Daily Papers

Training effective Text-to-SQL models remains challenging due to the scarcity of high-quality, diverse, and structurally complex datasets. Existing methods either rely on limited human-annotated corpora, or synthesize datasets directly by simply prompting LLMs without explicit control over SQL structures, often resulting in limited structural diversity and complexity. To address this, we introduce EvolSQL, a structure-aware data synthesis framework that evolves SQL queries from seed data into richer and more semantically diverse forms. EvolSQL starts with an exploratory Query-SQL expansion to broaden question diversity and improve schema coverage, and then applies an adaptive directional evolution strategy using six atomic transformation operators derived from the SQL Abstract Syntax Tree to progressively increase query complexity across relational, predicate, aggregation, and nesting dimensions. An execution-grounded SQL refinement module and schema-aware deduplication further ensure the creation of high-quality, structurally diverse mapping pairs. Experimental results show that a 7B model fine-tuned on our data outperforms one trained on the much larger SynSQL dataset using only 1/18 of the data.

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery to new material design. Current state-of-the-art models enforce roto-translational symmetries through equivariant neural network architectures, a hard-wired inductive bias that can often lead to reduced flexibility, computational efficiency, and scalability. In this work, we introduce TransIP: Transformer-based Inter-Atomic Potentials, a novel training paradigm for interatomic potentials achieving symmetry compliance without explicit architectural constraints. Our approach guides a generic non-equivariant Transformer-based model to learn SO(3)-equivariance by optimizing its representations in the embedding space. Trained on the recent Open Molecules (OMol25) collection, a large and diverse molecular dataset built specifically for MLIPs and covering different types of molecules (including small organics, biomolecular fragments, and electrolyte-like species), TransIP attains comparable performance in machine-learning force fields versus state-of-the-art equivariant baselines. Further, compared to a data augmentation baseline, TransIP achieves 40% to 60% improvement in performance across varying OMol25 dataset sizes. More broadly, our work shows that learned equivariance can be a powerful and efficient alternative to equivariant or augmentation-based MLIP models.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

The Kramers-Kronig relations are a pivotal foundation of linear optics and atomic physics, embedding a physical connection between the real and imaginary components of any causal response function. A mathematically equivalent, but simpler, approach instead utilises the Hilbert transform. In a previous study, the Hilbert transform was applied to absorption spectra in order to infer the sole refractive index of an atomic medium in the absence of an external magnetic field. The presence of a magnetic field causes the medium to become birefringent and dichroic, and therefore it is instead characterised by two refractive indices. In this study, we apply the same Hilbert transform technique to independently measure both refractive indices of a birefringent atomic medium, leading to an indirect measurement of atomic magneto-optical rotation. Key to this measurement is the insight that inputting specific light polarisations into an atomic medium induces absorption associated with only one of the refractive indices. We show this is true in two configurations, commonly referred to in literature as the Faraday and Voigt geometries, which differ by the magnetic field orientation with respect to the light wavevector. For both cases, we measure the two refractive indices independently for a Rb thermal vapour in a 0.6 T magnetic field, finding excellent agreement with theory. This study further emphasises the application of the Hilbert transform to the field of quantum and atomic optics in the linear regime.

Quantum algorithms for probing ground-state properties of quantum systems require good initial states. Projection-based methods such as eigenvalue filtering rely on inputs that have a significant overlap with the low-energy subspace, which can be challenging for large, strongly-correlated systems. This issue has motivated the study of physically-inspired dynamical approaches such as thermodynamic cooling. In this work, we introduce a ground-state preparation algorithm based on the simulation of quantum dynamics. Our main insight is to transform the Hamiltonian by a shifted sign function via quantum signal processing, effectively mapping eigenvalues into positive and negative subspaces separated by a large gap. This automatically ensures that all states within each subspace conserve energy with respect to the transformed Hamiltonian. Subsequent time-evolution with a perturbed Hamiltonian induces transitions to lower-energy states while preventing unwanted jumps to higher energy states. The approach does not rely on a priori knowledge of energy gaps and requires no additional qubits to model a bath. Furthermore, it makes mathcal{O}(d^{,3/2}/epsilon) queries to the time-evolution operator of the system and mathcal{O}(d^{,3/2}) queries to a block-encoding of the perturbation, for d cooling steps and an epsilon-accurate energy resolution. Our results provide a framework for combining quantum signal processing and Hamiltonian simulation to design heuristic quantum algorithms for ground-state preparation.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schr\"odinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. To address the slow convergence of the kappa=pm1 states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10^{-8} Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schr\"odinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

