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SubscribeLearned Perceptive Forward Dynamics Model for Safe and Platform-aware Robotic Navigation
Ensuring safe navigation in complex environments requires accurate real-time traversability assessment and understanding of environmental interactions relative to the robot`s capabilities. Traditional methods, which assume simplified dynamics, often require designing and tuning cost functions to safely guide paths or actions toward the goal. This process is tedious, environment-dependent, and not generalizable. To overcome these issues, we propose a novel learned perceptive Forward Dynamics Model (FDM) that predicts the robot`s future state conditioned on the surrounding geometry and history of proprioceptive measurements, proposing a more scalable, safer, and heuristic-free solution. The FDM is trained on multiple years of simulated navigation experience, including high-risk maneuvers, and real-world interactions to incorporate the full system dynamics beyond rigid body simulation. We integrate our perceptive FDM into a zero-shot Model Predictive Path Integral (MPPI) planning framework, leveraging the learned mapping between actions, future states, and failure probability. This allows for optimizing a simplified cost function, eliminating the need for extensive cost-tuning to ensure safety. On the legged robot ANYmal, the proposed perceptive FDM improves the position estimation by on average 41% over competitive baselines, which translates into a 27% higher navigation success rate in rough simulation environments. Moreover, we demonstrate effective sim-to-real transfer and showcase the benefit of training on synthetic and real data. Code and models are made publicly available under https://github.com/leggedrobotics/fdm.
Free$^2$Guide: Gradient-Free Path Integral Control for Enhancing Text-to-Video Generation with Large Vision-Language Models
Diffusion models have achieved impressive results in generative tasks like text-to-image (T2I) and text-to-video (T2V) synthesis. However, achieving accurate text alignment in T2V generation remains challenging due to the complex temporal dependency across frames. Existing reinforcement learning (RL)-based approaches to enhance text alignment often require differentiable reward functions or are constrained to limited prompts, hindering their scalability and applicability. In this paper, we propose Free^2Guide, a novel gradient-free framework for aligning generated videos with text prompts without requiring additional model training. Leveraging principles from path integral control, Free^2Guide approximates guidance for diffusion models using non-differentiable reward functions, thereby enabling the integration of powerful black-box Large Vision-Language Models (LVLMs) as reward model. Additionally, our framework supports the flexible ensembling of multiple reward models, including large-scale image-based models, to synergistically enhance alignment without incurring substantial computational overhead. We demonstrate that Free^2Guide significantly improves text alignment across various dimensions and enhances the overall quality of generated videos.
Path-Integral Approach to Quantum Acoustics
A path-integral approach to quantum acoustics is developed here. In contrast to the commonly utilized particle perspective, this emerging field brings forth a long neglected but essential wave paradigm for lattice vibrations. Within the coherent state picture, we formulate a non-Markovian, stochastic master equation that captures the exact dynamics of any system with coupling linear in the bath coordinates and nonlinear in the system coordinates. We further demonstrate the capability of the presented master equation by applying the corresponding procedure to the eminent Fr\"ohlich model. In general, we establish a solid foundation for quantum acoustics as a kindred framework to quantum optics, while paving the way for deeper first-principle explorations of non-perturbative system dynamics driven by lattice vibrations.
State-dependent diffusion: thermodynamic consistency and its path integral formulation
The friction coefficient of a particle can depend on its position as it does when the particle is near a wall. We formulate the dynamics of particles with such state-dependent friction coefficients in terms of a general Langevin equation with multiplicative noise, whose evaluation requires the introduction of specific rules. Two common conventions, the Ito and the Stratonovich, provide alternative rules for evaluation of the noise, but other conventions are possible. We show the requirement that a particle's distribution function approach the Boltzmann distribution at long times dictates that a drift term must be added to the Langevin equation. This drift term is proportional to the derivative of the diffusion coefficient times a factor that depends on the convention used to define the multiplicative noise. We explore the consequences of this result in a number examples with spatially varying diffusion coefficients. We also derive path integral representations for arbitrary interpretation of the noise, and use it in a perturbative study of correlations in a simple system.
Learning Feynman integrals from differential equations with neural networks
We present a new approach for evaluating Feynman integrals numerically. We apply the recently-proposed framework of physics-informed deep learning to train neural networks to approximate the solution to the differential equations satisfied by the Feynman integrals. This approach relies neither on a canonical form of the differential equations, which is often a bottleneck for the analytical techniques, nor on the availability of a large dataset, and after training yields essentially instantaneous evaluation times. We provide a proof-of-concept implementation within the PyTorch framework, and apply it to a number of one- and two-loop examples, achieving a mean magnitude of relative difference of around 1% at two loops in the physical phase space with network training times on the order of an hour on a laptop GPU.
Exploring Quantum Spacetime with Topological Data Analysis
In a novel application of the tools of topological data analysis (TDA) to nonperturbative quantum gravity, we introduce a new class of observables that allows us to assess whether quantum spacetime really resembles a ``quantum foam" near the Planck scale. The key idea is to investigate the Betti numbers of coarse-grained path integral histories, regularized in terms of dynamical triangulations, as a function of the coarse-graining scale. In two dimensions our analysis exhibits the well-known fractal structure of Euclidean quantum gravity.
amangkurat: A Python Library for Symplectic Pseudo-Spectral Solution of the Idealized (1+1)D Nonlinear Klein-Gordon Equation
This study introduces amangkurat, an open-source Python library designed for the robust numerical simulation of relativistic scalar field dynamics governed by the nonlinear Klein-Gordon equation in (1+1)D spacetime. The software implements a hybrid computational strategy that couples Fourier pseudo-spectral spatial discretization with a symplectic Størmer-Verlet temporal integrator, ensuring both exponential spatial convergence for smooth solutions and long-term preservation of Hamiltonian structure. To optimize performance, the solver incorporates adaptive timestepping based on Courant-Friedrichs-Lewy (CFL) stability criteria and utilizes Just-In-Time (JIT) compilation for parallelized force computation. The library's capabilities are validated across four canonical physical regimes: dispersive linear wave propagation, static topological kink preservation in phi-fourth theory, integrable breather dynamics in the sine-Gordon model, and non-integrable kink-antikink collisions. Beyond standard numerical validation, this work establishes a multi-faceted analysis framework employing information-theoretic entropy metrics (Shannon, Rényi, and Tsallis), kernel density estimation, and phase space reconstruction to quantify the distinct phenomenological signatures of these regimes. Statistical hypothesis testing confirms that these scenarios represent statistically distinguishable dynamical populations. Benchmarks on standard workstation hardware demonstrate that the implementation achieves high computational efficiency, making it a viable platform for exploratory research and education in nonlinear field theory.
Principal Landau Determinants
We reformulate the Landau analysis of Feynman integrals with the aim of advancing the state of the art in modern particle-physics computations. We contribute new algorithms for computing Landau singularities, using tools from polyhedral geometry and symbolic/numerical elimination. Inspired by the work of Gelfand, Kapranov, and Zelevinsky (GKZ) on generalized Euler integrals, we define the principal Landau determinant of a Feynman diagram. We illustrate with a number of examples that this algebraic formalism allows to compute many components of the Landau singular locus. We adapt the GKZ framework by carefully specializing Euler integrals to Feynman integrals. For instance, ultraviolet and infrared singularities are detected as irreducible components of an incidence variety, which project dominantly to the kinematic space. We compute principal Landau determinants for the infinite families of one-loop and banana diagrams with different mass configurations, and for a range of cutting-edge Standard Model processes. Our algorithms build on the Julia package Landau.jl and are implemented in the new open-source package PLD.jl available at https://mathrepo.mis.mpg.de/PLD/.
Causality and Renormalization in Finite-Time-Path Out-of-Equilibrium φ^3 QFT
Our aim is to contribute to quantum field theory (QFT) formalisms useful for descriptions of short time phenomena, dominant especially in heavy ion collisions. We formulate out-of-equilibrium QFT within the finite-time-path formalism (FTP) and renormalization theory (RT). The potential conflict of FTP and RT is investigated in g phi^3 QFT, by using the retarded/advanced (R/A) basis of Green functions and dimensional renormalization (DR). For example, vertices immediately after (in time) divergent self-energy loops do not conserve energy, as integrals diverge. We "repair" them, while keeping d<4, to obtain energy conservation at those vertices. Already in the S-matrix theory, the renormalized, finite part of Feynman self-energy Sigma_{F}(p_0) does not vanish when |p_0|rightarrowinfty and cannot be split to retarded and advanced parts. In the Glaser--Epstein approach, the causality is repaired in the composite object G_F(p_0)Sigma_{F}(p_0). In the FTP approach, after repairing the vertices, the corresponding composite objects are G_R(p_0)Sigma_{R}(p_0) and Sigma_{A}(p_0)G_A(p_0). In the limit drightarrow 4, one obtains causal QFT. The tadpole contribution splits into diverging and finite parts. The diverging, constant component is eliminated by the renormalization condition langle 0|phi|0rangle =0 of the S-matrix theory. The finite, oscillating energy-nonconserving tadpole contributions vanish in the limit trightarrow infty .
Probability and complex quantum trajectories
It is shown that in the complex trajectory representation of quantum mechanics, the Born's Psi^{\star}Ψprobability density can be obtained from the imaginary part of the velocity field of particles on the real axis. Extending this probability axiom to the complex plane, we first attempt to find a probability density by solving an appropriate conservation equation. The characteristic curves of this conservation equation are found to be the same as the complex paths of particles in the new representation. The boundary condition in this case is that the extended probability density should agree with the quantum probability rule along the real line. For the simple, time-independent, one-dimensional problems worked out here, we find that a conserved probability density can be derived from the velocity field of particles, except in regions where the trajectories were previously suspected to be nonviable. An alternative method to find this probability density in terms of a trajectory integral, which is easier to implement on a computer and useful for single particle solutions, is also presented. Most importantly, we show, by using the complex extension of Schrodinger equation, that the desired conservation equation can be derived from this definition of probability density.
Specializations of partial differential equations for Feynman integrals
Starting from the Mellin-Barnes integral representation of a Feynman integral depending on set of kinematic variables z_i, we derive a system of partial differential equations w.r.t.\ new variables x_j, which parameterize the differentiable constraints z_i=y_i(x_j). In our algorithm, the powers of propagators can be considered as arbitrary parameters. Our algorithm can also be used for the reduction of multiple hypergeometric sums to sums of lower dimension, finding special values and reduction equations of hypergeometric functions in a singular locus of continuous variables, or finding systems of partial differential equations for master integrals with arbitrary powers of propagators. As an illustration, we produce a differential equation of fourth order in one variable for the one-loop two-point Feynman diagram with two different masses and arbitrary propagator powers.
