arXiv subjects

Francesco Alesiani

Publications and source records attributed to Francesco Alesiani.

At least 19 recordsLinked to original sources

arXiv2026

BU-MBAR: A hybrid solution strategy for the MBAR equations

The multi-state Bennett acceptance ratio (MBAR) equations combine the data collected under different thermodynamic conditions in a statistically optimal way. Due to their practical importance, several solution strategies have been devised to optimize the convergence of the resulting set of coupled equations. However, even with graphics processing unit (GPU) acceleration, the convergence of these methods can still be either unstable or slow. We propose a new approach where the equations are interpreted as the limit of infinitesimal bin width of the respective weighted histogram analysis method (WHAM). In the proposed binned-to-unbinned MBAR (BU-MBAR) method, the bin width is adapted dynamically to ensure a stable and efficient convergence to the asymptotic solution.

physics.comp-ph↗

arXiv2026

Hyperspatial Sampling: Circumventing Free-Energy Barriers via Replica Exchange with Extra Dimensions

Simulating systems with rugged free-energy landscapes remains a central challenge in computational physics and chemistry. We introduce hyperspatial replica exchange (HS-REX), an enhanced sampling method in which the physical system is artificially extended by additional spatial dimensions. In higher dimensions, free-energy barriers can be circumvented through paths that are geometrically inaccessible in the original space. Restricting the penalty to only solute atoms dramatically reduces the number of replicas required for solvated systems compared to standard temperature replica exchange, a feature especially relevant for biological applications. As proof of concept, we demonstrate the method on a double-well model system and on alanine dipeptide in explicit water as benchmark system. In the latter case, HS-REX achieves enhanced conformational sampling of not only the slow backbone dihedral angles, but also both chiral configurations of the molecule, which are sterically inaccessible to standard sampling in three dimensions. This demonstrates enhanced ergodic sampling over conventional temperature replica exchange.

physics.comp-ph↗

arXiv2026

Logical Guidance for the Exact Composition of Diffusion Models

We propose LOGDIFF (Logical Guidance for the Exact Composition of Diffusion Models), a guidance framework for diffusion models that enables principled constrained generation with complex logical expressions at inference time. We study when exact score-based guidance for complex logical formulas can be obtained from guidance signals associated with atomic properties. First, we derive an exact Boolean calculus that provides a sufficient condition for exact logical guidance. Specifically, if a formula admits a circuit representation in which conjunctions combine conditionally independent subformulas and disjunctions combine subformulas that are either conditionally independent or mutually exclusive, exact logical guidance is achievable. In this case, the guidance signal can be computed exactly from atomic scores and posterior probabilities using an efficient recursive algorithm. Moreover, we show that, for commonly encountered classes of distributions, any desired Boolean formula is compilable into such a circuit representation. Second, by combining atomic guidance scores with posterior probability estimates, we introduce a hybrid guidance approach that bridges classifier guidance and classifier-free guidance, applicable to both compositional logical guidance and standard conditional generation. We demonstrate the effectiveness of our framework on multiple image and protein structure generation tasks.

cs.LG↗

arXiv2026

Clifford Kolmogorov-Arnold Networks

We introduce Clifford Kolmogorov-Arnold Network (ClKAN), a flexible and efficient architecture for function approximation in arbitrary Clifford Algebra spaces. We propose the use of Randomized Quasi-Monte Carlo grid generation as a solution to the exponential scaling associated with higher-dimensional algebras. Our ClKAN also introduces new batch normalization strategies to deal with variable domain input. ClKAN finds application in scientific discovery and engineering, and is validated in synthetic and physics-inspired tasks.

cs.LG↗

arXiv2025

Performance of universal machine-learned potentials with explicit long-range interactions in biomolecular simulations

Universal machine-learned potentials promise transferable accuracy across compositional and vibrational degrees of freedom, yet their application to biomolecular simulations remains underexplored. This work systematically evaluates equivariant message-passing architectures trained on the SPICE-v2 dataset with and without explicit long-range dispersion and electrostatics. We assess the impact of model size, training data composition, and electrostatic treatment across in- and out-of-distribution benchmark datasets, as well as molecular simulations of bulk liquid water, aqueous NaCl solutions, and biomolecules, including alanine tripeptide, the mini-protein Trp-cage, and Crambin. While larger models improve accuracy on benchmark datasets, this trend does not consistently extend to properties obtained from simulations. Predicted properties also depend on the composition of the training dataset. Long-range electrostatics show no systematic impact across systems. However, for Trp-cage, their inclusion yields increased conformational variability. Our results suggest that imbalanced datasets and immature evaluation practices currently challenge the applicability of universal machine-learned potentials to biomolecular simulations.

