Daily Papers

Recent text-to-CAD approaches have shown promising results by leveraging large language models, but they often struggle with maintaining structural consistency in complex designs and accurately grounding geometric parameters. To address these issues, we propose HierCAD, a hierarchical text-to-CAD framework that improves both structural reasoning and parameter prediction. HierCAD reformulates CAD generation as progressive reasoning by decomposing CAD construction trees into object-level procedural reasoning and part-level topology reasoning trajectories. To further improve generation fidelity, we introduce a unified Structure Alignment and Parameter Grounding (SAPG) learning strategy. Structure alignment aligns topology reasoning trajectories with their corresponding parametric CAD spans, while parameter grounding mitigates shortcut learning through structure-preserving parameter perturbations and ranking-based supervision. Experiments demonstrate that HierCAD outperforms prior state-of-the-art methods on both CAD sequence generation and reconstructed CAD model evaluation. Our code is available at https://github.com/Collab-Gen/HierCAD.

Sharpness Aware Minimization (SAM) enhances performance across various neural architectures and datasets. As models are continually scaled up to improve performance, a rigorous understanding of SAM's scaling behaviour is paramount. To this end, we study the infinite-width limit of neural networks trained with SAM, using the Tensor Programs framework. Our findings reveal that the dynamics of standard SAM effectively reduce to applying SAM solely in the last layer in wide neural networks, even with optimal hyperparameters. In contrast, we identify a stable parameterization with layerwise perturbation scaling, which we call Maximal Update and Perturbation Parameterization (μP^2), that ensures all layers are both feature learning and effectively perturbed in the limit. Through experiments with MLPs, ResNets and Vision Transformers, we empirically demonstrate that μP^2 achieves hyperparameter transfer of the joint optimum of learning rate and perturbation radius across model scales. Moreover, we provide an intuitive condition to derive μP^2 for other perturbation rules like Adaptive SAM and SAM-ON, also ensuring balanced perturbation effects across all layers.

We formulate gene regulatory network reconstruction from RNA velocity as a sparse dynamical inverse problem. We show that control-only data can be structurally nonidentifying and characterize excitation conditions under which controlled perturbations restore identifiability by generating complementary regulator trajectories. To enable stable reconstruction from noisy data, we develop an integral sparse estimator that avoids numerical differentiation and derive recovery bounds separating stochastic error from systematic contributions due to latent-time uncertainty, kinetic-parameter error, numerical quadrature, and model misspecification. Synthetic experiments illustrate perturbation-assisted identifiability, improved conditioning, and the robustness of integral reconstruction. Applied to perturbation-resolved RPE1 RNA-velocity data, the framework yields an empirically full-rank design whose conditioning improves with perturbational diversity and a reconstructed network core stable under perturbation subsampling. Held-out evaluation further shows that identifiability and reconstruction stability do not imply uniform predictive improvement. These results connect perturbational excitation, identifiability, and stable sparse recovery in regulatory dynamical systems.

We study the relation between equal-weight circle quadrature, Gauss--Chebyshev quadrature, and planar Minkowski reconstruction. The regular N-point grid is an mathbb S^1-design of strength N-1; a half-step rotation of the 2M-point grid projects to the classical M-point Gauss--Chebyshev rule. A common family of quadrature-error functionals gives exact identities for integration error, mixed-area error, and support-function error. For Nge3, the centered Minkowski polygon P_N with perimeter 2π has the exact Hausdorff distance from the unit disk B^2 \[ d_H(P_N,B^2)=1-\fracπ{N}\cot\fracπ{N} =π^2{3N^2}+O(N^{-4}). \] With Steiner centering, we obtain d_H(K_μ,K_ν)leπW_1(μ,ν) for balanced, nondegenerate probability measures, where W_1 uses geodesic distance. Its exponent is sharp even for smooth positive densities near the uniform measure. The identity W_1(ν_N,σ)=π/(2N) yields a general O(N^{-1}) bound for the regular grid. The sharper O(N^{-2}) rate follows from the sparse discrepancy spectrum and the inverse multiplier (1-k^2)^{-1}. Finally, a perturbation estimate gives sufficient conditions for preserving the quadratic rate and its leading constant.

Energy-based models (EBMs) implement inference as gradient descent on a learned Lyapunov function, yielding interpretable, structure-preserving alternatives to black-box neural ODEs and aligning naturally with physical AI. Yet their use in system identification remains limited, and existing architectures lack formal stability guarantees that globally preclude unstable modes. We address this gap by introducing an EBM framework for system identification with stable, dissipative, absorbing invariant dynamics. Unlike classical global Lyapunov stability, absorbing invariance expands the class of stability-preserving architectures, enabling more flexible and expressive EBMs. We extend EBM theory to nonsmooth activations by establishing negative energy dissipation via Clarke derivatives and deriving new conditions for radial unboundedness, exposing a stability-expressivity tradeoff in standard EBMs. To overcome this, we introduce a hybrid architecture with a dynamical visible layer and static hidden layers, prove absorbing invariance under mild assumptions, and show that these guarantees extend to port-Hamiltonian EBMs. Experiments on metric-deformed multi-well and ring systems validate the approach, showcasing how our hybrid EBM architecture combines expressivity with sound and provable safety guarantees by design.

Differentiable matching layers and residual connection paradigms, often implemented via entropy-regularized Optimal Transport (OT), serve as critical mechanisms in structural prediction and architectural scaling. However, recovering discrete permutations or maintaining identity mappings via annealing εto 0 is notoriously unstable. In this work, we identify a fundamental mechanism for this failure: Premature Mode Collapse. By analyzing the non-normal dynamics of the Sinkhorn fixed-point map, we reveal a theoretical thermodynamic speed limit: standard exponential cooling outpaces the contraction rate of the inference operator, which degrades as O(1/ε). To address this, we propose Efficient Piecewise Hybrid Adaptive Stability Control (EPH-ASC), an adaptive scheduling algorithm that monitors the stability of the inference process. We demonstrate that EPH-ASC is essential for stabilizing Manifold-Constrained Hyper-Connections (mHC) during large-scale training on the FineWeb-Edu dataset, effectively preventing late-stage gradient explosions by enforcing a linear stability law.

Data-driven surrogate models are an alternative to numerical homogenization of heterogeneous materials. In this contribution, a supervised learning approach is presented for predicting effective Lamé parameters of hyperelastic composites from low-dimensional microstructural descriptors. The data set is based on previously published numerical homogenization results for ensembles of two-phase stochastic microstructures generated by planar Boolean models, covering variations of inclusion shape, phase contrast, and area fraction; see Brändel, Brands, Maike, Rheinbach, Schröder, Schwarz and Stoyan (2022). A neural network is trained on combinations of scalar and curve-valued statistical descriptors, including the area fraction, a derived scalar shape descriptor τ, the two-point correlation function S_2(r), and the lineal-path function ell(z). Additional data representing limiting cases of the parameter space are incorporated to stabilize training and improve extrapolation behavior. The surrogate is evaluated by leave-one-grain-type-out cross-validation in order to assess generalization to unseen grain geometries. Numerical results demonstrate that additional descriptors can reduce relative errors. A predictor trained with τ and S_2(r) provides a compact representation with good quantitative accuracy and regular dense response behavior. Adding the lineal-path function ell(z) further reduces the error at the available data points, indicating that it is a promising additional descriptor; however, dense post-training response evaluations show that improved pointwise accuracy does not automatically guarantee physically admissible behavior between sampled parameter values. This motivates future work on physically constrained surrogate models, loss formulations, bounded output parametrizations, and a more systematic representation of curve-valued geometric descriptors.

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.

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.

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.

Numerical simulations in climate, chemistry, or astrophysics are computationally too expensive for uncertainty quantification or parameter-exploration at high-resolution. Reduced-order or surrogate models are multiple orders of magnitude faster, but traditional surrogates are inflexible or inaccurate and pure machine learning (ML)-based surrogates too data-hungry. We propose a hybrid, flexible surrogate model that exploits known physics for simulating large-scale dynamics and limits learning to the hard-to-model term, which is called parametrization or closure and captures the effect of fine- onto large-scale dynamics. Leveraging neural operators, we are the first to learn grid-independent, non-local, and flexible parametrizations. Our multiscale neural operator is motivated by a rich literature in multiscale modeling, has quasilinear runtime complexity, is more accurate or flexible than state-of-the-art parametrizations and demonstrated on the chaotic equation multiscale Lorenz96.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

The problem of attribution is concerned with identifying the parts of an input that are responsible for a model's output. An important family of attribution methods is based on measuring the effect of perturbations applied to the input. In this paper, we discuss some of the shortcomings of existing approaches to perturbation analysis and address them by introducing the concept of extremal perturbations, which are theoretically grounded and interpretable. We also introduce a number of technical innovations to compute extremal perturbations, including a new area constraint and a parametric family of smooth perturbations, which allow us to remove all tunable hyper-parameters from the optimization problem. We analyze the effect of perturbations as a function of their area, demonstrating excellent sensitivity to the spatial properties of the deep neural network under stimulation. We also extend perturbation analysis to the intermediate layers of a network. This application allows us to identify the salient channels necessary for classification, which, when visualized using feature inversion, can be used to elucidate model behavior. Lastly, we introduce TorchRay, an interpretability library built on PyTorch.

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.

In this paper, we study the problem of sampling from a probability distribution using Langevin-type dynamics. We consider overdamped Langevin dynamics perturbed by adding a Stratonovich perturbation that preserves reversibility. We prove an optimal scaling for the Stratonovich perturbation applied to Gaussian target distributions and derive an algorithm to construct such perturbation. Our theoretical results are supplemented by numerical experiments in which we compare our proposed method with nonreversible samplers and overdamped Langevin dynamics. Our numerical experiments demonstrate the efficiency of the approach beyond the quadratic case.

A fundamental tension exists in the large-step inference of diffusion models via their deterministic probability flow ordinary differential equation (PF-ODE) trajectories, which we identify as the contractivity trap: efficient inference favors large step sizes, while aggressive steps and highly expressive denoisers can undermine contraction-based stability certificates for error suppression. To address this, we propose SteinDiff, a step-wise inference-time stabilization framework that employs Stein-derived corrections without requiring reference samples. Specifically, SteinDiff introduces a geometry-aware residual correction mechanism that regularizes large-step solver updates without retraining. To this end, we derive a closed-form Stein correction coefficient for step-wise solver adjustment, enabling reference-free adaptation to local data geometry. We further establish a score-controlled perturbation bound under distributional shifts and provide a complementary Stein perspective on EDM-style parameterizations. Extensive experiments demonstrate that SteinDiff mitigates severe artifacts and improves generative quality across large-step inference settings.