We review Bohr's atomic model and its extension by Sommerfeld from a mathematical perspective of wave mechanics. The derivation of quantization rules and energy levels is revisited using semiclassical methods. Sommerfeld-type integrals are evaluated by elementary techniques, and connections with the Schr\"{o}dinger and Dirac equations are established. Historical developments and key transitions from classical to quantum theory are discussed to clarify the structure and significance of the old quantum mechanics.

We introduce a simple algorithm that efficiently computes tensor products of Pauli matrices. This is done by tailoring the calculations to this specific case, which allows to avoid unnecessary calculations. The strength of this strategy is benchmarked against state-of-the-art techniques, showing a remarkable acceleration. As a side product, we provide an optimized method for one key calculus in quantum simulations: the Pauli basis decomposition of Hamiltonians.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

We introduce an open-source package called QTraj that solves the Lindblad equation for heavy-quarkonium dynamics using the quantum trajectories algorithm. The package allows users to simulate the suppression of heavy-quarkonium states using externally-supplied input from 3+1D hydrodynamics simulations. The code uses a split-step pseudo-spectral method for updating the wave-function between jumps, which is implemented using the open-source multi-threaded FFTW3 package. This allows one to have manifestly unitary evolution when using real-valued potentials. In this paper, we provide detailed documentation of QTraj 1.0, installation instructions, and present various tests and benchmarks of the code.

A wide range of scientific problems, such as those described by continuous-time dynamical systems and partial differential equations (PDEs), are naturally formulated on function spaces. While function spaces are typically infinite-dimensional, deep learning has predominantly advanced through applications in computer vision and natural language processing that focus on mappings between finite-dimensional spaces. Such fundamental disparities in the nature of the data have limited neural networks from achieving a comparable level of success in scientific applications as seen in other fields. Neural operators are a principled way to generalize neural networks to mappings between function spaces, offering a pathway to replicate deep learning's transformative impact on scientific problems. For instance, neural operators can learn solution operators for entire classes of PDEs, e.g., physical systems with different boundary conditions, coefficient functions, and geometries. A key factor in deep learning's success has been the careful engineering of neural architectures through extensive empirical testing. Translating these neural architectures into neural operators allows operator learning to enjoy these same empirical optimizations. However, prior neural operator architectures have often been introduced as standalone models, not directly derived as extensions of existing neural network architectures. In this paper, we identify and distill the key principles for constructing practical implementations of mappings between infinite-dimensional function spaces. Using these principles, we propose a recipe for converting several popular neural architectures into neural operators with minimal modifications. This paper aims to guide practitioners through this process and details the steps to make neural operators work in practice. Our code can be found at https://github.com/neuraloperator/NNs-to-NOs

Rydberg atom arrays have emerged as a powerful platform to simulate a number of exotic quantum ground states and phase transitions. To verify these capabilities numerically, we develop a versatile quantum Monte Carlo sampling technique which operates in the reduced Hilbert space generated by enforcing the constraint of a Rydberg blockade. We use the framework of stochastic series expansion and show that in the restricted space, the configuration space of operator strings can be understood as a hard rod gas in d+1 dimensions. We use this mapping to develop cluster algorithms which can be visualized as various non-local movements of rods. We study the efficiency of each of our updates individually and collectively. To elucidate the utility of the algorithm, we show that it can efficiently generate the phase diagram of a Rydberg atom array, to temperatures much smaller than all energy scales involved, on a Kagom\'e link lattice. This is of broad interest as the presence of a Z_2 spin liquid has been hypothesized recently.

