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Oct 22

Fourth-order perturbation theory for the Frohlich polaron: Analytic structure of the weak-coupling series and the crossover to strong coupling

We calculate the Rayleigh-Schrodinger perturbation series for the ground-state energy and the effective mass of the three-dimensional Frohlich polaron through fourth order in the coupling constant alpha. The third- and fourth-order coefficients of the effective mass are new. Because the Frohlich interaction is a form-bounded perturbation of an isolated nondegenerate ground state at fixed total momentum, the series has a nonzero radius of convergence, and we analyze it with the ratio and Pade methods appropriate to convergent series. The coefficients are strikingly regular and are described by a simple power-law singularity at alpha near 8.5 with an exponent near 1.4. The couplings at which successive truncations of the inverse mass vanish, the first of which is the textbook breakdown value alpha = 6, are slowly converging estimates of this radius. Pade approximants built from the weak-coupling coefficients alone agree with diagrammatic Monte Carlo results for the mass to better than one percent for alpha up to 5. Exact results on the analyticity of the ground state and on the strong-coupling asymptotics imply that the coefficients cannot keep a constant sign, although all known coefficients do, so that the apparent singularity must be a complex-conjugate pair close to the positive real axis. It marks the crossover to strong coupling: the weak-coupling series locates this crossover accurately but cannot be continued through it.

  • 1 authors
·
Oct 6

Numerical Construction of Quasi-Periodic Solutions for Nonlinear PDEs: I. Bounded Perturbation

In this paper, we propose an alternating numerical scheme for constructing quasi-periodic solutions to a class of nonlinear partial differential equations (PDEs) with bounded perturbations, including the one-dimensional nonlinear Schrödinger (NLS) equations and nonlinear wave (NLW) equations under periodic and Dirichlet boundary conditions. A key observation concerning the resonant Q-equations allows us to establish directly a local diffeomorphism between the amplitudes and the drifted frequencies. This renders the proof considerably cleaner, since it avoids the Birkhoff normal form and the associated coordinate transformations required in classical KAM theory for PDEs.Unlike in the finite-dimensional setting, the lattice boxes must also include the spatial index, so that the multiscale induction has to be carried out in one additional dimension. This introduces two difficulties. First, the measure estimate for the excluded set of ``bad'' frequencies must account for the spatial index. For both the NLS and NLW equations, the linear frequencies and their differences are integers or close to integers; this allows the spatial dependence to be controlled through the modulus of the temporal index, so that the excluded measure remains under control. Second, a singular set may contain sites with the same temporal index but widely separated spatial indices, which obstructs the ``inversion implies localization'' process. For the one-dimensional NLS and NLW equations, however, such sites occur only in pairs with opposite spatial indices. They can therefore be separated by small boxes, after which the global inverse is obtained from the local inverses via the resolvent identity. Numerical experiments illustrate the scheme for nonlinear traveling and standing waves, exhibiting both the computed quasi-periodic solutions and the convergence of the iteration.

  • 2 authors
·
Oct 4

Hierarchical Melnikov Realization: Logarithmic Factor Improvement to Hilbert Number Lower Bounds

The second part of Hilbert's 16th problem is one of the most fundamental open problems in the qualitative theory of ordinary differential equations and dynamical systems. A central unresolved question is whether the Hilbert number H(d) is finite for arbitrary polynomial degree d. (A very recent manuscript from OpenAI asserts the finiteness of H(d); see the remark at the end of this paper.) In the absence of a general upper bound theory, most existing work constructs explicit perturbed polynomial systems to obtain improved lower bounds for H(d), while rigorous upper bound estimates remain largely unavailable. This paper focuses on improving the quantitative lower bound for polynomial systems through a systematic Hierarchical Melnikov Realization framework. We construct perturbed dynamics based on an anisotropic Chebyshev Hamiltonian, where hierarchically selected perturbation coefficients generate simple zeros of the first-order Melnikov function simultaneously across multiple disjoint period annuli. Two distinct 3-adic filtrations supply the necessary logarithmic correction factors, and a Borel--Gauss analysis establishes the required local rank condition under sufficiently strong anisotropy. As the main result of this work, we prove that H(d)=Ωbigl(d^2ln^2 dbigr), which improves the previously known lower bound by a factor of ln d. The full construction of limit cycles and the resulting dynamical bounds are formally certified using Lean 4 formal verification.

  • 2 authors
·
Oct 7

Convex-Hull-Neighborhood Smooth Dual Generalization: Controlling Local Correction Propagation in Offline RL

Offline reinforcement learning (offline RL) can benefit from nearby out-of-distribution (OOD) actions, but estimation errors at these actions may be amplified by bootstrapping. Existing regularization and local-generalization methods control either the admissible OOD region or the influence of generalized targets, often through separate mechanisms. We propose Convex Hull Neighborhood Smooth Dual Generalization (CSDG), which expresses the Bellman backup as an in-sample value target plus a CHN-local correction. This formulation makes the generalized contribution explicit and separates it from the in-sample reference path. The correction is obtained by smoothing in-sample-oriented and OOD-oriented candidates sampled at different perturbation radii. A mixture coefficient lambda scales its contribution to each backup, while the recursive discount remains gamma. Under boundedness and fixed perturbation kernels, we derive an exact one-step correction identity, a time-varying iterate bound, and a fixed-point bound that depends only on the branch discrepancy at the fixed point. We further characterize the implicit policies induced by the idealized operators and give a conditional non-degradation criterion. The practical algorithm approximates these quantities using asymmetric bounded noise and expectile regression, without exact support classification or an additional pessimistic OOD penalty. Experiments on Gym-MuJoCo and AntMaze show strong aggregate performance and stable value estimation. Code is available at: https://github.com/YOUNG-fnxm/CSDG

  • 6 authors
·
Aug 3

Perturbation Analysis of Neural Collapse

Training deep neural networks for classification often includes minimizing the training loss beyond the zero training error point. In this phase of training, a "neural collapse" behavior has been observed: the variability of features (outputs of the penultimate layer) of within-class samples decreases and the mean features of different classes approach a certain tight frame structure. Recent works analyze this behavior via idealized unconstrained features models where all the minimizers exhibit exact collapse. However, with practical networks and datasets, the features typically do not reach exact collapse, e.g., because deep layers cannot arbitrarily modify intermediate features that are far from being collapsed. In this paper, we propose a richer model that can capture this phenomenon by forcing the features to stay in the vicinity of a predefined features matrix (e.g., intermediate features). We explore the model in the small vicinity case via perturbation analysis and establish results that cannot be obtained by the previously studied models. For example, we prove reduction in the within-class variability of the optimized features compared to the predefined input features (via analyzing gradient flow on the "central-path" with minimal assumptions), analyze the minimizers in the near-collapse regime, and provide insights on the effect of regularization hyperparameters on the closeness to collapse. We support our theory with experiments in practical deep learning settings.

  • 3 authors
·
Oct 29, 2022

Resonance expansions and local-energy decay estimates for Dirac operators

We study resonance expansions and localised long-time dynamics for three-dimensional semiclassical Dirac operators. For smooth Hermitian matrix-valued perturbations which are analytic outside a compact set, we first obtain exponential cut-off resolvent bounds away from the resonance set and polynomial bounds in thin resonance-free rectangles adjacent to the real axis. Combining these estimates with a local Oc(h^{-3}) upper bound on the number of resonances, a pigeonhole selection of admissible contours, almost-analytic functional calculus, and a Cauchy--Green deformation, we derive resonance expansions for spectrally localised propagators. Positive-energy resonances contribute for large positive times, whereas negative-energy resonances contribute for large negative times. We then specialise to mass-type perturbations mbfβV(x) in a nontrapping energy window. Using the logarithmic resonance-free region established in our earlier work together with a quantitative FBI-transform/escape-function argument, we obtain a polynomial bound for the continued cut-off resolvent and deduce rapid local-energy decay. We subsequently refine this polynomial estimate by a finite-time propagation argument in the undistorted region. Introducing the maximal positive-sheet connection time T_χ associated with the spatial cutoff, we prove a geometric continued-resolvent estimate and, for every fixed M below the resonance-free depth constant, derive the explicit local-energy decay threshold T_N>T_χ+(N+1)/M. The same analysis gives a rigorous microlocal obstruction to a uniform [hlog(1/h)]^{-1} bound for the full distorted resolvent and identifies a finite-flight-time amplification mechanism for the sandwiched continued resolvent at logarithmic depth.

