHFLOW achieves state-of-the-art performance, reducing Hamiltonian error by 73% on MD17 and 53% on QH9 compared to the previous best model. Moreover, we further show that QHFLOW accelerates the DFT process without trading off the solution quality when initializing SCF iterations with the predicted Hamiltonian, significantly reducing the number of iterations and runtime.

Density functional theory (DFT) is a fundamental method for simulating quantum chemical properties, but it remains expensive due to the iterative self-consistent field (SCF) process required to solve the Kohn-Sham equations. Recently, deep learning methods are gaining attention as a way to bypass this step by directly predicting the Hamiltonian. However, they rely on deterministic regression and do not consider the highly structured nature of Hamiltonians. In this work, we propose QHFlow, a high-order equivariant flow matching framework that generates Hamiltonian matrices conditioned on molecular geometry. Flow matching models continuous-time trajectories between simple priors and complex targets, learning the structured distributions over Hamiltonians instead of direct regression. To further incorporate symmetry, we use a neural architecture that predicts SE(3)-equivariant vector fields, improving accuracy and generalization across diverse geometries. To further enhance physical fidelity, we additionally introduce a fine-tuning scheme to align predicted orbital energies with the target. QHFlow achieves state-of-the-art performance, reducing Hamiltonian error by 71% on MD17 and 53% on QH9. Moreover, we further show that QHFlow accelerates the DFT process without trading off the solution quality when initializing SCF iterations with the predicted Hamiltonian, significantly reducing the number of iterations and runtime.

We propose a novel method of understanding disease transformation from a healthy baseline with biomarker-level explainability. By modeling the biomarker covariance matrices of healthy controls and disease states, the perturbation can be individually characterized to accomplish mechanistic explanations of disease trajectories, both at a molecular level and for individual patients. Given a cohort of n patients each measured on p biomarkers, we define the biomarker "Hamiltonian" H = X^T X / n \in R^{p \times p}, where X \in R^{n \times p} is the covariant biomarker matrix. The eigenvectors of H define a set of normal modes of biomarker coordination, and the eigenvalues quantify the energy carried by each mode. In the healthy state, the reference Hamiltonian H_0 governs this structure where disease perturbs H_0 by an additive operator ΔH, thus shifting eigenvalues and rotating eigenvectors in proportion to the severity of pathological disruption. We formalize this framework, derive the spectral change given a disease perturbation, and demonstrate that the projection of a newly diagnosed patient's cumulative biomarker covariance structure onto disease-discriminant eigenmodes constitutes an optimal prognostic statistic for greater precision in disease prognosis. This work serves as a veritable white paper with application across a panoply of disease frameworks from cancer to neurodegenerative disorders.

In this section, we provide a short overview of the definitions relevant to the context of our work. The symmetry of an object is a transformation that leaves some of its properties unchanged.

We show the similarities between our method, Neural ODE, and differentiable physics in Figure 4. All the three approaches have a differentiable system governed by some kinds of differential equations. Our method parametrizes the dynamics using continuous basis functions; Neural ODE uses neural networks; and Differentiable physics describes the dynamics system using physics equations like Newton's Second Law, Navier-Stokes equations. Let Uv(t2,t1) be as defined in Theorem 3.2. Let Lbe defined as (4), and H(v,t) = P jfj(v,t)Hj.