Learning complex dynamics driven by partial differential equations directly from data holds great promise for fast and accurate simulations of complex physical systems. In most cases, this problem can be formulated as an operator learning task, where one aims to learn the operator representing the physics of interest, which entails discretization of the continuous system. However, preserving key continuous properties at the discrete level, such as boundary conditions, and addressing physical systems with complex geometries is challenging for most existing approaches. We introduce a family of operator learning architectures, structure-preserving operator networks (SPONs), that allows to preserve key mathematical and physical properties of the continuous system by leveraging finite element (FE) discretizations of the input-output spaces. SPONs are encode-process-decode architectures that are end-to-end differentiable, where the encoder and decoder follows from the discretizations of the input-output spaces. SPONs can operate on complex geometries, enforce certain boundary conditions exactly, and offer theoretical guarantees. Our framework provides a flexible way of devising structure-preserving architectures tailored to specific applications, and offers an explicit trade-off between performance and efficiency, all thanks to the FE discretization of the input-output spaces. Additionally, we introduce a multigrid-inspired SPON architecture that yields improved performance at higher efficiency. Finally, we release a software to automate the design and training of SPON architectures.

Predicting high-dimensional transcriptional responses to genetic perturbations is challenging due to severe experimental noise and sparse gene-level effects. Existing methods often suffer from mean collapse, where high correlation is achieved by predicting global average expression rather than perturbation-specific responses, leading to many false positives and limited biological interpretability. Recent approaches incorporate biological knowledge graphs into perturbation models, but these graphs are typically treated as dense and static, which can propagate noise and obscure true perturbation signals. We propose AdaPert, a perturbation-conditioned framework that addresses mean collapse by explicitly modeling sparsity and biological structure. AdaPert learns perturbation-specific subgraphs from biological knowledge graphs and applies adaptive learning to separate true signals from noise. Across multiple genetic perturbation benchmarks, AdaPert consistently outperforms existing baselines and achieves substantial improvements on DEG-aware evaluation metrics, indicating more accurate recovery of perturbation-specific transcriptional changes.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

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.

We develop a Gaussian comparison theory for posterior inference in non-Gaussian high-dimensional models. The framework allows for model misspecification and does not require the posterior distribution itself to be approximately Gaussian. Working directly with likelihood processes on separable function spaces, we establish explicit nonasymptotic free energy bounds controlled by first two moment discrepancies and local third moments. A perturbation-and-convexity argument transfers these comparisons to sandwich bounds for posterior mean squared error and posterior variance, including one-sided conclusions at nondifferentiable phase transitions. In high-dimensional product models, these conditions reduce to local moment controls and a canonical feature-radius scaling. Under weak regularity requirements, the resulting universality theory applies to a broad class of likelihood models, ranging from exponential families to more general regular local log-likelihoods. The framework is illustrated on sparse Bernoulli hypergraph inference.

Current LLM unlearning methods face a critical security vulnerability that undermines their fundamental purpose: while they appear to successfully remove sensitive or harmful knowledge, this ``forgotten" information remains precariously recoverable through relearning attacks. We identify that the root cause is that conventional methods optimizing the forgetting loss at individual data points will drive model parameters toward sharp minima in the loss landscape. In these unstable regions, even minimal parameter perturbations can drastically alter the model's behaviors. Consequently, relearning attacks exploit this vulnerability by using just a few fine-tuning samples to navigate the steep gradients surrounding these unstable regions, thereby rapidly recovering knowledge that was supposedly erased. This exposes a critical robustness gap between apparent unlearning and actual knowledge removal. To address this issue, we propose StableUN, a bi-level feedback-guided optimization framework that explicitly seeks more stable parameter regions via neighborhood-aware optimization. It integrates forgetting feedback, which uses adversarial perturbations to probe parameter neighborhoods, with remembering feedback to preserve model utility, aligning the two objectives through gradient projection. Experiments on WMDP and MUSE benchmarks demonstrate that our method is significantly more robust against both relearning and jailbreaking attacks while maintaining competitive utility performance.

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

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).

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

Predicting cellular responses to unseen chemical perturbations is challenging due to unknown targets and mechanisms, high-dimensional expression responses, and limited experimental coverage of the large small-molecule design space. We propose PerturbPFN, a PFN-style amortized model for unknown-target perturbation prediction under a hierarchical synthetic structural prior. Instead of directly regressing high-dimensional expression responses, PerturbPFN infers a latent system graph, sparse atomic intervention targets, and intervention strengths, then propagates their effects through an SCM decoder. The model is trained entirely on prior-predictive synthetic episodes generated from biologically motivated graph and expression simulators, enabling structured in-context learning without test-time gradient updates. We evaluate PerturbPFN on both real single-cell perturbation data and synthetic benchmarks, covering effect prediction, target identification, and regulatory structure discovery. Our results show that PerturbPFN offers a complementary trade-off to specialized baselines, achieving competitive perturbation prediction with low inference cost while exposing interpretable intermediate estimates of targets, strengths, and system structure.

Designing sampling algorithms for multimodal targets that remain stable under refinement of the finite-dimensional approximation of an underlying function-space problem is a central challenge. Annealed Langevin dynamics (ALD) is a natural alternative to classical Langevin in this context, since it is often observed to improve exploration across modes. Yet a gap remains between its empirical success and existing theory: under which conditions can ALD be guaranteed to remain stable across dimensions? In this paper, we bridge this gap by providing a uniform-in-dimension analysis of continuous-time ALD for Gaussian-mixture targets. Along an explicit annealing path obtained by gradually removing Gaussian smoothing from the target, we identify spectral conditions linking the smoothing covariance to the component covariances under which ALD achieves a prescribed accuracy in Kullback-Leibler divergence within a dimension-uniform time horizon. We then establish stability in a perturbative regime with imperfect initialization and approximate scores. Under a misspecified-mixture score model, we show that preconditioning ALD with an operator whose spectrum decays sufficiently fast prevents error terms from accumulating across coordinates and thereby preserves dimension-uniform control.

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.

Existing model reduction techniques for high-dimensional models of conservative partial differential equations (PDEs) encounter computational bottlenecks when dealing with systems featuring non-polynomial nonlinearities. This work presents a nonlinear model reduction method that employs lifting variable transformations to derive structure-preserving quadratic reduced-order models for conservative PDEs with general nonlinearities. We present an energy-quadratization strategy that defines the auxiliary variable in terms of the nonlinear term in the energy expression to derive an equivalent quadratic lifted system with quadratic system energy. The proposed strategy combined with proper orthogonal decomposition model reduction yields quadratic reduced-order models that conserve the quadratized lifted energy exactly in high dimensions. We demonstrate the proposed model reduction approach on four nonlinear conservative PDEs: the one-dimensional wave equation with exponential nonlinearity, the two-dimensional sine-Gordon equation, the two-dimensional Klein-Gordon equation with parametric dependence, and the two-dimensional Klein-Gordon-Zakharov equations. The numerical results show that the proposed lifting approach is competitive with the state-of-the-art structure-preserving hyper-reduction method in terms of both accuracy and computational efficiency in the online stage while providing significant computational gains in the offline stage.

A variety of methods have been proposed to try to explain how deep neural networks make their decisions. Key to those approaches is the need to sample the pixel space efficiently in order to derive importance maps. However, it has been shown that the sampling methods used to date introduce biases and other artifacts, leading to inaccurate estimates of the importance of individual pixels and severely limit the reliability of current explainability methods. Unfortunately, the alternative -- to exhaustively sample the image space is computationally prohibitive. In this paper, we introduce EVA (Explaining using Verified perturbation Analysis) -- the first explainability method guarantee to have an exhaustive exploration of a perturbation space. Specifically, we leverage the beneficial properties of verified perturbation analysis -- time efficiency, tractability and guaranteed complete coverage of a manifold -- to efficiently characterize the input variables that are most likely to drive the model decision. We evaluate the approach systematically and demonstrate state-of-the-art results on multiple benchmarks.

Existing evaluation methods largely rely on clean, static benchmarks, which can overestimate true model performance by failing to capture the noise and variability inherent in real-world user inputs. This is especially true for language models, which can face human-generated text queries containing mistakes, typos, or alternative ways of phrasing the same question. In this work, we introduce a theoretical framework for quantifying model sensitivity to prompt variants, or brittleness, that can enable us to disentangle data-induced difficulty from prompt-related variability. Using this framework, we design a novel evaluation pipeline, Brittlebench, to holistically evaluate the sensitivity of frontier models. We apply semantics-preserving perturbations to a suite of popular benchmarks, and observe model performance to degrade as much as 12%. However, these perturbations do not affect all models equally: even a single perturbation alters the relative ranking of models in 63% of cases, impacting conclusions about comparative model performance. Decomposing the total variance of both state-of-the-art open-weight and commercial models, we find that semantics-preserving input perturbations can account for up to half of the performance variance for a given model. Brittlebench highlights the need for more robust evaluations and models, and allows us to systematically understand model brittleness.

We develop a direct paradifferential approach to nonlinear graph integral operators arising in contour dynamics. The main methodological result is an abstract structure-preserving paralinearization theorem, valid in arbitrary dimension, for a class of homogeneous kernels whose nonlinear dependence on the graph is expressed through normalized finite differences. The theorem covers both critical principal-value kernels and subcritical locally integrable kernels, gives explicit formulas for the principal symbols, and separates the finite-order symbolic contribution generated by the homogeneous singularity from order-zero far-field terms and arbitrarily smoothing remainders. A structural feature of the reduction is the cancellation of the intermediate symbolic order; at the critical endpoint the construction also preserves the exact skew-adjoint structure of the original singular integral. As a main application, we consider the three-dimensional two-phase free-boundary Euler equations with constant interfacial background vorticity. We first derive an autonomous contour-dynamics equation in canonical surface variables and then apply the abstract theorem directly to the singular integral operators generated by the Birkhoff--Rott formulation. This yields the complete paradifferential structure of the system without taking the Dirichlet--Neumann reduction as a starting point. After introducing an Alinhac good unknown and diagonalizing the resulting system, we obtain local well-posedness for small Sobolev perturbations in the stable Kelvin--Rayleigh--Taylor regime, uniformly on compact subsets of the stable parameter set.

Existing works have extensively studied adversarial examples, which are minimal perturbations that can mislead the output of deep neural networks (DNNs) while remaining imperceptible to humans. However, in this work, we reveal the existence of a harmless perturbation space, in which perturbations drawn from this space, regardless of their magnitudes, leave the network output unchanged when applied to inputs. Essentially, the harmless perturbation space emerges from the usage of non-injective functions (linear or non-linear layers) within DNNs, enabling multiple distinct inputs to be mapped to the same output. For linear layers with input dimensions exceeding output dimensions, any linear combination of the orthogonal bases of the nullspace of the parameter consistently yields no change in their output. For non-linear layers, the harmless perturbation space may expand, depending on the properties of the layers and input samples. Inspired by this property of DNNs, we solve for a family of general perturbation spaces that are redundant for the DNN's decision, and can be used to hide sensitive data and serve as a means of model identification. Our work highlights the distinctive robustness of DNNs (i.e., consistency under large magnitude perturbations) in contrast to adversarial examples (vulnerability for small imperceptible noises).