  • 2 authors
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Sep 30

scDFM: Distributional Flow Matching Model for Robust Single-Cell Perturbation Prediction

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that perturbations often induce population-level shifts rather than changes in individual cells. Existing deep learning methods typically assume cell-level correspondences, limiting their ability to capture such global effects. We present scDFM, a generative framework based on conditional flow matching that models the full distribution of perturbed cells conditioned on control states. By incorporating a maximum mean discrepancy (MMD) objective, our method aligns perturbed and control populations beyond cell-level correspondences. To further improve robustness to sparsity and noise, we introduce the Perturbation-Aware Differential Transformer (PAD-Transformer), a backbone architecture that leverages gene interaction graphs and differential attention to capture context-specific expression changes. Across multiple genetic and drug perturbation benchmarks, scDFM consistently outperforms prior methods, demonstrating strong generalization in both unseen and combinatorial settings. In the combinatorial setting, it reduces mean squared error by 19.6% relative to the strongest baseline. These results highlight the importance of distribution-level generative modeling for robust in silico perturbation prediction. The code is available at https://github.com/AI4Science-WestlakeU/scDFM

  • 4 authors
·
Feb 5

Learning Perturbation-Specific Representations through Conditional Energy Prior for Cellular Response Prediction

AI-based cellular perturbation prediction is essential to accelerate drug discovery and therapeutic identification. However, perturbation-specific signals are generally obscured by cellular complexity, making it difficult for existing methods to correctly capture perturbation effects. To address this problem, we propose PerturbEnergy, which introduces a conditional energy-based prior over perturbation representations. It assigns lower energy (higher probability) to representations compatible with the given perturbation and higher energy to others, thereby explicitly tilting the latent space toward perturbation-preferred regions. Besides, PerturbEnergy can be integrated into autoencoder architectures as we find its Evidence Lower Bound (ELBO) is equivalent to the ELBO of the complete autoencoder. We further prove that optimizing PerturbEnergy increases the lower bound on the conditional mutual information between representation and perturbation. Extensive experiments on four benchmark datasets demonstrate the effectiveness of our PerturbEnergy: it improves perturbation recognition especially in latent space with improvement of up to 83.2\%; It also achieves state-of-the-art performance for predicting top-50/100/200 differentially expressed gene(DEG) response and remaining competitive on highly variable gene(HVG) prediction. The code is provided: https://github.com/BlueWhaleLab/PerturbEnergy

  • 2 authors
·
Oct 12

DRIFT: Disentangled Responsive-Invariant Flow Transport for Single-Cell Perturbation Prediction

Predicting cellular responses to perturbations is a central problem in cellular biology, with broad applications in systems biology and drug discovery. This task is challenging because cellular responses can be complex and cell-state dependent, intrinsic cell-to-cell variability can be confounded with perturbation effects, and destructive single-cell RNA sequencing precludes paired measurements of the same cell before and after treatment. Flow matching transports control cells to perturbed states flexibly, but acting on the full cell state can confound perturbation effects with pre-existing cell-to-cell variability. Disentangled approaches separate responsive from invariant components, but model perturbations through prescribed mechanisms, such as latent shifts or graph edits, limiting their flexibility. We address both limitations in a unified framework. A variational encoder disentangles each cell into an invariant block, capturing state unaffected by the perturbation, and a responsive block, capturing state it changes, through conditional priors and an information-theoretic invariance constraint. Conditional flow matching transports only the responsive block, conditioned on the perturbation and invariant state, yielding a flexible, data-driven model of perturbation effects without confounding pre-existing variability. Across several benchmarks, our method outperforms the strongest published method in settings involving combinatorial and unseen perturbation prediction.

  • 3 authors
·
Sep 27

SNIC bifurcation and its Application to MEMS

This project focuses on a method to extract a frequency comb in mechanical means, for general interest and numerous practical applications in MEMS. The method of execution is the implementation of a beam that is exhibiting non-linear dynamics that is perturbed and analyzed for its transverse vibrations. The perturbation is an external harmonic driver with a chosen small amplitude and frequency (which is slightly detuned from the beam eigenfrequency), that when engaged with the unperturbed beam oscillations, causes it reach a state of "injection pulling" - an effect that occurs when one harmonic oscillator is coupled with a second one and causes it to oscillate in a frequency near its own. This causes the beam to reach SNIC bifurcation, rendering a frequency comb as desired. Theoretical analysis showed that the problem can be modelled using a non-linear equation of the beam, that translates to a form of the non-linear Duffing equation. While a solution to the dynamics function of the beam is hard to obtain in practice due to mathematical difficulties, a slow evolution model is suggested that is composed of functions of a amplitude and phase. Using several additional mathematical assumptions, the amplitude is seen to be related to the phase, while the phase equation solution is seen to be of the form of Adler's equation. These assumptions ultimately reduce the entire behaviour of the beam to a relatively simple solution to the Adler equation, which has a known analytical solution. Computerized numerical simulations are run on it to check the results and compare them to the theory and desired outcome. The results agreed with the theory and produce the expected frequency comb, showing the assumptions to be valid in extracting the comb.

  • 1 authors
·
Aug 24, 2025

Endpoint-Stable Interval Inverse Inequalities for Multiscale Kernels with Positive Exponential Spectra

Inverse inequalities are essential for controlling derivative growth and ensuring stable sampling in kernel approximation. Existing whole-space and single-scale estimates provide an established analytical basis, but their extension to multiscale analytic spaces on finite intervals requires uniform control of boundary effects and cross-scale cancellation. This paper establishes unweighted interval \(L^2\) inverse inequalities for spaces generated by primitives of kernels with positive exponential spectra. By retaining exterior diagonal energy and controlling off-diagonal interactions through one-sided estimates with endpoint-distance weights, we derive uniform coefficient bounds for normalized high derivatives. A synthesis-operator perturbation argument extends these bounds to positive spectral mixtures, while adjacent-derivative comparison and interval interpolation yield an inverse bound of order \(h_*^{-1}\), where \(h_*\) is the smallest scale. Under geometric scale separation and within-scale centre separation, the constant is independent of the number of scales and centres and their distances from the endpoints, allowing endpoint centres and coincident centres across scales. The coefficient lower bound approaches the optimal limit \(1/2\). Two-centre constructions establish the sharpness of the scale exponent for every fixed kernel in the class and, for a single exponential spectrum, a sharp deficit of order \(q^{-1/2}\) from \(1/2\) for the best uniform coefficient lower bound, where \(q\) is the derivative order. Numerical illustrations for Cauchy and logistic kernels demonstrate coefficient stability in several multiscale configurations. These results extend interval inverse estimates to multiscale analytic kernel spaces with endpoint centres and provide quantitative conditions for deterministic sampling stability.

  • 2 authors
·
Oct 5

Finite-Precision Symmetric Krylov Methods: Exact Rounding Examples, Block Paige Identities,and a Variable-Block Lanczos Model

Short-recurrence Krylov methods that are equivalent in exact arithmetic often diverge in floating-point arithmetic. To illustrate this, we provide an exactly representable two-cycle for steepest descent with a recursively updated residual. A complementary convergence theorem gives a sufficient condition under which the stored residual decreases geometrically. We then show that a second positive definite family yields different outcomes for a Hestenes--Stiefel Conjugate Gradient (CG) implementation and a direct Lanczos--Galerkin approach. CG finds the exact solution after four updates, whereas the two-step projected system becomes inconsistent. Under stated perturbation and transfer hypotheses, a common spectral enclosure gives comparable convergence bounds. For a dense, left-to-right evaluation order, we prove a sufficient precision bound for a prescribed backward error within n updates for an ntimes n matrix, together with a computable stopping test and specified exponent-range assumptions. We use polynomial estimates and numerical experiments to examine the trade-off between working precision and the number of CG iterations needed to achieve a prescribed backward error. We also compare results on inexact matrix-vector products and preconditioning with the frameworks of Paige and Greenbaum. For block Lanczos, we analyze Householder orthogonalization and singular-value truncation as the block size changes. Under componentwise and normwise error bounds, the computed coefficients satisfy a controlled local recurrence and an exact block Lanczos relation for a nearby symmetric problem in a larger space. A block form of Paige's identity bounds the overlap with a Ritz vector along its residual coordinate direction. An inter-block recurrence describes the evolution of overlap, and a Gram-matrix argument gives a count of additional nearby Ritz values.

