Daily Papers

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and DeltaSCF results for the low lying excited states (S_{1} and T_{1}) of a set of gas phase acene molecules and OLED emitters, as well as with reference results from the literature. At the PBE level of theory, T-CDFT outperforms DeltaSCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge-transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT. T-CDFT is designed for large systems and has been implemented in the linear scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called nabla^2DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level (omegaB97X-D/def2-SVP) for each conformation. Moreover, nabla^2DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.

We present developments and applications for the diagonalization of shell-model hamiltonians in a discrete non-orthogonal basis (DNO-SM). The method, and its actual numerical implementation CARINA, based on mean-field and beyond-mean field techniques has already been applied in previous studies and is focused on basis states selection optimization. The method is benchmarked against a full set of sd shell exact diagonalizations, and is applied for the first time to the heavy deformed ^{254}No nucleus.

Fourier Neural Operators (FNOs) have proven to be an efficient and effective method for resolution-independent operator learning in a broad variety of application areas across scientific machine learning. A key reason for their success is their ability to accurately model long-range dependencies in spatio-temporal data by learning global convolutions in a computationally efficient manner. To this end, FNOs rely on the discrete Fourier transform (DFT), however, DFTs cause visual and spectral artifacts as well as pronounced dissipation when learning operators in spherical coordinates since they incorrectly assume a flat geometry. To overcome this limitation, we generalize FNOs on the sphere, introducing Spherical FNOs (SFNOs) for learning operators on spherical geometries. We apply SFNOs to forecasting atmospheric dynamics, and demonstrate stable auto\-regressive rollouts for a year of simulated time (1,460 steps), while retaining physically plausible dynamics. The SFNO has important implications for machine learning-based simulation of climate dynamics that could eventually help accelerate our response to climate change.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)^{1-3} offer a computationally efficient alternative to density functional theory (DFT)^4 for PES modeling across the periodic table. However, their accuracy today is fundamentally constrained due to a reliance on DFT relaxation data.^{5,6} Here, we introduce MatPES, a foundational PES dataset comprising sim 400,000 structures carefully sampled from 281 million molecular dynamics snapshots that span 16 billion atomic environments. We demonstrate that UMLIPs trained on the modestly sized MatPES dataset can rival, or even outperform, prior models trained on much larger datasets across a broad range of equilibrium, near-equilibrium, and molecular dynamics property benchmarks. We also introduce the first high-fidelity PES dataset based on the revised regularized strongly constrained and appropriately normed (r^2SCAN) functional^7 with greatly improved descriptions of interatomic bonding. The open source MatPES initiative emphasizes the importance of data quality over quantity in materials science and enables broad community-driven advancements toward more reliable, generalizable, and efficient UMLIPs for large-scale materials discovery and design.

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.

Symmetry learning has proven to be an effective approach for extracting the hidden structure of data, with the concept of equivariance relation playing the central role. However, most of the current studies are built on architectural theory and corresponding assumptions on the form of data. We propose Neural Fourier Transform (NFT), a general framework of learning the latent linear action of the group without assuming explicit knowledge of how the group acts on data. We present the theoretical foundations of NFT and show that the existence of a linear equivariant feature, which has been assumed ubiquitously in equivariance learning, is equivalent to the existence of a group invariant kernel on the dataspace. We also provide experimental results to demonstrate the application of NFT in typical scenarios with varying levels of knowledge about the acting group.

We propose a neural network for both forward and inverse continuous nonlinear Fourier transforms, NFT and INFT respectively. We demonstrate the network's capability to perform NFT and INFT for a random mix of NFDM-QAM signals. The network transformations (NFT and INFT) exhibit true characteristics of these transformations; they are significantly different for low and high-power input pulses. The network shows adequate accuracy with an RMSE of 5e-3 for forward and 3e-2 for inverse transforms. We further show that the trained network can be used to perform general nonlinear Fourier transforms on arbitrary pulses beyond the training pulse types.

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

We propose the use of low bit-depth Sigma-Delta and distributed noise-shaping methods for quantizing the Random Fourier features (RFFs) associated with shift-invariant kernels. We prove that our quantized RFFs -- even in the case of 1-bit quantization -- allow a high accuracy approximation of the underlying kernels, and the approximation error decays at least polynomially fast as the dimension of the RFFs increases. We also show that the quantized RFFs can be further compressed, yielding an excellent trade-off between memory use and accuracy. Namely, the approximation error now decays exponentially as a function of the bits used. Moreover, we empirically show by testing the performance of our methods on several machine learning tasks that our method compares favorably to other state of the art quantization methods in this context.

We consider the problem of computing the Walsh-Hadamard Transform (WHT) of some N-length input vector in the presence of noise, where the N-point Walsh spectrum is K-sparse with K = {O}(N^{delta}) scaling sub-linearly in the input dimension N for some 0<delta<1. Over the past decade, there has been a resurgence in research related to the computation of Discrete Fourier Transform (DFT) for some length-N input signal that has a K-sparse Fourier spectrum. In particular, through a sparse-graph code design, our earlier work on the Fast Fourier Aliasing-based Sparse Transform (FFAST) algorithm computes the K-sparse DFT in time {O}(Klog K) by taking {O}(K) noiseless samples. Inspired by the coding-theoretic design framework, Scheibler et al. proposed the Sparse Fast Hadamard Transform (SparseFHT) algorithm that elegantly computes the K-sparse WHT in the absence of noise using {O}(Klog N) samples in time {O}(Klog^2 N). However, the SparseFHT algorithm explicitly exploits the noiseless nature of the problem, and is not equipped to deal with scenarios where the observations are corrupted by noise. Therefore, a question of critical interest is whether this coding-theoretic framework can be made robust to noise. Further, if the answer is yes, what is the extra price that needs to be paid for being robust to noise? In this paper, we show, quite interestingly, that there is {\it no extra price} that needs to be paid for being robust to noise other than a constant factor. In other words, we can maintain the same sample complexity {O}(Klog N) and the computational complexity {O}(Klog^2 N) as those of the noiseless case, using our SParse Robust Iterative Graph-based Hadamard Transform (SPRIGHT) algorithm.

Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with system size partly relies upon a spatial distance limit on messages. While this focus on locality is a useful inductive bias, it also impedes the learning of long-range interactions such as electrostatics and van der Waals forces. To address this drawback, we propose Ewald message passing: a nonlocal Fourier space scheme which limits interactions via a cutoff on frequency instead of distance, and is theoretically well-founded in the Ewald summation method. It can serve as an augmentation on top of existing MPNN architectures as it is computationally inexpensive and agnostic to architectural details. We test the approach with four baseline models and two datasets containing diverse periodic (OC20) and aperiodic structures (OE62). We observe robust improvements in energy mean absolute errors across all models and datasets, averaging 10% on OC20 and 16% on OE62. Our analysis shows an outsize impact of these improvements on structures with high long-range contributions to the ground truth energy.

Spectral analysis provides one of the most effective paradigms for information-preserving dimensionality reduction, as simple descriptions of naturally occurring signals are often obtained via few terms of periodic basis functions. In this work, we study deep neural networks designed to harness the structure in frequency domain for efficient learning of long-range correlations in space or time: frequency-domain models (FDMs). Existing FDMs are based on complex-valued transforms i.e. Fourier Transforms (FT), and layers that perform computation on the spectrum and input data separately. This design introduces considerable computational overhead: for each layer, a forward and inverse FT. Instead, this work introduces a blueprint for frequency domain learning through a single transform: transform once (T1). To enable efficient, direct learning in the frequency domain we derive a variance-preserving weight initialization scheme and investigate methods for frequency selection in reduced-order FDMs. Our results noticeably streamline the design process of FDMs, pruning redundant transforms, and leading to speedups of 3x to 10x that increase with data resolution and model size. We perform extensive experiments on learning the solution operator of spatio-temporal dynamics, including incompressible Navier-Stokes, turbulent flows around airfoils and high-resolution video of smoke. T1 models improve on the test performance of FDMs while requiring significantly less computation (5 hours instead of 32 for our large-scale experiment), with over 20% reduction in average predictive error across tasks.

We present Neural Spectral Methods, a technique to solve parametric Partial Differential Equations (PDEs), grounded in classical spectral methods. Our method uses orthogonal bases to learn PDE solutions as mappings between spectral coefficients. In contrast to current machine learning approaches which enforce PDE constraints by minimizing the numerical quadrature of the residuals in the spatiotemporal domain, we leverage Parseval's identity and introduce a new training strategy through a spectral loss. Our spectral loss enables more efficient differentiation through the neural network, and substantially reduces training complexity. At inference time, the computational cost of our method remains constant, regardless of the spatiotemporal resolution of the domain. Our experimental results demonstrate that our method significantly outperforms previous machine learning approaches in terms of speed and accuracy by one to two orders of magnitude on multiple different problems. When compared to numerical solvers of the same accuracy, our method demonstrates a 10times increase in performance speed.

Automatic differentiation (autodiff) has revolutionized machine learning. It allows to express complex computations by composing elementary ones in creative ways and removes the burden of computing their derivatives by hand. More recently, differentiation of optimization problem solutions has attracted widespread attention with applications such as optimization layers, and in bi-level problems such as hyper-parameter optimization and meta-learning. However, so far, implicit differentiation remained difficult to use for practitioners, as it often required case-by-case tedious mathematical derivations and implementations. In this paper, we propose automatic implicit differentiation, an efficient and modular approach for implicit differentiation of optimization problems. In our approach, the user defines directly in Python a function F capturing the optimality conditions of the problem to be differentiated. Once this is done, we leverage autodiff of F and the implicit function theorem to automatically differentiate the optimization problem. Our approach thus combines the benefits of implicit differentiation and autodiff. It is efficient as it can be added on top of any state-of-the-art solver and modular as the optimality condition specification is decoupled from the implicit differentiation mechanism. We show that seemingly simple principles allow to recover many existing implicit differentiation methods and create new ones easily. We demonstrate the ease of formulating and solving bi-level optimization problems using our framework. We also showcase an application to the sensitivity analysis of molecular dynamics.

A Transformer-based deep direct sampling method is proposed for electrical impedance tomography, a well-known severely ill-posed nonlinear boundary value inverse problem. A real-time reconstruction is achieved by evaluating the learned inverse operator between carefully designed data and the reconstructed images. An effort is made to give a specific example to a fundamental question: whether and how one can benefit from the theoretical structure of a mathematical problem to develop task-oriented and structure-conforming deep neural networks? Specifically, inspired by direct sampling methods for inverse problems, the 1D boundary data in different frequencies are preprocessed by a partial differential equation-based feature map to yield 2D harmonic extensions as different input channels. Then, by introducing learnable non-local kernels, the direct sampling is recast to a modified attention mechanism. The new method achieves superior accuracy over its predecessors and contemporary operator learners and shows robustness to noises in benchmarks. This research shall strengthen the insights that, despite being invented for natural language processing tasks, the attention mechanism offers great flexibility to be modified in conformity with the a priori mathematical knowledge, which ultimately leads to the design of more physics-compatible neural architectures.

Dynamical systems provide a comprehensive way to study complex and changing behaviors across various sciences. Many modern systems are too complicated to analyze directly or we do not have access to models, driving significant interest in learning methods. Koopman operators have emerged as a dominant approach because they allow the study of nonlinear dynamics using linear techniques by solving an infinite-dimensional spectral problem. However, current algorithms face challenges such as lack of convergence, hindering practical progress. This paper addresses a fundamental open question: When can we robustly learn the spectral properties of Koopman operators from trajectory data of dynamical systems, and when can we not? Understanding these boundaries is crucial for analysis, applications, and designing algorithms. We establish a foundational approach that combines computational analysis and ergodic theory, revealing the first fundamental barriers -- universal for any algorithm -- associated with system geometry and complexity, regardless of data quality and quantity. For instance, we demonstrate well-behaved smooth dynamical systems on tori where non-trivial eigenfunctions of the Koopman operator cannot be determined by any sequence of (even randomized) algorithms, even with unlimited training data. Additionally, we identify when learning is possible and introduce optimal algorithms with verification that overcome issues in standard methods. These results pave the way for a sharp classification theory of data-driven dynamical systems based on how many limits are needed to solve a problem. These limits characterize all previous methods, presenting a unified view. Our framework systematically determines when and how Koopman spectral properties can be learned.

Diffusion models suffer from slow sample generation at inference time. Therefore, developing a principled framework for fast deterministic/stochastic sampling for a broader class of diffusion models is a promising direction. We propose two complementary frameworks for accelerating sample generation in pre-trained models: Conjugate Integrators and Splitting Integrators. Conjugate integrators generalize DDIM, mapping the reverse diffusion dynamics to a more amenable space for sampling. In contrast, splitting-based integrators, commonly used in molecular dynamics, reduce the numerical simulation error by cleverly alternating between numerical updates involving the data and auxiliary variables. After extensively studying these methods empirically and theoretically, we present a hybrid method that leads to the best-reported performance for diffusion models in augmented spaces. Applied to Phase Space Langevin Diffusion [Pandey & Mandt, 2023] on CIFAR-10, our deterministic and stochastic samplers achieve FID scores of 2.11 and 2.36 in only 100 network function evaluations (NFE) as compared to 2.57 and 2.63 for the best-performing baselines, respectively. Our code and model checkpoints will be made publicly available at https://github.com/mandt-lab/PSLD.