Building credible simulators from data is difficult because structure design, parameter calibration, and out-of-distribution (OOD) robustness are tightly coupled. We introduce SOCIA (Simulation Orchestration for Computational Intelligence with Agents), a framework that treats simulator construction as joint structure-parameter co-optimization: it elicits mechanism-rich blueprints, exposes explicit tunable parameters, and instantiates a calibration schema, producing an executable simulator with built-in calibration hooks. SOCIA couples Bayesian Optimization for sample-efficient point calibration with Simulation-Based Inference for uncertainty-aware fitting; diagnostics trigger targeted structural edits in an outer refinement loop to co-optimize design and parameters under tight budgets. Across three diverse tasks, SOCIA consistently outperforms strong baselines, excelling on both in-distribution (ID) fitting and OOD shift. Ablations that weaken structure, calibration design, or tuning yield near-monotone degradations, underscoring the necessity of unified structure-parameter optimization. We will release the code soon.

We study the problem of recovering the parameters of a multivariate Ornstein-Uhlenbeck (OU) process from steady-state observational and interventional data. In many applications, such as large-scale gene perturbation experiments, only stationary "snapshot" measurements are available, making standard stochastic differential equation estimation methods that rely on time-series trajectories inapplicable. We first establish an identifiability result: one intervention per strongly connected component (SCC) of the drift graph suffices to recover all OU process parameters generically up to a global scaling factor. This holds provided that the SCC condensation graph is connected with a single root and certain spectral nondegeneracy assumptions hold. We propose a recursive learning algorithm that orders SCCs topologically and, for each component, isolates its marginal dynamics and solves a linear system derived from the steady-state moment equations, leveraging parameters recovered for upstream components. Building on this theoretical foundation, we propose a regularized least-squares estimator that jointly minimizes residuals of the steady-state mean and covariance equations across observational and interventional data. Experimental results validate our theoretical findings in recovering parameters of the underlying OU process.

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.

We study the parameter dependence and transversality properties of trajectories of the controlled ODE $ U_x = P, qquad P_x = - f(U) - βP + tilde α(x)U, arising from traveling-wave solutions of a bistable reaction-diffusion equation with control. Optimal profiles minimizing the L^1-norm of the control \tilde α are determined by the unstable and stable manifolds Γ_u, Γ_s, the critical curve P^*(U) = Uf(U), and the associated function F(U) = dP^*{dU} + f(U){P^*(U)}. We establish generic transversality properties for these objects with respect to perturbations of the speed β and the nonlinear source f, together with quantitative estimates on the first- and second-order dependence of the invariant manifolds on these parameters. We also analyze the loss of regularity at the critical speed β^{**}, where the unstable manifold approaches the strongly stable manifold of the equilibrium (U^*,0)$. These results provide the ODE ingredients used in the analysis of the structure and regularity of optimal profiles in paper [S. Bianchini and C. Trifone. Traveling profiles and control cost for a PDE describing the evolution of invasive species. 2026. arXiv: 2606.23979 [math.OC]].

Modern recommender systems may output considerably different recommendations due to small perturbations in the training data. Changes in the data from a single user will alter the recommendations as well as the recommendations of other users. In applications like healthcare, housing, and finance, this sensitivity can have adverse effects on user experience. We propose a method to stabilize a given recommender system against such perturbations. This is a challenging task due to (1) the lack of a ``reference'' rank list that can be used to anchor the outputs; and (2) the computational challenges in ensuring the stability of rank lists with respect to all possible perturbations of training data. Our method, FINEST, overcomes these challenges by obtaining reference rank lists from a given recommendation model and then fine-tuning the model under simulated perturbation scenarios with rank-preserving regularization on sampled items. Our experiments on real-world datasets demonstrate that FINEST can ensure that recommender models output stable recommendations under a wide range of different perturbations without compromising next-item prediction accuracy.

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.

We present a novel structure-preserving framework for solving the Vlasov-Poisson-Landau system of equations using a particle in cell (PIC) discretization combined with discrete gradient time integrators. The Vlasov-Poisson-Landau system is an accurate model for studying hot plasma dynamics at a kinetic scale where small-angle Coulomb collisions dominate. Our scheme guarantees conservation of mass, momentum and energy as well as preservation of the monotonicity of entropy production in both the time-continuous and discrete systems. We employ the conservative integrator for both the Hamiltonian Vlasov-Poisson equations and the dissipative Landau equation using the PETSc library (www.mcs.anl.gov/petsc) to showcase structure-preserving properties.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

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.

The Multilevel Markov chain Monte Carlo algorithm accelerates Bayesian inversion by exploiting correlations between discretized quantities of interest across a hierarchy of model resolutions. A key practical parameter is the subsampling rate used to generate coarse-level proposals for the finer-level chains. Existing practice sets this rate equal to an integrated autocorrelation time as a proxy for proposal decorrelation, but this choice can be overly conservative and lead to substantial computational overhead. In this work we treat finite subsampling as an error-budget question. We derive a cost-error criterion for selecting a computationally efficient subsampling rate using estimates of sample variances, integrated autocorrelation times, and per-level costs. The criterion balances multilevel sampling errors across levels rather than enforcing approximate independence of the coarse proposals. We clarify the theoretical role of independence through an ideal reset-reference kernel, for which independent coarse proposals may be replaced by proposals generated from a reversible coarse-level kernel. We derive a Poisson-equation representation of the perturbation bias resulting from finite subsampling. Under a state-averaged lower-level forgetting assumption, this yields a conditional geometric perturbation-bias bound; in computation, the corresponding projected diagnostic is used as an empirical error-budget check. Numerical experiments on a highly autocorrelated elasticity beam benchmark show substantial reductions in computational cost compared with IAT-based subsampling. A second Darcy-flow inverse problem gives supporting evidence of qualitatively similar finite-subsampling behaviour in another elliptic benchmark.

A key challenge in machine learning is to explain how learning dynamics select among the many solutions that achieve identical loss values in overparameterized models - a phenomenon known as implicit bias. Controlling this bias provides a direct mechanism on learned representations, which are central to interpretability, robustness, and reasoning in modern AI systems. Yet, despite its importance, existing explanations remain largely ad hoc and lack a unifying mechanism. We develop a theoretical and constructive framework in which implicit bias emerges as a geometric correction induced by the interplay between gradient noise and continuous symmetries of the loss. We compute the induced bias across a range of architectures, predicting new behaviors and explaining known ones. The approach also enables inverse design: by engineering predictor - preserving parameterizations, it is possible to shape the bias, with sparsity and spectral sparsity emerging as canonical instances. Numerical experiments support the theory and validate the inverse - design framework in controlled settings.

Motivated by applications in Diophantine approximation, we develop a new fibering mechanism for non-degenerate manifolds in R^n, showing that they admit local decompositions into families of non-degenerate curves with uniform quantitative non-degeneracy properties. The manifolds are required to be C^N with the essentially optimal bound Ngeq maxlbrace n,l+1rbrace, where the manifold is l non-degenerate. Furthermore, we show that this uniform quantitative local control can be globalised into a qualitative statement, so that almost every point of a non-degenerate manifold lies on a non-degenerate curve contained in the manifold. Our approach is perturbative and shows that the fibering structure arising in the analytic setting is stable under sufficiently small C^N perturbations. The method provides a framework for extending fibering based results in Diophantine approximation from curves to manifolds. Such applications are considered in the paper.

Generative foundation models are increasingly scaled in both width and depth, posing significant challenges for stable feature learning and reliable hyperparameter (HP) transfer across model sizes. While maximal update parameterization (μP) has provided a principled solution to both problems for width scaling, existing extensions to the joint width-depth scaling regime remain fragmented, architecture- and optimizer-specific, and often rely on technically involved theories. In this work, we develop a simple and unified spectral framework for μP under joint width-depth scaling. Considering residual networks of varying block depths, we first introduce a spectral μP condition that precisely characterizes how the norms of weights and their per-step updates should scale with width and depth, unifying previously disparate μP formulations as special cases. Building on this condition, we then derive a general recipe for implementing μP across a broad class of optimizers by mapping the spectral constraints to concrete HP parameterizations. This approach not only recovers existing μP formulations (e.g., for SGD and AdamW) but also naturally extends to a wider range of optimizers. Finally, experiments on GPT-2 style language models demonstrate that the proposed spectral μP condition preserves stable feature learning and enables robust HP transfer under width-depth scaling.

The structure learning problem consists of fitting data generated by a Directed Acyclic Graph (DAG) to correctly reconstruct its arcs. In this context, differentiable approaches constrain or regularize the optimization problem using a continuous relaxation of the acyclicity property. The computational cost of evaluating graph acyclicity is cubic on the number of nodes and significantly affects scalability. In this paper we introduce COSMO, a constraint-free continuous optimization scheme for acyclic structure learning. At the core of our method, we define a differentiable approximation of an orientation matrix parameterized by a single priority vector. Differently from previous work, our parameterization fits a smooth orientation matrix and the resulting acyclic adjacency matrix without evaluating acyclicity at any step. Despite the absence of explicit constraints, we prove that COSMO always converges to an acyclic solution. In addition to being asymptotically faster, our empirical analysis highlights how COSMO performance on graph reconstruction compares favorably with competing structure learning methods.

Outer-learning algorithms use infinitesimal sensitivities to propose finite changes to initialization or training parameters. For hard-ReLU training, the derivative of the finite program and the derivative of its flow limit do not by themselves specify the response at a chosen radius. We characterize the intervening regime in which the perturbation radius is proportional to the GD step. Integer event rounding then survives at leading order: smooth Euler bias shifts each discrete phase, and upstream rounding moves downstream branch boundaries. We derive the crossing indices and a uniform endpoint expansion for finitely many separated transverse events in piecewise-C^2 dynamics, away from recursive phase boundaries. In contractive affine regions, an explicit remainder and complete branch verification certify finite candidate comparisons. Scalar phase frequencies and a coupled feedback ablation test the mechanism; frozen nonlinear-network experiments show radius-dependent prediction accuracy, including incomplete branch matches and failed-word tails. Together with local AD and uniform flow consistency, the result identifies sufficient response regimes: differentiating training is a choice of perturbation resolution as well as a choice of derivative.

We prove a weighted Wasserstein spectral gap for the three-dimensional primitive equations on mathscr E={uin H^1cap L^8: partial_zuin L^4} under finite-rank additive Brownian forcing that is phase-complete finite Fourier and satisfies a quantitative quadratic saturation condition. In particular, four real forcing directions suffice and this number is optimal within the phase-complete class. Consequently, the system is uniquely ergodic and exponentially mixing in the H^1 topology. The main difficulties stem from the lack of sufficiently strong moment bounds and the highly degenerate nature of the noise, placing the problem outside the direct reach of standard methods. We introduce a new quantitative stable--compact asymptotic coupling criterion that captures the delicate balance between the available control of the growth of initial perturbations and the accuracy--cost of compensating them by perturbing the noise. For the primitive equations, this leads to a quantitative infinite-dimensional Hörmander analysis requiring tracking the degree and coefficient cost of Lie-bracket polynomials with the Fourier frequency.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

This paper establishes Lipschitz stability for the simultaneous recovery of a variable density coefficient and the initial displacement in a damped biharmonic wave equation. The data consist of the boundary Cauchy data for the Laplacian of the solution, \(Δu |_{\partial Ω}\) and \( \partial_{n}(Δu)|_{\partial Ω}.\) We first prove that the associated system operator generates a contraction semigroup, which ensures the well-posedness of the forward problem. A key observability inequality is then derived via multiplier techniques. Building on this foundation, explicit stability estimates for the inverse problem are obtained. These estimates demonstrate that the biharmonic structure inherently enhances the stability of parameter identification, with the stability constants exhibiting an explicit dependence on the damping coefficient via the factor \( (1 + γ)^{1/2} \). This work provides a rigorous theoretical basis for applications in non-destructive testing and dynamic inversion.

Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several fine-tuning techniques have been developed to update the pre-trained model weights in a more resource-efficient manner, such as through low-rank adjustments. Yet, almost all of these methods focus on linear weights, neglecting the intricacies of parameter spaces in higher dimensions like 4D. Alternatively, some methods can be adapted for high-dimensional parameter space by compressing changes in the original space into two dimensions and then employing low-rank matrix decomposition. However, these approaches destructs the structural integrity of the involved high-dimensional spaces. To tackle the diversity of dimensional spaces across different foundation models and provide a more precise representation of the changes within these spaces, this paper introduces a generalized parameter-efficient fine-tuning framework, FLoRA, designed for various dimensional parameter space. Specifically, utilizing Tucker decomposition, FLoRA asserts that changes in each dimensional parameter space are based on a low-rank core space which maintains the consistent topological structure with the original space. It then models the changes through this core space alongside corresponding weights to reconstruct alterations in the original space. FLoRA effectively preserves the structural integrity of the change of original N-dimensional parameter space, meanwhile decomposes it via low-rank tensor decomposition. Extensive experiments on computer vision, natural language processing and multi-modal tasks validate FLoRA's effectiveness. Codes are available at https://github.com/SJTU-DeepVisionLab/FLoRA.

This paper introduces a new parameterization of deep neural networks (both fully-connected and convolutional) with guaranteed ell^2 Lipschitz bounds, i.e. limited sensitivity to input perturbations. The Lipschitz guarantees are equivalent to the tightest-known bounds based on certification via a semidefinite program (SDP). We provide a ``direct'' parameterization, i.e., a smooth mapping from mathbb R^N onto the set of weights satisfying the SDP-based bound. Moreover, our parameterization is complete, i.e. a neural network satisfies the SDP bound if and only if it can be represented via our parameterization. This enables training using standard gradient methods, without any inner approximation or computationally intensive tasks (e.g. projections or barrier terms) for the SDP constraint. The new parameterization can equivalently be thought of as either a new layer type (the sandwich layer), or a novel parameterization of standard feedforward networks with parameter sharing between neighbouring layers. A comprehensive set of experiments on image classification shows that sandwich layers outperform previous approaches on both empirical and certified robust accuracy. Code is available at https://github.com/acfr/LBDN.

Flow-based generative models have been employed for sampling the Boltzmann distribution, but their application to high-dimensional systems is hindered by the significant computational cost of obtaining the Jacobian of the flow. To overcome this challenge, we introduce the flow perturbation method, which incorporates optimized stochastic perturbations into the flow. By reweighting trajectories generated by the perturbed flow, our method achieves unbiased sampling of the Boltzmann distribution with orders of magnitude speedup compared to both brute force Jacobian calculations and the Hutchinson estimator. Notably, it accurately sampled the Chignolin protein with all atomic Cartesian coordinates explicitly represented, which, to our best knowledge, is the largest molecule ever Boltzmann sampled in such detail using generative models.

Learning to simulate complex physical systems from data has emerged as a promising way to overcome the limitations of traditional numerical solvers, which often require prohibitive computational costs for high-fidelity solutions. Recent Graph Neural Simulators (GNSs) accelerate simulations by learning dynamics on graph-structured data, yet often struggle to capture long-range interactions and suffer from error accumulation under autoregressive rollouts. To address these challenges, we propose Information-preserving Graph Neural Simulators (IGNS), a graph-based neural simulator built on the principles of Hamiltonian dynamics. This structure guarantees preservation of information across the graph, while extending to port-Hamiltonian systems allows the model to capture a broader class of dynamics, including non-conservative effects. IGNS further incorporates a warmup phase to initialize global context, geometric encoding to handle irregular meshes, and a multi-step training objective that facilitates PDE matching, where the trajectory produced by integrating the port-Hamiltonian core aligns with the ground-truth trajectory, thereby reducing rollout error. To evaluate these properties systematically, we introduce new benchmarks that target long-range dependencies and challenging external forcing scenarios. Across all tasks, IGNS consistently outperforms state-of-the-art GNSs, achieving higher accuracy and stability under challenging and complex dynamical systems. Our project page: https://thobotics.github.io/neural_pde_matching.

Smoothness and low dimensional structures play central roles in improving generalization and stability in learning and statistics. This work combines techniques from semi-infinite constrained learning and manifold regularization to learn representations that are globally smooth on a manifold. To do so, it shows that under typical conditions the problem of learning a Lipschitz continuous function on a manifold is equivalent to a dynamically weighted manifold regularization problem. This observation leads to a practical algorithm based on a weighted Laplacian penalty whose weights are adapted using stochastic gradient techniques. It is shown that under mild conditions, this method estimates the Lipschitz constant of the solution, learning a globally smooth solution as a byproduct. Experiments on real world data illustrate the advantages of the proposed method relative to existing alternatives.

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.

Finite element stress fields often exhibit strong local non-smoothness, where stress concentrations near holes, notches, and loading regions induce sharp spatial gradients and high-frequency graph components. Although graph neural networks naturally operate on irregular finite element meshes, conventional message passing is inherently smoothing and progressively attenuates such high-frequency information. Unitary propagation alleviates this problem by preserving spectral magnitudes, but typically relies on matrix functions and high-order approximations with O(Ked) propagation complexity. We propose LiftGCN, an efficient spectrally stable graph network based on Joukowski spectral lifting. LiftGCN maps the real spectrum of a normalized graph operator onto the unit circle through the Joukowski relation and realizes the resulting spectral transformation as a simple second-order recurrence, avoiding matrix exponentials, eigendecomposition, and high-order polynomial truncation. We show that the linear Joukowski backbone has unit-modulus characteristic roots and admits an energy-preserving structure under a positive-definite metric, preventing exponential attenuation of graph-frequency components with depth. Each layer requires only one sparse neighborhood aggregation, yielding O(ed) propagation complexity, while lightweight local nonlinear residuals provide expressive feature transformations. Experiments on finite element stress prediction demonstrate that LiftGCN achieves competitive overall accuracy while improving reconstruction of stress concentrations and local high-gradient structures with substantially reduced computational cost. Our code is available at https://github.com/ChenZeng001/LiftGCN.

Data-driven algorithm design automates hyperparameter tuning, but its statistical foundations remain limited because model performance can depend on hyperparameters in implicit and highly non-smooth ways. Existing guarantees focus on the simple case of a one-dimensional (scalar) hyperparameter. This leaves the practically important, multi-dimensional hyperparameter tuning setting unresolved. We address this open question by establishing the first general framework for establishing generalization guarantees for tuning multi-dimensional hyperparameters in data-driven settings. Our approach strengthens the generalization guarantee framework for semi-algebraic function classes by exploiting tools from real algebraic geometry, yielding sharper, more broadly applicable guarantees. For completeness, we also instantiate the first lower bound for this general setting. We further extend the analysis to hyperparameter tuning using the validation loss under minimal assumptions, and derive improved bounds when additional structure is available. Finally, we demonstrate the scope of the framework with new learnability results, including data-driven weighted group lasso and weighted fused lasso.

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.

Multiple epidemic waves are often taken as evidence that simple compartmental models are structurally inadequate. Yet the key question is not whether a simple model can reproduce multiple peaks, but how much time-varying structure is minimally required to preserve observed epidemic-wave patterns and what can legitimately be inferred from such a representation. Using the susceptible-infectious-removed (SIR) model, we develop a framework for peak-preserving dynamic parsimony linking dynamical systems, inverse problems, statistical inference, and infectious-disease modeling. We establish exact multi-wave representability under time-varying transmission, characterize conditions for epidemic peaks and resurgence, and show the incidence-only non-identifiability of time-varying transmission and removal rates. Our main methodological contribution is minimal peak-preserving complexity (MPPC): the smallest dimension of a positive time-varying transmission function whose posterior-predictive trajectories preserve salient features, including peak count, timing, height, trough depth, and whole-curve agreement. We estimate MPPC using peak-aware approximate Bayesian computation and evaluate it through six reproducible stress tests, a Philippine COVID-19 reported-case proof of concept, and short-term future-knot projection. Across diverse data-generating mechanisms, low-dimensional time-varying SIR models can preserve aggregate epidemic-wave topology with modest dynamic complexity. However, accurate trajectory compression does not imply recovery of the underlying mechanism or reliable long-term counterfactual prediction. The framework therefore separates four often-conflated questions: representability, minimal dynamic complexity, mechanistic identifiability, and projection validity, providing a basis for parsimonious modeling of complex epidemic trajectories.

We consider a family of linear systems A_mu alpha=C with system matrix A_mu depending on a parameter mu and for simplicity parameter-independent right-hand side C. These linear systems typically result from the finite-dimensional approximation of a parameter-dependent boundary-value problem. We derive a procedure based on the Empirical Interpolation Method to obtain a separated representation of the system matrix in the form A_muapproxsum_{m}beta_m(mu)A_{mu_m} for some selected values of the parameter. Such a separated representation is in particular useful in the Reduced Basis Method. The procedure is called nonintrusive since it only requires to access the matrices A_{mu_m}. As such, it offers a crucial advantage over existing approaches that instead derive separated representations requiring to enter the code at the level of assembly. Numerical examples illustrate the performance of our new procedure on a simple one-dimensional boundary-value problem and on three-dimensional acoustic scattering problems solved by a boundary element method.

Recovering a latent potential from observed flow on a directed graph (a discrete Poisson problem with Dirichlet boundaries) is ill-posed, and the standard fix backfires: ridge regularization shrinks toward a gauge-meaningless origin, collapsing and reversing the recovered ordering (+0.81to-0.42 rank correlation against a planted ground truth). The gauge-invariant graph Dirichlet energy removes the hazard and delivers parameter-insensitivity: the estimate is stable across four orders of magnitude in λ, whereas ridge inverts the ordering for every λ>0. We prove the reduced solve is SPD and preserves dynamic range exactly where ridge collapses it, and localize absorbing boundaries from flow alone via a Poisson residual. The H^1 seminorm is classical; what is new is the gauge diagnosis, the parameter-insensitivity it buys, and an ablation showing the result is robust to the extraction method. On three public clickstream corpora the gauge-invariant estimate retains 28--41% of the interior dynamic range while ridge collapses to as little as 0.2%. The same gauge invariance carries into graph neural networks -- neutralizing the constant mode per layer prevents the oversmoothing that collapses a deep directed GCN -- linking this classical inverse problem to a central question in graph learning.