physics.chem-ph↗

arXiv2025

Variational Kolmogorov-Arnold Network

Kolmogorov-Arnold Networks (KANs) offer a theoretically grounded alternative to multi-layer perceptrons by representing multivariate functions as compositions of univariate basis functions. However, a critical limitation of KANs is the need to manually specify the number of basis functions per layer -- a hyperparameter that directly controls model capacity and substantially impacts performance, yet whose optimal value varies unpredictably across tasks. We present InfinityKAN, a variational inference framework that eliminates this design choice by learning the number of basis functions during training. Our approach models the basis count as a latent variable with a truncated exponential prior, introducing a differentiable weighting function that enables gradient-based optimization. We establish the Lipschitz continuity of the variational objective, ensuring stable training dynamics. Experiments across 18 datasets spanning synthetic, image, tabular, and graph domains demonstrate that InfinityKAN matches or exceeds the performance of KANs while requiring no manual selection of the number of bases for each layer.

cs.LG↗

arXiv2025

Geometric Kolmogorov-Arnold Superposition Theorem

The Kolmogorov-Arnold Theorem (KAT), or more generally, the Kolmogorov Superposition Theorem (KST), establishes that any non-linear multivariate function can be exactly represented as a finite superposition of non-linear univariate functions. Unlike the universal approximation theorem, which provides only an approximate representation without guaranteeing a fixed network size, KST offers a theoretically exact decomposition. The Kolmogorov-Arnold Network (KAN) was introduced as a trainable model to implement KAT, and recent advancements have adapted KAN using concepts from modern neural networks. However, KAN struggles to effectively model physical systems that require inherent equivariance or invariance geometric symmetries as $E(3)$ transformations, a key property for many scientific and engineering applications. In this work, we propose a novel extension of KAT and KAN to incorporate equivariance and invariance over various group actions, including $O(n)$, $O(1,n)$, $S_n$, and general $GL$, enabling accurate and efficient modeling of these systems. Our approach provides a unified approach that bridges the gap between mathematical theory and practical architectures for physical systems, expanding the applicability of KAN to a broader class of problems. We provide experimental validation on molecular dynamical systems and particle physics.

cs.LG↗

arXiv2025

Adaptive Message Passing: A General Framework to Mitigate Oversmoothing, Oversquashing, and Underreaching

Long-range interactions are essential for the correct description of complex systems in many scientific fields. The price to pay for including them in the calculations, however, is a dramatic increase in the overall computational costs. Recently, deep graph networks have been employed as efficient, data-driven models for predicting properties of complex systems represented as graphs. These models rely on a message passing strategy that should, in principle, capture long-range information without explicitly modeling the corresponding interactions. In practice, most deep graph networks cannot really model long-range dependencies due to the intrinsic limitations of (synchronous) message passing, namely oversmoothing, oversquashing, and underreaching. This work proposes a general framework that learns to mitigate these limitations: within a variational inference framework, we endow message passing architectures with the ability to adapt their depth and filter messages along the way. With theoretical and empirical arguments, we show that this strategy better captures long-range interactions, by competing with the state of the art on five node and graph prediction datasets.

cs.LG↗

arXiv2025

Fast, Modular, and Differentiable Framework for Machine Learning-Enhanced Molecular Simulations

We present an end-to-end differentiable molecular simulation framework (DIMOS) for molecular dynamics and Monte Carlo simulations. DIMOS easily integrates machine-learning-based interatomic potentials and implements classical force fields including an efficient implementation of particle-mesh Ewald. Thanks to its modularity, both classical and machine-learning-based approaches can be easily combined into a hybrid description of the system (ML/MM). By supporting key molecular dynamics features such as efficient neighborlists and constraint algorithms for larger time steps, the framework makes steps in bridging the gap between hand-optimized simulation engines and the flexibility of a \verb|PyTorch| implementation. We show that due to improved linear instead of quadratic scaling as function of system size DIMOS is able to obtain speed-up factors of up to $170\times$ for classical force field simulations against another fully differentiable simulation framework. The advantage of differentiability is demonstrated by an end-to-end optimization of the proposal distribution in a Markov Chain Monte Carlo simulation based on Hamiltonian Monte Carlo (HMC). Using these optimized simulation parameters a $3\times$ acceleration is observed in comparison to ad-hoc chosen simulation parameters. The code is available at https://github.com/nec-research/DIMOS.

physics.comp-ph↗

arXiv2025

Adaptive Width Neural Networks

For almost 70 years, researchers have typically selected the width of neural networks' layers either manually or through automated hyperparameter tuning methods such as grid search and, more recently, neural architecture search. This paper challenges the status quo by introducing an easy-to-use technique to learn an unbounded width of a neural network's layer during training. The method jointly optimizes the width and the parameters of each layer via standard backpropagation. We apply the technique to a broad range of data domains such as tables, images, text, sequences, and graphs, showing how the width adapts to the task's difficulty. A by product of our width learning approach is the easy truncation of the trained network at virtually zero cost, achieving a smooth trade-off between performance and compute resources. Alternatively, one can dynamically compress the network until performances do not degrade. In light of recent foundation models trained on large datasets, requiring billions of parameters and where hyper-parameter tuning is unfeasible due to huge training costs, our approach introduces a viable alternative for width learning.

cs.LG↗

arXiv2024

Variational methods for Learning Multilevel Genetic Algorithms using the Kantorovich Monad

Levels of selection and multilevel evolutionary processes are essential concepts in evolutionary theory, and yet there is a lack of common mathematical models for these core ideas. Here, we propose a unified mathematical framework for formulating and optimizing multilevel evolutionary processes and genetic algorithms over arbitrarily many levels based on concepts from category theory and population genetics. We formulate a multilevel version of the Wright-Fisher process using this approach, and we show that this model can be analyzed to clarify key features of multilevel selection. Particularly, we derive an extended multilevel probabilistic version of Price's Equation via the Kantorovich Monad, and we use this to characterize regimes of parameter space within which selection acts antagonistically or cooperatively across levels. Finally, we show how our framework can provide a unified setting for learning genetic algorithms (GAs), and we show how we can use a Variational Optimization and a multi-level analogue of coalescent analysis to fit multilevel GAs to simulated data.

q-bio.PE↗

arXiv2024

Higher-Rank Irreducible Cartesian Tensors for Equivariant Message Passing

The ability to perform fast and accurate atomistic simulations is crucial for advancing the chemical sciences. By learning from high-quality data, machine-learned interatomic potentials achieve accuracy on par with ab initio and first-principles methods at a fraction of their computational cost. The success of machine-learned interatomic potentials arises from integrating inductive biases such as equivariance to group actions on an atomic system, e.g., equivariance to rotations and reflections. In particular, the field has notably advanced with the emergence of equivariant message passing. Most of these models represent an atomic system using spherical tensors, tensor products of which require complicated numerical coefficients and can be computationally demanding. Cartesian tensors offer a promising alternative, though state-of-the-art methods lack flexibility in message-passing mechanisms, restricting their architectures and expressive power. This work explores higher-rank irreducible Cartesian tensors to address these limitations. We integrate irreducible Cartesian tensor products into message-passing neural networks and prove the equivariance and traceless property of the resulting layers. Through empirical evaluations on various benchmark data sets, we consistently observe on-par or better performance than that of state-of-the-art spherical and Cartesian models.

cs.LG↗

arXiv2024

Uncertainty-biased molecular dynamics for learning uniformly accurate interatomic potentials

Efficiently creating a concise but comprehensive data set for training machine-learned interatomic potentials (MLIPs) is an under-explored problem. Active learning, which uses biased or unbiased molecular dynamics (MD) to generate candidate pools, aims to address this objective. Existing biased and unbiased MD-simulation methods, however, are prone to miss either rare events or extrapolative regions -- areas of the configurational space where unreliable predictions are made. This work demonstrates that MD, when biased by the MLIP's energy uncertainty, simultaneously captures extrapolative regions and rare events, which is crucial for developing uniformly accurate MLIPs. Furthermore, exploiting automatic differentiation, we enhance bias-forces-driven MD with the concept of bias stress. We employ calibrated gradient-based uncertainties to yield MLIPs with similar or, sometimes, better accuracy than ensemble-based methods at a lower computational cost. Finally, we apply uncertainty-biased MD to alanine dipeptide and MIL-53(Al), generating MLIPs that represent both configurational spaces more accurately than models trained with conventional MD.