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.

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

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.

Language-guided human motion synthesis has been a challenging task due to the inherent complexity and diversity of human behaviors. Previous methods face limitations in generalization to novel actions, often resulting in unrealistic or incoherent motion sequences. In this paper, we propose ATOM (ATomic mOtion Modeling) to mitigate this problem, by decomposing actions into atomic actions, and employing a curriculum learning strategy to learn atomic action composition. First, we disentangle complex human motions into a set of atomic actions during learning, and then assemble novel actions using the learned atomic actions, which offers better adaptability to new actions. Moreover, we introduce a curriculum learning training strategy that leverages masked motion modeling with a gradual increase in the mask ratio, and thus facilitates atomic action assembly. This approach mitigates the overfitting problem commonly encountered in previous methods while enforcing the model to learn better motion representations. We demonstrate the effectiveness of ATOM through extensive experiments, including text-to-motion and action-to-motion synthesis tasks. We further illustrate its superiority in synthesizing plausible and coherent text-guided human motion sequences.

We present a feasibility-seeking approach to neural network training. This mathematical optimization framework is distinct from conventional gradient-based loss minimization and uses projection operators and iterative projection algorithms. We reformulate training as a large-scale feasibility problem: finding network parameters and states that satisfy local constraints derived from its elementary operations. Training then involves projecting onto these constraints, a local operation that can be parallelized across the network. We introduce PJAX, a JAX-based software framework that enables this paradigm. PJAX composes projection operators for elementary operations, automatically deriving the solution operators for the feasibility problems (akin to autodiff for derivatives). It inherently supports GPU/TPU acceleration, provides a familiar NumPy-like API, and is extensible. We train diverse architectures (MLPs, CNNs, RNNs) on standard benchmarks using PJAX, demonstrating its functionality and generality. Our results show that this approach is as a compelling alternative to gradient-based training, with clear advantages in parallelism and the ability to handle non-differentiable operations.

Efficient quantum compiling tactics greatly enhance the capability of quantum computers to execute complicated quantum algorithms. Due to its fundamental importance, a plethora of quantum compilers has been designed in past years. However, there are several caveats to current protocols, which are low optimality, high inference time, limited scalability, and lack of universality. To compensate for these defects, here we devise an efficient and practical quantum compiler assisted by advanced deep reinforcement learning (RL) techniques, i.e., data generation, deep Q-learning, and AQ* search. In this way, our protocol is compatible with various quantum machines and can be used to compile multi-qubit operators. We systematically evaluate the performance of our proposal in compiling quantum operators with both inverse-closed and inverse-free universal basis sets. In the task of single-qubit operator compiling, our proposal outperforms other RL-based quantum compilers in the measure of compiling sequence length and inference time. Meanwhile, the output solution is near-optimal, guaranteed by the Solovay-Kitaev theorem. Notably, for the inverse-free universal basis set, the achieved sequence length complexity is comparable with the inverse-based setting and dramatically advances previous methods. These empirical results contribute to improving the inverse-free Solovay-Kitaev theorem. In addition, for the first time, we demonstrate how to leverage RL-based quantum compilers to accomplish two-qubit operator compiling. The achieved results open an avenue for integrating RL with quantum compiling to unify efficiency and practicality and thus facilitate the exploration of quantum advantages.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