  • 1 authors
·
Sep 7

Synergy-Aware Residual Flow Matching for Single-Cell Perturbation Prediction

Predicting single-cell responses to genetic and chemical perturbations is important for understanding regulatory mechanisms and prioritizing therapeutic interventions. Existing methods have made progress by modeling perturbation-conditioned expression shifts with neural networks, graph priors, foundation-model representations, or distributional generative models. However, combinatorial perturbation prediction remains challenging because much of the response can be explained by additive single-perturbation effects, while the biologically informative signal often lies in a smaller non-additive residual induced by perturbation interactions. Directly generating the full post-perturbation expression profile may therefore allocate substantial capacity to the dominant additive component and underemphasize synergy-specific structure. To address this issue, we propose SynGeneFlow, a synergy-aware flow matching framework that anchors the source distribution at an additive prior and learns a residual flow toward the true perturbed state. SynGeneFlow further incorporates perturbation-conditioned gene interaction modeling, where a static gene-gene mask provides biological structure and a perturbation-dependent deformation bias dynamically modulates gene-gene coupling. To preserve population-level response structure, we align both endpoint distributions and biological residual distributions with MMD-based regularization. We evaluate SynGeneFlow on genetic and drug perturbation benchmarks under observed-single, held-out, and cross-modality settings. The results demonstrate that residualizing flow matching around additive perturbation effects provides a biologically grounded and robust framework for single-cell perturbation response prediction.

  • 2 authors
·
Oct 17

A minimal model for rate-induced tipping to extinction

Rate-induced tipping ("R-tipping") in ecological modelling is characterised by too-rapid change of an environmental parameter causing collapse of a population without any bifurcation being crossed ("B-tipping"). A well-known example of a slow-fast predator-prey model in which R-tipping is observed [Vanselow, Wieczorek, Feudel, Journal of Theoretical Biology, 479, 64-72 (2019)] suffers from unecological "resurgence", whereby populations driven to functional extinction recover towards stable coexistence. We propose an analytically tractable model, incorporating a strong Allee effect into the prey dynamics in a slow-fast Lotka-Volterra-type predator-prey system, which induces bistability and thus renders the extinction state a genuine attractor. Applying geometric singular perturbation theory (GSPT), we describe the dynamics of the extended model that is obtained by "ramping" of the inverse prey carrying capacity. We show the presence of a parabolic-shaped, folded critical manifold which admits a folded saddle singularity, the strong canard of which separates solutions that track the moving coexistence state from those that tip to extinction. The analytical simplicity of our model allows us to derive explicit expressions for the critical rate that separates "tracking" from "tipping" dynamics. Finally, we argue that our system represents a minimal model for rate-induced tipping to extinction, in that it incorporates three essential ingredients: bistability, a folded critical manifold, and a folded-saddle-type canard.

  • 3 authors
·
Oct 7

Information-Theoretic Causal Bounds under Unmeasured Confounding

We develop a data-driven information-theoretic framework for sharp partial identification of causal effects under unmeasured confounding. Existing approaches often rely on restrictive assumptions, such as bounded or discrete outcomes; require external inputs (for example, instrumental variables, proxies, or user-specified sensitivity parameters); necessitate full structural causal model specifications; or focus solely on population-level averages while neglecting covariate-conditional effects. We overcome all four limitations simultaneously by establishing novel information-theoretic, data-driven divergence bounds. Our key theoretical contribution shows that the f-divergence between the observational distribution P(Y | A = a, X = x) and the interventional distribution P(Y | do(A = a), X = x) is upper bounded by a function of the propensity score alone. This result enables sharp partial identification of conditional causal effects directly from observational data, without requiring external sensitivity parameters, auxiliary variables, full structural specifications, or outcome boundedness assumptions. For practical implementation, we develop a semiparametric estimator satisfying Neyman orthogonality (Chernozhukov et al., 2018), which ensures root-n consistent inference even when nuisance functions are estimated via flexible machine learning methods. Simulation studies and real-world data applications, implemented in the GitHub repository (https://github.com/yonghanjung/Information-Theretic-Bounds), demonstrate that our framework provides tight and valid causal bounds across a wide range of data-generating processes.

  • 2 authors
·
Jan 23

PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

  • 6 authors
·
Feb 22

Global solutions to the two-dimensional compressible MHD equations with density-dependent bulk viscosity

We study the two-dimensional periodic resistive compressible magnetohydrodynamic equations with constant shear viscosity and magnetic diffusivity, bulk viscosity ρ^β, and pressure ρ^γ. For every β>1 and γ>1, we construct global finite-energy renormalized weak solutions from strictly positive bounded W^{1,q} densities, q>2, and arbitrary H^1 velocity and magnetic data. The construction combines approximation-independent finite density moments, generalized effective-flux identities, and a joint logarithmic renormalization of the density and its entropy defect. An augmented relative energy containing the β-power density potential yields weak--strong uniqueness against positive H^2 strong solutions for the same full pressure range. We also establish global strong existence for a large-background family when γ>max{5-2β,β+1}. Writing m=intρ_0, the density perturbation is bounded in the scaled norm m^{(γ-3)/2}|ρ_0-m|_{H^2}, while the fixed H^2 velocity and magnetic norms need not be small. For sufficiently large m, frequency-dependent acoustic dissipation, staged vorticity weights, and a separate initial-layer flux estimate close a simultaneous bootstrap. The admissible pressure exponents have infimum 7/3, with the endpoint excluded. For β>2 the relevant damping rate is the minimum of the viscous and pressure-relaxation rates; keeping both rates extends the argument without an upper restriction on β. The strong theorem has no upper restriction on γ under this scaled density hypothesis; for fixed additive density perturbations it applies in the stated lower range up to γ=3.

  • 3 authors
·
Oct 3

Equal Path Cost, Unequal Output Effects: Understanding Perturbation Propagation in Diffusion Models

Diffusion models have achieved remarkable success in generative modeling, with their sampling procedures routinely modified to control generation and improve efficiency. These modifications introduce perturbations along the sampling trajectory, raising a central question: how do such perturbations affect generated output? To address this question, we develop a theoretical framework to investigate perturbation propagation, combining dynamical analysis of the sampling process with an information-theoretic characterization of output responses. Within this framework, we quantify perturbation strength using the Kullback--Leibler (KL) divergence between perturbed and reference trajectory distributions, termed as path cost, which is shown to bound, but do not determine, changes in the output distribution. Building on this analysis, we derive a response identity that connects the propagation and accumulation of local perturbations with the information captured by a selected feature mean, explaining why changes in the output distribution can remain undetected by its first-order response. We test our theoretical analysis through controlled interventions at equal path cost in pretrained diffusion models, revealing distinct patterns of output sensitivity across sampling stages and spatial frequencies. To assess whether our framework can diagnose perturbations arising from practical approximations, we apply it to cache-based acceleration and show that our propagation analysis reliably identifies sampling intervals where caching causes larger image errors.

  • 4 authors
·
Oct 7

Steady-State Phase Transition States and Large-Time Asymptotics for the Cauchy Problem of Compressible Navier-Stokes Equations with van der Waals Equation of State

We study the Cauchy problem for the one-dimensional isothermal compressible Navier--Stokes system with the van der Waals equation of state, and analyze the well-posedness and asymptotic stability of steady-state phase-transition solutions at subcritical temperatures. Working in Lagrangian coordinates, we use variational techniques to construct piecewise smooth steady-state solutions corresponding to two-phase equilibrium states under finite-mass perturbations. Introducing artificial-viscosity regularization, we first establish existence of the global minimizer of the regularized variational problem, unique within each fixed symmetry class; passing to the vanishing artificial-viscosity limit then yields a physically admissible steady-state solution with two phase interfaces. For initial perturbations that are small with respect to energy, piecewise-gradient, total-variation, and integral norms but may exhibit large pointwise jumps across phase boundaries, we derive uniform a priori bounds for weak solutions near the two-phase equilibrium profile. We further prove that these global weak solutions converge to the steady-state two-phase equilibrium in L^infty(R) as ttoinfty, thereby characterizing their large-time asymptotic behavior. Physically, finite mass perturbations break the uniqueness of the uniform steady state and generate infinitely many piecewise constant two-phase equilibria satisfying the Maxwell equal-area rule. Artificial viscosity acts as a selection principle that singles out the physically relevant two-interface steady-state configuration, and this two-phase equilibrium is asymptotically stable under small integral perturbations that allow large-amplitude discontinuities at phase interfaces.