When considering a model architecture, there are several ways to reduce its memory footprint. Historically, popular approaches included selecting smaller architectures and creating sparse networks through pruning. More recently, randomized parameter-sharing (RPS) methods have gained traction for model compression at start of training. In this paper, we comprehensively assess the trade-off between memory and accuracy across RPS, pruning techniques, and building smaller models. Our findings demonstrate that RPS, which is both data and model-agnostic, consistently outperforms/matches smaller models and all moderately informed pruning strategies, such as MAG, SNIP, SYNFLOW, and GRASP, across the entire compression range. This advantage becomes particularly pronounced in higher compression scenarios. Notably, even when compared to highly informed pruning techniques like Lottery Ticket Rewinding (LTR), RPS exhibits superior performance in high compression settings. This points out inherent capacity advantage that RPS enjoys over sparse models. Theoretically, we establish RPS as a superior technique in terms of memory-efficient representation when compared to pruning for linear models. This paper argues in favor of paradigm shift towards RPS based models. During our rigorous evaluation of RPS, we identified issues in the state-of-the-art RPS technique ROAST, specifically regarding stability (ROAST's sensitivity to initialization hyperparameters, often leading to divergence) and Pareto-continuity (ROAST's inability to recover the accuracy of the original model at zero compression). We provably address both of these issues. We refer to the modified RPS, which incorporates our improvements, as STABLE-RPS.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

State-space models (SSMs) have recently emerged as a framework for learning long-range sequence tasks. An example is the structured state-space sequence (S4) layer, which uses the diagonal-plus-low-rank structure of the HiPPO initialization framework. However, the complicated structure of the S4 layer poses challenges; and, in an effort to address these challenges, models such as S4D and S5 have considered a purely diagonal structure. This choice simplifies the implementation, improves computational efficiency, and allows channel communication. However, diagonalizing the HiPPO framework is itself an ill-posed problem. In this paper, we propose a general solution for this and related ill-posed diagonalization problems in machine learning. We introduce a generic, backward-stable "perturb-then-diagonalize" (PTD) methodology, which is based on the pseudospectral theory of non-normal operators, and which may be interpreted as the approximate diagonalization of the non-normal matrices defining SSMs. Based on this, we introduce the S4-PTD and S5-PTD models. Through theoretical analysis of the transfer functions of different initialization schemes, we demonstrate that the S4-PTD/S5-PTD initialization strongly converges to the HiPPO framework, while the S4D/S5 initialization only achieves weak convergences. As a result, our new models show resilience to Fourier-mode noise-perturbed inputs, a crucial property not achieved by the S4D/S5 models. In addition to improved robustness, our S5-PTD model averages 87.6% accuracy on the Long-Range Arena benchmark, demonstrating that the PTD methodology helps to improve the accuracy of deep learning models.

Tensor randomized Kaczmarz (TRK) methods are efficient row-action solvers for tensor linear systems under the t-product framework. We study their behavior under a doubly noisy perturbation model. In this model, both the system tensor and the right-hand side tensor are corrupted. We first analyze standard TRK and derive an expected error recursion with two terms. One term is contractive, and the other is a persistent perturbation term. This explains the noise-limited and semi-convergent behavior that can occur when the observed tensor system is inconsistent. We then introduce a spectrally damped tensor randomized Kaczmarz method (SD-TRK). We prove an expected error recursion for SD-TRK that separates error propagation from noise injection. The bound makes explicit a speed-robustness trade-off. We also give an FFT-based implementation that applies the damped update slice-wise in the Fourier domain. This implementation allows frequency-dependent damping parameters in practice. Numerical experiments on synthetic tensor systems illustrate the stabilization behavior of SD-TRK relative to standard TRK in noisy and ill-conditioned settings. We also include a two-pass image reconstruction comparison under the same noisy reconstruction pipeline.

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.

Privacy-preserving machine learning algorithms are crucial for the increasingly common setting in which personal data, such as medical or financial records, are analyzed. We provide general techniques to produce privacy-preserving approximations of classifiers learned via (regularized) empirical risk minimization (ERM). These algorithms are private under the ε-differential privacy definition due to Dwork et al. (2006). First we apply the output perturbation ideas of Dwork et al. (2006), to ERM classification. Then we propose a new method, objective perturbation, for privacy-preserving machine learning algorithm design. This method entails perturbing the objective function before optimizing over classifiers. If the loss and regularizer satisfy certain convexity and differentiability criteria, we prove theoretical results showing that our algorithms preserve privacy, and provide generalization bounds for linear and nonlinear kernels. We further present a privacy-preserving technique for tuning the parameters in general machine learning algorithms, thereby providing end-to-end privacy guarantees for the training process. We apply these results to produce privacy-preserving analogues of regularized logistic regression and support vector machines. We obtain encouraging results from evaluating their performance on real demographic and benchmark data sets. Our results show that both theoretically and empirically, objective perturbation is superior to the previous state-of-the-art, output perturbation, in managing the inherent tradeoff between privacy and learning performance.

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.

In this paper, a new parameter perturbation attack on DNNs, called adversarial parameter attack, is proposed, in which small perturbations to the parameters of the DNN are made such that the accuracy of the attacked DNN does not decrease much, but its robustness becomes much lower. The adversarial parameter attack is stronger than previous parameter perturbation attacks in that the attack is more difficult to be recognized by users and the attacked DNN gives a wrong label for any modified sample input with high probability. The existence of adversarial parameters is proved. For a DNN F_{Theta} with the parameter set Theta satisfying certain conditions, it is shown that if the depth of the DNN is sufficiently large, then there exists an adversarial parameter set Theta_a for Theta such that the accuracy of F_{Theta_a} is equal to that of F_{Theta}, but the robustness measure of F_{Theta_a} is smaller than any given bound. An effective training algorithm is given to compute adversarial parameters and numerical experiments are used to demonstrate that the algorithms are effective to produce high quality adversarial parameters.

Hyper-Connections (HC) generalize residual connections into multiple streams, employing residual matrices for cross-stream feature mixing to enrich model expressivity. However, unconstrained mixing disrupts the identity mapping property intrinsic to the residual connection, causing unstable training. To address this, Manifold-Constrained Hyper-Connections (mHC) and its variant restrict these matrices to the Birkhoff polytope (doubly stochastic matrices) via Sinkhorn iterations or permutation-based parameterizations. We reveal three limitations of this polytope constraint: (1) identity degeneration, where learned matrices collapse around the identity and diminish cross-stream interactions, (2) an expressivity bottleneck, as the non-negativity constraint prevents subtractive feature disentanglement, and (3) parameterization inefficiencies, manifesting as unstable Sinkhorn iterations or the factorial-scaling overhead of permutation-based parameterizations. To overcome these flaws, we propose Spectral-Sphere-Constrained Hyper-Connections (sHC). By geometrically shifting the feasible set from a rigid polytope to a spectral norm sphere, sHC allows negative entries, unlocking subtractive interactions for selective feature diversification. This shift eliminates unstable Sinkhorn projections and factorial parameterization, enabling expressive, non-degenerate residual matrices while preserving training stability.

A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships. Existing graph-based models commonly use the same network to structure gene representations and mediate intergene interactions, thereby implicitly treating stable associations as perturbation-response pathways. Gene Ontology and control-derived coexpression networks encode relatively stable relationships rather than intervention-specific response directions or magnitudes. We therefore propose GeneGeoFlow, which conditions a control-anchored residual flow on gene-wise geometry derived from biological networks to learn intervention-specific transcriptional responses. GeneGeoFlow derives multi-scale spectral coordinates from Gene Ontology and control-derived coexpression networks. A perturbation-conditioned, gene-wise gating module selects relevant structural scales and network sources, yielding intervention-specific gene geometry. The resulting geometry conditions a control-anchored residual flow without explicitly propagating target-derived signals along the graph. Condition-wise optimal transport couples unpaired control and perturbed populations for training, while a Delta-correlation objective aligns the predicted and observed condition-level expression-shift directions. GeneGeoFlow achieves Pearson Delta scores of 0.8979 on the Norman additive benchmark and 0.9088 on five held-out drug combinations in the fixed ComboSciPlex test split. These results support perturbation-conditioned gene geometry as an effective structural prior for intervention-specific response prediction, without conflating stable gene relationships with response propagation.

This article investigates data-driven policy iteration (PI) for continuous-time linear systems without requiring an initially stabilizing policy. Standard infinite-horizon PI is not self-starting because its policy-evaluation step is well posed only when the feedback gain is stabilizing. However, verifying this property is difficult when the system matrices are unknown. To remove this requirement, we develop a finite-horizon bootstrap method. The key idea is to perform policy evaluation over a compact interval for a shifted system, where the evaluation equation is well defined for arbitrary bounded time-varying policies. We show that, for a sufficiently long horizon, the initial-time optimal gain of the shifted finite-horizon problem, when applied as a constant feedback gain, achieves a prescribed stability margin for the original system. We then derive a data-driven implementation from an off-policy identity evaluated along trajectories of the original plant. We use basis-function approximations to reconstruct the finite-horizon value matrix and policy, and we characterize the resulting error through a perturbed policy-improvement recursion. A data-driven Lyapunov certificate is further introduced to verify admissibility of the candidate gain before it is used to initialize infinite-horizon PI. Numerical studies of a batch reactor and a two-mass-spring system demonstrate the effectiveness of the proposed bootstrap method.

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.

Normalizing flows are a promising tool for modeling probability distributions in physical systems. While state-of-the-art flows accurately approximate distributions and energies, applications in physics additionally require smooth energies to compute forces and higher-order derivatives. Furthermore, such densities are often defined on non-trivial topologies. A recent example are Boltzmann Generators for generating 3D-structures of peptides and small proteins. These generative models leverage the space of internal coordinates (dihedrals, angles, and bonds), which is a product of hypertori and compact intervals. In this work, we introduce a class of smooth mixture transformations working on both compact intervals and hypertori. Mixture transformations employ root-finding methods to invert them in practice, which has so far prevented bi-directional flow training. To this end, we show that parameter gradients and forces of such inverses can be computed from forward evaluations via the inverse function theorem. We demonstrate two advantages of such smooth flows: they allow training by force matching to simulation data and can be used as potentials in molecular dynamics simulations.