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

Quantum computation is an emerging technology with important potential for solving certain problems pivotal in various scientific and engineering disciplines. This paper introduces an efficient quantum protocol for the explicit construction of the block-encoding for an important class of Hamiltonians. Using the Schrodingerisation technique -- which converts non-conservative PDEs into conservative ones -- this particular class of Hamiltonians is shown to be sufficient for simulating any linear partial differential equations that have coefficients which are polynomial functions. The class of Hamiltonians consist of discretisations of polynomial products and sums of position and momentum operators. This construction is explicit and leverages minimal one- and two-qubit operations. The explicit construction of this block-encoding forms a fundamental building block for constructing the unitary evolution operator for this Hamiltonian. The proposed algorithm exhibits polynomial scaling with respect to the spatial partitioning size, suggesting an exponential speedup over classical finite-difference methods. This work provides an important foundation for building explicit and efficient quantum circuits for solving partial differential equations.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Progress in the realisation of reliable large-scale quantum computers has motivated research into the design of quantum machine learning models. We present Quixer: a novel quantum transformer model which utilises the Linear Combination of Unitaries and Quantum Singular Value Transform primitives as building blocks. Quixer operates by preparing a superposition of tokens and applying a trainable non-linear transformation to this mix. We present the first results for a quantum transformer model applied to a practical language modelling task, obtaining results competitive with an equivalent classical baseline. In addition, we include resource estimates for evaluating the model on quantum hardware, and provide an open-source implementation for classical simulation. We conclude by highlighting the generality of Quixer, showing that its parameterised components can be substituted with fixed structures to yield new classes of quantum transformers.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

We introduce Orb-v3, the next generation of the Orb family of universal interatomic potentials. Models in this family expand the performance-speed-memory Pareto frontier, offering near SoTA performance across a range of evaluations with a >10x reduction in latency and > 8x reduction in memory. Our experiments systematically traverse this frontier, charting the trade-off induced by roto-equivariance, conservatism and graph sparsity. Contrary to recent literature, we find that non-equivariant, non-conservative architectures can accurately model physical properties, including those which require higher-order derivatives of the potential energy surface. This model release is guided by the principle that the most valuable foundation models for atomic simulation will excel on all fronts: accuracy, latency and system size scalability. The reward for doing so is a new era of computational chemistry driven by high-throughput and mesoscale all-atom simulations.

The energy levels of hydrogen-like atoms are obtained from the phase-space quantization, one of the pillars of the old quantum theory, by three different methods - (i) direct integration, (ii) Sommerfeld's original method, and (iii) complex integration. The difficulties come from the imposition of elliptical orbits to the electron, resulting in a variable radial component of the linear momentum. Details of the calculation, which constitute a recurrent gap in textbooks that deal with phase-space quantization, are shown in depth in an accessible fashion for students of introductory quantum mechanics courses.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Quantum computation is inherently hybrid, and fast classical manipulation of qubit operators is necessary to ensure scalability in quantum software. We introduce PauliEngine, a high-performance C++ framework that provides efficient primitives for Pauli string multiplication, commutators, symbolic phase tracking, and structural transformations. Built on a binary symplectic representation and optimized bit-wise operations, PauliEngine supports both numerical and symbolic coefficients and is accessible through a Python interface. Runtime benchmarks demonstrate substantial speedups over state-of-the-art implementations. PauliEngine provides a scalable backend for operator-based quantum software tools and simulations.

Quantum algorithms offer significant speedups over their classical counterparts for a variety of problems. The strongest arguments for this advantage are borne by algorithms for quantum search, quantum phase estimation, and Hamiltonian simulation, which appear as subroutines for large families of composite quantum algorithms. A number of these quantum algorithms were recently tied together by a novel technique known as the quantum singular value transformation (QSVT), which enables one to perform a polynomial transformation of the singular values of a linear operator embedded in a unitary matrix. In the seminal GSLW'19 paper on QSVT [Gily\'en, Su, Low, and Wiebe, ACM STOC 2019], many algorithms are encompassed, including amplitude amplification, methods for the quantum linear systems problem, and quantum simulation. Here, we provide a pedagogical tutorial through these developments, first illustrating how quantum signal processing may be generalized to the quantum eigenvalue transform, from which QSVT naturally emerges. Paralleling GSLW'19, we then employ QSVT to construct intuitive quantum algorithms for search, phase estimation, and Hamiltonian simulation, and also showcase algorithms for the eigenvalue threshold problem and matrix inversion. This overview illustrates how QSVT is a single framework comprising the three major quantum algorithms, thus suggesting a grand unification of quantum algorithms.

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.

The growing demand for Large Language Models (LLMs) in applications such as content generation, intelligent chatbots, and sentiment analysis poses considerable challenges for LLM service providers. To efficiently use GPU resources and boost throughput, batching multiple requests has emerged as a popular paradigm; to further speed up batching, LLM quantization techniques reduce memory consumption and increase computing capacity. However, prevalent quantization schemes (e.g., 8-bit weight-activation quantization) cannot fully leverage the capabilities of modern GPUs, such as 4-bit integer operators, resulting in sub-optimal performance. To maximize LLMs' serving throughput, we introduce Atom, a low-bit quantization method that achieves high throughput improvements with negligible accuracy loss. Atom significantly boosts serving throughput by using low-bit operators and considerably reduces memory consumption via low-bit quantization. It attains high accuracy by applying a novel mixed-precision and fine-grained quantization process. We evaluate Atom on 4-bit weight-activation quantization setups in the serving context. Atom improves end-to-end throughput by up to 7.73times compared to the FP16 and by 2.53times compared to INT8 quantization, while maintaining the same latency target.

The Schr\"odinger Bridge (SB) is a powerful framework for solving generative modeling tasks such as unpaired domain translation. Most SB-related research focuses on continuous data space R^{D} and leaves open theoretical and algorithmic questions about applying SB methods to discrete data, e.g, on finite spaces S^{D}. Notable examples of such sets S are codebooks of vector-quantized (VQ) representations of modern autoencoders, tokens in texts, categories of atoms in molecules, etc. In this paper, we provide a theoretical and algorithmic foundation for solving SB in discrete spaces using the recently introduced Iterative Markovian Fitting (IMF) procedure. Specifically, we theoretically justify the convergence of discrete-time IMF (D-IMF) to SB in discrete spaces. This enables us to develop a practical computational algorithm for SB which we call Categorical Schr\"odinger Bridge Matching (CSBM). We show the performance of CSBM via a series of experiments with synthetic data and VQ representations of images.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

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.

Machine learning force fields (MLFFs) have revolutionized molecular simulations by providing quantum mechanical accuracy at the speed of molecular mechanical computations. However, a fundamental reliance of these models on fixed-cutoff architectures limits their applicability to macromolecular systems where long-range interactions dominate. We demonstrate that this locality constraint causes force prediction errors to scale monotonically with system size, revealing a critical architectural bottleneck. To overcome this, we establish the systematically designed MolLR25 ({Mol}ecules with {L}ong-{R}ange effect) benchmark up to 1200 atoms, generated using high-fidelity DFT, and introduce E2Former-LSR, an equivariant transformer that explicitly integrates long-range attention blocks. E2Former-LSR exhibits stable error scaling, achieves superior fidelity in capturing non-covalent decay, and maintains precision on complex protein conformations. Crucially, its efficient design provides up to 30% speedup compared to purely local models. This work validates the necessity of non-local architectures for generalizable MLFFs, enabling high-fidelity molecular dynamics for large-scale chemical and biological systems.

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.

In the applications of proxy-SU(3) model in the context of determining (beta,gamma) values for nuclei across the periodic table, for understanding the preponderance of triaxial shapes in nuclei with Z ge 30, it is seen that one needs not only the highest weight (hw) or leading SU(3) irreducible representation (irrep) (lambda_H, mu_H) but also the lower SU(3) irreps (lambda ,mu) such that 2lambda + mu =2lambda_H + mu_H-3r with r=0,1 and 2 [Bonatsos et al., Symmetry {\bf 16}, 1625 (2024)]. These give the next highest weight (nhw) irrep, next-to-next highest irrep (nnhw) and so on. Recently, it is shown that for nuclei with 32 le Z,N le 46, there will be not only proxy-SU(3) but also proxy-SU(4) symmetry [Kota and Sahu, Physica Scripta {\bf 99}, 065306 (2024)]. Following these developments, presented in this paper are the SU(3) irreps (lambda ,mu) with 2lambda + mu =2lambda_H + mu_H-3r, r=0,1,2 for various isotopes of Ge, Se, Kr, Sr, Zr, Mo, Ru and Pd (with 32 le N le 46) assuming good proxy-SU(4) symmetry. A simple method for obtaining the SU(3) irreps is described and applied. The tabulations for proxy-SU(3) irreps provided in this paper will be useful in further investigations of triaxial shapes in these nuclei.

We implement physics-informed neural networks (PINNs) to solve the time-independent Schr\"odinger equation for three canonical one-dimensional quantum potentials: an infinite square well, a finite square well, and a finite barrier. The PINN models incorporate trial wavefunctions that exactly satisfy boundary conditions (Dirichlet zeros at domain boundaries), and they optimize a loss functional combining the PDE residual with a normalization constraint. For the infinite well, the ground-state energy is known (E = pi^2 in dimensionless units) and held fixed in training, whereas for the finite well and barrier, the eigenenergy is treated as a trainable parameter. We use fully-connected neural networks with smooth activation functions to represent the wavefunction and demonstrate that PINNs can learn the ground-state eigenfunctions and eigenvalues for these quantum systems. The results show that the PINN-predicted wavefunctions closely match analytical solutions or expected behaviors, and the learned eigenenergies converge to known values. We present training logs and convergence of the energy parameter, as well as figures comparing the PINN solutions to exact results. The discussion addresses the performance of PINNs relative to traditional numerical methods, highlighting challenges such as convergence to the correct eigenvalue, sensitivity to initialization, and the difficulty of modeling discontinuous potentials. We also discuss the importance of the normalization term to resolve the scaling ambiguity of the wavefunction. Finally, we conclude that PINNs are a viable approach for quantum eigenvalue problems, and we outline future directions including extensions to higher-dimensional and time-dependent Schr\"odinger equations.

We completely classify the atomic summands in a graph product (M,varphi) = *_{v in G} (M_v,varphi_v) of von Neumann algebras with faithful normal states. Each type I factor summand (N,psi) is a tensor product of type I factor summands (N_v,psi_v) in the individual algebras. The existence of such a summand and its weight in the direct sum can be determined from the (N_v,psi_v)'s using explicit polynomials associated to the graph.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

We propose using Normalizing Flows as a trainable kernel within the molecular dynamics update of Hamiltonian Monte Carlo (HMC). By learning (invertible) transformations that simplify our dynamics, we can outperform traditional methods at generating independent configurations. We show that, using a carefully constructed network architecture, our approach can be easily scaled to large lattice volumes with minimal retraining effort. The source code for our implementation is publicly available online at https://github.com/nftqcd/fthmc.

Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs often induced by a fixed radius cutoff or k-nearest neighbor scheme. While this design aligns with the locality present in many molecular tasks, a hard-coded graph can limit expressivity due to the fixed receptive field and slows down inference with sparse graph operations. In this work, we investigate whether pure, unmodified Transformers trained directly on Cartesian coordinatesx2013without predefined graphs or physical priorsx2013can approximate molecular energies and forces. As a starting point for our analysis, we demonstrate how to train a Transformer to competitive energy and force mean absolute errors under a matched training compute budget, relative to a state-of-the-art equivariant GNN on the OMol25 dataset. We discover that the Transformer learns physically consistent patternsx2013such as attention weights that decay inversely with interatomic distancex2013and flexibly adapts them across different molecular environments due to the absence of hard-coded biases. The use of a standard Transformer also unlocks predictable improvements with respect to scaling training resources, consistent with empirical scaling laws observed in other domains. Our results demonstrate that many favorable properties of GNNs can emerge adaptively in Transformers, challenging the necessity of hard-coded graph inductive biases and pointing toward standardized, scalable architectures for molecular modeling.