1d-qt-ideal-solver: 1D Idealized Quantum Tunneling Solver with Absorbing Boundaries
We present 1d-qt-ideal-solver, an open-source Python library for simulating one-dimensional quantum tunneling dynamics under idealized coherent conditions. The solver implements the split-operator method with second-order Trotter-Suzuki factorization, utilizing FFT-based spectral differentiation for the kinetic operator and complex absorbing potentials to eliminate boundary reflections. Numba just-in-time compilation achieves performance comparable to compiled languages while maintaining code accessibility. We validate the implementation through two canonical test cases: rectangular barriers modeling field emission through oxide layers and Gaussian barriers approximating scanning tunneling microscopy interactions. Both simulations achieve exceptional numerical fidelity with machine-precision energy conservation over femtosecond-scale propagation. Comparative analysis employing information-theoretic measures and nonparametric hypothesis tests reveals that rectangular barriers exhibit moderately higher transmission coefficients than Gaussian barriers in the over-barrier regime, though Jensen-Shannon divergence analysis indicates modest practical differences between geometries. Phase space analysis confirms complete decoherence when averaged over spatial-temporal domains. The library name reflects its scope: idealized signifies deliberate exclusion of dissipation, environmental coupling, and many-body interactions, limiting applicability to qualitative insights and pedagogical purposes rather than quantitative experimental predictions. Distributed under the MIT License, the library provides a deployable tool for teaching quantum mechanics and preliminary exploration of tunneling dynamics.
Path integrals and deformation quantization:the fermionic case
This thesis addresses a fundamental problem in deformation quantization: the difficulty of calculating the star-exponential, the symbol of the evolution operator, due to convergence issues. Inspired by the formalism that connects the star-exponential with the quantum propagator for bosonic systems, this work develops the analogous extension for the fermionic case. A rigorous method, based on Grassmann variables and coherent states, is constructed to obtain a closed-form expression for the fermionic star-exponential from its associated propagator. As a primary application, a fermionic version of the Feynman-Kac formula is derived within this formalism, allowing for the calculation of the ground state energy directly in phase space. Finally, the method is validated by successfully applying it to the simple and driven harmonic oscillators, where it is demonstrated that a simplified ("naive") approach (with an ad-hoc "remediation") is a valid weak-coupling limit of the rigorous ("meticulous") formalism, thereby providing a new and powerful computational tool for the study of fermionic systems.
Lie Group Decompositions for Equivariant Neural Networks
Invariance and equivariance to geometrical transformations have proven to be very useful inductive biases when training (convolutional) neural network models, especially in the low-data regime. Much work has focused on the case where the symmetry group employed is compact or abelian, or both. Recent work has explored enlarging the class of transformations used to the case of Lie groups, principally through the use of their Lie algebra, as well as the group exponential and logarithm maps. The applicability of such methods to larger transformation groups is limited by the fact that depending on the group of interest G, the exponential map may not be surjective. Further limitations are encountered when G is neither compact nor abelian. Using the structure and geometry of Lie groups and their homogeneous spaces, we present a framework by which it is possible to work with such groups primarily focusing on the Lie groups G = GL^{+}(n, R) and G = SL(n, R), as well as their representation as affine transformations R^{n} rtimes G. Invariant integration as well as a global parametrization is realized by decomposing the `larger` groups into subgroups and submanifolds which can be handled individually. Under this framework, we show how convolution kernels can be parametrized to build models equivariant with respect to affine transformations. We evaluate the robustness and out-of-distribution generalisation capability of our model on the standard affine-invariant benchmark classification task, where we outperform all previous equivariant models as well as all Capsule Network proposals.
Molchanov's Formula and Quantum Walks: A Probabilistic Approach
This paper establishes a robust link between quantum dynamics and classical ones by deriving probabilistic representation for both continuous time and discrete time quantum walks. We first adapt Molchanov formula, originally employed in the study of Schrodinger operators on multidimensional integer lattice, to characterize the evolution of continuous time quantum walks. Extending this framework, we develop a probabilistic method to represent discrete time quantum walks on an infinite integer line, bypassing the locality constraints that typically inhibit direct application of Molchanov formula. The validity of our representation is empirically confirmed through a benchmark analysis of the Hadamard walk, demonstrating high fidelity with traditional unitary evolution. Our results suggest that this probabilistic lens offer a powerful alternative for learning multidimensional quantum walks and provides new analytical pathways for investigating quantum systems via classical stochastic processes.
Folded context condensation in Path Integral formalism for infinite context transformers
This short note is written for rapid communication of long context training and to share the idea of how to train it with low memory usage. In the note, we generalize the attention algorithm and neural network of Generative Pre-Trained Transformers and reinterpret it in Path integral formalism. First, the role of the transformer is understood as the time evolution of the token state and second, it is suggested that the all key-token states in the same time as the query-token can attend to the attention with the query token states. As a result of the repetitive time evolution, it is discussed that the token states in the past sequence meats the token states in the present sequence so that the attention between separated sequences becomes possible for maintaining infinite contextual information just by using low memory for limited size of sequence. For the experiment, the 12 input token window size was taken and one GPU with 24GB memory was used for the pre-training. It was confirmed that more than 150 length context is preserved. The sampling result of the training, the code and the other details will be included in the revised version of this note later.
Six Birds: Foundations of Emergence Calculus
We develop a discipline-agnostic emergence calculus that treats theories as fixed points of idempotent operators acting on descriptions. We show that, once processes are composable but access to the underlying system is mediated by a bounded observational interface, a canonical toolkit of six closure-changing primitives (P1--P6) is unavoidable. The framework unifies order-theoretic closure operators with dynamics-induced endomaps E_{τ,f} built from a Markov kernel, a coarse-graining lens, and a time scale τ. We introduce a computable total-variation idempotence defect for E_{τ,f}; small retention error implies approximate idempotence and yields stable "objects" packaged at the chosen τ within a fixed lens. For directionality, we define an arrow-of-time functional as the path-space KL divergence between forward and time-reversed trajectories and prove it is monotone under coarse-graining (data processing); we also formalize a protocol-trap audit showing that protocol holonomy alone cannot sustain asymmetry without a genuine affinity in the lifted dynamics. Finally, we prove a finite forcing-style counting lemma: relative to a partition-based theory, definable predicate extensions are exponentially rare, giving a clean anti-saturation mechanism for strict ladder climbing.
Information structures and their cohomology
We introduce the category of information structures, whose objects are suitable diagrams of measurable sets that encode the possible outputs of a given family of observables and their mutual relationships of refinement; they serve as mathematical models of contextuality in classical and quantum settings. Each information structure can be regarded as a ringed site with trivial topology; the structure ring is generated by the observables themselves and its multiplication corresponds to joint measurement. We extend Baudot and Bennequin's definition of information cohomology to this setting, as a derived functor in the category of modules over the structure ring, and show explicitly that the bar construction gives a projective resolution in that category, recovering in this way the cochain complexes previously considered in the literature. Finally, we study the particular case of a one-parameter family of coefficients made of functions of probability distributions. The only 1-cocycles are Shannon entropy or Tsallis alpha-entropy, depending on the value of the parameter.
Topological Quantum Compilation Using Mixed-Integer Programming
We introduce the Mixed-Integer Quadratically Constrained Quadratic Programming framework for the quantum compilation problem and apply it in the context of topological quantum computing. In this setting, quantum gates are realized by sequences of elementary braids of quasiparticles with exotic fractional statistics in certain two-dimensional topological condensed matter systems, described by effective topological quantum field theories. We specifically focus on a non-semisimple version of topological field theory, which provides a foundation for an extended theory of Ising anyons and which has recently been shown by Iulianelli et al., Nature Communications {\bf 16}, 6408 (2025), to permit universal quantum computation. While the proofs of this pioneering result are existential in nature, the mixed integer programming provides an approach to explicitly construct quantum gates in topological systems. We demonstrate this by focusing specifically on the entangling controlled-NOT operation, and its local equivalence class, using braiding operations in the non-semisimple Ising system. This illustrates the utility of the Mixed-Integer Quadratically Constrained Quadratic Programming for topological quantum compilation.
Transport meets Variational Inference: Controlled Monte Carlo Diffusions
Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the Controlled Monte Carlo Diffusion sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{\"o}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.
Solving physics-based initial value problems with unsupervised machine learning
Initial value problems -- a system of ordinary differential equations and corresponding initial conditions -- can be used to describe many physical phenomena including those arise in classical mechanics. We have developed a novel approach to solve physics-based initial value problems using unsupervised machine learning. We propose a deep learning framework that models the dynamics of a variety of mechanical systems through neural networks. Our framework is flexible, allowing us to solve non-linear, coupled, and chaotic dynamical systems. We demonstrate the effectiveness of our approach on systems including a free particle, a particle in a gravitational field, a classical pendulum, and the H\'enon--Heiles system (a pair of coupled harmonic oscillators with a non-linear perturbation, used in celestial mechanics). Our results show that deep neural networks can successfully approximate solutions to these problems, producing trajectories which conserve physical properties such as energy and those with stationary action. We note that probabilistic activation functions, as defined in this paper, are required to learn any solutions of initial value problems in their strictest sense, and we introduce coupled neural networks to learn solutions of coupled systems.
A Stochastic Thermodynamics Approach to Price Impact and Round-Trip Arbitrage: Theory and Empirical Implications
This paper develops a comprehensive theoretical framework that imports concepts from stochastic thermodynamics to model price impact and characterize the feasibility of round-trip arbitrage in financial markets. A trading cycle is treated as a non-equilibrium thermodynamic process, where price impact represents dissipative work and market noise plays the role of thermal fluctuations. The paper proves a Financial Second Law: under general convex impact functionals, any round-trip trading strategy yields non-positive expected profit. This structural constraint is complemented by a fluctuation theorem that bounds the probability of profitable cycles in terms of dissipated work and market volatility. The framework introduces a statistical ensemble of trading strategies governed by a Gibbs measure, leading to a free energy decomposition that connects expected cost, strategy entropy, and a market temperature parameter. The framework provides rigorous, testable inequalities linking microstructural impact to macroscopic no-arbitrage conditions, offering a novel physics-inspired perspective on market efficiency. The paper derives explicit analytical results for prototypical trading strategies and discusses empirical validation protocols.
Variational Formulation of Local Molecular Field Theory
In this note, we show that the Local Molecular Field theory of Weeks et. al. can be re-derived as an extremum problem for an approximate Helmholtz free energy. Using the resulting free energy as a classical, fluid density functional yields an implicit solvent method identical in form to the Molecular Density Functional theory of Borgis et. al., but with an explicit formula for the 'ideal' free energy term. This new expression for the ideal free energy term can be computed from all-atom molecular dynamics of a solvent with only short-range interactions. The key hypothesis required to make the theory valid is that all smooth (and hence long-range) energy functions obey Gaussian statistics. This is essentially a random phase approximation for perturbations from a short-range only, 'reference,' fluid. This single hypothesis is enough to prove that the self-consistent LMF procedure minimizes a novel density functional whose 'ideal' free energy is the molecular system under a specific, reference Hamiltonian, as opposed to the non-interacting gas of conventional density functionals. Implementation of this new functional into existing software should be straightforward and robust.
pyhgf: A neural network library for predictive coding
Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.