The approximation of Partial Differential Equations (PDEs) using neural networks has seen significant advancements through Physics-Informed Neural Networks (PINNs). Despite their straightforward optimization framework and flexibility in implementing various PDEs, PINNs often suffer from limited accuracy due to the spectral bias of Multi-Layer Perceptrons (MLPs), which struggle to effectively learn high-frequency and non-linear components. Recently, parametric mesh representations in combination with neural networks have been investigated as a promising approach to eliminate the inductive biases of neural networks. However, they usually require very high-resolution grids and a large number of collocation points to achieve high accuracy while avoiding overfitting issues. In addition, the fixed positions of the mesh parameters restrict their flexibility, making it challenging to accurately approximate complex PDEs. To overcome these limitations, we propose Physics-Informed Gaussians (PIGs), which combine feature embeddings using Gaussian functions with a lightweight neural network. Our approach uses trainable parameters for the mean and variance of each Gaussian, allowing for dynamic adjustment of their positions and shapes during training. This adaptability enables our model to optimally approximate PDE solutions, unlike models with fixed parameter positions. Furthermore, the proposed approach maintains the same optimization framework used in PINNs, allowing us to benefit from their excellent properties. Experimental results show the competitive performance of our model across various PDEs, demonstrating its potential as a robust tool for solving complex PDEs. Our project page is available at https://namgyukang.github.io/Physics-Informed-Gaussians/

Nonlinear model order reduction has opened the door to parameter optimization and uncertainty quantification in complex physics problems governed by nonlinear equations. In particular, the computational cost of solving these equations can be reduced by means of local reduced-order bases. This article examines the benefits of a physics-informed cluster analysis for the construction of cluster-specific reduced-order bases. We illustrate that the choice of the dissimilarity measure for clustering is fundamental and highly affects the performances of the local reduced-order bases. It is shown that clustering with an angle-based dissimilarity on simulation data efficiently decreases the intra-cluster Kolmogorov N-width. Additionally, an a priori efficiency criterion is introduced to assess the relevance of a ROM-net, a methodology for the reduction of nonlinear physics problems introduced in our previous work in [T. Daniel, F. Casenave, N. Akkari, D. Ryckelynck, Model order reduction assisted by deep neural networks (ROM-net), Advanced Modeling and Simulation in Engineering Sciences 7 (16), 2020]. This criterion also provides engineers with a very practical method for ROM-nets' hyperparameters calibration under constrained computational costs for the training phase. On five different physics problems, our physics-informed clustering strategy significantly outperforms classic strategies for the construction of local reduced-order bases in terms of projection errors.

Generative machine learning methods, such as diffusion models and flow matching, have shown great potential in modeling complex system behaviors and building efficient surrogate models. However, these methods typically learn the underlying physics implicitly from data. We propose Physics-Based Flow Matching (PBFM), a novel generative framework that explicitly embeds physical constraints, both PDE residuals and algebraic relations, into the flow matching objective. We also introduce temporal unrolling at training time that improves the accuracy of the final, noise-free sample prediction. Our method jointly minimizes the flow matching loss and the physics-based residual loss without requiring hyperparameter tuning of their relative weights. Additionally, we analyze the role of the minimum noise level, sigma_{min}, in the context of physical constraints and evaluate a stochastic sampling strategy that helps to reduce physical residuals. Through extensive benchmarks on three representative PDE problems, we show that our approach yields up to an 8times more accurate physical residuals compared to FM, while clearly outperforming existing algorithms in terms of distributional accuracy. PBFM thus provides a principled and efficient framework for surrogate modeling, uncertainty quantification, and accelerated simulation in physics and engineering applications.

Fine-tuning pre-trained models has been ubiquitously proven to be effective in a wide range of NLP tasks. However, fine-tuning the whole model is parameter inefficient as it always yields an entirely new model for each task. Currently, many research works propose to only fine-tune a small portion of the parameters while keeping most of the parameters shared across different tasks. These methods achieve surprisingly good performance and are shown to be more stable than their corresponding fully fine-tuned counterparts. However, such kind of methods is still not well understood. Some natural questions arise: How does the parameter sparsity lead to promising performance? Why is the model more stable than the fully fine-tuned models? How to choose the tunable parameters? In this paper, we first categorize the existing methods into random approaches, rule-based approaches, and projection-based approaches based on how they choose which parameters to tune. Then, we show that all of the methods are actually sparse fine-tuned models and conduct a novel theoretical analysis of them. We indicate that the sparsity is actually imposing a regularization on the original model by controlling the upper bound of the stability. Such stability leads to better generalization capability which has been empirically observed in a lot of recent research works. Despite the effectiveness of sparsity grounded by our theory, it still remains an open problem of how to choose the tunable parameters. To better choose the tunable parameters, we propose a novel Second-order Approximation Method (SAM) which approximates the original problem with an analytically solvable optimization function. The tunable parameters are determined by directly optimizing the approximation function. The experimental results show that our proposed SAM model outperforms many strong baseline models and it also verifies our theoretical analysis.

Irregular multivariate time series impose a trade-off for long-horizon forecasting: discrete methods can distort temporal structure via re-gridding, while continuous-time models often require sequential solvers prone to drift. To bridge this gap, we present Latent Laplace Diffusion (LLapDiff), a generative framework that models the target as a low-dimensional latent trajectory, enabling horizon-wide generation without step-by-step integration over physical time. We guide the reverse process utilizing a stable modal parameterization motivated by stochastic port-Hamiltonian dynamics, and parameterize its mean evolution in the Laplace domain via learnable complex-conjugate poles, enabling direct evaluation over irregular timestamps. We also link continuous dynamics to irregular observations through renewal-averaging analysis, which maps sampling gaps to effective event-domain poles and motivates a gap-aware history summarizer. Extensive experiments show that LLapDiff improves over baselines in long-horizon forecasting, and its continuous-time generative nature supports missing-value imputation by querying the same model at historical timestamps. Code is available at https://github.com/pixelhero98/LLapDiffusion.

We present As-Plausible-as-Possible (APAP) mesh deformation technique that leverages 2D diffusion priors to preserve the plausibility of a mesh under user-controlled deformation. Our framework uses per-face Jacobians to represent mesh deformations, where mesh vertex coordinates are computed via a differentiable Poisson Solve. The deformed mesh is rendered, and the resulting 2D image is used in the Score Distillation Sampling (SDS) process, which enables extracting meaningful plausibility priors from a pretrained 2D diffusion model. To better preserve the identity of the edited mesh, we fine-tune our 2D diffusion model with LoRA. Gradients extracted by SDS and a user-prescribed handle displacement are then backpropagated to the per-face Jacobians, and we use iterative gradient descent to compute the final deformation that balances between the user edit and the output plausibility. We evaluate our method with 2D and 3D meshes and demonstrate qualitative and quantitative improvements when using plausibility priors over geometry-preservation or distortion-minimization priors used by previous techniques. Our project page is at: https://as-plausible-aspossible.github.io/

Second-order optimization has been developed to accelerate the training of deep neural networks and it is being applied to increasingly larger-scale models. In this study, towards training on further larger scales, we identify a specific parameterization for second-order optimization that promotes feature learning in a stable manner even if the network width increases significantly. Inspired by a maximal update parameterization, we consider a one-step update of the gradient and reveal the appropriate scales of hyperparameters including random initialization, learning rates, and damping terms. Our approach covers two major second-order optimization algorithms, K-FAC and Shampoo, and we demonstrate that our parameterization achieves higher generalization performance in feature learning. In particular, it enables us to transfer the hyperparameters across models with different widths.

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.

Neural models are usually adapted through changes in parameters shared among model components via fine-tuning, alignment-based training, and reinforcement learning. These changes have been found effective in short-term optimization. However, they result in long-term alterations in the model's base behavior. In this study, we introduce the concept of structural irreversibility as a characteristic of shared-parameter model adaptation. This concept refers to the intertwining of task-specific objectives with the representational identity of the model. We show that when parameters are directly mutated, the resulting model behaves divergently from the original model. This divergence cannot be reversed deterministically without an explicit parameter snapshot. We introduce reversible behavioral learning, in which model behaviors are structurally dissociated from identity parameters and can be deterministically unloaded through an explicit unload process. We also introduce the Recoverability Factor as a normalized measure of behavioral recoverability and provide additional diagnostics based on model divergence. Experiments show that reversible model adaptation achieves rollback within numerical precision, whereas shared-parameter mutation exhibits persistent post-reset divergence.

Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully descriptive of the system, must facilitate the training process and must be invertible, so that one can extract the atomic configurations corresponding to the output of the model. In general, this last requirement is not automatically satisfied by the most efficient structural descriptors, namely the representation is not directly invertible. Such drawback severely limits our freedom of choice in selecting the most appropriate descriptors for the problem, and thus our flexibility to construct generative models. In this work, we present a general optimization method capable of inverting any local many-body descriptor of the chemical environment, back to a cartesian representation. The algorithm is then implemented together with the bispectrum representation of the local structure and demonstrated for a number of molecules. The scheme presented here, thus, represents a general approach to the inversion of structural descriptors, enabling the construction of efficient structural generative models.

Mechanistic Interpretability aims to reverse engineer the algorithms implemented by neural networks by studying their weights and activations. An obstacle to reverse engineering neural networks is that many of the parameters inside a network are not involved in the computation being implemented by the network. These degenerate parameters may obfuscate internal structure. Singular learning theory teaches us that neural network parameterizations are biased towards being more degenerate, and parameterizations with more degeneracy are likely to generalize further. We identify 3 ways that network parameters can be degenerate: linear dependence between activations in a layer; linear dependence between gradients passed back to a layer; ReLUs which fire on the same subset of datapoints. We also present a heuristic argument that modular networks are likely to be more degenerate, and we develop a metric for identifying modules in a network that is based on this argument. We propose that if we can represent a neural network in a way that is invariant to reparameterizations that exploit the degeneracies, then this representation is likely to be more interpretable, and we provide some evidence that such a representation is likely to have sparser interactions. We introduce the Interaction Basis, a tractable technique to obtain a representation that is invariant to degeneracies from linear dependence of activations or Jacobians.

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

Scientific Machine Learning (SciML) is concerned with the development of learned emulators of physical systems governed by partial differential equations (PDE). In application domains such as weather forecasting, molecular dynamics, and inverse design, ML-based surrogate models are increasingly used to augment or replace inefficient and often non-differentiable numerical simulation algorithms. While a number of ML-based methods for approximating the solutions of PDEs have been proposed in recent years, they typically do not adapt to the parameters of the PDEs, making it difficult to generalize to PDE parameters not seen during training. We propose a Channel Attention mechanism guided by PDE Parameter Embeddings (CAPE) component for neural surrogate models and a simple yet effective curriculum learning strategy. The CAPE module can be combined with neural PDE solvers allowing them to adapt to unseen PDE parameters. The curriculum learning strategy provides a seamless transition between teacher-forcing and fully auto-regressive training. We compare CAPE in conjunction with the curriculum learning strategy using a popular PDE benchmark and obtain consistent and significant improvements over the baseline models. The experiments also show several advantages of CAPE, such as its increased ability to generalize to unseen PDE parameters without large increases inference time and parameter count.