A popular approach to sample a diffusion-based generative model is to solve an ordinary differential equation (ODE). In existing samplers, the coefficients of the ODE solvers are pre-determined by the ODE formulation, the reverse discrete timesteps, and the employed ODE methods. In this paper, we consider accelerating several popular ODE-based sampling processes (including EDM, DDIM, and DPM-Solver) by optimizing certain coefficients via improved integration approximation (IIA). We propose to minimize, for each time step, a mean squared error (MSE) function with respect to the selected coefficients. The MSE is constructed by applying the original ODE solver for a set of fine-grained timesteps, which in principle provides a more accurate integration approximation in predicting the next diffusion state. The proposed IIA technique does not require any change of a pre-trained model, and only introduces a very small computational overhead for solving a number of quadratic optimization problems. Extensive experiments show that considerably better FID scores can be achieved by using IIA-EDM, IIA-DDIM, and IIA-DPM-Solver than the original counterparts when the neural function evaluation (NFE) is small (i.e., less than 25).

We extend molecular bootstrap embedding to make it appropriate for implementation on a quantum computer. This enables solution of the electronic structure problem of a large molecule as an optimization problem for a composite Lagrangian governing fragments of the total system, in such a way that fragment solutions can harness the capabilities of quantum computers. By employing state-of-art quantum subroutines including the quantum SWAP test and quantum amplitude amplification, we show how a quadratic speedup can be obtained over the classical algorithm, in principle. Utilization of quantum computation also allows the algorithm to match -- at little additional computational cost -- full density matrices at fragment boundaries, instead of being limited to 1-RDMs. Current quantum computers are small, but quantum bootstrap embedding provides a potentially generalizable strategy for harnessing such small machines through quantum fragment matching.

Periodic signals play an important role in daily lives. Although conventional sequential models have shown remarkable success in various fields, they still come short in modeling periodicity; they either collapse, diverge or ignore details. In this paper, we introduce a novel framework inspired by Fourier series to generate periodic signals. We first decompose the given signals into multiple sines and cosines and then conditionally generate periodic signals with the output components. We have shown our model efficacy on three tasks: reconstruction, imputation and conditional generation. Our model outperforms baselines in all tasks and shows more stable and refined results.

Recently, various methods have been proposed to address the inconsistency issue of DDIM inversion to enable image editing, such as EDICT [36] and Null-text inversion [22]. However, the above methods introduce considerable computational overhead. In this paper, we propose a new technique, named bi-directional integration approximation (BDIA), to perform exact diffusion inversion with neglible computational overhead. Suppose we would like to estimate the next diffusion state z_{i-1} at timestep t_i with the historical information (i,z_i) and (i+1,z_{i+1}). We first obtain the estimated Gaussian noise boldsymbol{epsilon}(z_i,i), and then apply the DDIM update procedure twice for approximating the ODE integration over the next time-slot [t_i, t_{i-1}] in the forward manner and the previous time-slot [t_i, t_{t+1}] in the backward manner. The DDIM step for the previous time-slot is used to refine the integration approximation made earlier when computing z_i. A nice property of BDIA-DDIM is that the update expression for z_{i-1} is a linear combination of (z_{i+1}, z_i, boldsymbol{epsilon}(z_i,i)). This allows for exact backward computation of z_{i+1} given (z_i, z_{i-1}), thus leading to exact diffusion inversion. It is demonstrated with experiments that (round-trip) BDIA-DDIM is particularly effective for image editing. Our experiments further show that BDIA-DDIM produces markedly better image sampling qualities than DDIM for text-to-image generation. BDIA can also be applied to improve the performance of other ODE solvers in addition to DDIM. In our work, it is found that applying BDIA to the EDM sampling procedure produces consistently better performance over four pre-trained models.

Numerical approximations of partial differential equations (PDEs) are routinely employed to formulate the solution of physics, engineering and mathematical problems involving functions of several variables, such as the propagation of heat or sound, fluid flow, elasticity, electrostatics, electrodynamics, and more. While this has led to solving many complex phenomena, there are some limitations. Conventional approaches such as Finite Element Methods (FEMs) and Finite Differential Methods (FDMs) require considerable time and are computationally expensive. In contrast, data driven machine learning-based methods such as neural networks provide a faster, fairly accurate alternative, and have certain advantages such as discretization invariance and resolution invariance. This article aims to provide a comprehensive insight into how data-driven approaches can complement conventional techniques to solve engineering and physics problems, while also noting some of the major pitfalls of machine learning-based approaches. Furthermore, we highlight, a novel and fast machine learning-based approach (~1000x) to learning the solution operator of a PDE operator learning. We will note how these new computational approaches can bring immense advantages in tackling many problems in fundamental and applied physics.

In solving partial differential equations (PDEs), Fourier Neural Operators (FNOs) have exhibited notable effectiveness compared to Convolutional Neural Networks (CNNs). This paper presents clear empirical evidence through spectral analysis to elucidate the superiority of FNO over CNNs: FNO is significantly more capable of learning low-frequencies. This empirical evidence also unveils FNO's distinct low-frequency bias, which limits FNO's effectiveness in learning high-frequency information from PDE data. To tackle this challenge, we introduce SpecBoost, an ensemble learning framework that employs multiple FNOs to better capture high-frequency information. Specifically, a secondary FNO is utilized to learn the overlooked high-frequency information from the prediction residual of the initial FNO. Experiments demonstrate that SpecBoost noticeably enhances FNO's prediction accuracy on diverse PDE applications, achieving an up to 71% improvement.

We study the conformal bootstrap of 1D CFTs on the straight Maldacena-Wilson line in 4D {cal N}=4 super-Yang-Mills theory. We introduce an improved truncation scheme with an 'OPE tail' approximation and use it to reproduce the 'bootstrability' results of Cavagli\`a et al. for the OPE-coefficients squared of the first three unprotected operators. For example, for the first OPE-coefficient squared at 't Hooft coupling (4pi)^2, linear-functional methods with two sum rules from integrated correlators give the rigorous result 0.294014873 pm 4.88 cdot 10^{-8}, whereas our methods give with machine-precision computations 0.294014228 pm 6.77 cdot 10^{-7}. For our numerical searches, we benchmark the Reinforcement Learning Soft Actor-Critic algorithm against an Interior Point Method algorithm (IPOPT) and comment on the merits of each algorithm.

We derive a Fast Multipole Method (FMM) where a low-rank approximation of the kernel is obtained using the Empirical Interpolation Method (EIM). Contrary to classical interpolation-based FMM, where the interpolation points and basis are fixed beforehand, the EIM is a nonlinear approximation method which constructs interpolation points and basis which are adapted to the kernel under consideration. The basis functions are obtained using evaluations of the kernel itself. We restrict ourselves to translation-invariant kernels, for which a modified version of the EIM approximation can be used in a multilevel FMM context; we call the obtained algorithm Empirical Interpolation Fast Multipole Method (EIFMM). An important feature of the EIFMM is a built-in error estimation of the interpolation error made by the low-rank approximation of the far-field behavior of the kernel: the algorithm selects the optimal number of interpolation points required to ensure a given accuracy for the result, leading to important gains for inhomogeneous kernels.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

We present the first framework to solve linear inverse problems leveraging pre-trained latent diffusion models. Previously proposed algorithms (such as DPS and DDRM) only apply to pixel-space diffusion models. We theoretically analyze our algorithm showing provable sample recovery in a linear model setting. The algorithmic insight obtained from our analysis extends to more general settings often considered in practice. Experimentally, we outperform previously proposed posterior sampling algorithms in a wide variety of problems including random inpainting, block inpainting, denoising, deblurring, destriping, and super-resolution.

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.

We consider solving partial differential equations (PDEs) with Fourier neural operators (FNOs), which operate in the frequency domain. Since the laws of physics do not depend on the coordinate system used to describe them, it is desirable to encode such symmetries in the neural operator architecture for better performance and easier learning. While encoding symmetries in the physical domain using group theory has been studied extensively, how to capture symmetries in the frequency domain is under-explored. In this work, we extend group convolutions to the frequency domain and design Fourier layers that are equivariant to rotations, translations, and reflections by leveraging the equivariance property of the Fourier transform. The resulting G-FNO architecture generalizes well across input resolutions and performs well in settings with varying levels of symmetry. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

Singly-TASE operators for the numerical solution of stiff differential equations were proposed by Calvo et al. in J.Sci. Comput. 2023 to reduce the computational cost of Runge-Kutta-TASE (RKTASE) methods when the involved linear systems are solved by some LU factorization. In this paper we propose a modification of these methods to improve the efficiency by considering different TASE operators for each stage of the Runge-Kutta. We prove that the resulting RKTASE methods are equivalent to W-methods (Steihaug and Wolfbrandt, Mathematics of Computation,1979) and this allows us to obtain the order conditions of the proposed Modified Singly-RKTASE methods (MSRKTASE) through the theory developed for the W-methods. We construct new MSRKTASE methods of order two and three and demonstrate their effectiveness through numerical experiments on both linear and nonlinear stiff systems. The results show that the MSRKTASE schemes significantly enhance efficiency and accuracy compared to previous Singly-RKTASE schemes.

The past few years have witnessed the great success of Diffusion models~(DMs) in generating high-fidelity samples in generative modeling tasks. A major limitation of the DM is its notoriously slow sampling procedure which normally requires hundreds to thousands of time discretization steps of the learned diffusion process to reach the desired accuracy. Our goal is to develop a fast sampling method for DMs with a much less number of steps while retaining high sample quality. To this end, we systematically analyze the sampling procedure in DMs and identify key factors that affect the sample quality, among which the method of discretization is most crucial. By carefully examining the learned diffusion process, we propose Diffusion Exponential Integrator Sampler~(DEIS). It is based on the Exponential Integrator designed for discretizing ordinary differential equations (ODEs) and leverages a semilinear structure of the learned diffusion process to reduce the discretization error. The proposed method can be applied to any DMs and can generate high-fidelity samples in as few as 10 steps. In our experiments, it takes about 3 minutes on one A6000 GPU to generate 50k images from CIFAR10. Moreover, by directly using pre-trained DMs, we achieve the state-of-art sampling performance when the number of score function evaluation~(NFE) is limited, e.g., 4.17 FID with 10 NFEs, 3.37 FID, and 9.74 IS with only 15 NFEs on CIFAR10. Code is available at https://github.com/qsh-zh/deis

We explore the integration of Kolmogorov Networks (KANs) into molecular dynamics (MD) simulations to improve interatomic potentials. We propose that widely used potentials, such as the Lennard-Jones (LJ) potential, the embedded atom model (EAM), and artificial neural network (ANN) potentials, can be interpreted within the KAN framework. Specifically, we demonstrate that the descriptors for ANN potentials, typically constructed using polynomials, can be redefined using KAN's non-linear functions. By employing linear or cubic spline interpolations for these KAN functions, we show that the computational cost of evaluating ANN potentials and their derivatives is reduced.

It is well noted that coordinate based MLPs benefit -- in terms of preserving high-frequency information -- through the encoding of coordinate positions as an array of Fourier features. Hitherto, the rationale for the effectiveness of these positional encodings has been solely studied through a Fourier lens. In this paper, we strive to broaden this understanding by showing that alternative non-Fourier embedding functions can indeed be used for positional encoding. Moreover, we show that their performance is entirely determined by a trade-off between the stable rank of the embedded matrix and the distance preservation between embedded coordinates. We further establish that the now ubiquitous Fourier feature mapping of position is a special case that fulfills these conditions. Consequently, we present a more general theory to analyze positional encoding in terms of shifted basis functions. To this end, we develop the necessary theoretical formulae and empirically verify that our theoretical claims hold in practice. Codes available at https://github.com/osiriszjq/Rethinking-positional-encoding.

Deep models have achieved impressive progress in solving partial differential equations (PDEs). A burgeoning paradigm is learning neural operators to approximate the input-output mappings of PDEs. While previous deep models have explored the multiscale architectures and various operator designs, they are limited to learning the operators as a whole in the coordinate space. In real physical science problems, PDEs are complex coupled equations with numerical solvers relying on discretization into high-dimensional coordinate space, which cannot be precisely approximated by a single operator nor efficiently learned due to the curse of dimensionality. We present Latent Spectral Models (LSM) toward an efficient and precise solver for high-dimensional PDEs. Going beyond the coordinate space, LSM enables an attention-based hierarchical projection network to reduce the high-dimensional data into a compact latent space in linear time. Inspired by classical spectral methods in numerical analysis, we design a neural spectral block to solve PDEs in the latent space that approximates complex input-output mappings via learning multiple basis operators, enjoying nice theoretical guarantees for convergence and approximation. Experimentally, LSM achieves consistent state-of-the-art and yields a relative gain of 11.5% averaged on seven benchmarks covering both solid and fluid physics. Code is available at https://github.com/thuml/Latent-Spectral-Models.

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.

Generative diffusion models have emerged as a powerful tool for high-quality image synthesis, yet their iterative nature demands significant computational resources. This paper proposes an efficient time step sampling method based on an image spectral analysis of the diffusion process, aimed at optimizing the denoising process. Instead of the traditional uniform distribution-based time step sampling, we introduce a Beta distribution-like sampling technique that prioritizes critical steps in the early and late stages of the process. Our hypothesis is that certain steps exhibit significant changes in image content, while others contribute minimally. We validated our approach using Fourier transforms to measure frequency response changes at each step, revealing substantial low-frequency changes early on and high-frequency adjustments later. Experiments with ADM and Stable Diffusion demonstrated that our Beta Sampling method consistently outperforms uniform sampling, achieving better FID and IS scores, and offers competitive efficiency relative to state-of-the-art methods like AutoDiffusion. This work provides a practical framework for enhancing diffusion model efficiency by focusing computational resources on the most impactful steps, with potential for further optimization and broader application.