  • 4 authors
·
Oct 4

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

  • 7 authors
·
May 26

JAWS: Enhancing Long-term Rollout of Neural Operators via Spatially-Adaptive Jacobian Regularization

Data-driven surrogate models improve the efficiency of simulating continuous dynamical systems, yet their autoregressive rollouts are often limited by instability and spectral blow-up. While global regularization techniques can enforce contractive dynamics, they uniformly damp high-frequency features, introducing a contraction-dissipation dilemma. Furthermore, long-horizon trajectory optimization methods that explicitly correct drift are bottlenecked by memory constraints. In this work, we propose Jacobian-Adaptive Weighting for Stability (JAWS), a probabilistic regularization strategy designed to mitigate these limitations. By framing operator learning as Maximum A Posteriori (MAP) estimation with spatially heteroscedastic uncertainty, JAWS dynamically modulates the regularization strength based on local physical complexity. This allows the model to enforce contraction in smooth regions to suppress noise, while relaxing constraints near singular features to preserve gradients, effectively realizing a behavior similar to numerical shock-capturing schemes. Experiments demonstrate that this spatially-adaptive prior serves as an effective spectral pre-conditioner, which reduces the base operator's burden of handling high-frequency instabilities. This reduction enables memory-efficient, short-horizon trajectory optimization to match or exceed the long-term accuracy of long-horizon baselines. Evaluated on the 1D viscous Burgers' equation, our hybrid approach improves long-term stability, shock fidelity, and out-of-distribution generalization while reducing training computational costs.

  • 2 authors
·
Mar 4

StEik: Stabilizing the Optimization of Neural Signed Distance Functions and Finer Shape Representation

We present new insights and a novel paradigm (StEik) for learning implicit neural representations (INR) of shapes. In particular, we shed light on the popular eikonal loss used for imposing a signed distance function constraint in INR. We show analytically that as the representation power of the network increases, the optimization approaches a partial differential equation (PDE) in the continuum limit that is unstable. We show that this instability can manifest in existing network optimization, leading to irregularities in the reconstructed surface and/or convergence to sub-optimal local minima, and thus fails to capture fine geometric and topological structure. We show analytically how other terms added to the loss, currently used in the literature for other purposes, can actually eliminate these instabilities. However, such terms can over-regularize the surface, preventing the representation of fine shape detail. Based on a similar PDE theory for the continuum limit, we introduce a new regularization term that still counteracts the eikonal instability but without over-regularizing. Furthermore, since stability is now guaranteed in the continuum limit, this stabilization also allows for considering new network structures that are able to represent finer shape detail. We introduce such a structure based on quadratic layers. Experiments on multiple benchmark data sets show that our new regularization and network are able to capture more precise shape details and more accurate topology than existing state-of-the-art.

  • 4 authors
·
Nov 10, 2023

Robust Learnability of Sample-Compressible Distributions under Noisy or Adversarial Perturbations

Learning distribution families over R^d is a fundamental problem in unsupervised learning and statistics. A central question in this setting is whether a given family of distributions possesses sufficient structure to be (at least) information-theoretically learnable and, if so, to characterize its sample complexity. In 2018, Ashtiani et al. reframed sample compressibility, originally due to Littlestone and Warmuth (1986), as a structural property of distribution classes, proving that it guarantees PAC-learnability. This discovery subsequently enabled a series of recent advancements in deriving nearly tight sample complexity bounds for various high-dimensional open problems. It has been further conjectured that the converse also holds: every learnable class admits a tight sample compression scheme. In this work, we establish that sample compressible families remain learnable even from perturbed samples, subject to a set of necessary and sufficient conditions. We analyze two models of data perturbation: (i) an additive independent noise model, and (ii) an adversarial corruption model, where an adversary manipulates a limited subset of the samples unknown to the learner. Our results are general and rely on as minimal assumptions as possible. We develop a perturbation-quantization framework that interfaces naturally with the compression scheme and leads to sample complexity bounds that scale gracefully with the noise level and corruption budget. As concrete applications, we establish new sample complexity bounds for learning finite mixtures of high-dimensional uniform distributions under both noise and adversarial perturbations, as well as for learning Gaussian mixture models from adversarially corrupted samples, resolving two open problems in the literature.

  • 2 authors
·
Jun 6, 2025

Necessary Conditions for Free End-Time Sweeping Process Problems

This paper derives necessary optimality conditions for free end-time optimal control problems governed by sweeping process dynamics. In contrast to classical optimal control problems, the presence of the normal cone term in the state equation introduces discontinuities with respect to the state variable and prevents the standard Lipschitz regularity assumptions typically used in optimal control theory. As a result, both the analysis of trajectories and the formulation of optimality conditions require refined tools. We address problems with general endpoint constraints and time-dependent data, considering both the case in which the dynamics are Lipschitz continuous in time and the more challenging setting of merely measurable time dependence. Special attention is devoted to the additional transversality conditions associated with the free end-time variable. In the Lipschitz case, these conditions are expressed in terms of a function of bounded variation that coincides almost everywhere with the maximized Hamiltonian. In the measurable case, we show that a suitable interpretation can be obtained via the notions of sub- and super-essential values of the maximized Hamiltonian, recently introduced in the literature, leading to strengthened transversality conditions. These conditions also involve an additional term reflecting the interaction between the costate arc and the normal cone to the moving set at the optimal endpoints. Our approach combines suitable perturbation techniques with a penalization method tailored to sweeping processes. The moving set is modelled as a finite intersection of inequality-defined sets satisfying suitable constraint qualifications, including a positive linear independence condition and a diagonal dominance property of the associated Gramian matrix. We also introduce a local version of the constraint qualification condition. Our results apply to a broad class of problems, including those involving unbounded moving sets such as polyhedra. The resulting optimality system extends and sharpens recent results for classical free end-time problems to the non-Lipschitz, discontinuous framework of sweeping processes. The relevance of the transversality conditions obtained in this article is illustrated through two simple examples.

  • 3 authors
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Oct 6

Semigroup Solutions for A Multilayered Filtration System

We investigate solutions to a coupled system of partial differential equations that describe a multilayered filtration system. Namely, we study the interaction of a viscous incompressible flow with bulk poroelasticity, via a poroelastic interface. The configuration consists of two 3D toroidal subdomains connected via a plate interface, which permits elastic deformation and perfusive fluid dynamics. The governing dynamics comprise Stokes equations in the bulk fluid region, Biot's equations in the bulk poroelastic region, and the recent poroplate of Mikelić at the interface. Coupling occurs on the top and lower surfaces of the plate, and involves conservation of mass, stress balance, and a certain slip condition for the fluid free-flow. We seek strong (and mild) solutions in the Hilbert space framework via the Lumer-Phillips theorem. The resolvent analysis employs a nonstandard mixed variational formulation which captures the complex, multi-physics coupling at the interface. We explicitly characterize the infinitesimal generator associated to the linear Cauchy problem and establish the generation of a C_0-semigroup on a suitably chosen finite-energy space. With the semigroup in hand, we may treat elastic nonlinearities for plate displacements through perturbation theory. These result parallel those for Biot-Stokes filtration systems, and complement the recently established weak solution theory for multilayer filtrations. The agency of the semigroup straightforwardly admits structural (plate) nonlinearity into the dynamics. Future stability and regularity analyses for multilayer filtrations are also made possible by these results, as well as a comparison of spectral and regularity properties between filtration configurations, and the elucidation of the mitigating poroplate dynamics as possibly regularizing and stabilizing.

  • 3 authors
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Jan 31

Closed-form Continuous-time Neural Models

Continuous-time neural processes are performant sequential decision-makers that are built by differential equations (DE). However, their expressive power when they are deployed on computers is bottlenecked by numerical DE solvers. This limitation has significantly slowed down the scaling and understanding of numerous natural physical phenomena such as the dynamics of nervous systems. Ideally, we would circumvent this bottleneck by solving the given dynamical system in closed form. This is known to be intractable in general. Here, we show it is possible to closely approximate the interaction between neurons and synapses -- the building blocks of natural and artificial neural networks -- constructed by liquid time-constant networks (LTCs) efficiently in closed-form. To this end, we compute a tightly-bounded approximation of the solution of an integral appearing in LTCs' dynamics, that has had no known closed-form solution so far. This closed-form solution substantially impacts the design of continuous-time and continuous-depth neural models; for instance, since time appears explicitly in closed-form, the formulation relaxes the need for complex numerical solvers. Consequently, we obtain models that are between one and five orders of magnitude faster in training and inference compared to differential equation-based counterparts. More importantly, in contrast to ODE-based continuous networks, closed-form networks can scale remarkably well compared to other deep learning instances. Lastly, as these models are derived from liquid networks, they show remarkable performance in time series modeling, compared to advanced recurrent models.

  • 8 authors
·
Mar 1, 2022

Finite-Sample Approximation of Hessian-Guided Perturbed Wasserstein Gradient Flows

Wasserstein gradient flow extends gradient descent to probability measures. Its Hessian-guided perturbed variant (PWGF) adds Gaussian perturbations to escape saddle points in nonconvex problems. We investigate when its approximation by finitely many interacting particles remains accurate over growing time horizons. Our analysis retains the curvature accumulated along the population-driven reference path: negative curvature can amplify approximation errors, while subsequent positive curvature can damp their influence. This captures favorable scenarios in which temporary instability is compatible with accurate tracking over growing horizons. Under regularity assumptions and a prescribed common perturbation schedule, we prove particle and objective-value tracking bounds on a high-probability event for reference paths satisfying explicit conditions on accumulated curvature. To handle state-dependent Gaussian jumps, we construct a population-first coupling that preserves the reference particles' conditional independence and reduces jump errors to covariance comparison. We verify the conditions in a variance-plus-cosine model, where curvature recovery yields a growing-horizon tracking guarantee. We also establish local attraction, transverse descent, and positive second variation in two regions of a regularized matrix-factorization model, motivating a positive-negative-positive curvature pattern.

  • 3 authors
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Oct 6

Stable by Construction: Variational Latent Markov Operators for Long-Horizon PDE Prediction

Neural PDE solvers provide efficient surrogates for time-dependent physical systems, but autoregressive prediction over long horizons remains challenging because local errors can induce distribution shift and accumulate under recursive deployment. We develop a variational approach to this problem by introducing latent Markov dynamics in which physical states are represented by latent distributions and evolved through probabilistic transitions. The framework is formulated directly on function spaces and specialized to functional Gaussian models, where structured latent perturbations induce a spectral geometry and variational transition alignment regularizes the learned dynamics. We further analyze how these mechanisms affect autoregressive error propagation, providing a theoretical connection between variational training and long-horizon prediction. We instantiate the framework as the Variational Autoencoding Markov Operator (VAMO), which combines spatially resolved latent fields, structured Gaussian perturbations, and a neural-operator transition. Empirically, we demonstrate the effectiveness of VAMO on several fluid-dynamics benchmarks with prediction horizons extending substantially beyond those represented during training, where it consistently reduces error accumulation and improves rollout stability over several deterministic and noise-injection baselines. Overall, these results highlight variational modeling as a complementary approach to robust long-horizon neural PDE dynamics.

  • 3 authors
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Sep 14

A Numerical Realization of Suzuki's Weil-Quadratic-Form Operator: The Archimedean Spectral Law, its Universality, and an Operator Form of Weil's Positivity Criterion

This paper presents the first numerical realization of Suzuki's Weil-Quadratic-Form operator, a candidate for the Hilbert--Pólya program linking spectral positivity to the Riemann Hypothesis (RH). Suzuki's 2026 construction was purely theoretical; here, the operator is instantiated via P1 finite-element discretization and Richardson extrapolation. Key results include: (R1) In the prime-free regime, the spectrum follows a closed Archimedean law A_k(a) = log(1/a) + log(k-2) + B_0 + O(a), with B_0 = log q - 2log 2, confirmed to 30-digit precision. (R2) A Mellin double-pole argument proves the head coefficient B(ν) and shows B_0 depends only on the conductor q, independent of the Archimedean parameter. (R2b) The degree d of an L-function appears directly as the logarithmic slope of the spectrum. (R3) Total spectral intensity follows the prime number theorem, S(a) sim (2a)^3/6. (R4) Nontrivial zeros are not eigenvalues but occur in the explicit-formula error term of the prime symbol. (R5) The best-match line σ^*(a) descends toward the critical line. (R6) Weil's positivity criterion is realized in operator form: bounded residual growth corresponds to all zeros on the line, while an injected off-line zero causes exponential blow-up. (R7) The lowest eigenvalue λ_1(a) is strictly positive, decays superexponentially, and passes smoothly through the first prime threshold. (R8) The characteristic function W(a,0;z) is computed for the first time, with all zeros confirmed real. (R9) Indirect traces of GUE statistics appear in the moment structure, even where direct detection is blocked. The authors emphasize that this work does not prove RH. All results are Archimedean and universal, with significance lying in the faithful numerical realization of classical identities rather than new arithmetic.

  • 7 authors
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Jul 22

Generalizable single-cell perturbation response prediction using energy-guided flow matching

Predicting phenotypic and transcriptional responses to perturbations at single-cell resolution provides a powerful tool for probing biological systems. However, existing methods typically rely on fixed mappings learned during training, making it challenging to calibrate distribution shifts or adapt to novel perturbation conditions during inference. Here, we present scEGFlow, an energy-guided flow matching framework that dynamically bridges control and perturbed cellular states. scEGFlow models continuous transitions from control cell populations to perturbed states using conditional flow matching. It then applies condition-specific energy gradients to correct and steer these predictions, enabling flexible adjustments without retraining the flow model. Evaluations across benchmarks spanning imaging phenotypes and transcriptomic profiles show that scEGFlow outperforms existing methods in reconstructing response distributions under both seen and unseen perturbation conditions, faithfully preserving cellular manifold geometry and population heterogeneity. This advantage is notable when adapting to new conditions with only a few measured cells, consistently improving prediction accuracy. Furthermore, scEGFlow accurately recapitulates perturbation-induced up- and down-regulation patterns across consensus gene expression signatures, where energy guidance improves the agreement between predicted and observed regulatory directions. Ultimately, these findings demonstrate that scEGFlow provides a modular, generalizable, and steerable solution for single-cell perturbation modeling. By grounding generative flows in learned biological landscapes, this architecture establishes a new computational paradigm for navigating and manipulating cellular behavior in silico.

  • 6 authors
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Sep 26

The Implicit Regularization of Dynamical Stability in Stochastic Gradient Descent

In this paper, we study the implicit regularization of stochastic gradient descent (SGD) through the lens of {\em dynamical stability} (Wu et al., 2018). We start by revising existing stability analyses of SGD, showing how the Frobenius norm and trace of Hessian relate to different notions of stability. Notably, if a global minimum is linearly stable for SGD, then the trace of Hessian must be less than or equal to 2/eta, where eta denotes the learning rate. By contrast, for gradient descent (GD), the stability imposes a similar constraint but only on the largest eigenvalue of Hessian. We then turn to analyze the generalization properties of these stable minima, focusing specifically on two-layer ReLU networks and diagonal linear networks. Notably, we establish the {\em equivalence} between these metrics of sharpness and certain parameter norms for the two models, which allows us to show that the stable minima of SGD provably generalize well. By contrast, the stability-induced regularization of GD is provably too weak to ensure satisfactory generalization. This discrepancy provides an explanation of why SGD often generalizes better than GD. Note that the learning rate (LR) plays a pivotal role in the strength of stability-induced regularization. As the LR increases, the regularization effect becomes more pronounced, elucidating why SGD with a larger LR consistently demonstrates superior generalization capabilities. Additionally, numerical experiments are provided to support our theoretical findings.

  • 2 authors
·
May 27, 2023

A Kinetic Concentration criterion for Large-data Boltzmann Dynamics

We establish a conditional theory of genuinely non-perturbative global dynamics for the cutoff Boltzmann equation with hard potentials on the three-dimensional torus. We prove that any global mild solution satisfying \[ \sup_{t\ge0}\int_{\mathbb R^3}W(v)\sup_{x\in\mathbb T^3}F(t,x,v)\,dv<\infty, \] for a suitable stretched-exponential weight \(W\), enjoys uniform weighted \(L^\infty\) control, is unique in the dissipative mild class, and converges exponentially to the global Maxwellian. In particular, these conclusions hold for arbitrary-amplitude solutions admitting a uniform stretched-exponential velocity upper bound. The key mechanism is a *tail-to-coercivity principle*: uniform velocity-tail control generates positive lower bounds for the local density and nonlinear collision frequency, without imposing macroscopic coercivity a priori. A double-Duhamel positivity argument also generates a Gaussian lower bound at arbitrarily short positive times, allowing initial data with local vacuum. We establish a polynomially weighted counterpart under an additional spatially uniform lower velocity profile, obtaining analogous weighted \(L^\infty\) bounds, uniqueness, and exponential relaxation. Our results provide a low-regularity alternative to conditional theories requiring smoothness and pointwise macroscopic bounds. They reveal how a single velocity-tail condition controls large-data Boltzmann dynamics and suggest a route toward problems with physical boundary conditions.

  • 5 authors
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Oct 7

Incremental Sheaf Cohomology on Cellular Complexes: O(1)-in-n Lazy Edit Processing under Bounded Local Geometry

We present an algorithmic framework for incremental maintenance of first sheaf cohomology H^1(X; F) on dynamically evolving 1-dimensional cellular complexes equipped with finite-dimensional cellular sheaves. The classical computation of H^1 via factorization of the coboundary matrix requires O(n^3) time; when the complex evolves with a stream of m edits, full recomputation after each edit costs O(mn^3). Under a bounded local geometry assumption -- bounded cell size v_{max}, bounded stalk dimension d, and bounded nerve degree D -- each edit (vertex insertion, edge insertion, restriction map update) affects only a bounded set of local coboundary blocks. The algorithm therefore processes lazy streaming edits in O(1) time with respect to the total complex size n (with cost polynomial in the local geometry parameters v_{max}, d, and D, which are treated as constants independent of n), deferring local eigensolves and Mayer-Vietoris global assembly to synchronization points (Flush). At synchronization, the maintained state agrees with the corresponding batch assembly of the partitioned sheaf model; we observe zero measured drift in all batch-verified runs (through V = 10^6). We also give an amortized O(|E|) streaming construction for the cellular decomposition and discuss an adversarial algebraic-RAM barrier arguing that unpartitioned non-trivial sheaves (d geq 2, non-identity restriction maps) do not admit the same locality. Experiments on Barabasi-Albert graphs with up to 5 times 10^6 vertices and 1.7 times 10^7 streaming edits show 35 μs median lazy per-edit update latency (excluding flush); query time (global assembly at synchronization) is O(n) per flush in the implemented full-traversal path. Exact synchronization costs are reported separately.

  • 1 authors
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Jun 5

Well-Posedness of a Coupled Brinkman--Biofilm--Nutrient System with Volume-Fraction Constraints

We investigate a coupled system of partial differential equations modeling the interaction between Brinkman flow, biofilm evolution, and nutrient transport in a porous medium. The model captures the mutual influence between the fluid velocity and the biofilm through drag and diffusion coefficients that depend on the local biofilm volume fraction. A hard constraint on the admissible range of the biofilm fraction is incorporated through the subdifferential of an indicator functional, which leads naturally to an evolution variational inequality formulation for the biofilm dynamics. Assuming standard coercivity, ellipticity, and growth conditions on the model coefficients and reaction terms, we prove the global-in-time existence of weak solutions. The analysis relies on a decomposition of the system into three interconnected subproblems: the Brinkman equation with a fixed biofilm profile, the constrained biofilm evolution treated through maximal monotone operator theory, and the nutrient equation viewed as a semilinear parabolic problem. These components are then coupled through a Leray--Schauder type fixed-point argument, with the passage to the limit justified by Aubin--Lions and Simon compactness results. We further establish the nonnegativity of the nutrient concentration under a natural quasi-positivity assumption on the reaction term. Finally, we provide conditional uniqueness results for weak solutions in two spatial dimensions under additional smallness assumptions.

  • 2 authors
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Jun 30

SPIN: Image Immunization Against Diffusion Editing via Single-Step Projection in Stochastic Neighborhoods

Diffusion models have greatly advanced instruction-guided image editing, while also raising concerns about unauthorized image manipulation. Image immunization addresses this risk by adding imperceptible perturbations to an input image to disrupt subsequent edits. Since editing requests are unknown at image release, protection should remain effective beyond the instruction used to construct the perturbation. Existing immunization methods either require costly full-trajectory backpropagation or use intermediate objectives whose effects may be weakened by subsequent denoising. Meanwhile, a single inference path provides limited feedback about alternative denoising continuations. To address these challenges, we propose SPIN, a framework for image immunization via one-step projection over local stochastic trajectory neighborhoods. Starting from an early denoising state, SPIN generates stochastic neighboring states under the same instruction and predicts their clean latents through one-step projection without full unrolling. We then optimize a bounded input perturbation to maximize the average deviation of these predictions from a clean-edit reference, encouraging the perturbation to disrupt multiple possible editing outcomes. Experiments on two image editors demonstrate substantial gains in protection performance, with SPIN outperforming compared methods across all six metrics under seen instructions and in the more challenging unseen instruction setting.

  • 6 authors
·
Oct 4

Plunge bounds for Fourier concentration operators: geometry, smoothing, and wave packets

We prove a single-logarithm bound for the eigenvalues in the plunge region of Fourier concentration operators, removing the extra logarithmic factor in the Kulikov--Dam Larsen bound for two general admissible sets throughout each fixed exponential window. For bounded spatial and frequency sets A,BsubsetR^d of positive measure with finite upper codimension-one Minkowski boundary content, the number Λ_varepsilon(cA,B) of eigenvalues in (varepsilon,1-varepsilon) satisfies Λ_varepsilon(cA,B)le C(d,A,B,β)c^{d-1}D(1+log_+(c/D)), where D=log(1/(varepsilon(1-varepsilon))), for every fixed β>0, cge2, 0<varepsilon<1/2, and Dleβc, with log_+t=max(0,log t). The argument uses positive band-limited smoothing and requires no symmetry, convexity, or connectedness. In dimension two, the corresponding exponential-window estimate has a constant uniform in the window parameter. We also determine the optimal coordinate-Lipschitz constant d-1 for recursive decompositions of balls and standard simplices in every dimension, and obtain box-frequency estimates with explicit geometric constants. For C^1 convex bodies in three dimensions, the optimal infimum of recursive coordinate slopes is 2. Uniform real-order Bessel estimates give independent disk and ball bounds at every spectral threshold, including an explicit deep-tail term. For smooth strictly convex planar frequency bodies with positive curvature, we prove correlation estimates for aligned Gaussian packets at arbitrary relative scales and quantitative lower bounds on the cost of estimating spatial blocks separately. Together these results connect the global spectral bound with sharp geometric constructions and the cancellation retained by grouping boundary interactions.

  • 1 authors
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Oct 6

STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations

Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their genomic locus, including different transcription start sites and regulatory elements. Gene-level perturbation models collapse these distinct interventions into the same representation. We introduce STRAND, a generative model that predicts single-cell transcriptional responses by conditioning on regulatory DNA sequence. STRAND represents a perturbation by encoding the sequence at its genomic locus and uses this representation to parameterize a conditional transport process from control to perturbed cell states. Representing perturbations by sequence, rather than by a fixed set of gene identifiers, supports zero-shot inference at loci not seen during training and expands inference-time genomic coverage from ~1.5% for gene-level single-cell foundation models to ~95% of the genome. We evaluate STRAND on CRISPR perturbation datasets in K562, Jurkat, and RPE1 cells. STRAND improves discrimination scores by up to 33% in low-sample regimes, achieves the best average rank on unseen gene perturbation benchmarks, and improves transfer to novel cell lines by up to 0.14 in Pearson correlation. Ablations isolate the gains to sequence conditioning and transport, and case studies show that STRAND resolves functionally alternative transcription start sites missed by gene-level models.

  • 8 authors
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Feb 9

PerturbBridge: Direct Phenotypic Supervision for Cellular Perturbation Generation

Virtual cell models should capture phenotypes induced by specific perturbations. However, image-based models are typically trained and evaluated to match real-image distributions, which alone does not explicitly prioritize perturbation-specific biological responses. Recent approaches add biological signals through reinforcement-learning post-training or inference-time steering, raising a central question: where should biological response information enter the generative pipeline? We introduce PerturbBridge, a stochastic data-to-data bridge model that directly supervises perturbation-specific phenotypes in predicted perturbed images during training. PerturbBridge jointly optimizes bridge regression and differentiable biological response losses, with biological gradients passing through a frozen image encoder. We further introduce perturbation-response evaluations based on downstream classification and retrieval. Across three microscopy benchmarks for perturbation profiling and subcellular imaging, PerturbBridge surpasses CellFlux in biological fidelity, image quality, and sampling efficiency. On BBBC021, mechanism-of-action classification improves by 5.66 and 7.5 percentage points with morphological and learned visual features, respectively. On JUMP and AllenCell, retrieval Hit@10 and Hit@1 improve by 1.77 and 7.15 percentage points, respectively. On BBBC021 and JUMP, PerturbBridge achieves lower FID with 80% fewer model evaluations than CellFlux. Overall, these results show that directly supervising perturbation responses during training improves phenotypic fidelity while enabling efficient cellular image generation. Code is available at https://github.com/yyc1215lll-creator/PerturbBridge.

