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.

We formulate the first differentiable analog quantum computing framework with specific parameterization design at the analog signal (pulse) level to better exploit near-term quantum devices via variational methods. We further propose a scalable approach to estimate the gradients of quantum dynamics using a forward pass with Monte Carlo sampling, which leads to a quantum stochastic gradient descent algorithm for scalable gradient-based training in our framework. Applying our framework to quantum optimization and control, we observe a significant advantage of differentiable analog quantum computing against SOTAs based on parameterized digital quantum circuits by orders of magnitude.

Algorithm 6 Generating the (non-differentiable) Hamiltonian AIS variational bound. Figure 1 shows the results. The first row shows the results obtained by tuning the pair (,η) and each other parameter individually for different values of K, and the second row shows the results obtained by tuning increasingly more parameters. It can be observed that tuning β and q(z) lead to the largest gains in performance. Figure 4: Tuning more parameters leads to significantly better results.

Physics-informed neural networks (PINNs) offer a unified framework for solving both forward and inverse problems of differential equations, yet their performance and physical consistency strongly depend on how governing laws are incorporated. In this work, we present a systematic comparison of different thermodynamic structure-informed neural networks by incorporating various thermodynamics formulations, including Newtonian, Lagrangian, and Hamiltonian mechanics for conservative systems, as well as the Onsager variational principle and extended irreversible thermodynamics for dissipative systems. Through comprehensive numerical experiments on representative ordinary and partial differential equations, we quantitatively evaluate the impact of these formulations on accuracy, physical consistency, noise robustness, and interpretability. The results show that Newtonian-residual-based PINNs can reconstruct system states but fail to reliably recover key physical and thermodynamic quantities, whereas structure-preserving formulation significantly enhances parameter identification, thermodynamic consistency, and robustness. These findings provide practical guidance for principled design of thermodynamics-consistency model, and lay the groundwork for integrating more general nonequilibrium thermodynamic structures into physics-informed machine learning.

In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Models (DEQs) for predicting Density Functional Theory (DFT) Hamiltonians. The DEQH model inherently captures the self-consistency nature of Hamiltonian, a critical aspect often overlooked by traditional machine learning approaches for Hamiltonian prediction. By employing DEQ within our model architecture, we circumvent the need for DFT calculations during the training phase to introduce the Hamiltonian's self-consistency, thus addressing computational bottlenecks associated with large or complex systems. We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians. When benchmarked on the MD17 and QH9 datasets, DEQHNet, an instantiation of the DEQH framework, has demonstrated a significant improvement in prediction accuracy. Beyond a predictor, the DEQH model is a Hamiltonian solver, in the sense that it uses the fixed-point solving capability of the deep equilibrium model to iteratively solve for the Hamiltonian.

Symmetries have proven useful in machine learning models, improving generalisation and overall performance.

We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians.