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Mar 14

Transition-Based Constrained DFT for the Robust and Reliable Treatment of Excitations in Supramolecular Systems

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.

Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs

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).

The Open Catalyst 2020 (OC20) Dataset and Community Challenges

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.

SPRIGHT: A Fast and Robust Framework for Sparse Walsh-Hadamard Transform

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.

Transform Once: Efficient Operator Learning in Frequency Domain

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.

Efficient and Modular Implicit Differentiation

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.

Limits and Powers of Koopman Learning

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.

Exact Diffusion Inversion via Bi-directional Integration Approximation

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.

Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields

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/.

Fast Sampling of Diffusion Models with Exponential Integrator

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

Solving High-Dimensional PDEs with Latent Spectral Models

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.

Robustifying State-space Models for Long Sequences via Approximate Diagonalization

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.

Open Materials 2024 (OMat24) Inorganic Materials Dataset and Models

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.

Diffusion Probabilistic Model Made Slim

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.

Solving High Frequency and Multi-Scale PDEs with Gaussian Processes

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.

Enabling Efficient Equivariant Operations in the Fourier Basis via Gaunt Tensor Products

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

Low-Bitwidth Floating Point Quantization for Efficient High-Quality Diffusion Models

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.

Scalable Diffusion for Materials Generation

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.

Generating π-Functional Molecules Using STGG+ with Active Learning

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).

DPM-Solver-v3: Improved Diffusion ODE Solver with Empirical Model Statistics

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.

Stochastic Interpolants: A Unifying Framework for Flows and Diffusions

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.

An inorganic ABX3 perovskite materials dataset for target property prediction and classification using machine learning

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.

Post-training Quantization on Diffusion Models

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 .

Training Deep Surrogate Models with Large Scale Online Learning

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.

Feynman-Kac Correctors in Diffusion: Annealing, Guidance, and Product of Experts

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.

Experimental Design for Multi-Channel Imaging via Task-Driven Feature Selection

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

DPM-Solver++: Fast Solver for Guided Sampling of Diffusion Probabilistic Models

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.

Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

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.

CHGNet: Pretrained universal neural network potential for charge-informed atomistic modeling

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.

On the Stability of Expressive Positional Encodings for Graph Neural Networks

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.

Pseudo Numerical Methods for Diffusion Models on Manifolds

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.

A Unified Sampling Framework for Solver Searching of Diffusion Probabilistic Models

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.

High-performance symbolic-numerics via multiple dispatch

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.

FABind: Fast and Accurate Protein-Ligand Binding

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

Deep Learning for Protein-Ligand Docking: Are We There Yet?

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.

Fast, Expressive SE(n) Equivariant Networks through Weight-Sharing in Position-Orientation Space

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

Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking

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.

Accurate Computation of the Logarithm of Modified Bessel Functions on GPUs

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.

Locally Regularized Neural Differential Equations: Some Black Boxes Were Meant to Remain Closed!

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.

Denoising MCMC for Accelerating Diffusion-Based Generative 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

Rise and Fall of Anderson Localization by Lattice Vibrations: A Time-Dependent Machine Learning Approach

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.

Practical Benchmarking of Randomized Measurement Methods for Quantum Chemistry Hamiltonians

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.

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding

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}.

FlashFFTConv: Efficient Convolutions for Long Sequences with Tensor Cores

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.

DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps

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.

Poseidon: Efficient Foundation Models for PDEs

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.

How Powerful are Shallow Neural Networks with Bandlimited Random Weights?

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.

Spectral-Refiner: Fine-Tuning of Accurate Spatiotemporal Neural Operator for Turbulent Flows

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.

Dense Hebbian neural networks: a replica symmetric picture of supervised learning

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.

Von Mises Mixture Distributions for Molecular Conformation Generation

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.

LLM-FP4: 4-Bit Floating-Point Quantized Transformers

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.

Physics-informed cluster analysis and a priori efficiency criterion for the construction of local reduced-order bases

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.

PDE-Refiner: Achieving Accurate Long Rollouts with Neural PDE Solvers

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.

Post-Training Quantization with Low-precision Minifloats and Integers on FPGAs

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.