The ability to discover new materials with desirable properties is critical for numerous applications from helping mitigate climate change to advances in next generation computing hardware. AI has the potential to accelerate materials discovery and design by more effectively exploring the chemical space compared to other computational methods or by trial-and-error. While substantial progress has been made on AI for materials data, benchmarks, and models, a barrier that has emerged is the lack of publicly available training data and open pre-trained models. To address this, we present a Meta FAIR release of the Open Materials 2024 (OMat24) large-scale open dataset and an accompanying set of pre-trained models. OMat24 contains over 110 million density functional theory (DFT) calculations focused on structural and compositional diversity. Our EquiformerV2 models achieve state-of-the-art performance on the Matbench Discovery leaderboard and are capable of predicting ground-state stability and formation energies to an F1 score above 0.9 and an accuracy of 20 meV/atom, respectively. We explore the impact of model size, auxiliary denoising objectives, and fine-tuning on performance across a range of datasets including OMat24, MPtraj, and Alexandria. The open release of the OMat24 dataset and models enables the research community to build upon our efforts and drive further advancements in AI-assisted materials science.

Despite the recent visually-pleasing results achieved, the massive computational cost has been a long-standing flaw for diffusion probabilistic models (DPMs), which, in turn, greatly limits their applications on resource-limited platforms. Prior methods towards efficient DPM, however, have largely focused on accelerating the testing yet overlooked their huge complexity and sizes. In this paper, we make a dedicated attempt to lighten DPM while striving to preserve its favourable performance. We start by training a small-sized latent diffusion model (LDM) from scratch, but observe a significant fidelity drop in the synthetic images. Through a thorough assessment, we find that DPM is intrinsically biased against high-frequency generation, and learns to recover different frequency components at different time-steps. These properties make compact networks unable to represent frequency dynamics with accurate high-frequency estimation. Towards this end, we introduce a customized design for slim DPM, which we term as Spectral Diffusion (SD), for light-weight image synthesis. SD incorporates wavelet gating in its architecture to enable frequency dynamic feature extraction at every reverse steps, and conducts spectrum-aware distillation to promote high-frequency recovery by inverse weighting the objective based on spectrum magni tudes. Experimental results demonstrate that, SD achieves 8-18x computational complexity reduction as compared to the latent diffusion models on a series of conditional and unconditional image generation tasks while retaining competitive image fidelity.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

Low-rank adaptation~(LoRA) has recently gained much interest in fine-tuning foundation models. It effectively reduces the number of trainable parameters by incorporating low-rank matrices A and B to represent the weight change, i.e., Delta W=BA. Despite LoRA's progress, it faces storage challenges when handling extensive customization adaptations or larger base models. In this work, we aim to further compress trainable parameters by enjoying the powerful expressiveness of the Fourier transform. Specifically, we introduce FourierFT, which treats Delta W as a matrix in the spatial domain and learns only a small fraction of its spectral coefficients. With the trained spectral coefficients, we implement the inverse discrete Fourier transform to recover Delta W. Empirically, our FourierFT method shows comparable or better performance with fewer parameters than LoRA on various tasks, including natural language understanding, natural language generation, instruction tuning, and image classification. For example, when performing instruction tuning on the LLaMA2-7B model, FourierFT surpasses LoRA with only 0.064M trainable parameters, compared to LoRA's 33.5M. Our code is released at https://github.com/Chaos96/fourierft.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Diffusion Transformers (DiTs) have recently gained substantial attention in both industrial and academic fields for their superior visual generation capabilities, outperforming traditional diffusion models that use U-Net. However,the enhanced performance of DiTs also comes with high parameter counts and implementation costs, seriously restricting their use on resource-limited devices such as mobile phones. To address these challenges, we introduce the Hybrid Floating-point Quantization for DiT(HQ-DiT), an efficient post-training quantization method that utilizes 4-bit floating-point (FP) precision on both weights and activations for DiT inference. Compared to fixed-point quantization (e.g., INT8), FP quantization, complemented by our proposed clipping range selection mechanism, naturally aligns with the data distribution within DiT, resulting in a minimal quantization error. Furthermore, HQ-DiT also implements a universal identity mathematical transform to mitigate the serious quantization error caused by the outliers. The experimental results demonstrate that DiT can achieve extremely low-precision quantization (i.e., 4 bits) with negligible impact on performance. Our approach marks the first instance where both weights and activations in DiTs are quantized to just 4 bits, with only a 0.12 increase in sFID on ImageNet.

We present a new approach for evaluating Feynman integrals numerically. We apply the recently-proposed framework of physics-informed deep learning to train neural networks to approximate the solution to the differential equations satisfied by the Feynman integrals. This approach relies neither on a canonical form of the differential equations, which is often a bottleneck for the analytical techniques, nor on the availability of a large dataset, and after training yields essentially instantaneous evaluation times. We provide a proof-of-concept implementation within the PyTorch framework, and apply it to a number of one- and two-loop examples, achieving a mean magnitude of relative difference of around 1% at two loops in the physical phase space with network training times on the order of an hour on a laptop GPU.

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.

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.33% of the time, while achieving a 1331x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 85,658 unique configurations.

Machine learning based solvers have garnered much attention in physical simulation and scientific computing, with a prominent example, physics-informed neural networks (PINNs). However, PINNs often struggle to solve high-frequency and multi-scale PDEs, which can be due to spectral bias during neural network training. To address this problem, we resort to the Gaussian process (GP) framework. To flexibly capture the dominant frequencies, we model the power spectrum of the PDE solution with a student t mixture or Gaussian mixture. We apply the inverse Fourier transform to obtain the covariance function (by Wiener-Khinchin theorem). The covariance derived from the Gaussian mixture spectrum corresponds to the known spectral mixture kernel. Next, we estimate the mixture weights in the log domain, which we show is equivalent to placing a Jeffreys prior. It automatically induces sparsity, prunes excessive frequencies, and adjusts the remaining toward the ground truth. Third, to enable efficient and scalable computation on massive collocation points, which are critical to capture high frequencies, we place the collocation points on a grid, and multiply our covariance function at each input dimension. We use the GP conditional mean to predict the solution and its derivatives so as to fit the boundary condition and the equation itself. As a result, we can derive a Kronecker product structure in the covariance matrix. We use Kronecker product properties and multilinear algebra to promote computational efficiency and scalability, without low-rank approximations. We show the advantage of our method in systematic experiments. The code is released at https://github.com/xuangu-fang/Gaussian-Process-Slover-for-High-Freq-PDE.

We consider in this work quantities that can be obtained as limits of powers of parametrized matrices, for instance the inverse matrix or the logarithm of the determinant. Under the assumption of affine dependence in the parameters, we use the Empirical Interpolation Method (EIM) to derive an approximation for powers of these matrices, from which we derive a nonintrusive approximation for the aforementioned limits. We derive upper bounds of the error made by the obtained formula. Finally, numerical comparisons with classical intrusive and nonintrusive approximation techniques are provided: in the considered test-cases, our algorithm performs well compared to the nonintrusive ones.

Developing equivariant neural networks for the E(3) group plays an important role in modeling 3D data across real-world applications. Enforcing this equivariance primarily involves the tensor products of irreducible representations (irreps). However, the computational complexity of such operations increases significantly as higher-order tensors are used. In this work, we propose a systematic approach to substantially accelerate the computation of the tensor products of irreps. We mathematically connect the commonly used Clebsch-Gordan coefficients to the Gaunt coefficients, which are integrals of products of three spherical harmonics. Through Gaunt coefficients, the tensor product of irreps becomes equivalent to the multiplication between spherical functions represented by spherical harmonics. This perspective further allows us to change the basis for the equivariant operations from spherical harmonics to a 2D Fourier basis. Consequently, the multiplication between spherical functions represented by a 2D Fourier basis can be efficiently computed via the convolution theorem and Fast Fourier Transforms. This transformation reduces the complexity of full tensor products of irreps from O(L^6) to O(L^3), where L is the max degree of irreps. Leveraging this approach, we introduce the Gaunt Tensor Product, which serves as a new method to construct efficient equivariant operations across different model architectures. Our experiments on the Open Catalyst Project and 3BPA datasets demonstrate both the increased efficiency and improved performance of our approach.

Score-based diffusion models, while achieving remarkable empirical performance, often suffer from low sampling speed, due to extensive function evaluations needed during the sampling phase. Despite a flurry of recent activities towards speeding up diffusion generative modeling in practice, theoretical underpinnings for acceleration techniques remain severely limited. In this paper, we design novel training-free algorithms to accelerate popular deterministic (i.e., DDIM) and stochastic (i.e., DDPM) samplers. Our accelerated deterministic sampler converges at a rate O(1/{T}^2) with T the number of steps, improving upon the O(1/T) rate for the DDIM sampler; and our accelerated stochastic sampler converges at a rate O(1/T), outperforming the rate O(1/T) for the DDPM sampler. The design of our algorithms leverages insights from higher-order approximation, and shares similar intuitions as popular high-order ODE solvers like the DPM-Solver-2. Our theory accommodates ell_2-accurate score estimates, and does not require log-concavity or smoothness on the target distribution.

Diffusion models are emerging models that generate images by iteratively denoising random Gaussian noise using deep neural networks. These models typically exhibit high computational and memory demands, necessitating effective post-training quantization for high-performance inference. Recent works propose low-bitwidth (e.g., 8-bit or 4-bit) quantization for diffusion models, however 4-bit integer quantization typically results in low-quality images. We observe that on several widely used hardware platforms, there is little or no difference in compute capability between floating-point and integer arithmetic operations of the same bitwidth (e.g., 8-bit or 4-bit). Therefore, we propose an effective floating-point quantization method for diffusion models that provides better image quality compared to integer quantization methods. We employ a floating-point quantization method that was effective for other processing tasks, specifically computer vision and natural language tasks, and tailor it for diffusion models by integrating weight rounding learning during the mapping of the full-precision values to the quantized values in the quantization process. We comprehensively study integer and floating-point quantization methods in state-of-the-art diffusion models. Our floating-point quantization method not only generates higher-quality images than that of integer quantization methods, but also shows no noticeable degradation compared to full-precision models (32-bit floating-point), when both weights and activations are quantized to 8-bit floating-point values, while has minimal degradation with 4-bit weights and 8-bit activations.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

The Empirical Interpolation Method (EIM) is a greedy procedure that constructs approximate representations of two-variable functions in separated form. In its classical presentation, the two variables play a non-symmetric role. In this work, we give an equivalent definition of the EIM approximation, in which the two variables play symmetric roles. Then, we give a proof for the existence of this approximation, and extend it up to the convergence of the EIM, and for any norm chosen to compute the error in the greedy step. Finally, we introduce a way to compute a separated representation in the case where the number of selected values is different for each variable. In the case of a physical field measured by sensors, this is useful to discard a broken sensor while keeping the information provided by the associated selected field.

Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are still limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace SO(3) convolutions with eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements -- attention re-normalization, separable S^2 activation and separable layer normalization. Putting this all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on the large-scale OC20 dataset by up to 12% on forces, 4% on energies, offers better speed-accuracy trade-offs, and 2times reduction in DFT calculations needed for computing adsorption energies.

Generating novel molecules with out-of-distribution properties is a major challenge in molecular discovery. While supervised learning methods generate high-quality molecules similar to those in a dataset, they struggle to generalize to out-of-distribution properties. Reinforcement learning can explore new chemical spaces but often conducts 'reward-hacking' and generates non-synthesizable molecules. In this work, we address this problem by integrating a state-of-the-art supervised learning method, STGG+, in an active learning loop. Our approach iteratively generates, evaluates, and fine-tunes STGG+ to continuously expand its knowledge. We denote this approach STGG+AL. We apply STGG+AL to the design of organic pi-functional materials, specifically two challenging tasks: 1) generating highly absorptive molecules characterized by high oscillator strength and 2) designing absorptive molecules with reasonable oscillator strength in the near-infrared (NIR) range. The generated molecules are validated and rationalized in-silico with time-dependent density functional theory. Our results demonstrate that our method is highly effective in generating novel molecules with high oscillator strength, contrary to existing methods such as reinforcement learning (RL) methods. We open-source our active-learning code along with our Conjugated-xTB dataset containing 2.9 million pi-conjugated molecules and the function for approximating the oscillator strength and absorption wavelength (based on sTDA-xTB).

Diffusion probabilistic models (DPMs) have exhibited excellent performance for high-fidelity image generation while suffering from inefficient sampling. Recent works accelerate the sampling procedure by proposing fast ODE solvers that leverage the specific ODE form of DPMs. However, they highly rely on specific parameterization during inference (such as noise/data prediction), which might not be the optimal choice. In this work, we propose a novel formulation towards the optimal parameterization during sampling that minimizes the first-order discretization error of the ODE solution. Based on such formulation, we propose DPM-Solver-v3, a new fast ODE solver for DPMs by introducing several coefficients efficiently computed on the pretrained model, which we call empirical model statistics. We further incorporate multistep methods and a predictor-corrector framework, and propose some techniques for improving sample quality at small numbers of function evaluations (NFE) or large guidance scales. Experiments show that DPM-Solver-v3 achieves consistently better or comparable performance in both unconditional and conditional sampling with both pixel-space and latent-space DPMs, especially in 5sim10 NFEs. We achieve FIDs of 12.21 (5 NFE), 2.51 (10 NFE) on unconditional CIFAR10, and MSE of 0.55 (5 NFE, 7.5 guidance scale) on Stable Diffusion, bringing a speed-up of 15\%sim30\% compared to previous state-of-the-art training-free methods. Code is available at https://github.com/thu-ml/DPM-Solver-v3.

Previous literature offers limited clues on how to learn a periodic function using modern neural networks. We start with a study of the extrapolation properties of neural networks; we prove and demonstrate experimentally that the standard activations functions, such as ReLU, tanh, sigmoid, along with their variants, all fail to learn to extrapolate simple periodic functions. We hypothesize that this is due to their lack of a "periodic" inductive bias. As a fix of this problem, we propose a new activation, namely, x + sin^2(x), which achieves the desired periodic inductive bias to learn a periodic function while maintaining a favorable optimization property of the ReLU-based activations. Experimentally, we apply the proposed method to temperature and financial data prediction.

Discovering the underlying behavior of complex systems is an important topic in many science and engineering disciplines. In this paper, we propose a novel neural network framework, finite difference neural networks (FDNet), to learn partial differential equations from data. Specifically, our proposed finite difference inspired network is designed to learn the underlying governing partial differential equations from trajectory data, and to iteratively estimate the future dynamical behavior using only a few trainable parameters. We illustrate the performance (predictive power) of our framework on the heat equation, with and without noise and/or forcing, and compare our results to the Forward Euler method. Moreover, we show the advantages of using a Hessian-Free Trust Region method to train the network.

We propose a new method called the N-particle underdamped Langevin algorithm for optimizing a special class of non-linear functionals defined over the space of probability measures. Examples of problems with this formulation include training mean-field neural networks, maximum mean discrepancy minimization and kernel Stein discrepancy minimization. Our algorithm is based on a novel spacetime discretization of the mean-field underdamped Langevin dynamics, for which we provide a new, fast mixing guarantee. In addition, we demonstrate that our algorithm converges globally in total variation distance, bridging the theoretical gap between the dynamics and its practical implementation.

The Reduced Basis Method can be exploited in an efficient way only if the so-called affine dependence assumption on the operator and right-hand side of the considered problem with respect to the parameters is satisfied. When it is not, the Empirical Interpolation Method is usually used to recover this assumption approximately. In both cases, the Reduced Basis Method requires to access and modify the assembly routines of the corresponding computational code, leading to an intrusive procedure. In this work, we derive variants of the EIM algorithm and explain how they can be used to turn the Reduced Basis Method into a nonintrusive procedure. We present examples of aeroacoustic problems solved by integral equations and show how our algorithms can benefit from the linear algebra tools available in the considered code.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

A class of generative models that unifies flow-based and diffusion-based methods is introduced. These models extend the framework proposed in Albergo & Vanden-Eijnden (2023), enabling the use of a broad class of continuous-time stochastic processes called `stochastic interpolants' to bridge any two arbitrary probability density functions exactly in finite time. These interpolants are built by combining data from the two prescribed densities with an additional latent variable that shapes the bridge in a flexible way. The time-dependent probability density function of the stochastic interpolant is shown to satisfy a first-order transport equation as well as a family of forward and backward Fokker-Planck equations with tunable diffusion coefficient. Upon consideration of the time evolution of an individual sample, this viewpoint immediately leads to both deterministic and stochastic generative models based on probability flow equations or stochastic differential equations with an adjustable level of noise. The drift coefficients entering these models are time-dependent velocity fields characterized as the unique minimizers of simple quadratic objective functions, one of which is a new objective for the score of the interpolant density. We show that minimization of these quadratic objectives leads to control of the likelihood for generative models built upon stochastic dynamics, while likelihood control for deterministic dynamics is more stringent. We also discuss connections with other methods such as score-based diffusion models, stochastic localization processes, probabilistic denoising techniques, and rectifying flows. In addition, we demonstrate that stochastic interpolants recover the Schr\"odinger bridge between the two target densities when explicitly optimizing over the interpolant. Finally, algorithmic aspects are discussed and the approach is illustrated on numerical examples.

Machine learning for differential equations paves the way for computationally efficient alternatives to numerical solvers, with potentially broad impacts in science and engineering. Though current algorithms typically require simulated training data tailored to a given setting, one may instead wish to learn useful information from heterogeneous sources, or from real dynamical systems observations that are messy or incomplete. In this work, we learn general-purpose representations of PDEs from heterogeneous data by implementing joint embedding methods for self-supervised learning (SSL), a framework for unsupervised representation learning that has had notable success in computer vision. Our representation outperforms baseline approaches to invariant tasks, such as regressing the coefficients of a PDE, while also improving the time-stepping performance of neural solvers. We hope that our proposed methodology will prove useful in the eventual development of general-purpose foundation models for PDEs.

Partial differential equations (PDEs) are important tools to model physical systems, and including them into machine learning models is an important way of incorporating physical knowledge. Given any system of linear PDEs with constant coefficients, we propose a family of Gaussian process (GP) priors, which we call EPGP, such that all realizations are exact solutions of this system. We apply the Ehrenpreis-Palamodov fundamental principle, which works like a non-linear Fourier transform, to construct GP kernels mirroring standard spectral methods for GPs. Our approach can infer probable solutions of linear PDE systems from any data such as noisy measurements, or pointwise defined initial and boundary conditions. Constructing EPGP-priors is algorithmic, generally applicable, and comes with a sparse version (S-EPGP) that learns the relevant spectral frequencies and works better for big data sets. We demonstrate our approach on three families of systems of PDE, the heat equation, wave equation, and Maxwell's equations, where we improve upon the state of the art in computation time and precision, in some experiments by several orders of magnitude.

We introduce the use of Crystal Graph Convolutional Neural Networks (CGCNN), Fully Connected Neural Networks (FCNN) and XGBoost to predict thermoelectric properties. The dataset for the CGCNN is independent of Density Functional Theory (DFT) and only relies on the crystal and atomic information, while that for the FCNN is based on a rich attribute list mined from Materialsproject.org. The results show that the optimized FCNN is three layer deep and is able to predict the scattering-time independent thermoelectric powerfactor much better than the CGCNN (or XGBoost), suggesting that bonding and density of states descriptors informed from materials science knowledge obtained partially from DFT are vital to predict functional properties.

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

We introduce ensembles within score-based sampling methods to develop gradient-free approximate sampling techniques that leverage the collective dynamics of particle ensembles to compute approximate reverse diffusion drifts. We introduce the underlying methodology, emphasizing its relationship with generative diffusion models and the previously introduced F\"ollmer sampler. We demonstrate the efficacy of ensemble strategies through various examples, ranging from low- to medium-dimensionality sampling problems, including multi-modal and highly non-Gaussian probability distributions, and provide comparisons to traditional methods like NUTS. Our findings highlight the potential of ensemble strategies for modeling complex probability distributions in situations where gradients are unavailable. Finally, we showcase its application in the context of Bayesian inversion problems within the geophysical sciences.

Denoising diffusion (score-based) generative models have recently achieved significant accomplishments in generating realistic and diverse data. These approaches define a forward diffusion process for transforming data into noise and a backward denoising process for sampling data from noise. Unfortunately, the generation process of current denoising diffusion models is notoriously slow due to the lengthy iterative noise estimations, which rely on cumbersome neural networks. It prevents the diffusion models from being widely deployed, especially on edge devices. Previous works accelerate the generation process of diffusion model (DM) via finding shorter yet effective sampling trajectories. However, they overlook the cost of noise estimation with a heavy network in every iteration. In this work, we accelerate generation from the perspective of compressing the noise estimation network. Due to the difficulty of retraining DMs, we exclude mainstream training-aware compression paradigms and introduce post-training quantization (PTQ) into DM acceleration. However, the output distributions of noise estimation networks change with time-step, making previous PTQ methods fail in DMs since they are designed for single-time step scenarios. To devise a DM-specific PTQ method, we explore PTQ on DM in three aspects: quantized operations, calibration dataset, and calibration metric. We summarize and use several observations derived from all-inclusive investigations to formulate our method, which especially targets the unique multi-time-step structure of DMs. Experimentally, our method can directly quantize full-precision DMs into 8-bit models while maintaining or even improving their performance in a training-free manner. Importantly, our method can serve as a plug-and-play module on other fast-sampling methods, e.g., DDIM. The code is available at https://github.com/42Shawn/PTQ4DM .

The spatiotemporal resolution of Partial Differential Equations (PDEs) plays important roles in the mathematical description of the world's physical phenomena. In general, scientists and engineers solve PDEs numerically by the use of computationally demanding solvers. Recently, deep learning algorithms have emerged as a viable alternative for obtaining fast solutions for PDEs. Models are usually trained on synthetic data generated by solvers, stored on disk and read back for training. This paper advocates that relying on a traditional static dataset to train these models does not allow the full benefit of the solver to be used as a data generator. It proposes an open source online training framework for deep surrogate models. The framework implements several levels of parallelism focused on simultaneously generating numerical simulations and training deep neural networks. This approach suppresses the I/O and storage bottleneck associated with disk-loaded datasets, and opens the way to training on significantly larger datasets. Experiments compare the offline and online training of four surrogate models, including state-of-the-art architectures. Results indicate that exposing deep surrogate models to more dataset diversity, up to hundreds of GB, can increase model generalization capabilities. Fully connected neural networks, Fourier Neural Operator (FNO), and Message Passing PDE Solver prediction accuracy is improved by 68%, 16% and 7%, respectively.

Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods seldom consider the space group constraint which is crucial in describing the geometry of crystals and closely relevant to many desirable properties. However, considering space group constraint is challenging owing to its diverse and nontrivial forms. In this paper, we reduce the space group constraint into an equivalent formulation that is more tractable to be handcrafted into the generation process. In particular, we translate the space group constraint into two parts: the basis constraint of the invariant logarithmic space of the lattice matrix and the Wyckoff position constraint of the fractional coordinates. Upon the derived constraints, we then propose DiffCSP++, a novel diffusion model that has enhanced a previous work DiffCSP by further taking space group constraint into account. Experiments on several popular datasets verify the benefit of the involvement of the space group constraint, and show that our DiffCSP++ achieves promising performance on crystal structure prediction, ab initio crystal generation and controllable generation with customized space groups.

Large linear systems play an important role in high-energy theory, appearing in amplitude bootstraps and during integral reduction. This paper introduces FiniteFieldSolve, a general-purpose toolkit for exactly solving large linear systems over the rationals. The solver interfaces directly with Mathematica, is straightforward to install, and seamlessly replaces Mathematica's native solvers. In testing, FiniteFieldSolve is approximately two orders of magnitude faster than Mathematica and uses an order of magnitude less memory. The package also compares favorably against other public solvers in FiniteFieldSolve's intended use cases. As the name of the package suggests, solutions are obtained via well-known finite field methods. These methods suffer from introducing an inordinate number of modulo (or integer division) operations with respect to different primes. By automatically recompiling itself for each prime, FiniteFieldSolve converts the division operations into much faster combinations of instructions, dramatically improving performance. The technique of compiling the prime can be applied to any finite field solver, where the time savings will be solver dependent. The operation of the package is illustrated through a detailed example of an amplitude bootstrap.

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

In this paper, we find a sample complexity bound for learning a simplex from noisy samples. Assume a dataset of size n is given which includes i.i.d. samples drawn from a uniform distribution over an unknown simplex in R^K, where samples are assumed to be corrupted by a multi-variate additive Gaussian noise of an arbitrary magnitude. We prove the existence of an algorithm that with high probability outputs a simplex having a ell_2 distance of at most varepsilon from the true simplex (for any varepsilon>0). Also, we theoretically show that in order to achieve this bound, it is sufficient to have ngeleft(K^2/varepsilon^2right)e^{Omegaleft(K/SNR^2right)} samples, where SNR stands for the signal-to-noise ratio. This result solves an important open problem and shows as long as SNRgeOmegaleft(K^{1/2}right), the sample complexity of the noisy regime has the same order to that of the noiseless case. Our proofs are a combination of the so-called sample compression technique in ashtiani2018nearly, mathematical tools from high-dimensional geometry, and Fourier analysis. In particular, we have proposed a general Fourier-based technique for recovery of a more general class of distribution families from additive Gaussian noise, which can be further used in a variety of other related problems.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Diffusion probabilistic models (DPMs) have achieved impressive success in high-resolution image synthesis, especially in recent large-scale text-to-image generation applications. An essential technique for improving the sample quality of DPMs is guided sampling, which usually needs a large guidance scale to obtain the best sample quality. The commonly-used fast sampler for guided sampling is DDIM, a first-order diffusion ODE solver that generally needs 100 to 250 steps for high-quality samples. Although recent works propose dedicated high-order solvers and achieve a further speedup for sampling without guidance, their effectiveness for guided sampling has not been well-tested before. In this work, we demonstrate that previous high-order fast samplers suffer from instability issues, and they even become slower than DDIM when the guidance scale grows large. To further speed up guided sampling, we propose DPM-Solver++, a high-order solver for the guided sampling of DPMs. DPM-Solver++ solves the diffusion ODE with the data prediction model and adopts thresholding methods to keep the solution matches training data distribution. We further propose a multistep variant of DPM-Solver++ to address the instability issue by reducing the effective step size. Experiments show that DPM-Solver++ can generate high-quality samples within only 15 to 20 steps for guided sampling by pixel-space and latent-space DPMs.

Model order reduction has been extensively studied over the last two decades. Projection-based methods such as the Proper Orthogonal Decomposition and the Reduced Basis Method enjoy the important advantages of Galerkin methods in the derivation of the reduced problem, but are limited to linear data compression for which the reduced solution is sought as a linear combination of spatial modes. Nonlinear data compression must be used when the solution manifold is not embedded in a low-dimensional subspace. Early methods involve piecewise linear data compression, by constructing a dictionary of reduced-order models tailored to a partition of the solution manifold. In this work, we introduce the concept of optimal partition of the solution manifold in terms of normalized Kolmogorov widths, and prove that the optimal partitions can be found by means of a representative-based clustering algorithm using the sine dissimilarity measure on the solution manifold.

Strong correlation brings a rich array of emergent phenomena, as well as a daunting challenge to theoretical physics study. In condensed matter physics, the fractional quantum Hall effect is a prominent example of strong correlation, with Landau level mixing being one of the most challenging aspects to address using traditional computational methods. Deep learning real-space neural network wavefunction methods have emerged as promising architectures to describe electron correlations in molecules and materials, but their power has not been fully tested for exotic quantum states. In this work, we employ real-space neural network wavefunction techniques to investigate fractional quantum Hall systems. On both 1/3 and 2/5 filling systems, we achieve energies consistently lower than exact diagonalization results which only consider the lowest Landau level. We also demonstrate that the real-space neural network wavefunction can naturally capture the extent of Landau level mixing up to a very high level, overcoming the limitations of traditional methods. Our work underscores the potential of neural networks for future studies of strongly correlated systems and opens new avenues for exploring the rich physics of the fractional quantum Hall effect.

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide spatial range. Traditional docking by searching for possible binding sites and conformations is computationally complex and results poorly under blind docking. Quantum-inspired algorithms combining quantum properties and annealing show great advantages in solving combinatorial optimization problems. Inspired by this, we achieve an improved in blind docking by using quantum-inspired combined with gradients learned by deep learning in the encoded molecular space. Numerical simulation shows that our method outperforms traditional docking algorithms and deep learning-based algorithms over 10\%. Compared to the current state-of-the-art deep learning-based docking algorithm DiffDock, the success rate of Top-1 (RMSD<2) achieves an improvement from 33\% to 35\% in our same setup. In particular, a 6\% improvement is realized in the high-precision region(RMSD<1) on molecules data unseen in DiffDock, which demonstrates the well-generalized of our method.

Computing the numerical solution to high-dimensional tensor differential equations can lead to prohibitive computational costs and memory requirements. To reduce the memory and computational footprint, dynamical low-rank approximation (DLRA) has proven to be a promising approach. DLRA represents the solution as a low-rank tensor factorization and evolves the resulting low-rank factors in time. A central challenge in DLRA is to find time integration schemes that are robust to the arising small singular values. A robust parallel basis update & Galerkin integrator, which simultaneously evolves all low-rank factors, has recently been derived for matrix differential equations. This work extends the parallel low-rank matrix integrator to Tucker tensors and general tree tensor networks, yielding an algorithm in which all bases and connecting tensors are evolved in parallel over a time step. We formulate the algorithm, provide a robust error bound, and demonstrate the efficiency of the new integrators for problems in quantum many-body physics, uncertainty quantification, and radiative transfer.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab-initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses, and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory static and relaxation trajectories of sim 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.

Diffusion model-based inverse problem solvers have shown impressive performance, but are limited in speed, mostly as they require reverse diffusion sampling starting from noise. Several recent works have tried to alleviate this problem by building a diffusion process, directly bridging the clean and the corrupted for specific inverse problems. In this paper, we first unify these existing works under the name Direct Diffusion Bridges (DDB), showing that while motivated by different theories, the resulting algorithms only differ in the choice of parameters. Then, we highlight a critical limitation of the current DDB framework, namely that it does not ensure data consistency. To address this problem, we propose a modified inference procedure that imposes data consistency without the need for fine-tuning. We term the resulting method data Consistent DDB (CDDB), which outperforms its inconsistent counterpart in terms of both perception and distortion metrics, thereby effectively pushing the Pareto-frontier toward the optimum. Our proposed method achieves state-of-the-art results on both evaluation criteria, showcasing its superiority over existing methods.

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.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

The reduced basis method is a model reduction technique yielding substantial savings of computational time when a solution to a parametrized equation has to be computed for many values of the parameter. Certification of the approximation is possible by means of an a posteriori error bound. Under appropriate assumptions, this error bound is computed with an algorithm of complexity independent of the size of the full problem. In practice, the evaluation of the error bound can become very sensitive to round-off errors. We propose herein an explanation of this fact. A first remedy has been proposed in [F. Casenave, Accurate a posteriori error evaluation in the reduced basis method. C. R. Math. Acad. Sci. Paris 350 (2012) 539--542.]. Herein, we improve this remedy by proposing a new approximation of the error bound using the Empirical Interpolation Method (EIM). This method achieves higher levels of accuracy and requires potentially less precomputations than the usual formula. A version of the EIM stabilized with respect to round-off errors is also derived. The method is illustrated on a simple one-dimensional diffusion problem and a three-dimensional acoustic scattering problem solved by a boundary element method.

Toeplitz Neural Networks (TNNs) have exhibited outstanding performance in various sequence modeling tasks. They outperform commonly used Transformer-based models while benefiting from log-linear space-time complexities. On the other hand, State Space Models (SSMs) achieve lower performance than TNNs in language modeling but offer the advantage of constant inference complexity. In this paper, we aim to combine the strengths of TNNs and SSMs by converting TNNs to SSMs during inference, thereby enabling TNNs to achieve the same constant inference complexities as SSMs. To accomplish this, we formulate the conversion process as an optimization problem and provide a closed-form solution. We demonstrate how to transform the target equation into a Vandermonde linear system problem, which can be efficiently solved using the Discrete Fourier Transform (DFT). Notably, our method requires no training and maintains numerical stability. It can be also applied to any LongConv-based model. To assess its effectiveness, we conduct extensive experiments on language modeling tasks across various settings. Additionally, we compare our method to other gradient-descent solutions, highlighting the superior numerical stability of our approach. The source code is available at https://github.com/OpenNLPLab/ETSC-Exact-Toeplitz-to-SSM-Conversion.

Denoising Diffusion Probabilistic Models (DDPMs) can generate high-quality samples such as image and audio samples. However, DDPMs require hundreds to thousands of iterations to produce final samples. Several prior works have successfully accelerated DDPMs through adjusting the variance schedule (e.g., Improved Denoising Diffusion Probabilistic Models) or the denoising equation (e.g., Denoising Diffusion Implicit Models (DDIMs)). However, these acceleration methods cannot maintain the quality of samples and even introduce new noise at a high speedup rate, which limit their practicability. To accelerate the inference process while keeping the sample quality, we provide a fresh perspective that DDPMs should be treated as solving differential equations on manifolds. Under such a perspective, we propose pseudo numerical methods for diffusion models (PNDMs). Specifically, we figure out how to solve differential equations on manifolds and show that DDIMs are simple cases of pseudo numerical methods. We change several classical numerical methods to corresponding pseudo numerical methods and find that the pseudo linear multi-step method is the best in most situations. According to our experiments, by directly using pre-trained models on Cifar10, CelebA and LSUN, PNDMs can generate higher quality synthetic images with only 50 steps compared with 1000-step DDIMs (20x speedup), significantly outperform DDIMs with 250 steps (by around 0.4 in FID) and have good generalization on different variance schedules. Our implementation is available at https://github.com/luping-liu/PNDM.

We approach designing a state-space model for deep learning applications through its dual representation, the transfer function, and uncover a highly efficient sequence parallel inference algorithm that is state-free: unlike other proposed algorithms, state-free inference does not incur any significant memory or computational cost with an increase in state size. We achieve this using properties of the proposed frequency domain transfer function parametrization, which enables direct computation of its corresponding convolutional kernel's spectrum via a single Fast Fourier Transform. Our experimental results across multiple sequence lengths and state sizes illustrates, on average, a 35% training speed improvement over S4 layers -- parametrized in time-domain -- on the Long Range Arena benchmark, while delivering state-of-the-art downstream performances over other attention-free approaches. Moreover, we report improved perplexity in language modeling over a long convolutional Hyena baseline, by simply introducing our transfer function parametrization. Our code is available at https://github.com/ruke1ire/RTF.

Recent years have witnessed the rapid progress and broad application of diffusion probabilistic models (DPMs). Sampling from DPMs can be viewed as solving an ordinary differential equation (ODE). Despite the promising performance, the generation of DPMs usually consumes much time due to the large number of function evaluations (NFE). Though recent works have accelerated the sampling to around 20 steps with high-order solvers, the sample quality with less than 10 NFE can still be improved. In this paper, we propose a unified sampling framework (USF) to study the optional strategies for solver. Under this framework, we further reveal that taking different solving strategies at different timesteps may help further decrease the truncation error, and a carefully designed solver schedule has the potential to improve the sample quality by a large margin. Therefore, we propose a new sampling framework based on the exponential integral formulation that allows free choices of solver strategy at each step and design specific decisions for the framework. Moreover, we propose S^3, a predictor-based search method that automatically optimizes the solver schedule to get a better time-quality trade-off of sampling. We demonstrate that S^3 can find outstanding solver schedules which outperform the state-of-the-art sampling methods on CIFAR-10, CelebA, ImageNet, and LSUN-Bedroom datasets. Specifically, we achieve 2.69 FID with 10 NFE and 6.86 FID with 5 NFE on CIFAR-10 dataset, outperforming the SOTA method significantly. We further apply S^3 to Stable-Diffusion model and get an acceleration ratio of 2times, showing the feasibility of sampling in very few steps without retraining the neural network.

Two-point zeroth order methods are important in many applications of zeroth-order optimization, such as robotics, wind farms, power systems, online optimization, and adversarial robustness to black-box attacks in deep neural networks, where the problem may be high-dimensional and/or time-varying. Most problems in these applications are nonconvex and contain saddle points. While existing works have shown that zeroth-order methods utilizing Omega(d) function valuations per iteration (with d denoting the problem dimension) can escape saddle points efficiently, it remains an open question if zeroth-order methods based on two-point estimators can escape saddle points. In this paper, we show that by adding an appropriate isotropic perturbation at each iteration, a zeroth-order algorithm based on 2m (for any 1 leq m leq d) function evaluations per iteration can not only find epsilon-second order stationary points polynomially fast, but do so using only Oleft(d{mepsilon^{2}psi}right) function evaluations, where psi geq Omegaleft(epsilonright) is a parameter capturing the extent to which the function of interest exhibits the strict saddle property.

Distillation techniques have substantially improved the sampling speed of diffusion models, allowing of the generation within only one step or a few steps. However, these distillation methods require extensive training for each dataset, sampler, and network, which limits their practical applicability. To address this limitation, we propose a straightforward distillation approach, Distilled-ODE solvers (D-ODE solvers), that optimizes the ODE solver rather than training the denoising network. D-ODE solvers are formulated by simply applying a single parameter adjustment to existing ODE solvers. Subsequently, D-ODE solvers with smaller steps are optimized by ODE solvers with larger steps through distillation over a batch of samples. Our comprehensive experiments indicate that D-ODE solvers outperform existing ODE solvers, including DDIM, PNDM, DPM-Solver, DEIS, and EDM, especially when generating samples with fewer steps. Our method incur negligible computational overhead compared to previous distillation techniques, enabling simple and rapid integration with previous samplers. Qualitative analysis further shows that D-ODE solvers enhance image quality while preserving the sampling trajectory of ODE solvers.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

We study differentially private (DP) algorithms for recovering clusters in well-clustered graphs, which are graphs whose vertex set can be partitioned into a small number of sets, each inducing a subgraph of high inner conductance and small outer conductance. Such graphs have widespread application as a benchmark in the theoretical analysis of spectral clustering. We provide an efficient (epsilon,delta)-DP algorithm tailored specifically for such graphs. Our algorithm draws inspiration from the recent work of Chen et al., who developed DP algorithms for recovery of stochastic block models in cases where the graph comprises exactly two nearly-balanced clusters. Our algorithm works for well-clustered graphs with k nearly-balanced clusters, and the misclassification ratio almost matches the one of the best-known non-private algorithms. We conduct experimental evaluations on datasets with known ground truth clusters to substantiate the prowess of our algorithm. We also show that any (pure) epsilon-DP algorithm would result in substantial error.

Deep learning has been wildly successful in practice and most state-of-the-art machine learning methods are based on neural networks. Lacking, however, is a rigorous mathematical theory that adequately explains the amazing performance of deep neural networks. In this article, we present a relatively new mathematical framework that provides the beginning of a deeper understanding of deep learning. This framework precisely characterizes the functional properties of neural networks that are trained to fit to data. The key mathematical tools which support this framework include transform-domain sparse regularization, the Radon transform of computed tomography, and approximation theory, which are all techniques deeply rooted in signal processing. This framework explains the effect of weight decay regularization in neural network training, the use of skip connections and low-rank weight matrices in network architectures, the role of sparsity in neural networks, and explains why neural networks can perform well in high-dimensional problems.

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

This paper introduces a novel method for eigenvalue computation using a distributed cooperative neural network framework. Unlike traditional techniques that face scalability challenges in large systems, our decentralized algorithm enables multiple autonomous agents to collaboratively estimate the smallest eigenvalue of large matrices. Each agent employs a localized neural network, refining its estimates through communication with neighboring agents. Our empirical results confirm the algorithm's convergence towards the true eigenvalue, with estimates clustered closely around the true value. Even in the presence of communication delays or network disruptions, the method demonstrates strong robustness and scalability. Theoretical analysis further validates the accuracy and stability of the proposed approach, while empirical tests highlight its efficiency and precision, surpassing traditional centralized algorithms in large-scale eigenvalue computations.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the ``clean'' molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (i.e., diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.

Crystalline materials are a fundamental component in next-generation technologies, yet modeling their distribution presents unique computational challenges. Of the plausible arrangements of atoms in a periodic lattice only a vanishingly small percentage are thermodynamically stable, which is a key indicator of the materials that can be experimentally realized. Two fundamental tasks in this area are to (a) predict the stable crystal structure of a known composition of elements and (b) propose novel compositions along with their stable structures. We present FlowMM, a pair of generative models that achieve state-of-the-art performance on both tasks while being more efficient and more flexible than competing methods. We generalize Riemannian Flow Matching to suit the symmetries inherent to crystals: translation, rotation, permutation, and periodic boundary conditions. Our framework enables the freedom to choose the flow base distributions, drastically simplifying the problem of learning crystal structures compared with diffusion models. In addition to standard benchmarks, we validate FlowMM's generated structures with quantum chemistry calculations, demonstrating that it is about 3x more efficient, in terms of integration steps, at finding stable materials compared to previous open methods.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

Bessel functions are critical in scientific computing for applications such as machine learning, protein structure modeling, and robotics. However, currently, available routines lack precision or fail for certain input ranges, such as when the order v is large, and GPU-specific implementations are limited. We address the precision limitations of current numerical implementations while dramatically improving the runtime. We propose two novel algorithms for computing the logarithm of modified Bessel functions of the first and second kinds by computing intermediate values on a logarithmic scale. Our algorithms are robust and never have issues with underflows or overflows while having relative errors on the order of machine precision, even for inputs where existing libraries fail. In C++/CUDA, our algorithms have median and maximum speedups of 45x and 6150x for GPU and 17x and 3403x for CPU, respectively, over the ranges of inputs and third-party libraries tested. Compared to SciPy, the algorithms have median and maximum speedups of 77x and 300x for GPU and 35x and 98x for CPU, respectively, over the tested inputs. The ability to robustly compute a solution and the low relative errors allow us to fit von Mises-Fisher, vMF, distributions to high-dimensional neural network features. This is, e.g., relevant for uncertainty quantification in metric learning. We obtain image feature data by processing CIFAR10 training images with the convolutional layers of a pre-trained ResNet50. We successfully fit vMF distributions to 2048-, 8192-, and 32768-dimensional image feature data using our algorithms. Our approach provides fast and accurate results while existing implementations in SciPy and mpmath fail to fit successfully. Our approach is readily implementable on GPUs, and we provide a fast open-source implementation alongside this paper.

Physics-Informed Neural Networks (PINNs) have emerged as a promising deep learning framework for approximating numerical solutions to partial differential equations (PDEs). However, conventional PINNs, relying on multilayer perceptrons (MLP), neglect the crucial temporal dependencies inherent in practical physics systems and thus fail to propagate the initial condition constraints globally and accurately capture the true solutions under various scenarios. In this paper, we introduce a novel Transformer-based framework, termed PINNsFormer, designed to address this limitation. PINNsFormer can accurately approximate PDE solutions by utilizing multi-head attention mechanisms to capture temporal dependencies. PINNsFormer transforms point-wise inputs into pseudo sequences and replaces point-wise PINNs loss with a sequential loss. Additionally, it incorporates a novel activation function, Wavelet, which anticipates Fourier decomposition through deep neural networks. Empirical results demonstrate that PINNsFormer achieves superior generalization ability and accuracy across various scenarios, including PINNs failure modes and high-dimensional PDEs. Moreover, PINNsFormer offers flexibility in integrating existing learning schemes for PINNs, further enhancing its performance.

Implicit layer deep learning techniques, like Neural Differential Equations, have become an important modeling framework due to their ability to adapt to new problems automatically. Training a neural differential equation is effectively a search over a space of plausible dynamical systems. However, controlling the computational cost for these models is difficult since it relies on the number of steps the adaptive solver takes. Most prior works have used higher-order methods to reduce prediction timings while greatly increasing training time or reducing both training and prediction timings by relying on specific training algorithms, which are harder to use as a drop-in replacement due to strict requirements on automatic differentiation. In this manuscript, we use internal cost heuristics of adaptive differential equation solvers at stochastic time points to guide the training toward learning a dynamical system that is easier to integrate. We "close the black-box" and allow the use of our method with any adjoint technique for gradient calculations of the differential equation solution. We perform experimental studies to compare our method to global regularization to show that we attain similar performance numbers without compromising the flexibility of implementation on ordinary differential equations (ODEs) and stochastic differential equations (SDEs). We develop two sampling strategies to trade off between performance and training time. Our method reduces the number of function evaluations to 0.556-0.733x and accelerates predictions by 1.3-2x.

Diffusion models are a family of generative models that yield record-breaking performance in tasks such as image synthesis, video generation, and molecule design. Despite their capabilities, their efficiency, especially in the reverse denoising process, remains a challenge due to slow convergence rates and high computational costs. In this work, we introduce an approach that leverages continuous dynamical systems to design a novel denoising network for diffusion models that is more parameter-efficient, exhibits faster convergence, and demonstrates increased noise robustness. Experimenting with denoising probabilistic diffusion models, our framework operates with approximately a quarter of the parameters and 30% of the Floating Point Operations (FLOPs) compared to standard U-Nets in Denoising Diffusion Probabilistic Models (DDPMs). Furthermore, our model is up to 70% faster in inference than the baseline models when measured in equal conditions while converging to better quality solutions.

In this note we examine the autoregressive generalization of the FNet algorithm, in which self-attention layers from the standard Transformer architecture are substituted with a trivial sparse-uniformsampling procedure based on Fourier transforms. Using the Wikitext-103 benchmark, we demonstratethat FNetAR retains state-of-the-art performance (25.8 ppl) on the task of causal language modelingcompared to a Transformer-XL baseline (24.2 ppl) with only half the number self-attention layers,thus providing further evidence for the superfluity of deep neural networks with heavily compoundedattention mechanisms. The autoregressive Fourier transform could likely be used for parameterreduction on most Transformer-based time-series prediction models.

Diffusion models are powerful generative models that simulate the reverse of diffusion processes using score functions to synthesize data from noise. The sampling process of diffusion models can be interpreted as solving the reverse stochastic differential equation (SDE) or the ordinary differential equation (ODE) of the diffusion process, which often requires up to thousands of discretization steps to generate a single image. This has sparked a great interest in developing efficient integration techniques for reverse-S/ODEs. Here, we propose an orthogonal approach to accelerating score-based sampling: Denoising MCMC (DMCMC). DMCMC first uses MCMC to produce samples in the product space of data and variance (or diffusion time). Then, a reverse-S/ODE integrator is used to denoise the MCMC samples. Since MCMC traverses close to the data manifold, the computation cost of producing a clean sample for DMCMC is much less than that of producing a clean sample from noise. To verify the proposed concept, we show that Denoising Langevin Gibbs (DLG), an instance of DMCMC, successfully accelerates all six reverse-S/ODE integrators considered in this work on the tasks of CIFAR10 and CelebA-HQ-256 image generation. Notably, combined with integrators of Karras et al. (2022) and pre-trained score models of Song et al. (2021b), DLG achieves SOTA results. In the limited number of score function evaluation (NFE) settings on CIFAR10, we have 3.86 FID with approx 10 NFE and 2.63 FID with approx 20 NFE. On CelebA-HQ-256, we have 6.99 FID with approx 160 NFE, which beats the current best record of Kim et al. (2022) among score-based models, 7.16 FID with 4000 NFE. Code: https://github.com/1202kbs/DMCMC

The intricate relationship between electrons and the crystal lattice is a linchpin in condensed matter, traditionally described by the Fr\"ohlich model encompassing the lowest-order lattice-electron coupling. Recently developed quantum acoustics, emphasizing the wave nature of lattice vibrations, has enabled the exploration of previously uncharted territories of electron-lattice interaction not accessible with conventional tools such as perturbation theory. In this context, our agenda here is two-fold. First, we showcase the application of machine learning methods to categorize various interaction regimes within the subtle interplay of electrons and the dynamical lattice landscape. Second, we shed light on a nebulous region of electron dynamics identified by the machine learning approach and then attribute it to transient localization, where strong lattice vibrations result in a momentary Anderson prison for electronic wavepackets, which are later released by the evolution of the lattice. Overall, our research illuminates the spectrum of dynamics within the Fr\"ohlich model, such as transient localization, which has been suggested as a pivotal factor contributing to the mysteries surrounding strange metals. Furthermore, this paves the way for utilizing time-dependent perspectives in machine learning techniques for designing materials with tailored electron-lattice properties.

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.

Many hybrid quantum-classical algorithms for the application of ground state energy estimation in quantum chemistry involve estimating the expectation value of a molecular Hamiltonian with respect to a quantum state through measurements on a quantum device. To guide the selection of measurement methods designed for this observable estimation problem, we propose a benchmark called CSHOREBench (Common States and Hamiltonians for ObseRvable Estimation Benchmark) that assesses the performance of these methods against a set of common molecular Hamiltonians and common states encountered during the runtime of hybrid quantum-classical algorithms. In CSHOREBench, we account for resource utilization of a quantum computer through measurements of a prepared state, and a classical computer through computational runtime spent in proposing measurements and classical post-processing of acquired measurement outcomes. We apply CSHOREBench considering a variety of measurement methods on Hamiltonians of size up to 16 qubits. Our discussion is aided by using the framework of decision diagrams which provides an efficient data structure for various randomized methods and illustrate how to derandomize distributions on decision diagrams. In numerical simulations, we find that the methods of decision diagrams and derandomization are the most preferable. In experiments on IBM quantum devices against small molecules, we observe that decision diagrams reduces the number of measurements made by classical shadows by more than 80%, that made by locally biased classical shadows by around 57%, and consistently require fewer quantum measurements along with lower classical computational runtime than derandomization. Furthermore, CSHOREBench is empirically efficient to run when considering states of random quantum ansatz with fixed depth.

Hyperparameter optimization (HPO) is concerned with the automated search for the most appropriate hyperparameter configuration (HPC) of a parameterized machine learning algorithm. A state-of-the-art HPO method is Hyperband, which, however, has its own parameters that influence its performance. One of these parameters, the maximal budget, is especially problematic: If chosen too small, the budget needs to be increased in hindsight and, as Hyperband is not incremental by design, the entire algorithm must be re-run. This is not only costly but also comes with a loss of valuable knowledge already accumulated. In this paper, we propose incremental variants of Hyperband that eliminate these drawbacks, and show that these variants satisfy theoretical guarantees qualitatively similar to those for the original Hyperband with the "right" budget. Moreover, we demonstrate their practical utility in experiments with benchmark data sets.

Computing the matrix square root or its inverse in a differentiable manner is important in a variety of computer vision tasks. Previous methods either adopt the Singular Value Decomposition (SVD) to explicitly factorize the matrix or use the Newton-Schulz iteration (NS iteration) to derive the approximate solution. However, both methods are not computationally efficient enough in either the forward pass or in the backward pass. In this paper, we propose two more efficient variants to compute the differentiable matrix square root. For the forward propagation, one method is to use Matrix Taylor Polynomial (MTP), and the other method is to use Matrix Pad\'e Approximants (MPA). The backward gradient is computed by iteratively solving the continuous-time Lyapunov equation using the matrix sign function. Both methods yield considerable speed-up compared with the SVD or the Newton-Schulz iteration. Experimental results on the de-correlated batch normalization and second-order vision transformer demonstrate that our methods can also achieve competitive and even slightly better performances. The code is available at https://github.com/KingJamesSong/FastDifferentiableMatSqrt{https://github.com/KingJamesSong/FastDifferentiableMatSqrt}.

Harmonic retrieval techniques are the foundation of radio channel sounding, estimation and modeling. This paper introduces a Deep Learning approach for two-dimensional spectral estimation from frequency and time samples of a radio channel transfer function. Our work can estimate two-dimensional parameters from a signal containing an unknown number of paths. In contrast to existing deep learning-based methods, the signal parameters are not estimated via classification but instead in a quasi-grid-free manner. This alleviates the bias, spectral leakage, and ghost targets that grid-based approaches inherently produce. The proposed architecture also reliably estimates the number of spectral components in the measurement. Hence, the architecture jointly solves the model order selection problem and the parameter estimation task. Additionally, we propose a multi-channel windowing of the data during preprocessing, increasing the resulting estimator's robustness. We verify the performance compared to existing harmonic retrieval methods and also show how it can be integrated into an existing maximum likelihood estimator for efficient initialization of a gradient-based iteration.

Recent advancements in neural vocoding are predominantly driven by Generative Adversarial Networks (GANs) operating in the time-domain. While effective, this approach neglects the inductive bias offered by time-frequency representations, resulting in reduntant and computionally-intensive upsampling operations. Fourier-based time-frequency representation is an appealing alternative, aligning more accurately with human auditory perception, and benefitting from well-established fast algorithms for its computation. Nevertheless, direct reconstruction of complex-valued spectrograms has been historically problematic, primarily due to phase recovery issues. This study seeks to close this gap by presenting Vocos, a new model that directly generates Fourier spectral coefficients. Vocos not only matches the state-of-the-art in audio quality, as demonstrated in our evaluations, but it also substantially improves computational efficiency, achieving an order of magnitude increase in speed compared to prevailing time-domain neural vocoding approaches. The source code and model weights have been open-sourced at https://github.com/charactr-platform/vocos.

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

Implicit neural representations (INRs) have arisen as useful methods for representing signals on Euclidean domains. By parameterizing an image as a multilayer perceptron (MLP) on Euclidean space, INRs effectively represent signals in a way that couples spatial and spectral features of the signal that is not obvious in the usual discrete representation, paving the way for continuous signal processing and machine learning approaches that were not previously possible. Although INRs using sinusoidal activation functions have been studied in terms of Fourier theory, recent works have shown the advantage of using wavelets instead of sinusoids as activation functions, due to their ability to simultaneously localize in both frequency and space. In this work, we approach such INRs and demonstrate how they resolve high-frequency features of signals from coarse approximations done in the first layer of the MLP. This leads to multiple prescriptions for the design of INR architectures, including the use of complex wavelets, decoupling of low and band-pass approximations, and initialization schemes based on the singularities of the desired signal.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

We develop a spacetime neural network method with second order optimization for solving quantum dynamics from the high dimensional Schr\"{o}dinger equation. In contrast to the standard iterative first order optimization and the time-dependent variational principle, our approach utilizes the implicit mid-point method and generates the solution for all spatial and temporal values simultaneously after optimization. We demonstrate the method in the Schr\"{o}dinger equation with a self-normalized autoregressive spacetime neural network construction. Future explorations for solving different high dimensional differential equations are discussed.