Linear relaxation based perturbation analysis (LiRPA) for neural networks, which computes provable linear bounds of output neurons given a certain amount of input perturbation, has become a core component in robustness verification and certified defense. The majority of LiRPA-based methods focus on simple feed-forward networks and need particular manual derivations and implementations when extended to other architectures. In this paper, we develop an automatic framework to enable perturbation analysis on any neural network structures, by generalizing existing LiRPA algorithms such as CROWN to operate on general computational graphs. The flexibility, differentiability and ease of use of our framework allow us to obtain state-of-the-art results on LiRPA based certified defense on fairly complicated networks like DenseNet, ResNeXt and Transformer that are not supported by prior works. Our framework also enables loss fusion, a technique that significantly reduces the computational complexity of LiRPA for certified defense. For the first time, we demonstrate LiRPA based certified defense on Tiny ImageNet and Downscaled ImageNet where previous approaches cannot scale to due to the relatively large number of classes. Our work also yields an open-source library for the community to apply LiRPA to areas beyond certified defense without much LiRPA expertise, e.g., we create a neural network with a probably flat optimization landscape by applying LiRPA to network parameters. Our opensource library is available at https://github.com/KaidiXu/auto_LiRPA.

We introduce a novel approach for analyzing the training dynamics of ReLU networks by examining the characteristic activation boundaries of individual ReLU neurons. Our proposed analysis reveals a critical instability in common neural network parameterizations and normalizations during stochastic optimization, which impedes fast convergence and hurts generalization performance. Addressing this, we propose Geometric Parameterization (GmP), a novel neural network parameterization technique that effectively separates the radial and angular components of weights in the hyperspherical coordinate system. We show theoretically that GmP resolves the aforementioned instability issue. We report empirical results on various models and benchmarks to verify GmP's theoretical advantages of optimization stability, convergence speed and generalization performance.

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

There is an emerging interest in generating robust counterfactual explanations that would remain valid if the model is updated or changed even slightly. Towards finding robust counterfactuals, existing literature often assumes that the original model m and the new model M are bounded in the parameter space, i.e., |Params(M){-}Params(m)|{<}Delta. However, models can often change significantly in the parameter space with little to no change in their predictions or accuracy on the given dataset. In this work, we introduce a mathematical abstraction termed naturally-occurring model change, which allows for arbitrary changes in the parameter space such that the change in predictions on points that lie on the data manifold is limited. Next, we propose a measure -- that we call Stability -- to quantify the robustness of counterfactuals to potential model changes for differentiable models, e.g., neural networks. Our main contribution is to show that counterfactuals with sufficiently high value of Stability as defined by our measure will remain valid after potential ``naturally-occurring'' model changes with high probability (leveraging concentration bounds for Lipschitz function of independent Gaussians). Since our quantification depends on the local Lipschitz constant around a data point which is not always available, we also examine practical relaxations of our proposed measure and demonstrate experimentally how they can be incorporated to find robust counterfactuals for neural networks that are close, realistic, and remain valid after potential model changes.

Recent benchmarks reveal that models for single-cell perturbation response are often outperformed by simply predicting the dataset mean. We trace this anomaly to a metric artifact: control-referenced deltas and unweighted error metrics reward mode collapse whenever the control is biased or the biological signal is sparse. Large-scale in silico simulations and analysis of two real-world perturbation datasets confirm that shared reference shifts, not genuine biological change, drives high performance in these evaluations. We introduce differentially expressed gene (DEG)-aware metrics, weighted mean-squared error (WMSE) and weighted delta R^{2} (R^{2}_{w}(Δ)) with respect to all perturbations, that measure error in niche signals with high sensitivity. We further introduce negative and positive performance baselines to calibrate these metrics. With these improvements, the mean baseline sinks to null performance while genuine predictors are correctly rewarded. Finally, we show that using WMSE as a loss function reduces mode collapse and improves model performance.

Learning physical simulations has been an essential and central aspect of many recent research efforts in machine learning, particularly for Navier-Stokes-based fluid mechanics. Classic numerical solvers have traditionally been computationally expensive and challenging to use in inverse problems, whereas Neural solvers aim to address both concerns through machine learning. We propose a general formulation for continuous convolutions using separable basis functions as a superset of existing methods and evaluate a large set of basis functions in the context of (a) a compressible 1D SPH simulation, (b) a weakly compressible 2D SPH simulation, and (c) an incompressible 2D SPH Simulation. We demonstrate that even and odd symmetries included in the basis functions are key aspects of stability and accuracy. Our broad evaluation shows that Fourier-based continuous convolutions outperform all other architectures regarding accuracy and generalization. Finally, using these Fourier-based networks, we show that prior inductive biases, such as window functions, are no longer necessary. An implementation of our approach, as well as complete datasets and solver implementations, is available at https://github.com/tum-pbs/SFBC.

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

Alternating projections (AP) near a clean intersection of smooth manifolds can converge slowly when the Friedrichs angle is small. We develop the Fixed-Point Manifold Acceleration (FPMA) framework for {local convergence and polynomial acceleration of} smooth maps that fix a manifold pointwise. {Under suitable regularity and uniform normal spectral stability, FPMA establishes local R-linear convergence and a smooth limiting map inducing a local retraction. At fixed points, consistent polynomial acceleration with p(1)=1 preserves the selected limit's first-order response to normal initial perturbations whenever the transformed normal blocks are uniformly spectrally stable. Under sufficient smoothness, we give a curvature criterion for second-order induced retractions and show that stable consistent polynomial acceleration preserves both the quadratic retraction expansion and this criterion. {As a special case, we establish new local R-linear convergence guarantees for fixed-degree Chebyshev-accelerated exact AP and second-order induced retractions. For uniform Friedrichs angle θ_Fin(0,π/2), acceleration strictly improves the local convergence rate per AP evaluation. The large-degree limiting spectral factor at fixed θ_F predicts O(θ_F^{-1}) evaluations for fixed relative error reduction as θ_Fdownarrow0, versus O(θ_F^{-2}) for ordinary AP.}} {The framework also covers} inexact, relaxed, and generalized AP {under their respective regularity and stability conditions.}

Local loss-landscape stabilization under sample growth is typically measured either pointwise or through isotropic averaging in the full parameter space. Despite practical value, both choices probe directions that contribute little to the dominant local deformation of strongly anisotropic neural landscapes. We recast stabilization as an observational problem and introduce a unified family of criteria parameterized by an aggregation order and a probing distribution; within this family we propose a curvature-aligned criterion Δ_2^{(D)} that probes the loss increment field in the top-D eigenspace of the empirical Hessian near a trained solution. Solely from a local quadratic model, we prove that Δ_2^{(D)} preserves the O(k^{-2}) mean-squared rate of the full-space criterion while replacing ambient-dimension curvature dependence with dependence on the subspace dimension D; a corollary gives a closed-form spectral expression and a proposition identifies the top-D eigenspace as extremal within the eigenspace-aligned family. We also derive scalable estimators based on Hessian-vector products, subspace Monte Carlo, and a closed-form Gaussian-moment proxy. On a decoder-only transformer, a curvature-aligned probe occupying a tiny fraction of parameter space already reproduces the full-space mean-squared signal to within numerical noise throughout the validated local regime, and the closed-form estimator is orders of magnitude faster than direct Monte Carlo after subspace construction.

We address the computational challenges of solving parametric PDEs with non parametrized geometric variations and non-reducible problems, such as those involving shocks and discontinuities of variable positions. Traditional dimensionality reduction methods like POD struggle with these scenarios due to slowly decaying Kolmogorov widths. To overcome this, we propose a novel non-linear dimensionality reduction technique to reduce the required modes for representation. The non-linear reduction is obtained through a POD after applying a transformation on the fields, which we call optimal mappings, and is a solution to an optimization problem in infinite dimension. The proposed learning framework combines morphing techniques, non-linear dimensionality reduction, and Gaussian Process Regression (GPR). The problem is reformulated on a reference geometry before applying the dimensionality reduction. Our method learns both the optimal mapping, and the solution fields, using a series of GPR models, enabling efficient and accurate modeling of complex parametric PDEs with geometrical variability. The results obtained concur with current state-of-the-art models. We mainly compare our method with the winning solution of the ML4CFD NeurIPS 2024 competition.

Recent years have witnessed significant progress in developing efficient training and fast sampling approaches for diffusion models. A recent remarkable advancement is the use of stochastic differential equations (SDEs) to describe data perturbation and generative modeling in a unified mathematical framework. In this paper, we reveal several intriguing geometric structures of diffusion models and contribute a simple yet powerful interpretation to their sampling dynamics. Through carefully inspecting a popular variance-exploding SDE and its marginal-preserving ordinary differential equation (ODE) for sampling, we discover that the data distribution and the noise distribution are smoothly connected with an explicit, quasi-linear sampling trajectory, and another implicit denoising trajectory, which even converges faster in terms of visual quality. We also establish a theoretical relationship between the optimal ODE-based sampling and the classic mean-shift (mode-seeking) algorithm, with which we can characterize the asymptotic behavior of diffusion models and identify the score deviation. These new geometric observations enable us to improve previous sampling algorithms, re-examine latent interpolation, as well as re-explain the working principles of distillation-based fast sampling techniques.

In this paper, we investigate the long-term memory learning capabilities of state-space models (SSMs) from the perspective of parameterization. We prove that state-space models without any reparameterization exhibit a memory limitation similar to that of traditional RNNs: the target relationships that can be stably approximated by state-space models must have an exponential decaying memory. Our analysis identifies this "curse of memory" as a result of the recurrent weights converging to a stability boundary, suggesting that a reparameterization technique can be effective. To this end, we introduce a class of reparameterization techniques for SSMs that effectively lift its memory limitations. Besides improving approximation capabilities, we further illustrate that a principled choice of reparameterization scheme can also enhance optimization stability. We validate our findings using synthetic datasets and language models.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

The Sharpness Aware Minimization (SAM) optimization algorithm has been shown to control large eigenvalues of the loss Hessian and provide generalization benefits in a variety of settings. The original motivation for SAM was a modified loss function which penalized sharp minima; subsequent analyses have also focused on the behavior near minima. However, our work reveals that SAM provides a strong regularization of the eigenvalues throughout the learning trajectory. We show that in a simplified setting, SAM dynamically induces a stabilization related to the edge of stability (EOS) phenomenon observed in large learning rate gradient descent. Our theory predicts the largest eigenvalue as a function of the learning rate and SAM radius parameters. Finally, we show that practical models can also exhibit this EOS stabilization, and that understanding SAM must account for these dynamics far away from any minima.

Objective perturbation adds a random linear term to a regularized empirical risk and releases the exact perturbed minimizer. We study the finite computation obtained by releasing the N-th iterate of deterministic gradient descent on wmapsto F(w;S)+langle z,wrangle, where zsimmathcal N(0,σ^2I_d) is drawn once before optimization. For strongly convex and smooth objectives with Lipschitz Hessian, we prove an explicit condition under which the map zmapsto w_N is a C^1-diffeomorphism on the bounded domains used in the privacy argument, with a quantitative lower bound on the smallest singular value of its Jacobian. This permits a direct change-of-variables analysis of the finite iterate. For generalized linear models, the resulting privacy-profile bound has no explicit ambient-dimension factor once the iteration condition holds, and its finite-iteration correction decreases geometrically. By letting the free truncation parameter grow slowly with N, we recover the corresponding exact-minimizer certificate in the limit. We also bound the expected excess empirical risk by dσ^2/(2μ) plus a geometrically decreasing optimization term, and transfer the result to population risk without an additional multiplicative condition-number factor in the leading statistical terms.