  • 6 authors
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Oct 11

MintFlow: Minimal Trajectory Intervention for Constrained Flow Matching

Flow matching models excel at generative modeling, and many downstream applications require their samples to satisfy prescribed constraints, such as observed measurements and physical laws. However, existing constrained samplers often face a trade-off: enforcing constraints can substantially displace samples from the pretrained data distribution. To address this trade-off, we introduce MintFlow, a training-free constrained sampling framework that formulates constraint enforcement as a minimal intervention on the pretrained flow trajectory. MintFlow seeks the minimal perturbation of an intermediate flow state such that its subsequent evolution under the pretrained flow field satisfies the target constraint. By minimally perturbing the flow state while keeping the pretrained flow field unchanged, MintFlow enforces the constraint while minimizing unnecessary deviation from the pretrained distribution. An adjoint formulation yields a closed-form expression for this perturbation, eliminating expensive iterative optimization. Furthermore, MintFlow adaptively selects the intervention time to balance the required perturbation magnitude with its amplification by the remaining flow. Across a range of tasks in generative vision and physical system modeling, MintFlow achieves competitive constraint satisfaction while preserving the pretrained generative distribution substantially better than state-of-the-art constrained methods.

  • 5 authors
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Sep 29

Extensions of Schoen--Simon--Yau and Schoen--Simon theorems via iteration à la De Giorgi

We give an alternative proof of the Schoen--Simon--Yau curvature estimates and associated Bernstein-type theorems (1975), and extend the original result by including the case of 6-dimensional (stable minimal) immersions. The key step is an ε-regularity theorem, that assumes smallness of the scale-invariant L^2 norm of the second fundamental form. Further, we obtain a graph description, in the Lipschitz multi-valued sense, for any stable minimal immersion of dimension ngeq 2, that may have a singular set Σ of locally finite H^{n-2}-measure, and that is weakly close to a hyperplane. (In fact, if H^{n-2}(Σ)=0, the conclusion is strengthened to a union of smooth graphs.) This follows directly from an ε-regularity theorem, that assumes smallness of the scale-invariant L^2 tilt-excess (verified when the hypersurface is weakly close to a hyperplane). Specialising the multi-valued decomposition to the case of embeddings, we recover the Schoen--Simon theorem (1981). In both ε-regularity theorems the relevant quantity (respectively, length of the second fundamental form and tilt function) solves a non-linear PDE on the immersed minimal hypersurface. The proof is carried out intrinsically (without linearising the PDE) by implementing an iteration method à la De Giorgi (from the linear De Giorgi--Nash--Moser theory). Stability implies estimates (intrinsic weak Caccioppoli inequalities) that make the iteration effective despite the non-linear framework. (In both ε-regularity theorems the method gives explicit constants that quantify the required smallness.)

  • 1 authors
·
Sep 11, 2025

Don't Waste the Noise: Importance-Guided Perturbation Allocation under Joint Global and Local Constraints

Adversarial optimization under a shared ell_1 budget requires deciding not only how much perturbation to use, but also where that limited budget should be spent. This allocation problem becomes particularly important when individual input coordinates are subject to local magnitude constraints, which restrict the extent to which perturbation can be concentrated on a small number of locations. We introduce an importance-guided allocation mechanism that uses a fixed clean-gradient prior to steer perturbation toward model-sensitive regions while leaving the feasible perturbation set unchanged. A centered allocation objective encourages perturbation at above-average importance locations and discourages unnecessary expenditure elsewhere, thereby redistributing rather than enlarging the available budget. Across ten robust model--dataset configurations under a common capacity-limited threat setting, the proposed method improves attack success over matched APGD- and PMA-based baselines by 2.52 to 17.70 percentage points. Allocation analysis shows that these gains are accompanied by substantially greater perturbation mass in high-importance regions without increased global ell_1 consumption. Mechanism ablations further show that centered non-uniform redistribution provides part of the benefit, while model-derived importance yields an additional improvement. These results identify perturbation allocation as a distinct and practically relevant dimension of adversarial optimization under shared-budget, locally constrained threat models.

  • 2 authors
·
Sep 30

Evaluating the Robustness of Proof Autoformalization in Lean 4

Proof autoformalization aims to translate a mathematical informal proof written in natural language into a formal proof in a formal language such as Lean~4. Several works have developed LLM-based models for proof autoformalization. However, existing evaluations have typically focused on translating well-formed informal proofs from curated datasets. We argue that a robust proof autoformalizer must remain faithful even for informal proofs that diverge from these idealized ones, and we present the first study on the robustness of proof autoformalization models. We formulate two categories of perturbations and evaluate robustness under each: a global perturbation paraphrases the informal proof in a different style, under which the formalization should remain consistent; a local perturbation alters a value, symbol, or proof step, possibly in a counterfactual way, and a robust formalization should faithfully reflect the perturbation rather than reverting to the original one or inferring a different one on its own. We build a benchmark with both perturbations on miniF2F and MATH-500, and automatically measure how stable a proof autoformalization's correctness is under global perturbations and how faithfully its output reflects local perturbations. We evaluate seven recent models, all of which are sensitive to global perturbations and mostly fail to remain faithful under local perturbations. Code and data are available via https://github.com/ucr-rai/robust-proof-autoformalization.

  • 3 authors
·
Jun 11

Parabolic-elliptic and indirect-direct simplifications in chemotaxis systems driven by indirect signalling

Singular limits for the following indirect signalling chemotaxis system align* \left\{ array{lllllll} \partial_t n = \Delta n - \nabla \cdot (n \nabla c ) & in \Omega\times(0,\infty) , \varepsilon \partial_t c = \Delta c - c + w & in \Omega\times(0,\infty), \varepsilon \partial_t w = \tau \Delta w - w + n & in \Omega\times (0,\infty), \partial_\nu n = \partial_\nu c = \partial_\nu w = 0, &on \partial\Omega\times (0,\infty) %(n,c,w)_{t=0} = (n_0,c_0,w_0) & on \Omega, array \right. align* are investigated. More precisely, we study parabolic-elliptic simplification, or PES, varepsilonto 0^+ with fixed tau>0 up to the critical dimension N=4, and indirect-direct simplification, or IDS, (varepsilon,tau)to (0^+,0^+) up to the critical dimension N=2. These are relevant in biological situations where the signalling process is on a much faster time scale compared to the species diffusion and all interactions. Showing singular limits in critical dimensions is challenging. To deal with the PES, we carefully combine the entropy function, an Adam-type inequality, the regularisation of slow evolution, and an energy equation method to obtain strong convergence in representative spaces. For the IDS, a bootstrap argument concerning the L^p-energy function is devised, which allows us to obtain suitable uniform bounds for the singular limits. Moreover, in both scenarios, we also present the convergence rates, where the effect of the initial layer and the convergence to the critical manifold are also revealed.

  • 4 authors
·
Aug 2, 2025

A Machine-Checked Itô Calculus for Brownian Motion

We develop the Itô calculus of Brownian motion, machine-checked in Lean~4 over Mathlib and the BrownianMotion package. On a bounded interval [0,T] the Itô integral is built as a Hilbert-space isometry, from a predictable-rectangle π-system through the density of simple adapted processes. Realized as a process, it is a continuous L^2 martingale. One structural identity drives this: the integral at time t is the conditional-expectation projection of its terminal value onto F_t, and from it adaptedness, the martingale property, the contraction bound, and both the terminal and time-indexed Itô isometries follow as corollaries. On this integral we prove Itô's formula for C^3 functions with bounded derivatives, including the time-dependent form df = f_x,dB + (f_t + tfrac12 f_{xx}),dt, by a discrete-to-continuous argument through weighted quadratic variation with explicit L^2 remainder bounds. We then pass from the L^2 theory to the pathwise. The integral process has an almost-surely continuous modification, and its everywhere-continuous representative is a local martingale for the null-augmented Brownian filtration; gluing the bounded-horizon representatives along the half-line yields the Itô integral as a continuous local martingale on all of R_{ge 0}, the form it takes in the classical theory. To our knowledge these are the first machine-checked constructions of the Itô integral and of Itô's formula in any proof assistant, and the first to reach a pathwise-continuous local martingale. The boundary is explicit. The L^2 integral and Itô's formula are developed on [0,T] with bounded-derivative integrands; the unrestricted C^2 formula, integrators beyond brownian motion, and right-continuity of the filtration lie outside the development.