A Comparative Study of Quantum Optimization Techniques for Solving Combinatorial Optimization Benchmark Problems
Quantum optimization holds promise for addressing classically intractable combinatorial problems, yet a standardized framework for benchmarking its performance, particularly in terms of solution quality, computational speed, and scalability is still lacking. In this work, we introduce a comprehensive benchmarking framework designed to systematically evaluate a range of quantum optimization techniques against well-established NP-hard combinatorial problems. Our framework focuses on key problem classes, including the Multi-Dimensional Knapsack Problem (MDKP), Maximum Independent Set (MIS), Quadratic Assignment Problem (QAP), and Market Share Problem (MSP). Our study evaluates gate-based quantum approaches, including the Variational Quantum Eigensolver (VQE) and its CVaR-enhanced variant, alongside advanced quantum algorithms such as the Quantum Approximate Optimization Algorithm (QAOA) and its extensions. To address resource constraints, we incorporate qubit compression techniques like Pauli Correlation Encoding (PCE) and Quantum Random Access Optimization (QRAO). Experimental results, obtained from simulated quantum environments and classical solvers, provide key insights into feasibility, optimality gaps, and scalability. Our findings highlight both the promise and current limitations of quantum optimization, offering a structured pathway for future research and practical applications in quantum-enhanced decision-making.
The Free Energy Principle for Perception and Action: A Deep Learning Perspective
The free energy principle, and its corollary active inference, constitute a bio-inspired theory that assumes biological agents act to remain in a restricted set of preferred states of the world, i.e., they minimize their free energy. Under this principle, biological agents learn a generative model of the world and plan actions in the future that will maintain the agent in an homeostatic state that satisfies its preferences. This framework lends itself to being realized in silico, as it comprehends important aspects that make it computationally affordable, such as variational inference and amortized planning. In this work, we investigate the tool of deep learning to design and realize artificial agents based on active inference, presenting a deep-learning oriented presentation of the free energy principle, surveying works that are relevant in both machine learning and active inference areas, and discussing the design choices that are involved in the implementation process. This manuscript probes newer perspectives for the active inference framework, grounding its theoretical aspects into more pragmatic affairs, offering a practical guide to active inference newcomers and a starting point for deep learning practitioners that would like to investigate implementations of the free energy principle.
Generative Latent Space Dynamics of Electron Density
Modeling the time-dependent evolution of electron density is essential for understanding quantum mechanical behaviors of condensed matter and enabling predictive simulations in spectroscopy, photochemistry, and ultrafast science. Yet, while machine learning methods have advanced static density prediction, modeling its spatiotemporal dynamics remains largely unexplored. In this work, we introduce a generative framework that combines a 3D convolutional autoencoder with a latent diffusion model (LDM) to learn electron density trajectories from ab-initio molecular dynamics (AIMD) simulations. Our method encodes electron densities into a compact latent space and predicts their future states by sampling from the learned conditional distribution, enabling stable long-horizon rollouts without drift or collapse. To preserve statistical fidelity, we incorporate a scaled Jensen-Shannon divergence regularization that aligns generated and reference density distributions. On AIMD trajectories of liquid lithium at 800 K, our model accurately captures both the spatial correlations and the log-normal-like statistical structure of the density. The proposed framework has the potential to accelerate the simulation of quantum dynamics and overcome key challenges faced by current spatiotemporal machine learning methods as surrogates of quantum mechanical simulators.
A Periodic Bayesian Flow for Material Generation
Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song et al., 2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., ~100x speedup 10 v.s. 2000 steps network forwards) compared with previous diffusion-based methods on MP-20 dataset. Code is available at https://github.com/wu-han-lin/CrysBFN.
Categorical Schrödinger Bridge Matching
The Schr\"odinger Bridge (SB) is a powerful framework for solving generative modeling tasks such as unpaired domain translation. Most SB-related research focuses on continuous data space R^{D} and leaves open theoretical and algorithmic questions about applying SB methods to discrete data, e.g, on finite spaces S^{D}. Notable examples of such sets S are codebooks of vector-quantized (VQ) representations of modern autoencoders, tokens in texts, categories of atoms in molecules, etc. In this paper, we provide a theoretical and algorithmic foundation for solving SB in discrete spaces using the recently introduced Iterative Markovian Fitting (IMF) procedure. Specifically, we theoretically justify the convergence of discrete-time IMF (D-IMF) to SB in discrete spaces. This enables us to develop a practical computational algorithm for SB which we call Categorical Schr\"odinger Bridge Matching (CSBM). We show the performance of CSBM via a series of experiments with synthetic data and VQ representations of images.
What type of inference is planning?
Multiple types of inference are available for probabilistic graphical models, e.g., marginal, maximum-a-posteriori, and even marginal maximum-a-posteriori. Which one do researchers mean when they talk about ``planning as inference''? There is no consistency in the literature, different types are used, and their ability to do planning is further entangled with specific approximations or additional constraints. In this work we use the variational framework to show that, just like all commonly used types of inference correspond to different weightings of the entropy terms in the variational problem, planning corresponds exactly to a different set of weights. This means that all the tricks of variational inference are readily applicable to planning. We develop an analogue of loopy belief propagation that allows us to perform approximate planning in factored-state Markov decisions processes without incurring intractability due to the exponentially large state space. The variational perspective shows that the previous types of inference for planning are only adequate in environments with low stochasticity, and allows us to characterize each type by its own merits, disentangling the type of inference from the additional approximations that its practical use requires. We validate these results empirically on synthetic MDPs and tasks posed in the International Planning Competition.
QINNs: Quantum-Informed Neural Networks
Classical deep neural networks can learn rich multi-particle correlations in collider data, but their inductive biases are rarely anchored in physics structure. We propose quantum-informed neural networks (QINNs), a general framework that brings quantum information concepts and quantum observables into purely classical models. While the framework is broad, in this paper, we study one concrete realisation that encodes each particle as a qubit and uses the Quantum Fisher Information Matrix (QFIM) as a compact, basis-independent summary of particle correlations. Using jet tagging as a case study, QFIMs act as lightweight embeddings in graph neural networks, increasing model expressivity and plasticity. The QFIM reveals distinct patterns for QCD and hadronic top jets that align with physical expectations. Thus, QINNs offer a practical, interpretable, and scalable route to quantum-informed analyses, that is, tomography, of particle collisions, particularly by enhancing well-established deep learning approaches.
Generating Molecular Conformer Fields
In this paper we tackle the problem of generating conformers of a molecule in 3D space given its molecular graph. We parameterize these conformers as continuous functions that map elements from the molecular graph to points in 3D space. We then formulate the problem of learning to generate conformers as learning a distribution over these functions using a diffusion generative model, called Molecular Conformer Fields (MCF). Our approach is simple and scalable, and achieves state-of-the-art performance on challenging molecular conformer generation benchmarks while making no assumptions about the explicit structure of molecules (e.g. modeling torsional angles). MCF represents an advance in extending diffusion models to handle complex scientific problems in a conceptually simple, scalable and effective manner.
On Kinetic Optimal Probability Paths for Generative Models
Recent successful generative models are trained by fitting a neural network to an a-priori defined tractable probability density path taking noise to training examples. In this paper we investigate the space of Gaussian probability paths, which includes diffusion paths as an instance, and look for an optimal member in some useful sense. In particular, minimizing the Kinetic Energy (KE) of a path is known to make particles' trajectories simple, hence easier to sample, and empirically improve performance in terms of likelihood of unseen data and sample generation quality. We investigate Kinetic Optimal (KO) Gaussian paths and offer the following observations: (i) We show the KE takes a simplified form on the space of Gaussian paths, where the data is incorporated only through a single, one dimensional scalar function, called the data separation function. (ii) We characterize the KO solutions with a one dimensional ODE. (iii) We approximate data-dependent KO paths by approximating the data separation function and minimizing the KE. (iv) We prove that the data separation function converges to 1 in the general case of arbitrary normalized dataset consisting of n samples in d dimension as n/drightarrow 0. A consequence of this result is that the Conditional Optimal Transport (Cond-OT) path becomes kinetic optimal as n/drightarrow 0. We further support this theory with empirical experiments on ImageNet.
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design
Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.
Deep Learning Meets Sparse Regularization: A Signal Processing Perspective
Deep learning has been wildly successful in practice and most state-of-the-art machine learning methods are based on neural networks. Lacking, however, is a rigorous mathematical theory that adequately explains the amazing performance of deep neural networks. In this article, we present a relatively new mathematical framework that provides the beginning of a deeper understanding of deep learning. This framework precisely characterizes the functional properties of neural networks that are trained to fit to data. The key mathematical tools which support this framework include transform-domain sparse regularization, the Radon transform of computed tomography, and approximation theory, which are all techniques deeply rooted in signal processing. This framework explains the effect of weight decay regularization in neural network training, the use of skip connections and low-rank weight matrices in network architectures, the role of sparsity in neural networks, and explains why neural networks can perform well in high-dimensional problems.
Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations
SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks in which CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single shared parameter set without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS/tree/main/OpenMol/TDN{https://github.com/divelab/AIRS/}).
Cauchy activation function and XNet
We have developed a novel activation function, named the Cauchy Activation Function. This function is derived from the Cauchy Integral Theorem in complex analysis and is specifically tailored for problems requiring high precision. This innovation has led to the creation of a new class of neural networks, which we call (Comple)XNet, or simply XNet. We will demonstrate that XNet is particularly effective for high-dimensional challenges such as image classification and solving Partial Differential Equations (PDEs). Our evaluations show that XNet significantly outperforms established benchmarks like MNIST and CIFAR-10 in computer vision, and offers substantial advantages over Physics-Informed Neural Networks (PINNs) in both low-dimensional and high-dimensional PDE scenarios.
Spacetime Neural Network for High Dimensional Quantum Dynamics
We develop a spacetime neural network method with second order optimization for solving quantum dynamics from the high dimensional Schr\"{o}dinger equation. In contrast to the standard iterative first order optimization and the time-dependent variational principle, our approach utilizes the implicit mid-point method and generates the solution for all spatial and temporal values simultaneously after optimization. We demonstrate the method in the Schr\"{o}dinger equation with a self-normalized autoregressive spacetime neural network construction. Future explorations for solving different high dimensional differential equations are discussed.
Entering the Era of Discrete Diffusion Models: A Benchmark for Schrödinger Bridges and Entropic Optimal Transport
The Entropic Optimal Transport (EOT) problem and its dynamic counterpart, the Schrödinger bridge (SB) problem, play an important role in modern machine learning, linking generative modeling with optimal transport theory. While recent advances in discrete diffusion and flow models have sparked growing interest in applying SB methods to discrete domains, there is still no reliable way to evaluate how well these methods actually solve the underlying problem. We address this challenge by introducing a benchmark for SB on discrete spaces. Our construction yields pairs of probability distributions with analytically known SB solutions, enabling rigorous evaluation. As a byproduct of building this benchmark, we obtain two new SB algorithms, DLightSB and DLightSB-M, and additionally extend prior related work to construct the α-CSBM algorithm. We demonstrate the utility of our benchmark by evaluating both existing and new solvers in high-dimensional discrete settings. This work provides the first step toward proper evaluation of SB methods on discrete spaces, paving the way for more reproducible future studies.
Simulation of integrated nonlinear quantum optics: from nonlinear interferometer to temporal walk-off compensator
Nonlinear quantum photonics serves as a cornerstone in photonic quantum technologies, such as universal quantum computing and quantum communications. The emergence of integrated photonics platform not only offers the advantage of large-scale manufacturing but also provides a variety of engineering methods. Given the complexity of integrated photonics engineering, a comprehensive simulation framework is essential to fully harness the potential of the platform. In this context, we introduce a nonlinear quantum photonics simulation framework which can accurately model a variety of features such as adiabatic waveguide, material anisotropy, linear optics components, photon losses, and detectors. Furthermore, utilizing the framework, we have developed a device scheme, chip-scale temporal walk-off compensation, that is useful for various quantum information processing tasks. Applying the simulation framework, we show that the proposed device scheme can enhance the squeezing parameter of photon-pair sources and the conversion efficiency of quantum frequency converters without relying on higher pump power.