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.

Robotic systems often exhibit unstable modes, along which small perturbations and disturbances can cause unbounded growth unless corrected through feedback. Controlling such systems from high-dimensional visual observations requires representations that preserve these modes. Joint-embedding predictive architectures (JEPAs) provide a natural framework for learning such representations and their dynamics from visual data. However, we demonstrate that next step prediction combined with anti-collapse regularization does not guarantee that controllable unstable modes are preserved: the training loss can be minimized while these modes are collapsed, making stabilization from the learned representation impossible. To address this, we augment world-model training with an action reconstruction objective (i.e., an inverse dynamics loss) that encourages control-aware representations, namely, visual representations that preserve crucial features for control. We prove that exact action reconstruction makes the encoder injective on the finite-horizon reachable subspace. Thus, the encoder cannot discard any state direction reachable by an action sequence within H steps. Moreover, we show that, as H grows, the dominant eigenspace of the finite-horizon controllability Gramian converges to the controllable unstable subspace. We establish our theoretical results for linear systems and demonstrate empirically that our findings extend to nonlinear visual control tasks (CartPole, Walker2D, and PointMaze), highlighting the benefits of control-aware representation learning.

Straight line equation y=mx with slope m, when singularly perturbed as ay^3+y=mx with a positive parameter a, results in S-shaped curves or S-curves on a real plane. As arightarrow 0, we get back y=mx which is a cumulative distribution function of a continuous uniform distribution that describes the occurrence of every event in an interval to be equally probable. As arightarrowinfty, the derivative of y has finite support only at y=0 resembling a degenerate distribution. Based on these arguments, in this work, we propose that these S-curves can represent maximum entropy uniform distribution to a zero entropy single value. We also argue that these S-curves are superposable as they are only parametrically nonlinear but fundamentally linear. So far, the superposed forms have been used to capture the patterns of natural systems such as nonlinear dynamics of biological growth and kinetics of enzyme reactions. Here, we attempt to use the S-curve and its superposed form as statistical models. We fit the models on a classical dataset containing flower measurements of iris plants and analyze their usefulness in pattern recognition. Based on these models, we claim that any non-uniform pattern can be represented as a singular perturbation to uniform distribution. However, our parametric estimation procedure have some limitations such as sensitivity to initial conditions depending on the data at hand.

Weak perturbations of equal size can produce terminal Wasserstein errors of different orders. For Gaussian-smoothed infinitely divisible laws, we differentiate distribution functions with respect to variance-weighted Lévy characteristics, including distributional directions generated by moving atoms. We obtain first- and second-order expansions uniform over Lipschitz tests. Gaussian analyticity identifies the signed second coefficient of the Wasserstein-1 distance when the first response is nonzero. When it vanishes, a finite second displacement moment yields a quadratic response, strictly positive for nonzero displacement dispersion. For local balanced remeshing, the error is comparable to the grid-alignment variance, giving sharp quadratic grid rates for compactly supported densities and nonaligned atomic sequences. We derive metric speed and length along admissible non-atomic curves and a response-based linear program with a certified oracle gap and consistent quadrature. We also establish the sharp vanishing-smoothing transition and a multivariate second-order expansion. The Supplement treats state-dependent responses and further stability estimates.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) Non-uniqueness: there are many different eigendecompositions of the same Laplacian, and (2) Instability: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a "hard partition" of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to "softly partition" eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods.

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.

We investigate statistical properties of a likelihood approach to nonparametric estimation of a singular distribution using deep generative models. More specifically, a deep generative model is used to model high-dimensional data that are assumed to concentrate around some low-dimensional structure. Estimating the distribution supported on this low-dimensional structure, such as a low-dimensional manifold, is challenging due to its singularity with respect to the Lebesgue measure in the ambient space. In the considered model, a usual likelihood approach can fail to estimate the target distribution consistently due to the singularity. We prove that a novel and effective solution exists by perturbing the data with an instance noise, which leads to consistent estimation of the underlying distribution with desirable convergence rates. We also characterize the class of distributions that can be efficiently estimated via deep generative models. This class is sufficiently general to contain various structured distributions such as product distributions, classically smooth distributions and distributions supported on a low-dimensional manifold. Our analysis provides some insights on how deep generative models can avoid the curse of dimensionality for nonparametric distribution estimation. We conduct a thorough simulation study and real data analysis to empirically demonstrate that the proposed data perturbation technique improves the estimation performance significantly.

Fix a strip width \(ρ>0\), a Diophantine frequency \(α\), an integer \(N\ge2\), and \(λ>1\). For the family \[ V_{\varepsilon,δ}(x) =2λ\cos(2πN x)+\varepsilonδ(x), \] we prove that there is an open prevalent set \(\mathcal P_{\rm strat}\) of real-analytic strip-\(ρ\) perturbations such that every \(δ\in\mathcal P_{\rm strat}\) admits \(\varepsilon_0(δ)>0\) for which \[ gathered Leb\left\{ E\inΣ(V_{\varepsilon,δ},α): ω(α,E;V_{\varepsilon,δ})=s \right\}>0, 0<\varepsilon<\varepsilon_0(δ), \qquad s=1,\ldots,N. gathered \] The proof relates acceleration to the total multiplicity of real zeros of analytic overlap coefficients for first-return cocycles. Under quantitative control of the return products, Poisson integration and Kac normalization identify acceleration with half this multiplicity. A positive analytic dual state gives the finite-volume spectral gaps and Schur curvature needed at the upper spectral edge. Schur variations separate the perturbed maxima, and parameter exclusion preserves \(s\) pairs of simple zeros on a positive-measure spectral set.

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.

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.

Ensemble Kalman Inversion (EKI) is a derivative-free, ensemble-based method for inverse and optimization problems. Its continuous-time formulation can be interpreted as an interacting particle system driven by a Kalman-type preconditioned descent direction. A well-known limitation of this dynamics is the possible premature collapse of the covariance of the ensemble, which makes the method sensitive to the initial ensemble. We introduce a second-order particle system in which the particles evolve according to an inertial dynamics. The model combines a Kalman-type relaxation force with damping, attraction towards the ensemble mean, and a short-range repulsive interaction designed to counteract ensemble collapse. The resulting dynamics can be interpreted as a heavy-ball reformulation of continuous-time EKI enriched by competing attractive and repulsive mechanisms. For linear inverse problems, we analyze the induced mean and fluctuation dynamics and identify a parameter regime in which fully collapsed configurations are linearly unstable. We further characterize asymptotic equilibria through a constrained optimality condition on the subspace retained by the limiting ensemble covariance and derive an exponential decay estimate. Numerical experiments illustrate the effect of inertia and repulsion on the ensemble dynamics and compare the proposed second-order method with first-order EKI-type

We present anyakrakusuma, an open-source Python library that solves the discrete static Schrödinger bridge problem, the entropically regularized counterpart of optimal transport, through a log-domain Sinkhorn--Knopp iteration and reconstructs the entropic interpolation between two empirical point clouds. The solver is paired with a diagnostic pipeline that characterizes the optimal coupling and the intermediate distributions through information-theoretic and geometric measures. We exercise the library on four idealized planar cases spanning a circle-to-circle dilation, a spiral-to-mixture fragmentation, a rigid reorientation of two moons, and a Lissajous-to-trefoil deformation. The log-domain formulation is necessary rather than merely convenient at the parameters studied, where the cost-to-regularization ratio reaches four hundred and the Gibbs kernel underflows double precision across most of its range; the iteration nonetheless attains a marginal residual of 10^{-9} and unit marginal fidelity in every case. Residual histories decay geometrically over approximately eight decades at per-iteration contraction factors between 0.966 and 0.976, which are local rates near the fixed point that lie many orders of magnitude below the worst-case Hilbert-metric bound. The covariance analysis recovers an imposed ninety-degree reorientation to within 0.07^circ, roughly forty times smaller than its uncertainty, across a masked interval of near-isotropy on which the principal axis is unobservable. The diagnostics are reported with explicit attention to the regimes in which each is well defined, including the differential entropy, which is meaningful only on the open interpolation interval. The presented cases are constructed rather than measured; quantitative application to empirical point clouds requires further study.

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.

Model quantization reduces neural network parameter precision to achieve compression, but often compromises accuracy. Existing post-training quantization (PTQ) methods employ iterative parameter updates to preserve accuracy under high compression ratios, incurring significant computational complexity and resource overhead, which limits applicability in resource-constrained edge computing and real-time inference scenarios. This paper proposes an efficient PTQ method guided by parameter sensitivity analysis. The approach prioritizes quantization of high-sensitivity parameters, leveraging unquantized low-sensitivity parameters to compensate for quantization errors, thereby mitigating accuracy degradation. Furthermore, by exploiting column-wise clustering of parameter sensitivity, the method introduces a row-parallel quantization framework with a globally shared inverse Hessian matrix update mechanism, reducing computational complexity by an order of magnitude. Experimental results on ResNet-50 and YOLOv5s demonstrate a 20-200-fold quantization speedup over the Optimal Brain Quantization baseline, with mean accuracy loss below 0.3%, confirming the method's efficacy in balancing efficiency and accuracy.

Structural optimization is a popular method for designing objects such as bridge trusses, airplane wings, and optical devices. Unfortunately, the quality of solutions depends heavily on how the problem is parameterized. In this paper, we propose using the implicit bias over functions induced by neural networks to improve the parameterization of structural optimization. Rather than directly optimizing densities on a grid, we instead optimize the parameters of a neural network which outputs those densities. This reparameterization leads to different and often better solutions. On a selection of 116 structural optimization tasks, our approach produces the best design 50% more often than the best baseline method.

Optimal configuration of the learning rate (LR) is a fundamental yet formidable challenge in large-scale pre-training. Given the stringent trade-off between training costs and model performance, the pivotal question is whether the optimal LR can be accurately extrapolated from low-cost experiments. In this paper, we formalize this investigation into two distinct research paradigms: Fitting and Transfer. Within the Fitting Paradigm, we innovatively introduce a Scaling Law for search factor, effectively reducing the search complexity from O(n^3) to O(n*C_D*C_η) via predictive modeling. Within the Transfer Paradigm, we extend the principles of μTransfer to the Mixture of Experts (MoE) architecture, broadening its applicability to encompass model depth, weight decay, and token horizons. By pushing the boundaries of existing hyperparameter research in terms of scale, we conduct a comprehensive comparison between these two paradigms. Our empirical results challenge the scalability of the widely adopted μ Transfer in large-scale pre-training scenarios. Furthermore, we provide a rigorous analysis through the dual lenses of training stability and feature learning to elucidate the underlying reasons why module-wise parameter tuning underperforms in large-scale settings. This work offers systematic practical guidelines and a fresh theoretical perspective for optimizing industrial-level pre-training.