Taming the Loss Landscape of PINNs with Noisy Feynman-Kac Supervision: Operator Preconditioning and Non-Asymptotic Error Bounds

Physics-Informed Neural Networks (PINNs) often train slowly or fail to converge on challenging partial differential equations (PDEs), a behavior recently linked to severely ill-conditioned loss landscapes inherited from the underlying differential operator. We study PINNs augmented with a pointwise data-fidelity term, added at a few points in the domain to the standard residual and boundary losses. We show that this supervision term acts as an operator-level preconditioner: for suitable weights, our comparison bounds guarantee a substantially smaller condition number than under the standard PINN loss, independently of how the pointwise labels are obtained. For a broad class of PDEs admitting a Feynman-Kac (FK) representation, we generate such labels by Monte Carlo averages of the FK functional, resulting in what we call ``FK-PINNs", and using the excess risk decomposition approach, we derive non-asymptotic L^2(Ω)-error bounds for FK-PINNs with tanh activation trained by finitely many steps of gradient descent. Along the way, we establish pseudo-dimension bounds for first- and second-order derivatives of tanh neural networks, which are of independent interest and, to the best of our knowledge, new. Numerical experiments on Poisson, Schrödinger, mean exit time, and committor problems corroborate the theory, and show that FK-PINNs can successfully solve PDEs for which standard PINNs exhibit severe failure modes.

  • 4 authors
·
May 29

On the transmission of floating-point perturbations in flow-dependent filter-width formulations in Large-Eddy Simulation

Heterogeneous high--performance computing architectures expose numerical algorithms to perturbations arising from the non--associativity of floating--point arithmetic. In Large--Eddy Simulation (LES), similar numerical effects may become relevant when they affect the filter--width entering the subgrid scale (SGS) model. This work investigates this mechanism for the least--squares (LSQ) based filter--width formulation, focusing on how floating--point effects are generated, transmitted, and coupled with the resolved flow. We show that, for fixed resolved kinematics, the LSQ filter--width is logarithmically non-expansive but not strictly contractive with respect to perturbations of the mesh metrics. Consequently, small disturbances may be transmitted with little attenuation through strongly directional filter-width responses. To mitigate this sensitivity, we introduce a scalar max--min compression of the directional mesh scales together with a bounded modulation based on the resolved velocity gradient. The resulting formulation reroutes floating--point perturbations through the filter-width operator, improving robustness while preserving the flow--dependent character of the original LSQ construction. The framework is assessed on heterogeneous CPU and GPU architectures for flow past a circular cylinder at Re=3900 and the Taylor--Green vortex at Re=1600. In the former, nearly one--to--one transmission of relative metric disturbances can become relevant when the transmitted perturbations interact with shear-layer transition. By contrast, on orthogonal Taylor--Green vortex grids, the accumulation pathway is structurally absent and no comparable macroscopic response develops. These results suggest floating--point sensitivity matters for LES filter--width formulations in heterogeneous computing environments.

  • 4 authors
·
Sep 30

Uncertainty propagation in auto-regressive random neural network models

We develop analytical and particle-based methods for uncertainty propagation in random neural network models, where both the inputs and network parameters are allowed to be random. Building on the piecewise-linear structure of the Leaky ReLU activation function, we derive a local approximation of the neural network output with respect to perturbations in both its inputs and parameters. This approximation is exact for perturbations that preserve the network activation pattern, and it allows us to compute analytical expressions for the probability density function and characteristic function of the network output, together with closed-form approximations for its mean and covariance. We extend this uncertainty propagation framework to autonomous dynamical systems whose one-step evolution map is represented by a random neural network. Repeated application of this map defines an autoregressive model, for which we derive recursive equations to propagate uncertainty in both the state and network parameters over time. These equations explicitly account for the state-parameter cross-covariance that develops under successive iterations of the network. Numerical experiments on the Lorenz-63 system and the Kuramoto-Sivashinsky equation demonstrate accurate uncertainty propagation through the predictability horizon and the applicability of the proposed framework to high-dimensional dynamical systems.

  • 2 authors
·
Aug 19

TopoReformer: Mitigating Adversarial Attacks Using Topological Purification in OCR Models

Adversarially perturbed images of text can cause sophisticated OCR systems to produce misleading or incorrect transcriptions from seemingly invisible changes to humans. Some of these perturbations even survive physical capture, posing security risks to high-stakes applications such as document processing, license plate recognition, and automated compliance systems. Existing defenses, such as adversarial training, input preprocessing, or post-recognition correction, are often model-specific, computationally expensive, and affect performance on unperturbed inputs while remaining vulnerable to unseen or adaptive attacks. To address these challenges, TopoReformer is introduced, a model-agnostic reformation pipeline that mitigates adversarial perturbations while preserving the structural integrity of text images. Topology studies properties of shapes and spaces that remain unchanged under continuous deformations, focusing on global structures such as connectivity, holes, and loops rather than exact distance. Leveraging these topological features, TopoReformer employs a topological autoencoder to enforce manifold-level consistency in latent space and improve robustness without explicit gradient regularization. The proposed method is benchmarked on EMNIST, MNIST, against standard adversarial attacks (FGSM, PGD, Carlini-Wagner), adaptive attacks (EOT, BDPA), and an OCR-specific watermark attack (FAWA).

Neural Network Approximations of PDEs Beyond Linearity: A Representational Perspective

A burgeoning line of research leverages deep neural networks to approximate the solutions to high dimensional PDEs, opening lines of theoretical inquiry focused on explaining how it is that these models appear to evade the curse of dimensionality. However, most prior theoretical analyses have been limited to linear PDEs. In this work, we take a step towards studying the representational power of neural networks for approximating solutions to nonlinear PDEs. We focus on a class of PDEs known as nonlinear elliptic variational PDEs, whose solutions minimize an Euler-Lagrange energy functional E(u) = int_Omega L(x, u(x), nabla u(x)) - f(x) u(x)dx. We show that if composing a function with Barron norm b with partial derivatives of L produces a function of Barron norm at most B_L b^p, the solution to the PDE can be epsilon-approximated in the L^2 sense by a function with Barron norm Oleft(left(dB_Lright)^{max{p log(1/ epsilon), p^{log(1/epsilon)}}}right). By a classical result due to Barron [1993], this correspondingly bounds the size of a 2-layer neural network needed to approximate the solution. Treating p, epsilon, B_L as constants, this quantity is polynomial in dimension, thus showing neural networks can evade the curse of dimensionality. Our proof technique involves neurally simulating (preconditioned) gradient in an appropriate Hilbert space, which converges exponentially fast to the solution of the PDE, and such that we can bound the increase of the Barron norm at each iterate. Our results subsume and substantially generalize analogous prior results for linear elliptic PDEs over a unit hypercube.

  • 4 authors
·
Oct 21, 2022

Stochastic gradient descent on the epigenetic landscape: a unified framework for cellular plasticity, tumor heterogeneity, and the asymptotic irrelevance of fitness

Phenotypic plasticity, the ability of cells to switch between states, is central to development, differentiation, and therapy resistance. Although it is modeled at several scales, from compartmental ODEs to phenotype-structured PDEs and single-cell stochastic equations, a framework connecting these descriptions is missing. We present such a framework. Starting from a general n-compartment ODE model encompassing nonlinear growth and linear transitions between phenotypes, we show, with a new, elementary and generalizable proof of a recent theorem, that under uniform competition, the long-term population distribution is solely governed by transition rates. All phenotypes become selectively neutral at saturation, and the imprint of fitness differences during growth fades at an explicit rate. Restricting transitions to neighboring states transforms the model into a discretization of a phenotype-structured reaction-diffusion-advection PDE. In this continuum model, diffusion and advection are identified from switching rates, and fitness remains asymptotically irrelevant. Interpreting the advection velocity as the negative gradient of an effective epigenetic potential transforms the PDE into a Fokker--Planck equation and converts single-cell trajectories into stochastic gradient descent (SGD) in the Langevin sense on the phenotypic landscape. Non-local transitions, such as mutations, are incorporated via an integro-differential term, yielding a unified model with reaction, gradient flow, diffusion, and jumps. State-dependent noise reshapes the effective landscape without altering the underlying potential. This gives cancer a route to elevated plasticity that static, single-cell snapshots cannot distinguish from a changed landscape. This framework provides a physical interpretation of Waddington's landscape, where cells perform SGD, and cancer corresponds to a corrupted landscape.

  • 1 authors
·
Sep 28