Energy-guided Entropic Neural Optimal Transport
Energy-based models (EBMs) are known in the Machine Learning community for decades. Since the seminal works devoted to EBMs dating back to the noughties, there have been a lot of efficient methods which solve the generative modelling problem by means of energy potentials (unnormalized likelihood functions). In contrast, the realm of Optimal Transport (OT) and, in particular, neural OT solvers is much less explored and limited by few recent works (excluding WGAN-based approaches which utilize OT as a loss function and do not model OT maps themselves). In our work, we bridge the gap between EBMs and Entropy-regularized OT. We present a novel methodology which allows utilizing the recent developments and technical improvements of the former in order to enrich the latter. From the theoretical perspective, we prove generalization bounds for our technique. In practice, we validate its applicability in toy 2D and image domains. To showcase the scalability, we empower our method with a pre-trained StyleGAN and apply it to high-res AFHQ 512times 512 unpaired I2I translation. For simplicity, we choose simple short- and long-run EBMs as a backbone of our Energy-guided Entropic OT approach, leaving the application of more sophisticated EBMs for future research. Our code is available at: https://github.com/PetrMokrov/Energy-guided-Entropic-OT
MLMC: Machine Learning Monte Carlo for Lattice Gauge Theory
We present a trainable framework for efficiently generating gauge configurations, and discuss ongoing work in this direction. In particular, we consider the problem of sampling configurations from a 4D SU(3) lattice gauge theory, and consider a generalized leapfrog integrator in the molecular dynamics update that can be trained to improve sampling efficiency. Code is available online at https://github.com/saforem2/l2hmc-qcd.
Let the Quantum Creep In: Designing Quantum Neural Network Models by Gradually Swapping Out Classical Components
Artificial Intelligence (AI), with its multiplier effect and wide applications in multiple areas, could potentially be an important application of quantum computing. Since modern AI systems are often built on neural networks, the design of quantum neural networks becomes a key challenge in integrating quantum computing into AI. To provide a more fine-grained characterisation of the impact of quantum components on the performance of neural networks, we propose a framework where classical neural network layers are gradually replaced by quantum layers that have the same type of input and output while keeping the flow of information between layers unchanged, different from most current research in quantum neural network, which favours an end-to-end quantum model. We start with a simple three-layer classical neural network without any normalisation layers or activation functions, and gradually change the classical layers to the corresponding quantum versions. We conduct numerical experiments on image classification datasets such as the MNIST, FashionMNIST and CIFAR-10 datasets to demonstrate the change of performance brought by the systematic introduction of quantum components. Through this framework, our research sheds new light on the design of future quantum neural network models where it could be more favourable to search for methods and frameworks that harness the advantages from both the classical and quantum worlds.
First principles simulations of dense hydrogen
Accurate knowledge of the properties of hydrogen at high compression is crucial for astrophysics (e.g. planetary and stellar interiors, brown dwarfs, atmosphere of compact stars) and laboratory experiments, including inertial confinement fusion. There exists experimental data for the equation of state, conductivity, and Thomson scattering spectra. However, the analysis of the measurements at extreme pressures and temperatures typically involves additional model assumptions, which makes it difficult to assess the accuracy of the experimental data. rigorously. On the other hand, theory and modeling have produced extensive collections of data. They originate from a very large variety of models and simulations including path integral Monte Carlo (PIMC) simulations, density functional theory (DFT), chemical models, machine-learned models, and combinations thereof. At the same time, each of these methods has fundamental limitations (fermion sign problem in PIMC, approximate exchange-correlation functionals of DFT, inconsistent interaction energy contributions in chemical models, etc.), so for some parameter ranges accurate predictions are difficult. Recently, a number of breakthroughs in first principle PIMC and DFT simulations were achieved which are discussed in this review. Here we use these results to benchmark different simulation methods. We present an update of the hydrogen phase diagram at high pressures, the expected phase transitions, and thermodynamic properties including the equation of state and momentum distribution. Furthermore, we discuss available dynamic results for warm dense hydrogen, including the conductivity, dynamic structure factor, plasmon dispersion, imaginary-time structure, and density response functions. We conclude by outlining strategies to combine different simulations to achieve accurate theoretical predictions.
nabla^2DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials
Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called nabla^2DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level (omegaB97X-D/def2-SVP) for each conformation. Moreover, nabla^2DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.
Solving a Machine Learning Regression Problem Based on the Theory of Random Functions
This paper studies a machine learning regression problem as a multivariate approximation problem using the framework of the theory of random functions. An ab initio derivation of a regression method is proposed, starting from postulates of indifference. It is shown that if a probability measure on an infinite-dimensional function space possesses natural symmetries (invariance under translation, rotation, scaling, and Gaussianity), then the entire solution scheme, including the kernel form, the type of regularization, and the noise parameterization, follows analytically from these postulates. The resulting kernel coincides with a generalized polyharmonic spline; however, unlike existing approaches, it is not chosen empirically but arises as a consequence of the indifference principle. This result provides a theoretical foundation for a broad class of smoothing and interpolation methods, demonstrating their optimality in the absence of a priori information.
SETOL: A Semi-Empirical Theory of (Deep) Learning
We present a SemiEmpirical Theory of Learning (SETOL) that explains the remarkable performance of State-Of-The-Art (SOTA) Neural Networks (NNs). We provide a formal explanation of the origin of the fundamental quantities in the phenomenological theory of Heavy-Tailed Self-Regularization (HTSR): the heavy-tailed power-law layer quality metrics, alpha and alpha-hat. In prior work, these metrics have been shown to predict trends in the test accuracies of pretrained SOTA NN models, importantly, without needing access to either testing or training data. Our SETOL uses techniques from statistical mechanics as well as advanced methods from random matrix theory and quantum chemistry. The derivation suggests new mathematical preconditions for ideal learning, including a new metric, ERG, which is equivalent to applying a single step of the Wilson Exact Renormalization Group. We test the assumptions and predictions of SETOL on a simple 3-layer multilayer perceptron (MLP), demonstrating excellent agreement with the key theoretical assumptions. For SOTA NN models, we show how to estimate the individual layer qualities of a trained NN by simply computing the empirical spectral density (ESD) of the layer weight matrices and plugging this ESD into our SETOL formulas. Notably, we examine the performance of the HTSR alpha and the SETOL ERG layer quality metrics, and find that they align remarkably well, both on our MLP and on SOTA NNs.
Kolmogorov--Arnold networks in molecular dynamics
We explore the integration of Kolmogorov Networks (KANs) into molecular dynamics (MD) simulations to improve interatomic potentials. We propose that widely used potentials, such as the Lennard-Jones (LJ) potential, the embedded atom model (EAM), and artificial neural network (ANN) potentials, can be interpreted within the KAN framework. Specifically, we demonstrate that the descriptors for ANN potentials, typically constructed using polynomials, can be redefined using KAN's non-linear functions. By employing linear or cubic spline interpolations for these KAN functions, we show that the computational cost of evaluating ANN potentials and their derivatives is reduced.
Depthwise Hyperparameter Transfer in Residual Networks: Dynamics and Scaling Limit
The cost of hyperparameter tuning in deep learning has been rising with model sizes, prompting practitioners to find new tuning methods using a proxy of smaller networks. One such proposal uses muP parameterized networks, where the optimal hyperparameters for small width networks transfer to networks with arbitrarily large width. However, in this scheme, hyperparameters do not transfer across depths. As a remedy, we study residual networks with a residual branch scale of 1/text{depth} in combination with the muP parameterization. We provide experiments demonstrating that residual architectures including convolutional ResNets and Vision Transformers trained with this parameterization exhibit transfer of optimal hyperparameters across width and depth on CIFAR-10 and ImageNet. Furthermore, our empirical findings are supported and motivated by theory. Using recent developments in the dynamical mean field theory (DMFT) description of neural network learning dynamics, we show that this parameterization of ResNets admits a well-defined feature learning joint infinite-width and infinite-depth limit and show convergence of finite-size network dynamics towards this limit.
Generative Modeling with Phase Stochastic Bridges
Diffusion models (DMs) represent state-of-the-art generative models for continuous inputs. DMs work by constructing a Stochastic Differential Equation (SDE) in the input space (ie, position space), and using a neural network to reverse it. In this work, we introduce a novel generative modeling framework grounded in phase space dynamics, where a phase space is defined as {an augmented space encompassing both position and velocity.} Leveraging insights from Stochastic Optimal Control, we construct a path measure in the phase space that enables efficient sampling. {In contrast to DMs, our framework demonstrates the capability to generate realistic data points at an early stage of dynamics propagation.} This early prediction sets the stage for efficient data generation by leveraging additional velocity information along the trajectory. On standard image generation benchmarks, our model yields favorable performance over baselines in the regime of small Number of Function Evaluations (NFEs). Furthermore, our approach rivals the performance of diffusion models equipped with efficient sampling techniques, underscoring its potential as a new tool generative modeling.
MeLM, a generative pretrained language modeling framework that solves forward and inverse mechanics problems
We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.
Grad DFT: a software library for machine learning enhanced density functional theory
Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.
QTRAJ 1.0: A Lindblad equation solver for heavy-quarkonium dynamics
We introduce an open-source package called QTraj that solves the Lindblad equation for heavy-quarkonium dynamics using the quantum trajectories algorithm. The package allows users to simulate the suppression of heavy-quarkonium states using externally-supplied input from 3+1D hydrodynamics simulations. The code uses a split-step pseudo-spectral method for updating the wave-function between jumps, which is implemented using the open-source multi-threaded FFTW3 package. This allows one to have manifestly unitary evolution when using real-valued potentials. In this paper, we provide detailed documentation of QTraj 1.0, installation instructions, and present various tests and benchmarks of the code.
Adapting Quantum Machine Learning for Energy Dissociation of Bonds
Accurate prediction of bond dissociation energies (BDEs) underpins mechanistic insight and the rational design of molecules and materials. We present a systematic, reproducible benchmark comparing quantum and classical machine learning models for BDE prediction using a chemically curated feature set encompassing atomic properties (atomic numbers, hybridization), bond characteristics (bond order, type), and local environmental descriptors. Our quantum framework, implemented in Qiskit Aer on six qubits, employs ZZFeatureMap encodings with variational ansatz (RealAmplitudes) across multiple architectures Variational Quantum Regressors (VQR), Quantum Support Vector Regressors (QSVR), Quantum Neural Networks (QNN), Quantum Convolutional Neural Networks (QCNN), and Quantum Random Forests (QRF). These are rigorously benchmarked against strong classical baselines, including Support Vector Regression (SVR), Random Forests (RF), and Multi-Layer Perceptrons (MLP). Comprehensive evaluation spanning absolute and relative error metrics, threshold accuracies, and error distributions shows that top-performing quantum models (QCNN, QRF) match the predictive accuracy and robustness of classical ensembles and deep networks, particularly within the chemically prevalent mid-range BDE regime. These findings establish a transparent baseline for quantum-enhanced molecular property prediction and outline a practical foundation for advancing quantum computational chemistry toward near chemical accuracy.