Diffusion models, which employ stochastic differential equations to sample images through integrals, have emerged as a dominant class of generative models. However, the rationality of the diffusion process itself receives limited attention, leaving the question of whether the problem is well-posed and well-conditioned. In this paper, we uncover a vexing propensity of diffusion models: they frequently exhibit the infinite Lipschitz near the zero point of timesteps. This poses a threat to the stability and accuracy of the diffusion process, which relies on integral operations. We provide a comprehensive evaluation of the issue from both theoretical and empirical perspectives. To address this challenge, we propose a novel approach, dubbed E-TSDM, which eliminates the Lipschitz singularity of the diffusion model near zero. Remarkably, our technique yields a substantial improvement in performance, e.g., on the high-resolution FFHQ dataset (256times256). Moreover, as a byproduct of our method, we manage to achieve a dramatic reduction in the Frechet Inception Distance of other acceleration methods relying on network Lipschitz, including DDIM and DPM-Solver, by over 33%. We conduct extensive experiments on diverse datasets to validate our theory and method. Our work not only advances the understanding of the general diffusion process, but also provides insights for the design of diffusion models.

Graph neural networks (GNNs) are one of the most popular research topics for deep learning. GNN methods typically have been designed on top of the graph signal processing theory. In particular, diffusion equations have been widely used for designing the core processing layer of GNNs, and therefore they are inevitably vulnerable to the notorious oversmoothing problem. Recently, a couple of papers paid attention to reaction equations in conjunctions with diffusion equations. However, they all consider limited forms of reaction equations. To this end, we present a reaction-diffusion equation-based GNN method that considers all popular types of reaction equations in addition to one special reaction equation designed by us. To our knowledge, our paper is one of the most comprehensive studies on reaction-diffusion equation-based GNNs. In our experiments with 9 datasets and 28 baselines, our method, called GREAD, outperforms them in a majority of cases. Further synthetic data experiments show that it mitigates the oversmoothing problem and works well for various homophily rates.

Denoising diffusion bridge models (DDBMs) are a powerful variant of diffusion models for interpolating between two arbitrary paired distributions given as endpoints. Despite their promising performance in tasks like image translation, DDBMs require a computationally intensive sampling process that involves the simulation of a (stochastic) differential equation through hundreds of network evaluations. In this work, we take the first step in fast sampling of DDBMs without extra training, motivated by the well-established recipes in diffusion models. We generalize DDBMs via a class of non-Markovian diffusion bridges defined on the discretized timesteps concerning sampling, which share the same marginal distributions and training objectives, give rise to generative processes ranging from stochastic to deterministic, and result in diffusion bridge implicit models (DBIMs). DBIMs are not only up to 25times faster than the vanilla sampler of DDBMs but also induce a novel, simple, and insightful form of ordinary differential equation (ODE) which inspires high-order numerical solvers. Moreover, DBIMs maintain the generation diversity in a distinguished way, by using a booting noise in the initial sampling step, which enables faithful encoding, reconstruction, and semantic interpolation in image translation tasks. Code is available at https://github.com/thu-ml/DiffusionBridge.

Marine mammal communication is a complex field, hindered by the diversity of vocalizations and environmental factors. The Watkins Marine Mammal Sound Database (WMMD) is an extensive labeled dataset used in machine learning applications. However, the methods for data preparation, preprocessing, and classification found in the literature are quite disparate. This study first focuses on a brief review of the state-of-the-art benchmarks on the dataset, with an emphasis on clarifying data preparation and preprocessing methods. Subsequently, we propose the application of the Wavelet Scattering Transform (WST) in place of standard methods based on the Short-Time Fourier Transform (STFT). The study also tackles a classification task using an ad-hoc deep architecture with residual layers. We outperform the existing classification architecture by 6% in accuracy using WST and 8% using Mel spectrogram preprocessing, effectively reducing by half the number of misclassified samples, and reaching a top accuracy of 96%.

Recent developments in Parameter-Efficient Fine-Tuning (PEFT) methods for pretrained deep neural networks have captured widespread interest. In this work, we study the enhancement of current PEFT methods by incorporating the spectral information of pretrained weight matrices into the fine-tuning procedure. We investigate two spectral adaptation mechanisms, namely additive tuning and orthogonal rotation of the top singular vectors, both are done via first carrying out Singular Value Decomposition (SVD) of pretrained weights and then fine-tuning the top spectral space. We provide a theoretical analysis of spectral fine-tuning and show that our approach improves the rank capacity of low-rank adapters given a fixed trainable parameter budget. We show through extensive experiments that the proposed fine-tuning model enables better parameter efficiency and tuning performance as well as benefits multi-adapter fusion. The code will be open-sourced for reproducibility.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

Reversing a diffusion process by learning its score forms the heart of diffusion-based generative modeling and for estimating properties of scientific systems. The diffusion processes that are tractable center on linear processes with a Gaussian stationary distribution. This limits the kinds of models that can be built to those that target a Gaussian prior or more generally limits the kinds of problems that can be generically solved to those that have conditionally linear score functions. In this work, we introduce a family of tractable denoising score matching objectives, called local-DSM, built using local increments of the diffusion process. We show how local-DSM melded with Taylor expansions enables automated training and score estimation with nonlinear diffusion processes. To demonstrate these ideas, we use automated-DSM to train generative models using non-Gaussian priors on challenging low dimensional distributions and the CIFAR10 image dataset. Additionally, we use the automated-DSM to learn the scores for nonlinear processes studied in statistical physics.

Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. This paper focuses on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D^3G. Unlike previous methods that aim to learn a single model that is domain invariant, D^3G leverages domain similarities based on domain metadata to learn domain-specific models. Concretely, D^3G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly obtained and learned from domain metadata. Under mild assumptions, we theoretically prove that using domain relations to reweight training-domain-specific functions achieves stronger out-of-domain generalization compared to the conventional averaging approach. Empirically, we evaluate the effectiveness of D^3G using real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein binding affinity prediction. Our results show that D^3G consistently outperforms state-of-the-art methods.

We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and the neural network potential is optimized to match the corresponding equilibrium potential at every intermediate time-step. Once the interpolating potentials and samples are well-aligned, the free-energy difference can be estimated using (neural) thermodynamic integration. To target molecular systems, we simultaneously couple Lennard-Jones and electrostatic interactions and model the rigid-body rotation of molecules. We report accurate results for several benchmark systems: a Lennard-Jones particle in a Lennard-Jones fluid, as well as the insertion of both water and methane solutes in a water solvent at atomistic resolution using a simple three-body neural-network potential.

Despite the success of physics-informed neural networks (PINNs) in approximating partial differential equations (PDEs), PINNs can sometimes fail to converge to the correct solution in problems involving complicated PDEs. This is reflected in several recent studies on characterizing the "failure modes" of PINNs, although a thorough understanding of the connection between PINN failure modes and sampling strategies is missing. In this paper, we provide a novel perspective of failure modes of PINNs by hypothesizing that training PINNs relies on successful "propagation" of solution from initial and/or boundary condition points to interior points. We show that PINNs with poor sampling strategies can get stuck at trivial solutions if there are propagation failures, characterized by highly imbalanced PDE residual fields. To mitigate propagation failures, we propose a novel Retain-Resample-Release sampling (R3) algorithm that can incrementally accumulate collocation points in regions of high PDE residuals with little to no computational overhead. We provide an extension of R3 sampling to respect the principle of causality while solving time-dependent PDEs. We theoretically analyze the behavior of R3 sampling and empirically demonstrate its efficacy and efficiency in comparison with baselines on a variety of PDE problems.

Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-binding domains of proteins, and we show that existing machine learning-based docking models have very weak generalization abilities. We carefully analyze the scaling laws of ML-based docking and show that, by scaling data and model size, as well as integrating synthetic data strategies, we are able to significantly increase the generalization capacity and set new state-of-the-art performance across benchmarks. Further, we propose Confidence Bootstrapping, a new training paradigm that solely relies on the interaction between diffusion and confidence models and exploits the multi-resolution generation process of diffusion models. We demonstrate that Confidence Bootstrapping significantly improves the ability of ML-based docking methods to dock to unseen protein classes, edging closer to accurate and generalizable blind docking methods.

In this paper, we investigate the behavior of gradient descent algorithms in physics-informed machine learning methods like PINNs, which minimize residuals connected to partial differential equations (PDEs). Our key result is that the difficulty in training these models is closely related to the conditioning of a specific differential operator. This operator, in turn, is associated to the Hermitian square of the differential operator of the underlying PDE. If this operator is ill-conditioned, it results in slow or infeasible training. Therefore, preconditioning this operator is crucial. We employ both rigorous mathematical analysis and empirical evaluations to investigate various strategies, explaining how they better condition this critical operator, and consequently improve training.

This paper introduces a novel theoretical simplification of the Diffusion Schr\"odinger Bridge (DSB) that facilitates its unification with Score-based Generative Models (SGMs), addressing the limitations of DSB in complex data generation and enabling faster convergence and enhanced performance. By employing SGMs as an initial solution for DSB, our approach capitalizes on the strengths of both frameworks, ensuring a more efficient training process and improving the performance of SGM. We also propose a reparameterization technique that, despite theoretical approximations, practically improves the network's fitting capabilities. Our extensive experimental evaluations confirm the effectiveness of the simplified DSB, demonstrating its significant improvements. We believe the contributions of this work pave the way for advanced generative modeling. The code is available at https://github.com/checkcrab/SDSB.

Convolution models with long filters have demonstrated state-of-the-art reasoning abilities in many long-sequence tasks but lag behind the most optimized Transformers in wall-clock time. A major bottleneck is the Fast Fourier Transform (FFT)--which allows long convolutions to run in O(N logN) time in sequence length N but has poor hardware utilization. In this paper, we study how to optimize the FFT convolution. We find two key bottlenecks: the FFT does not effectively use specialized matrix multiply units, and it incurs expensive I/O between layers of the memory hierarchy. In response, we propose FlashFFTConv. FlashFFTConv uses a matrix decomposition that computes the FFT using matrix multiply units and enables kernel fusion for long sequences, reducing I/O. We also present two sparse convolution algorithms--1) partial convolutions and 2) frequency-sparse convolutions--which can be implemented simply by skipping blocks in the matrix decomposition, enabling further opportunities for memory and compute savings. FlashFFTConv speeds up exact FFT convolutions by up to 7.93times over PyTorch and achieves up to 4.4times speedup end-to-end. Given the same compute budget, FlashFFTConv allows Hyena-GPT-s to achieve 2.3 points better perplexity on the PILE and M2-BERT-base to achieve 3.3 points higher GLUE score--matching models with twice the parameter count. FlashFFTConv also achieves 96.1% accuracy on Path-512, a high-resolution vision task where no model had previously achieved better than 50%. Furthermore, partial convolutions enable longer-sequence models--yielding the first DNA model that can process the longest human genes (2.3M base pairs)--and frequency-sparse convolutions speed up pretrained models while maintaining or improving model quality.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

A large class of inverse problems for PDEs are only well-defined as mappings from operators to functions. Existing operator learning frameworks map functions to functions and need to be modified to learn inverse maps from data. We propose a novel architecture termed Neural Inverse Operators (NIOs) to solve these PDE inverse problems. Motivated by the underlying mathematical structure, NIO is based on a suitable composition of DeepONets and FNOs to approximate mappings from operators to functions. A variety of experiments are presented to demonstrate that NIOs significantly outperform baselines and solve PDE inverse problems robustly, accurately and are several orders of magnitude faster than existing direct and PDE-constrained optimization methods.

Diffusion probabilistic models (DPMs) are emerging powerful generative models. Despite their high-quality generation performance, DPMs still suffer from their slow sampling as they generally need hundreds or thousands of sequential function evaluations (steps) of large neural networks to draw a sample. Sampling from DPMs can be viewed alternatively as solving the corresponding diffusion ordinary differential equations (ODEs). In this work, we propose an exact formulation of the solution of diffusion ODEs. The formulation analytically computes the linear part of the solution, rather than leaving all terms to black-box ODE solvers as adopted in previous works. By applying change-of-variable, the solution can be equivalently simplified to an exponentially weighted integral of the neural network. Based on our formulation, we propose DPM-Solver, a fast dedicated high-order solver for diffusion ODEs with the convergence order guarantee. DPM-Solver is suitable for both discrete-time and continuous-time DPMs without any further training. Experimental results show that DPM-Solver can generate high-quality samples in only 10 to 20 function evaluations on various datasets. We achieve 4.70 FID in 10 function evaluations and 2.87 FID in 20 function evaluations on the CIFAR10 dataset, and a 4sim 16times speedup compared with previous state-of-the-art training-free samplers on various datasets.

Diffusion models are powerful generative models but suffer from slow sampling, often taking 1000 sequential denoising steps for one sample. As a result, considerable efforts have been directed toward reducing the number of denoising steps, but these methods hurt sample quality. Instead of reducing the number of denoising steps (trading quality for speed), in this paper we explore an orthogonal approach: can we run the denoising steps in parallel (trading compute for speed)? In spite of the sequential nature of the denoising steps, we show that surprisingly it is possible to parallelize sampling via Picard iterations, by guessing the solution of future denoising steps and iteratively refining until convergence. With this insight, we present ParaDiGMS, a novel method to accelerate the sampling of pretrained diffusion models by denoising multiple steps in parallel. ParaDiGMS is the first diffusion sampling method that enables trading compute for speed and is even compatible with existing fast sampling techniques such as DDIM and DPMSolver. Using ParaDiGMS, we improve sampling speed by 2-4x across a range of robotics and image generation models, giving state-of-the-art sampling speeds of 0.2s on 100-step DiffusionPolicy and 16s on 1000-step StableDiffusion-v2 with no measurable degradation of task reward, FID score, or CLIP score.

We introduce Poseidon, a foundation model for learning the solution operators of PDEs. It is based on a multiscale operator transformer, with time-conditioned layer norms that enable continuous-in-time evaluations. A novel training strategy leveraging the semi-group property of time-dependent PDEs to allow for significant scaling-up of the training data is also proposed. Poseidon is pretrained on a diverse, large scale dataset for the governing equations of fluid dynamics. It is then evaluated on a suite of 15 challenging downstream tasks that include a wide variety of PDE types and operators. We show that Poseidon exhibits excellent performance across the board by outperforming baselines significantly, both in terms of sample efficiency and accuracy. Poseidon also generalizes very well to new physics that is not seen during pretraining. Moreover, Poseidon scales with respect to model and data size, both for pretraining and for downstream tasks. Taken together, our results showcase the surprising ability of Poseidon to learn effective representations from a very small set of PDEs during pretraining in order to generalize well to unseen and unrelated PDEs downstream, demonstrating its potential as an effective, general purpose PDE foundation model. Finally, the Poseidon model as well as underlying pretraining and downstream datasets are open sourced, with code being available at https://github.com/camlab-ethz/poseidon and pretrained models and datasets at https://huggingface.co/camlab-ethz.

The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard discretization techniques. In the present paper we propose a homogenization technique for computing effective diffusion constants. This is accomplished by using a two-step strategy. The first step consists of an analytic homogenization from the smallest to an intermediate scale. The homogenization error is estimated by comparing the analytic diffusion constant with a numerical estimate obtained by using real cell geometries. The second step consists of a random homogenization. Since no analytical solution is known to this homogenization problem, a numerical approximation algorithm is proposed. Although rather expensive this algorithm provides a reasonable estimate of the homogenized diffusion constant.

In this paper we tackle the problem of generating conformers of a molecule in 3D space given its molecular graph. We parameterize these conformers as continuous functions that map elements from the molecular graph to points in 3D space. We then formulate the problem of learning to generate conformers as learning a distribution over these functions using a diffusion generative model, called Molecular Conformer Fields (MCF). Our approach is simple and scalable, and achieves state-of-the-art performance on challenging molecular conformer generation benchmarks while making no assumptions about the explicit structure of molecules (e.g. modeling torsional angles). MCF represents an advance in extending diffusion models to handle complex scientific problems in a conceptually simple, scalable and effective manner.

We investigate the expressive power of depth-2 bandlimited random neural networks. A random net is a neural network where the hidden layer parameters are frozen with random assignment, and only the output layer parameters are trained by loss minimization. Using random weights for a hidden layer is an effective method to avoid non-convex optimization in standard gradient descent learning. It has also been adopted in recent deep learning theories. Despite the well-known fact that a neural network is a universal approximator, in this study, we mathematically show that when hidden parameters are distributed in a bounded domain, the network may not achieve zero approximation error. In particular, we derive a new nontrivial approximation error lower bound. The proof utilizes the technique of ridgelet analysis, a harmonic analysis method designed for neural networks. This method is inspired by fundamental principles in classical signal processing, specifically the idea that signals with limited bandwidth may not always be able to perfectly recreate the original signal. We corroborate our theoretical results with various simulation studies, and generally, two main take-home messages are offered: (i) Not any distribution for selecting random weights is feasible to build a universal approximator; (ii) A suitable assignment of random weights exists but to some degree is associated with the complexity of the target function.

Recent advancements in operator-type neural networks have shown promising results in approximating the solutions of spatiotemporal Partial Differential Equations (PDEs). However, these neural networks often entail considerable training expenses, and may not always achieve the desired accuracy required in many scientific and engineering disciplines. In this paper, we propose a new Spatiotemporal Fourier Neural Operator (SFNO) that learns maps between Bochner spaces, and a new learning framework to address these issues. This new paradigm leverages wisdom from traditional numerical PDE theory and techniques to refine the pipeline of commonly adopted end-to-end neural operator training and evaluations. Specifically, in the learning problems for the turbulent flow modeling by the Navier-Stokes Equations (NSE), the proposed architecture initiates the training with a few epochs for SFNO, concluding with the freezing of most model parameters. Then, the last linear spectral convolution layer is fine-tuned without the frequency truncation. The optimization uses a negative Sobolev norm for the first time as the loss in operator learning, defined through a reliable functional-type a posteriori error estimator whose evaluation is almost exact thanks to the Parseval identity. This design allows the neural operators to effectively tackle low-frequency errors while the relief of the de-aliasing filter addresses high-frequency errors. Numerical experiments on commonly used benchmarks for the 2D NSE demonstrate significant improvements in both computational efficiency and accuracy, compared to end-to-end evaluation and traditional numerical PDE solvers.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

We consider dense, associative neural-networks trained by a teacher (i.e., with supervision) and we investigate their computational capabilities analytically, via statistical-mechanics of spin glasses, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as quality and quantity of the training dataset, network storage and noise, that is valid in the limit of large network size and structureless datasets: these networks may work in a ultra-storage regime (where they can handle a huge amount of patterns, if compared with shallow neural networks) or in a ultra-detection regime (where they can perform pattern recognition at prohibitive signal-to-noise ratios, if compared with shallow neural networks). Guided by the random theory as a reference framework, we also test numerically learning, storing and retrieval capabilities shown by these networks on structured datasets as MNist and Fashion MNist. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate supervised learning in neural networks, beyond the shallow limit, in general.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

Isolated quantum many-body systems which thermalize under their own dynamics are expected to act as their own thermal baths, thereby bringing their local subsystems to thermal equilibrium. Here we show that the infinite-dimensional limit of a quantum lattice model, as described by Dynamical Mean-Field theory (DMFT), provides a natural framework to understand this self-consistent thermalization process. Using the Fermi-Hubbard model as working example, we demonstrate that the emergence of a self-consistent bath thermalising the system is characterized by a sharp thermalization front, moving balistically and separating the initial condition from the long-time thermal fixed point. We characterize the full DMFT dynamics through an effective temperature for which we derive a travelling-wave equation of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) type. This equation allows to predict the asymptotic shape of the front and its velocity, which match perfectly the full DMFT numerics. Our results provide a new angle to understand the onset of quantum thermalisation in closed isolated systems.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

We propose LLM-FP4 for quantizing both weights and activations in large language models (LLMs) down to 4-bit floating-point values, in a post-training manner. Existing post-training quantization (PTQ) solutions are primarily integer-based and struggle with bit widths below 8 bits. Compared to integer quantization, floating-point (FP) quantization is more flexible and can better handle long-tail or bell-shaped distributions, and it has emerged as a default choice in many hardware platforms. One characteristic of FP quantization is that its performance largely depends on the choice of exponent bits and clipping range. In this regard, we construct a strong FP-PTQ baseline by searching for the optimal quantization parameters. Furthermore, we observe a high inter-channel variance and low intra-channel variance pattern in activation distributions, which adds activation quantization difficulty. We recognize this pattern to be consistent across a spectrum of transformer models designed for diverse tasks, such as LLMs, BERT, and Vision Transformer models. To tackle this, we propose per-channel activation quantization and show that these additional scaling factors can be reparameterized as exponential biases of weights, incurring a negligible cost. Our method, for the first time, can quantize both weights and activations in the LLaMA-13B to only 4-bit and achieves an average score of 63.1 on the common sense zero-shot reasoning tasks, which is only 5.8 lower than the full-precision model, significantly outperforming the previous state-of-the-art by 12.7 points. Code is available at: https://github.com/nbasyl/LLM-FP4.

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.

We revisit quantum phase estimation algorithms for the purpose of obtaining the energy levels of many-body Hamiltonians and pay particular attention to the statistical analysis of their outputs. We introduce the mean phase direction of the parent distribution associated with eigenstate inputs as a new post-processing tool. By connecting it with the unknown phase, we find that if used as its direct estimator, it exceeds the accuracy of the standard majority rule using one less bit of resolution, making evident that it can also be inverted to provide unbiased estimation. Moreover, we show how to directly use this quantity to accurately find the energy levels when the initialized state is an eigenstate of the simulated propagator during the whole time evolution, which allows for shallower algorithms. We then use IBM Q hardware to carry out the digital quantum simulation of three toy models: a two-level system, a two-spin Ising model and a two-site Hubbard model at half-filling. Methodologies are provided to implement Trotterization and reduce the variability of results in noisy intermediate scale quantum computers.

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

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.

Score-based generative models (SGMs) have recently shown impressive results for difficult generative tasks such as the unconditional and conditional generation of natural images and audio signals. In this work, we extend these models to the complex short-time Fourier transform (STFT) domain, proposing a novel training task for speech enhancement using a complex-valued deep neural network. We derive this training task within the formalism of stochastic differential equations (SDEs), thereby enabling the use of predictor-corrector samplers. We provide alternative formulations inspired by previous publications on using generative diffusion models for speech enhancement, avoiding the need for any prior assumptions on the noise distribution and making the training task purely generative which, as we show, results in improved enhancement performance.

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.

Time-dependent partial differential equations (PDEs) are ubiquitous in science and engineering. Recently, mostly due to the high computational cost of traditional solution techniques, deep neural network based surrogates have gained increased interest. The practical utility of such neural PDE solvers relies on their ability to provide accurate, stable predictions over long time horizons, which is a notoriously hard problem. In this work, we present a large-scale analysis of common temporal rollout strategies, identifying the neglect of non-dominant spatial frequency information, often associated with high frequencies in PDE solutions, as the primary pitfall limiting stable, accurate rollout performance. Based on these insights, we draw inspiration from recent advances in diffusion models to introduce PDE-Refiner; a novel model class that enables more accurate modeling of all frequency components via a multistep refinement process. We validate PDE-Refiner on challenging benchmarks of complex fluid dynamics, demonstrating stable and accurate rollouts that consistently outperform state-of-the-art models, including neural, numerical, and hybrid neural-numerical architectures. We further demonstrate that PDE-Refiner greatly enhances data efficiency, since the denoising objective implicitly induces a novel form of spectral data augmentation. Finally, PDE-Refiner's connection to diffusion models enables an accurate and efficient assessment of the model's predictive uncertainty, allowing us to estimate when the surrogate becomes inaccurate.

Optimizing neural networks with loss that contain high-dimensional and high-order differential operators is expensive to evaluate with back-propagation due to O(d^{k}) scaling of the derivative tensor size and the O(2^{k-1}L) scaling in the computation graph, where d is the dimension of the domain, L is the number of ops in the forward computation graph, and k is the derivative order. In previous works, the polynomial scaling in d was addressed by amortizing the computation over the optimization process via randomization. Separately, the exponential scaling in k for univariate functions (d=1) was addressed with high-order auto-differentiation (AD). In this work, we show how to efficiently perform arbitrary contraction of the derivative tensor of arbitrary order for multivariate functions, by properly constructing the input tangents to univariate high-order AD, which can be used to efficiently randomize any differential operator. When applied to Physics-Informed Neural Networks (PINNs), our method provides >1000times speed-up and >30times memory reduction over randomization with first-order AD, and we can now solve 1-million-dimensional PDEs in 8 minutes on a single NVIDIA A100 GPU. This work opens the possibility of using high-order differential operators in large-scale problems.

Post-Training Quantization (PTQ) is a powerful technique for model compression, reducing the precision of neural networks without additional training overhead. Recent works have investigated adopting 8-bit floating-point quantization (FP8) in the context of PTQ for model inference. However, the exploration of floating-point formats smaller than 8 bits and their comparison with integer quantization remains relatively limited. In this work, we present minifloats, which are reduced-precision floating-point formats capable of further reducing the memory footprint, latency, and energy cost of a model while approaching full-precision model accuracy. Our work presents a novel PTQ design-space exploration, comparing minifloat and integer quantization schemes across a range of 3 to 8 bits for both weights and activations. We examine the applicability of various PTQ techniques to minifloats, including weight equalization, bias correction, SmoothQuant, gradient-based learned rounding, and the GPTQ method. Our experiments validate the effectiveness of low-precision minifloats when compared to their integer counterparts across a spectrum of accuracy-precision trade-offs on a set of reference deep learning vision workloads. Finally, we evaluate our results against an FPGA-based hardware cost model, showing that integer quantization often remains the Pareto-optimal option, given its relatively smaller hardware resource footprint.

The optimization of the latents and parameters of diffusion models with respect to some differentiable metric defined on the output of the model is a challenging and complex problem. The sampling for diffusion models is done by solving either the probability flow ODE or diffusion SDE wherein a neural network approximates the score function allowing a numerical ODE/SDE solver to be used. However, naive backpropagation techniques are memory intensive, requiring the storage of all intermediate states, and face additional complexity in handling the injected noise from the diffusion term of the diffusion SDE. We propose a novel family of bespoke ODE solvers to the continuous adjoint equations for diffusion models, which we call AdjointDEIS. We exploit the unique construction of diffusion SDEs to further simplify the formulation of the continuous adjoint equations using exponential integrators. Moreover, we provide convergence order guarantees for our bespoke solvers. Significantly, we show that continuous adjoint equations for diffusion SDEs actually simplify to a simple ODE. Lastly, we demonstrate the effectiveness of AdjointDEIS for guided generation with an adversarial attack in the form of the face morphing problem. Our code will be released on our project page https://zblasingame.github.io/AdjointDEIS/