physics.comp-ph↗

arXiv2024

PDEBENCH: An Extensive Benchmark for Scientific Machine Learning

Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and representative of a wide range of problems. We introduce PDEBench, a benchmark suite of time-dependent simulation tasks based on Partial Differential Equations (PDEs). PDEBench comprises both code and data to benchmark the performance of novel machine learning models against both classical numerical simulations and machine learning baselines. Our proposed set of benchmark problems contribute the following unique features: (1) A much wider range of PDEs compared to existing benchmarks, ranging from relatively common examples to more realistic and difficult problems; (2) much larger ready-to-use datasets compared to prior work, comprising multiple simulation runs across a larger number of initial and boundary conditions and PDE parameters; (3) more extensible source codes with user-friendly APIs for data generation and baseline results with popular machine learning models (FNO, U-Net, PINN, Gradient-Based Inverse Method). PDEBench allows researchers to extend the benchmark freely for their own purposes using a standardized API and to compare the performance of new models to existing baseline methods. We also propose new evaluation metrics with the aim to provide a more holistic understanding of learning methods in the context of Scientific ML. With those metrics we identify tasks which are challenging for recent ML methods and propose these tasks as future challenges for the community. The code is available at https://github.com/pdebench/PDEBench.

cs.LG↗

arXiv2024

Graph Reasoning Networks

Graph neural networks (GNNs) are the predominant approach for graph-based machine learning. While neural networks have shown great performance at learning useful representations, they are often criticized for their limited high-level reasoning abilities. In this work, we present Graph Reasoning Networks (GRNs), a novel approach to combine the strengths of fixed and learned graph representations and a reasoning module based on a differentiable satisfiability solver. While results on real-world datasets show comparable performance to GNN, experiments on synthetic datasets demonstrate the potential of the newly proposed method.

cs.LG↗

arXiv2023

Continual Invariant Risk Minimization

Empirical risk minimization can lead to poor generalization behavior on unseen environments if the learned model does not capture invariant feature representations. Invariant risk minimization (IRM) is a recent proposal for discovering environment-invariant representations. IRM was introduced by Arjovsky et al. (2019) and extended by Ahuja et al. (2020). IRM assumes that all environments are available to the learning system at the same time. With this work, we generalize the concept of IRM to scenarios where environments are observed sequentially. We show that existing approaches, including those designed for continual learning, fail to identify the invariant features and models across sequentially presented environments. We extend IRM under a variational Bayesian and bilevel framework, creating a general approach to continual invariant risk minimization. We also describe a strategy to solve the optimization problems using a variant of the alternating direction method of multiplier (ADMM). We show empirically using multiple datasets and with multiple sequential environments that the proposed methods outperform or is competitive with prior approaches.

cs.LG↗

arXiv2023

Self-Tuning Hamiltonian Monte Carlo for Accelerated Sampling

The performance of Hamiltonian Monte Carlo simulations crucially depends on both the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune such parameters, based on a local loss function which promotes the fast exploration of phase-space. We show that a good correspondence between loss and autocorrelation time can be established, allowing for gradient-based optimization using a fully-differentiable set-up. The loss is constructed in such a way that it also allows for gradient-driven learning of a distribution over the number of integration steps. Our approach is demonstrated for the one-dimensional harmonic oscillator and alanine dipeptide, a small protein common as a test case for simulation methods. Through the application to the harmonic oscillator, we highlight the importance of not using a fixed timestep to avoid a rugged loss surface with many local minima, otherwise trapping the optimization. In the case of alanine dipeptide, by tuning the only free parameter of our loss definition, we find a good correspondence between it and the autocorrelation times, resulting in a $>100$ fold speed up in optimization of simulation parameters compared to a grid-search. For this system, we also extend the integrator to allow for atom-dependent timesteps, providing a further reduction of $25\%$ in autocorrelation times.

physics.comp-ph↗

arXiv2023

Learning Neural PDE Solvers with Parameter-Guided Channel Attention

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.

cs.LG↗