Fast and Accurate Prediction of Material Properties with Three-Body Tight-Binding Model for the Periodic Table
Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.
Out of equilibrium Phase Diagram of the Quantum Random Energy Model
In this paper we study the out-of-equilibrium phase diagram of the quantum version of Derrida's Random Energy Model, which is the simplest model of mean-field spin glasses. We interpret its corresponding quantum dynamics in Fock space as a one-particle problem in very high dimension to which we apply different theoretical methods tailored for high-dimensional lattices: the Forward-Scattering Approximation, a mapping to the Rosenzweig-Porter model, and the cavity method. Our results indicate the existence of two transition lines and three distinct dynamical phases: a completely many-body localized phase at low energy, a fully ergodic phase at high energy, and a multifractal "bad metal" phase at intermediate energy. In the latter, eigenfunctions occupy a diverging volume, yet an exponentially vanishing fraction of the total Hilbert space. We discuss the limitations of our approximations and the relationship with previous studies.
Multi-Fidelity Physics-Informed Neural Networks with Bayesian Uncertainty Quantification and Adaptive Residual Learning for Efficient Solution of Parametric Partial Differential Equations
Physics-informed neural networks (PINNs) have emerged as a powerful paradigm for solving partial differential equations (PDEs) by embedding physical laws directly into neural network training. However, solving high-fidelity PDEs remains computationally prohibitive, particularly for parametric systems requiring multiple evaluations across varying parameter configurations. This paper presents MF-BPINN, a novel multi-fidelity framework that synergistically combines physics-informed neural networks with Bayesian uncertainty quantification and adaptive residual learning. Our approach leverages abundant low-fidelity simulations alongside sparse high-fidelity data through a hierarchical neural architecture that learns nonlinear correlations across fidelity levels. We introduce an adaptive residual network with learnable gating mechanisms that dynamically balances linear and nonlinear fidelity discrepancies. Furthermore, we develop a rigorous Bayesian framework employing Hamiltonian Monte Carlo.
Efficient Integrators for Diffusion Generative Models
Diffusion models suffer from slow sample generation at inference time. Therefore, developing a principled framework for fast deterministic/stochastic sampling for a broader class of diffusion models is a promising direction. We propose two complementary frameworks for accelerating sample generation in pre-trained models: Conjugate Integrators and Splitting Integrators. Conjugate integrators generalize DDIM, mapping the reverse diffusion dynamics to a more amenable space for sampling. In contrast, splitting-based integrators, commonly used in molecular dynamics, reduce the numerical simulation error by cleverly alternating between numerical updates involving the data and auxiliary variables. After extensively studying these methods empirically and theoretically, we present a hybrid method that leads to the best-reported performance for diffusion models in augmented spaces. Applied to Phase Space Langevin Diffusion [Pandey & Mandt, 2023] on CIFAR-10, our deterministic and stochastic samplers achieve FID scores of 2.11 and 2.36 in only 100 network function evaluations (NFE) as compared to 2.57 and 2.63 for the best-performing baselines, respectively. Our code and model checkpoints will be made publicly available at https://github.com/mandt-lab/PSLD.
Matrix approach to generalized ensemble theory
We provide a concise framework for generalized ensemble theory through a matrix-based approach. By introducing an observation matrix, any discrete probability distribution, including those for non-equilibrium steady states, can be expressed as a generalized Boltzmann distribution, with observables and conjugate variables as the basis and coordinates in a linear space. In this framework, we identify the minimal sufficient statistics required for inferring the Boltzmann distribution. Furthermore, we show that the Hadamard and Vandermonde matrices are suitable observation matrices for spin systems and random walks. In master equation systems, the probability flux observation matrix facilitates the identification of detailed balance violations. Our findings provide a new approach to developing generalized ensemble theory for non-equilibrium steady-state systems.
Graph Generation with Diffusion Mixture
Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.
Improving thermal state preparation of Sachdev-Ye-Kitaev model with reinforcement learning on quantum hardware
The Sachdev-Ye-Kitaev (SYK) model, known for its strong quantum correlations and chaotic behavior, serves as a key platform for quantum gravity studies. However, variationally preparing thermal states on near-term quantum processors for large systems (N>12, where N is the number of Majorana fermions) presents a significant challenge due to the rapid growth in the complexity of parameterized quantum circuits. This paper addresses this challenge by integrating reinforcement learning (RL) with convolutional neural networks, employing an iterative approach to optimize the quantum circuit and its parameters. The refinement process is guided by a composite reward signal derived from entropy and the expectation values of the SYK Hamiltonian. This approach reduces the number of CNOT gates by two orders of magnitude for systems Ngeq12 compared to traditional methods like first-order Trotterization. We demonstrate the effectiveness of the RL framework in both noiseless and noisy quantum hardware environments, maintaining high accuracy in thermal state preparation. This work advances a scalable, RL-based framework with applications for quantum gravity studies and out-of-time-ordered thermal correlators computation in quantum many-body systems on near-term quantum hardware. The code is available at https://github.com/Aqasch/solving_SYK_model_with_RL.
Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.
Quantum Monte Carlo simulations in the restricted Hilbert space of Rydberg atom arrays
Rydberg atom arrays have emerged as a powerful platform to simulate a number of exotic quantum ground states and phase transitions. To verify these capabilities numerically, we develop a versatile quantum Monte Carlo sampling technique which operates in the reduced Hilbert space generated by enforcing the constraint of a Rydberg blockade. We use the framework of stochastic series expansion and show that in the restricted space, the configuration space of operator strings can be understood as a hard rod gas in d+1 dimensions. We use this mapping to develop cluster algorithms which can be visualized as various non-local movements of rods. We study the efficiency of each of our updates individually and collectively. To elucidate the utility of the algorithm, we show that it can efficiently generate the phase diagram of a Rydberg atom array, to temperatures much smaller than all energy scales involved, on a Kagom\'e link lattice. This is of broad interest as the presence of a Z_2 spin liquid has been hypothesized recently.
Latent Field Discovery In Interacting Dynamical Systems With Neural Fields
Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.
The role of quantum information in thermodynamics --- a topical review
This topical review article gives an overview of the interplay between quantum information theory and thermodynamics of quantum systems. We focus on several trending topics including the foundations of statistical mechanics, resource theories, entanglement in thermodynamic settings, fluctuation theorems and thermal machines. This is not a comprehensive review of the diverse field of quantum thermodynamics; rather, it is a convenient entry point for the thermo-curious information theorist. Furthermore this review should facilitate the unification and understanding of different interdisciplinary approaches emerging in research groups around the world.
Manifold Diffusion Fields
We present Manifold Diffusion Fields (MDF), an approach to learn generative models of continuous functions defined over Riemannian manifolds. Leveraging insights from spectral geometry analysis, we define an intrinsic coordinate system on the manifold via the eigen-functions of the Laplace-Beltrami Operator. MDF represents functions using an explicit parametrization formed by a set of multiple input-output pairs. Our approach allows to sample continuous functions on manifolds and is invariant with respect to rigid and isometric transformations of the manifold. Empirical results on several datasets and manifolds show that MDF can capture distributions of such functions with better diversity and fidelity than previous approaches.
Force-Free Molecular Dynamics Through Autoregressive Equivariant Networks
Molecular dynamics (MD) simulations play a crucial role in scientific research. Yet their computational cost often limits the timescales and system sizes that can be explored. Most data-driven efforts have been focused on reducing the computational cost of accurate interatomic forces required for solving the equations of motion. Despite their success, however, these machine learning interatomic potentials (MLIPs) are still bound to small time-steps. In this work, we introduce TrajCast, a transferable and data-efficient framework based on autoregressive equivariant message passing networks that directly updates atomic positions and velocities lifting the constraints imposed by traditional numerical integration. We benchmark our framework across various systems, including a small molecule, crystalline material, and bulk liquid, demonstrating excellent agreement with reference MD simulations for structural, dynamical, and energetic properties. Depending on the system, TrajCast allows for forecast intervals up to 30times larger than traditional MD time-steps, generating over 15 ns of trajectory data per day for a solid with more than 4,000 atoms. By enabling efficient large-scale simulations over extended timescales, TrajCast can accelerate materials discovery and explore physical phenomena beyond the reach of traditional simulations and experiments. An open-source implementation of TrajCast is accessible under https://github.com/IBM/trajcast.
Uncertainty quantification in a mechanical submodel driven by a Wasserstein-GAN
The analysis of parametric and non-parametric uncertainties of very large dynamical systems requires the construction of a stochastic model of said system. Linear approaches relying on random matrix theory and principal componant analysis can be used when systems undergo low-frequency vibrations. In the case of fast dynamics and wave propagation, we investigate a random generator of boundary conditions for fast submodels by using machine learning. We show that the use of non-linear techniques in machine learning and data-driven methods is highly relevant. Physics-informed neural networks is a possible choice for a data-driven method to replace linear modal analysis. An architecture that support a random component is necessary for the construction of the stochastic model of the physical system for non-parametric uncertainties, since the goal is to learn the underlying probabilistic distribution of uncertainty in the data. Generative Adversarial Networks (GANs) are suited for such applications, where the Wasserstein-GAN with gradient penalty variant offers improved convergence results for our problem. The objective of our approach is to train a GAN on data from a finite element method code (Fenics) so as to extract stochastic boundary conditions for faster finite element predictions on a submodel. The submodel and the training data have both the same geometrical support. It is a zone of interest for uncertainty quantification and relevant to engineering purposes. In the exploitation phase, the framework can be viewed as a randomized and parametrized simulation generator on the submodel, which can be used as a Monte Carlo estimator.
Probabilistic Digital Twin for Misspecified Structural Dynamical Systems via Latent Force Modeling and Bayesian Neural Networks
This work presents a probabilistic digital twin framework for response prediction in dynamical systems governed by misspecified physics. The approach integrates Gaussian Process Latent Force Models (GPLFM) and Bayesian Neural Networks (BNNs) to enable end-to-end uncertainty-aware inference and prediction. In the diagnosis phase, model-form errors (MFEs) are treated as latent input forces to a nominal linear dynamical system and jointly estimated with system states using GPLFM from sensor measurements. A BNN is then trained on posterior samples to learn a probabilistic nonlinear mapping from system states to MFEs, while capturing diagnostic uncertainty. For prognosis, this mapping is used to generate pseudo-measurements, enabling state prediction via Kalman filtering. The framework allows for systematic propagation of uncertainty from diagnosis to prediction, a key capability for trustworthy digital twins. The framework is demonstrated using four nonlinear examples: a single degree of freedom (DOF) oscillator, a multi-DOF system, and two established benchmarks -- the Bouc-Wen hysteretic system and the Silverbox experimental dataset -- highlighting its predictive accuracy and robustness to model misspecification.
MODNet -- accurate and interpretable property predictions for limited materials datasets by feature selection and joint-learning
In order to make accurate predictions of material properties, current machine-learning approaches generally require large amounts of data, which are often not available in practice. In this work, an all-round framework is presented which relies on a feedforward neural network, the selection of physically-meaningful features and, when applicable, joint-learning. Next to being faster in terms of training time, this approach is shown to outperform current graph-network models on small datasets. In particular, the vibrational entropy at 305 K of crystals is predicted with a mean absolute test error of 0.009 meV/K/atom (four times lower than previous studies). Furthermore, joint-learning reduces the test error compared to single-target learning and enables the prediction of multiple properties at once, such as temperature functions. Finally, the selection algorithm highlights the most important features and thus helps understanding the underlying physics.
Quantum Thermalization via Travelling Waves
Isolated quantum many-body systems which thermalize under their own dynamics are expected to act as their own thermal baths, thereby bringing their local subsystems to thermal equilibrium. Here we show that the infinite-dimensional limit of a quantum lattice model, as described by Dynamical Mean-Field theory (DMFT), provides a natural framework to understand this self-consistent thermalization process. Using the Fermi-Hubbard model as working example, we demonstrate that the emergence of a self-consistent bath thermalising the system is characterized by a sharp thermalization front, moving balistically and separating the initial condition from the long-time thermal fixed point. We characterize the full DMFT dynamics through an effective temperature for which we derive a travelling-wave equation of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) type. This equation allows to predict the asymptotic shape of the front and its velocity, which match perfectly the full DMFT numerics. Our results provide a new angle to understand the onset of quantum thermalisation in closed isolated systems.
Fast, Expressive SE(n) Equivariant Networks through Weight-Sharing in Position-Orientation Space
Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.
ADAPT: Lightweight, Long-Range Machine Learning Force Fields Without Graphs
Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.
Physics-informed Reduced Order Modeling of Time-dependent PDEs via Differentiable Solvers
Reduced-order modeling (ROM) of time-dependent and parameterized differential equations aims to accelerate the simulation of complex high-dimensional systems by learning a compact latent manifold representation that captures the characteristics of the solution fields and their time-dependent dynamics. Although high-fidelity numerical solvers generate the training datasets, they have thus far been excluded from the training process, causing the learned latent dynamics to drift away from the discretized governing physics. This mismatch often limits generalization and forecasting capabilities. In this work, we propose Physics-informed ROM (Φ-ROM) by incorporating differentiable PDE solvers into the training procedure. Specifically, the latent space dynamics and its dependence on PDE parameters are shaped directly by the governing physics encoded in the solver, ensuring a strong correspondence between the full and reduced systems. Our model outperforms state-of-the-art data-driven ROMs and other physics-informed strategies by accurately generalizing to new dynamics arising from unseen parameters, enabling long-term forecasting beyond the training horizon, maintaining continuity in both time and space, and reducing the data cost. Furthermore, Φ-ROM learns to recover and forecast the solution fields even when trained or evaluated with sparse and irregular observations of the fields, providing a flexible framework for field reconstruction and data assimilation. We demonstrate the framework's robustness across various PDE solvers and highlight its broad applicability by providing an open-source JAX implementation that is readily extensible to other PDE systems and differentiable solvers, available at https://phi-rom.github.io.
Autoregressive Transformer Neural Network for Simulating Open Quantum Systems via a Probabilistic Formulation
The theory of open quantum systems lays the foundations for a substantial part of modern research in quantum science and engineering. Rooted in the dimensionality of their extended Hilbert spaces, the high computational complexity of simulating open quantum systems calls for the development of strategies to approximate their dynamics. In this paper, we present an approach for tackling open quantum system dynamics. Using an exact probabilistic formulation of quantum physics based on positive operator-valued measure (POVM), we compactly represent quantum states with autoregressive transformer neural networks; such networks bring significant algorithmic flexibility due to efficient exact sampling and tractable density. We further introduce the concept of String States to partially restore the symmetry of the autoregressive transformer neural network and improve the description of local correlations. Efficient algorithms have been developed to simulate the dynamics of the Liouvillian superoperator using a forward-backward trapezoid method and find the steady state via a variational formulation. Our approach is benchmarked on prototypical one and two-dimensional systems, finding results which closely track the exact solution and achieve higher accuracy than alternative approaches based on using Markov chain Monte Carlo to sample restricted Boltzmann machines. Our work provides general methods for understanding quantum dynamics in various contexts, as well as techniques for solving high-dimensional probabilistic differential equations in classical setups.
Improved sampling via learned diffusions
Recently, a series of papers proposed deep learning-based approaches to sample from unnormalized target densities using controlled diffusion processes. In this work, we identify these approaches as special cases of the Schr\"odinger bridge problem, seeking the most likely stochastic evolution between a given prior distribution and the specified target. We further generalize this framework by introducing a variational formulation based on divergences between path space measures of time-reversed diffusion processes. This abstract perspective leads to practical losses that can be optimized by gradient-based algorithms and includes previous objectives as special cases. At the same time, it allows us to consider divergences other than the reverse Kullback-Leibler divergence that is known to suffer from mode collapse. In particular, we propose the so-called log-variance loss, which exhibits favorable numerical properties and leads to significantly improved performance across all considered approaches.
Flexible MOF Generation with Torsion-Aware Flow Matching
Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.
Old Quantum Mechanics by Bohr and Sommerfeld from a Modern Perspective
We review Bohr's atomic model and its extension by Sommerfeld from a mathematical perspective of wave mechanics. The derivation of quantization rules and energy levels is revisited using semiclassical methods. Sommerfeld-type integrals are evaluated by elementary techniques, and connections with the Schr\"{o}dinger and Dirac equations are established. Historical developments and key transitions from classical to quantum theory are discussed to clarify the structure and significance of the old quantum mechanics.
Path Choice Matters for Clear Attribution in Path Methods
Rigorousness and clarity are both essential for interpretations of DNNs to engender human trust. Path methods are commonly employed to generate rigorous attributions that satisfy three axioms. However, the meaning of attributions remains ambiguous due to distinct path choices. To address the ambiguity, we introduce Concentration Principle, which centrally allocates high attributions to indispensable features, thereby endowing aesthetic and sparsity. We then present SAMP, a model-agnostic interpreter, which efficiently searches the near-optimal path from a pre-defined set of manipulation paths. Moreover, we propose the infinitesimal constraint (IC) and momentum strategy (MS) to improve the rigorousness and optimality. Visualizations show that SAMP can precisely reveal DNNs by pinpointing salient image pixels. We also perform quantitative experiments and observe that our method significantly outperforms the counterparts. Code: https://github.com/zbr17/SAMP.
Dense Hebbian neural networks: a replica symmetric picture of unsupervised learning
We consider dense, associative neural-networks trained with no supervision and we investigate their computational capabilities analytically, via a statistical-mechanics approach, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as the quality and quantity of the training dataset and the network storage, valid in the limit of large network size and structureless datasets. Moreover, we establish a bridge between macroscopic observables standardly used in statistical mechanics and loss functions typically used in the machine learning. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate neural networks in general.
Control flow in active inference systems
Living systems face both environmental complexity and limited access to free-energy resources. Survival under these conditions requires a control system that can activate, or deploy, available perception and action resources in a context specific way. We show here that when systems are described as executing active inference driven by the free-energy principle (and hence can be considered Bayesian prediction-error minimizers), their control flow systems can always be represented as tensor networks (TNs). We show how TNs as control systems can be implmented within the general framework of quantum topological neural networks, and discuss the implications of these results for modeling biological systems at multiple scales.
Radiating Love: adiabatic tidal fluxes and modes up to next-to-next-to-leading post-Newtonian order
We present the analytic evaluation of the gravitational energy and of the angular momentum flux with tidal effects for inspiraling compact binaries, at next-to-next-to-leading post-Newtoian (2PN) order, within the effective field theory diagrammatic approach. We first compute the stress-energy tensor for a binary system, that requires the evaluation of two-point Feynman integrals, up to two loops. Then, we extract the multipole moments of the system, which we present for generic orbits in center-of-mass coordinates, and which are needed for the evaluation of the total gravitational energy and the angular momentum flux, for generic orbits. Finally, we provide the expression of gauge invariant quantities such as the fluxes, and the mode amplitudes and phase of the emitted gravitational wave, for circular orbits. Our findings are useful to update earlier theoretical studies as well as related phenomenological analyses, and waveform models
Optimizing AI Reasoning: A Hamiltonian Dynamics Approach to Multi-Hop Question Answering
This paper introduces an innovative approach to analyzing and improving multi-hop reasoning in AI systems by drawing inspiration from Hamiltonian mechanics. We propose a novel framework that maps reasoning chains in embedding spaces to Hamiltonian systems, allowing us to leverage powerful analytical tools from classical physics. Our method defines a Hamiltonian function that balances the progression of reasoning (kinetic energy) against the relevance to the question at hand (potential energy). Using this framework, we analyze a large dataset of reasoning chains from a multi-hop question-answering task, revealing intriguing patterns that distinguish valid from invalid reasoning. We show that valid reasoning chains have lower Hamiltonian energy and move in ways that make the best trade-off between getting more information and answering the right question. Furthermore, we demonstrate the application of this framework to steer the creation of more efficient reasoning algorithms within AI systems. Our results not only provide new insights into the nature of valid reasoning but also open up exciting possibilities for physics-inspired approaches to understanding and improving artificial intelligence.
Solving Key Challenges in Collider Physics with Foundation Models
Foundation Models are neural networks that are capable of simultaneously solving many problems. Large Language Foundation Models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new Foundation Model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet Foundation Models beyond proof-of-principle studies and into the toolkit of practitioners.
Quantum Multi-Model Fitting
Geometric model fitting is a challenging but fundamental computer vision problem. Recently, quantum optimization has been shown to enhance robust fitting for the case of a single model, while leaving the question of multi-model fitting open. In response to this challenge, this paper shows that the latter case can significantly benefit from quantum hardware and proposes the first quantum approach to multi-model fitting (MMF). We formulate MMF as a problem that can be efficiently sampled by modern adiabatic quantum computers without the relaxation of the objective function. We also propose an iterative and decomposed version of our method, which supports real-world-sized problems. The experimental evaluation demonstrates promising results on a variety of datasets. The source code is available at: https://github.com/FarinaMatteo/qmmf.
Commutative Width and Depth Scaling in Deep Neural Networks
This paper is the second in the series Commutative Scaling of Width and Depth (WD) about commutativity of infinite width and depth limits in deep neural networks. Our aim is to understand the behaviour of neural functions (functions that depend on a neural network model) as width and depth go to infinity (in some sense), and eventually identify settings under which commutativity holds, i.e. the neural function tends to the same limit no matter how width and depth limits are taken. In this paper, we formally introduce and define the commutativity framework, and discuss its implications on neural network design and scaling. We study commutativity for the neural covariance kernel which reflects how network layers separate data. Our findings extend previous results established in [55] by showing that taking the width and depth to infinity in a deep neural network with skip connections, when branches are suitably scaled to avoid exploding behaviour, result in the same covariance structure no matter how that limit is taken. This has a number of theoretical and practical implications that we discuss in the paper. The proof techniques in this paper are novel and rely on tools that are more accessible to readers who are not familiar with stochastic calculus (used in the proofs of WD(I))).
Minkowski Functionals for composite smooth random fields
Minkowski functionals quantify the morphology of smooth random fields. They are widely used to probe statistical properties of cosmological fields. Analytic formulae for ensemble expectations of Minkowski functionals are well known for Gaussian and mildly non-Gaussian fields. In this paper we extend the formulae to composite fields which are sums of two fields and explicitly derive the expressions for the sum of uncorrelated mildly non-Gaussian and Gaussian fields. These formulae are applicable to observed data which is usually a sum of the true signal and one or more secondary fields that can be either noise, or some residual contaminating signal. Our formulae provide explicit quantification of the effect of the secondary field on the morphology and statistical nature of the true signal. As examples, we apply the formulae to determine how the presence of Gaussian noise can bias the morphological properties and statistical nature of Gaussian and non-Gaussian CMB temperature maps.
Thermodynamic Performance Limits for Score-Based Diffusion Models
We establish a fundamental connection between score-based diffusion models and non-equilibrium thermodynamics by deriving performance limits based on entropy rates. Our main theoretical contribution is a lower bound on the negative log-likelihood of the data that relates model performance to entropy rates of diffusion processes. We numerically validate this bound on a synthetic dataset and investigate its tightness. By building a bridge to entropy rates - system, intrinsic, and exchange entropy - we provide new insights into the thermodynamic operation of these models, drawing parallels to Maxwell's demon and implications for thermodynamic computing hardware. Our framework connects generative modeling performance to fundamental physical principles through stochastic thermodynamics.
Effects of Plasticity Functions on Neural Assemblies
We explore the effects of various plasticity functions on assemblies of neurons. To bridge the gap between experimental and computational theories we make use of a conceptual framework, the Assembly Calculus, which is a formal system for the description of brain function based on assemblies of neurons. The Assembly Calculus includes operations for projecting, associating, and merging assemblies of neurons. Our research is focused on simulating different plasticity functions with Assembly Calculus. Our main contribution is the modification and evaluation of the projection operation. We experiment with Oja's and Spike Time-Dependent Plasticity (STDP) rules and test the effect of various hyper-parameters.
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method
While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.
Exact Gradients for Stochastic Spiking Neural Networks Driven by Rough Signals
We introduce a mathematically rigorous framework based on rough path theory to model stochastic spiking neural networks (SSNNs) as stochastic differential equations with event discontinuities (Event SDEs) and driven by c\`adl\`ag rough paths. Our formalism is general enough to allow for potential jumps to be present both in the solution trajectories as well as in the driving noise. We then identify a set of sufficient conditions ensuring the existence of pathwise gradients of solution trajectories and event times with respect to the network's parameters and show how these gradients satisfy a recursive relation. Furthermore, we introduce a general-purpose loss function defined by means of a new class of signature kernels indexed on c\`adl\`ag rough paths and use it to train SSNNs as generative models. We provide an end-to-end autodifferentiable solver for Event SDEs and make its implementation available as part of the diffrax library. Our framework is, to our knowledge, the first enabling gradient-based training of SSNNs with noise affecting both the spike timing and the network's dynamics.
Entropic Neural Optimal Transport via Diffusion Processes
We propose a novel neural algorithm for the fundamental problem of computing the entropic optimal transport (EOT) plan between continuous probability distributions which are accessible by samples. Our algorithm is based on the saddle point reformulation of the dynamic version of EOT which is known as the Schr\"odinger Bridge problem. In contrast to the prior methods for large-scale EOT, our algorithm is end-to-end and consists of a single learning step, has fast inference procedure, and allows handling small values of the entropy regularization coefficient which is of particular importance in some applied problems. Empirically, we show the performance of the method on several large-scale EOT tasks. https://github.com/ngushchin/EntropicNeuralOptimalTransport
A Simple Introduction to the SiMPL Method for Density-Based Topology Optimization
We introduce a novel method for solving density-based topology optimization problems: Sigmoidal Mirror descent with a Projected Latent variable (SiMPL). The SiMPL method (pronounced as ``the simple method'') optimizes a design using only first-order derivative information of the objective function. The bound constraints on the density field are enforced with the help of the (negative) Fermi--Dirac entropy, which is also used to define a non-symmetric distance function called a Bregman divergence on the set of admissible designs. This Bregman divergence leads to a simple update rule that is further simplified with the help of a so-called latent variable. Because the SiMPL method involves discretizing the latent variable, it produces a sequence of pointwise-feasible iterates, even when high-order finite elements are used in the discretization. Numerical experiments demonstrate that the method outperforms other popular first-order optimization algorithms. To outline the general applicability of the technique, we include examples with (self-load) compliance minimization and compliant mechanism optimization problems.
Directional Message Passing for Molecular Graphs
Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.
Statistical mechanics of continual learning: variational principle and mean-field potential
An obstacle to artificial general intelligence is set by continual learning of multiple tasks of different nature. Recently, various heuristic tricks, both from machine learning and from neuroscience angles, were proposed, but they lack a unified theory ground. Here, we focus on continual learning in single-layered and multi-layered neural networks of binary weights. A variational Bayesian learning setting is thus proposed, where the neural networks are trained in a field-space, rather than gradient-ill-defined discrete-weight space, and furthermore, weight uncertainty is naturally incorporated, and modulates synaptic resources among tasks. From a physics perspective, we translate the variational continual learning into Franz-Parisi thermodynamic potential framework, where previous task knowledge acts as a prior and a reference as well. We thus interpret the continual learning of the binary perceptron in a teacher-student setting as a Franz-Parisi potential computation. The learning performance can then be analytically studied with mean-field order parameters, whose predictions coincide with numerical experiments using stochastic gradient descent methods. Based on the variational principle and Gaussian field approximation of internal preactivations in hidden layers, we also derive the learning algorithm considering weight uncertainty, which solves the continual learning with binary weights using multi-layered neural networks, and performs better than the currently available metaplasticity algorithm. Our proposed principled frameworks also connect to elastic weight consolidation, weight-uncertainty modulated learning, and neuroscience inspired metaplasticity, providing a theory-grounded method for the real-world multi-task learning with deep networks.
Generalizing Neural Wave Functions
Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.
Exact Coset Sampling for Quantum Lattice Algorithms
We give a simple, fully correct, and assumption-light replacement for the contested "domain-extension" in Step 9 of a recent windowed-QFT lattice algorithm with complex-Gaussian windows~chen2024quantum. The published Step~9 suffers from a periodicity/support mismatch. We present a pair-shift difference construction that coherently cancels all unknown offsets, produces an exact uniform CRT-coset state over Z_{P}, and then uses the QFT to enforce the intended modular linear relation. The unitary is reversible, uses poly(log M_2) gates, and preserves the algorithm's asymptotics. Project Page: https://github.com/yifanzhang-pro/quantum-lattice.
Quantum-Enhanced Conformal Methods for Multi-Output Uncertainty: A Holistic Exploration and Experimental Analysis
In this paper, we propose a unified approach to harness quantum conformal methods for multi-output distributions, with a particular emphasis on two experimental paradigms: (i) a standard 2-qubit circuit scenario producing a four-dimensional outcome distribution, and (ii) a multi-basis measurement setting that concatenates measurement probabilities in different bases (Z, X, Y) into a twelve-dimensional output space. By combining a multioutput regression model (e.g., random forests) with distributional conformal prediction, we validate coverage and interval-set sizes on both simulated quantum data and multi-basis measurement data. Our results confirm that classical conformal prediction can effectively provide coverage guarantees even when the target probabilities derive from inherently quantum processes. Such synergy opens the door to next-generation quantum-classical hybrid frameworks, providing both improved interpretability and rigorous coverage for quantum machine learning tasks. All codes and full reproducible Colab notebooks are made available at https://github.com/detasar/QECMMOU.
A Conceptual Introduction to Hamiltonian Monte Carlo
Hamiltonian Monte Carlo has proven a remarkable empirical success, but only recently have we begun to develop a rigorous understanding of why it performs so well on difficult problems and how it is best applied in practice. Unfortunately, that understanding is confined within the mathematics of differential geometry which has limited its dissemination, especially to the applied communities for which it is particularly important. In this review I provide a comprehensive conceptual account of these theoretical foundations, focusing on developing a principled intuition behind the method and its optimal implementations rather of any exhaustive rigor. Whether a practitioner or a statistician, the dedicated reader will acquire a solid grasp of how Hamiltonian Monte Carlo works, when it succeeds, and, perhaps most importantly, when it fails.
Cutting Slack: Quantum Optimization with Slack-Free Methods for Combinatorial Benchmarks
Constraint handling remains a key bottleneck in quantum combinatorial optimization. While slack-variable-based encodings are straightforward, they significantly increase qubit counts and circuit depth, challenging the scalability of quantum solvers. In this work, we investigate a suite of Lagrangian-based optimization techniques including dual ascent, bundle methods, cutting plane approaches, and augmented Lagrangian formulations for solving constrained combinatorial problems on quantum simulators and hardware. Our framework is applied to three representative NP-hard problems: the Travelling Salesman Problem (TSP), the Multi-Dimensional Knapsack Problem (MDKP), and the Maximum Independent Set (MIS). We demonstrate that MDKP and TSP, with their inequality-based or degree-constrained structures, allow for slack-free reformulations, leading to significant qubit savings without compromising performance. In contrast, MIS does not inherently benefit from slack elimination but still gains in feasibility and objective quality from principled Lagrangian updates. We benchmark these methods across classically hard instances, analyzing trade-offs in qubit usage, feasibility, and optimality gaps. Our results highlight the flexibility of Lagrangian formulations as a scalable alternative to naive QUBO penalization, even when qubit savings are not always achievable. This work provides practical insights for deploying constraint-aware quantum optimization pipelines, with applications in logistics, network design, and resource allocation.
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.
Energy-conserving equivariant GNN for elasticity of lattice architected metamaterials
Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.
From Block Diagrams to Bloch Spheres: Graphical Quantum Circuit Simulation in LabVIEW
As quantum computing transitions from theoretical physics to engineering applications, there is a growing need for accessible simulation tools that bridge the gap between abstract linear algebra and practical implementation. While text-based frameworks (like Qiskit or Cirq) are standard, they often present a steep learning curve for students and engineers accustomed to graphical system design. This paper introduces QuVI (Quantum Virtual Instrument), an open-source quantum circuit toolkit developed natively within the NI LabVIEW environment. Moving beyond initial proof-of-concept models, QuVI establishes a robust framework that leverages LabVIEW's "dataflow" paradigm, in which wires represent data and nodes represent operations, to provide an intuitive, visual analog to standard quantum circuit notation while enabling the seamless integration of classical control structures like loops and conditionals. The toolkit's capabilities are demonstrated by constructing and visualizing fundamental quantum algorithms and verifying results against theoretical predictions. By translating "Block Diagrams" directly into quantum state evolutions ("Bloch Spheres"), QuVI offers educators and researchers a powerful platform for prototyping quantum logic without leaving the graphical engineering workspace.
Light Schrödinger Bridge
Despite the recent advances in the field of computational Schr\"odinger Bridges (SB), most existing SB solvers are still heavy-weighted and require complex optimization of several neural networks. It turns out that there is no principal solver which plays the role of simple-yet-effective baseline for SB just like, e.g., k-means method in clustering, logistic regression in classification or Sinkhorn algorithm in discrete optimal transport. We address this issue and propose a novel fast and simple SB solver. Our development is a smart combination of two ideas which recently appeared in the field: (a) parameterization of the Schr\"odinger potentials with sum-exp quadratic functions and (b) viewing the log-Schr\"odinger potentials as the energy functions. We show that combined together these ideas yield a lightweight, simulation-free and theoretically justified SB solver with a simple straightforward optimization objective. As a result, it allows solving SB in moderate dimensions in a matter of minutes on CPU without a painful hyperparameter selection. Our light solver resembles the Gaussian mixture model which is widely used for density estimation. Inspired by this similarity, we also prove an important theoretical result showing that our light solver is a universal approximator of SBs. Furthemore, we conduct the analysis of the generalization error of our light solver. The code for our solver can be found at https://github.com/ngushchin/LightSB
The probabilistic world
Physics is based on probabilities as fundamental entities of a mathematical description. Expectation values of observables are computed according to the classical statistical rule. The overall probability distribution for one world covers all times. The quantum formalism arises once one focuses on the evolution of the time-local probabilistic information. Wave functions or the density matrix allow the formulation of a general linear evolution law for classical statistics. The quantum formalism for classical statistics is a powerful tool which allows us to implement for generalized Ising models the momentum observable with the associated Fourier representation. The association of operators to observables permits the computation of expectation values in terms of the density matrix by the usual quantum rule. We show that probabilistic cellular automata are quantum systems in a formulation with discrete time steps and real wave functions. With a complex structure the evolution operator for automata can be expressed in terms of a Hamiltonian involving fermionic creation and annihilation operators. The time-local probabilistic information amounts to a subsystem of the overall probabilistic system which is correlated with its environment consisting of the past and future. Such subsystems typically involve probabilistic observables for which only a probability distribution for their possible measurement values is available. Incomplete statistics does not permit to compute classical correlation functions for arbitrary subsystem-observables. Bell's inequalities are not generally applicable.
PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation
Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.
Intensional Inheritance Between Concepts: An Information-Theoretic Interpretation
This paper addresses the problem of formalizing and quantifying the concept of "intensional inheritance" between two concepts. We begin by conceiving the intensional inheritance of W from F as the amount of information the proposition "x is F " provides about the proposition "x is W. To flesh this out, we consider concepts F and W defined by sets of properties left{F_{1}, F_{2}, ldots, F_{n}right} and left{W_{1}, W_{2}, ldots, W_{m}right} with associated degrees left{d_{1}, d_{2}, ldots, d_{n}right} and left{e_{1}, e_{2}, ldots, e_{m}right}, respectively, where the properties may overlap. We then derive formulas for the intensional inheritance using both Shannon information theory and algorithmic information theory, incorporating interaction information among properties. We examine a special case where all properties are mutually exclusive and calculate the intensional inheritance in this case in both frameworks. We also derive expressions for P(W mid F) based on the mutual information formula. Finally we consider the relationship between intensional inheritance and conventional set-theoretic "extensional" inheritance, concluding that in our information-theoretic framework, extensional inheritance emerges as a special case of intensional inheritance.
Probing Off-diagonal Eigenstate Thermalization with Tensor Networks
Energy filter methods in combination with quantum simulation can efficiently access the properties of quantum many-body systems at finite energy densities [Lu et al. PRX Quantum 2, 020321 (2021)]. Classically simulating this algorithm with tensor networks can be used to investigate the microcanonical properties of large spin chains, as recently shown in [Yang et al. Phys. Rev. B 106, 024307 (2022)]. Here we extend this strategy to explore the properties of off-diagonal matrix elements of observables in the energy eigenbasis, fundamentally connected to the thermalization behavior and the eigenstate thermalization hypothesis. We test the method on integrable and non-integrable spin chains of up to 60 sites, much larger than accessible with exact diagonalization. Our results allow us to explore the scaling of the off-diagonal functions with the size and energy difference, and to establish quantitative differences between integrable and non-integrable cases.
Applications of Machine Learning to Lattice Quantum Field Theory
There is great potential to apply machine learning in the area of numerical lattice quantum field theory, but full exploitation of that potential will require new strategies. In this white paper for the Snowmass community planning process, we discuss the unique requirements of machine learning for lattice quantum field theory research and outline what is needed to enable exploration and deployment of this approach in the future.
Enabling Efficient Equivariant Operations in the Fourier Basis via Gaunt Tensor Products
Developing equivariant neural networks for the E(3) group plays an important role in modeling 3D data across real-world applications. Enforcing this equivariance primarily involves the tensor products of irreducible representations (irreps). However, the computational complexity of such operations increases significantly as higher-order tensors are used. In this work, we propose a systematic approach to substantially accelerate the computation of the tensor products of irreps. We mathematically connect the commonly used Clebsch-Gordan coefficients to the Gaunt coefficients, which are integrals of products of three spherical harmonics. Through Gaunt coefficients, the tensor product of irreps becomes equivalent to the multiplication between spherical functions represented by spherical harmonics. This perspective further allows us to change the basis for the equivariant operations from spherical harmonics to a 2D Fourier basis. Consequently, the multiplication between spherical functions represented by a 2D Fourier basis can be efficiently computed via the convolution theorem and Fast Fourier Transforms. This transformation reduces the complexity of full tensor products of irreps from O(L^6) to O(L^3), where L is the max degree of irreps. Leveraging this approach, we introduce the Gaunt Tensor Product, which serves as a new method to construct efficient equivariant operations across different model architectures. Our experiments on the Open Catalyst Project and 3BPA datasets demonstrate both the increased efficiency and improved performance of our approach.
On the generation of periodic discrete structures with identical two-point correlation
Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.
Quantum Visual Fields with Neural Amplitude Encoding
Quantum Implicit Neural Representations (QINRs) include components for learning and execution on gate-based quantum computers. While QINRs recently emerged as a promising new paradigm, many challenges concerning their architecture and ansatz design, the utility of quantum-mechanical properties, training efficiency and the interplay with classical modules remain. This paper advances the field by introducing a new type of QINR for 2D image and 3D geometric field learning, which we collectively refer to as Quantum Visual Field (QVF). QVF encodes classical data into quantum statevectors using neural amplitude encoding grounded in a learnable energy manifold, ensuring meaningful Hilbert space embeddings. Our ansatz follows a fully entangled design of learnable parametrised quantum circuits, with quantum (unitary) operations performed in the real Hilbert space, resulting in numerically stable training with fast convergence. QVF does not rely on classical post-processing -- in contrast to the previous QINR learning approach -- and directly employs projective measurement to extract learned signals encoded in the ansatz. Experiments on a quantum hardware simulator demonstrate that QVF outperforms the existing quantum approach and widely used classical foundational baselines in terms of visual representation accuracy across various metrics and model characteristics, such as learning of high-frequency details. We also show applications of QVF in 2D and 3D field completion and 3D shape interpolation, highlighting its practical potential.
Covariant quantum kernels for data with group structure
The use of kernel functions is a common technique to extract important features from data sets. A quantum computer can be used to estimate kernel entries as transition amplitudes of unitary circuits. Quantum kernels exist that, subject to computational hardness assumptions, cannot be computed classically. It is an important challenge to find quantum kernels that provide an advantage in the classification of real-world data. We introduce a class of quantum kernels that can be used for data with a group structure. The kernel is defined in terms of a unitary representation of the group and a fiducial state that can be optimized using a technique called kernel alignment. We apply this method to a learning problem on a coset-space that embodies the structure of many essential learning problems on groups. We implement the learning algorithm with 27 qubits on a superconducting processor.
Can "consciousness" be observed from large language model (LLM) internal states? Dissecting LLM representations obtained from Theory of Mind test with Integrated Information Theory and Span Representation analysis
Integrated Information Theory (IIT) provides a quantitative framework for explaining consciousness phenomenon, positing that conscious systems comprise elements integrated through causal properties. We apply IIT 3.0 and 4.0 -- the latest iterations of this framework -- to sequences of Large Language Model (LLM) representations, analyzing data derived from existing Theory of Mind (ToM) test results. Our study systematically investigates whether the differences of ToM test performances, when presented in the LLM representations, can be revealed by IIT estimates, i.e., Phi^{max} (IIT 3.0), Phi (IIT 4.0), Conceptual Information (IIT 3.0), and Phi-structure (IIT 4.0). Furthermore, we compare these metrics with the Span Representations independent of any estimate for consciousness. This additional effort aims to differentiate between potential "consciousness" phenomena and inherent separations within LLM representational space. We conduct comprehensive experiments examining variations across LLM transformer layers and linguistic spans from stimuli. Our results suggest that sequences of contemporary Transformer-based LLM representations lack statistically significant indicators of observed "consciousness" phenomena but exhibit intriguing patterns under spatio-permutational analyses. The Appendix and code are available as Supplementary Materials at: https://doi.org/10.1016/j.nlp.2025.100163.
Symmetry-invariant quantum machine learning force fields
Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.
Composition and Control with Distilled Energy Diffusion Models and Sequential Monte Carlo
Diffusion models may be formulated as a time-indexed sequence of energy-based models, where the score corresponds to the negative gradient of an energy function. As opposed to learning the score directly, an energy parameterization is attractive as the energy itself can be used to control generation via Monte Carlo samplers. Architectural constraints and training instability in energy parameterized models have so far yielded inferior performance compared to directly approximating the score or denoiser. We address these deficiencies by introducing a novel training regime for the energy function through distillation of pre-trained diffusion models, resembling a Helmholtz decomposition of the score vector field. We further showcase the synergies between energy and score by casting the diffusion sampling procedure as a Feynman Kac model where sampling is controlled using potentials from the learnt energy functions. The Feynman Kac model formalism enables composition and low temperature sampling through sequential Monte Carlo.
Equivariant Matrix Function Neural Networks
Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.
Hitchhiker's guide on Energy-Based Models: a comprehensive review on the relation with other generative models, sampling and statistical physics
Energy-Based Models (EBMs) have emerged as a powerful framework in the realm of generative modeling, offering a unique perspective that aligns closely with principles of statistical mechanics. This review aims to provide physicists with a comprehensive understanding of EBMs, delineating their connection to other generative models such as Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), and Normalizing Flows. We explore the sampling techniques crucial for EBMs, including Markov Chain Monte Carlo (MCMC) methods, and draw parallels between EBM concepts and statistical mechanics, highlighting the significance of energy functions and partition functions. Furthermore, we delve into state-of-the-art training methodologies for EBMs, covering recent advancements and their implications for enhanced model performance and efficiency. This review is designed to clarify the often complex interconnections between these models, which can be challenging due to the diverse communities working on the topic.
The Virtual Quantum Optics Laboratory
We present a web-based software tool, the Virtual Quantum Optics Laboratory (VQOL), that may be used for designing and executing realistic simulations of quantum optics experiments. A graphical user interface allows one to rapidly build and configure a variety of different optical experiments, while the runtime environment provides unique capabilities for visualization and analysis. All standard linear optical components are available as well as sources of thermal, coherent, and entangled Gaussian states. A unique aspect of VQOL is the introduction of non-Gaussian measurements using detectors modeled as deterministic devices that "click" when the amplitude of the light falls above a given threshold. We describe the underlying theoretical models and provide several illustrative examples. We find that VQOL provides a a faithful representation of many experimental quantum optics phenomena and may serve as both a useful instructional tool for students as well as a valuable research tool for practitioners.