Although quantum simulation can give insight into elusive or intractable physical phenomena, many quantum simulators are unavoidably limited in the models they mimic. Such is also the case for atom arrays interacting via Rydberg states - a platform potentially capable of simulating any kind of spin exchange model, albeit with currently unattainable experimental capabilities. Here, we propose a new route towards simulating generic spin exchange Hamiltonians in atom arrays, using Floquet engineering with both global and local control. To demonstrate the versatility and applicability of our approach, we numerically investigate the generation of several spin exchange models which have yet to be realized in atom arrays, using only previously-demonstrated experimental capabilities. Our proposed scheme can be readily explored in many existing setups, providing a path to investigate a large class of exotic quantum spin models.

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.

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).

We develop a theory of pseudo-differential operators associated with the gyrator transform on modulation spaces. The gyrator transform is a two-dimensional linear canonical transform which can be viewed as a rotation in the time-frequency plane and is closely related to the fractional Fourier transform. Motivated by the global structure of the gyrator kernel, we work with Shubin global symbol classes on R^4. We first recall basic properties of modulation spaces and establish continuity and invertibility of the gyrator transform on these spaces, using its representation as a metaplectic operator. Then we introduce pseudo-differential operators defined via the gyrator transform and a Shubin symbol, and we prove boundedness results on modulation spaces and on gyrator-based modulation-Sobolev spaces. Our work extends and generalises earlier results of Mahato, Arya and Prasad on Schwartz and Sobolev spaces MahatoGyrator to the more flexible framework of modulation spaces.

We present 1d-qt-ideal-solver, an open-source Python library for simulating one-dimensional quantum tunneling dynamics under idealized coherent conditions. The solver implements the split-operator method with second-order Trotter-Suzuki factorization, utilizing FFT-based spectral differentiation for the kinetic operator and complex absorbing potentials to eliminate boundary reflections. Numba just-in-time compilation achieves performance comparable to compiled languages while maintaining code accessibility. We validate the implementation through two canonical test cases: rectangular barriers modeling field emission through oxide layers and Gaussian barriers approximating scanning tunneling microscopy interactions. Both simulations achieve exceptional numerical fidelity with machine-precision energy conservation over femtosecond-scale propagation. Comparative analysis employing information-theoretic measures and nonparametric hypothesis tests reveals that rectangular barriers exhibit moderately higher transmission coefficients than Gaussian barriers in the over-barrier regime, though Jensen-Shannon divergence analysis indicates modest practical differences between geometries. Phase space analysis confirms complete decoherence when averaged over spatial-temporal domains. The library name reflects its scope: idealized signifies deliberate exclusion of dissipation, environmental coupling, and many-body interactions, limiting applicability to qualitative insights and pedagogical purposes rather than quantitative experimental predictions. Distributed under the MIT License, the library provides a deployable tool for teaching quantum mechanics and preliminary exploration of tunneling dynamics.

Physics is based on probabilities as fundamental entities of a mathematical description. Expectation values of observables are computed according to the classical statistical rule. The overall probability distribution for one world covers all times. The quantum formalism arises once one focuses on the evolution of the time-local probabilistic information. Wave functions or the density matrix allow the formulation of a general linear evolution law for classical statistics. The quantum formalism for classical statistics is a powerful tool which allows us to implement for generalized Ising models the momentum observable with the associated Fourier representation. The association of operators to observables permits the computation of expectation values in terms of the density matrix by the usual quantum rule. We show that probabilistic cellular automata are quantum systems in a formulation with discrete time steps and real wave functions. With a complex structure the evolution operator for automata can be expressed in terms of a Hamiltonian involving fermionic creation and annihilation operators. The time-local probabilistic information amounts to a subsystem of the overall probabilistic system which is correlated with its environment consisting of the past and future. Such subsystems typically involve probabilistic observables for which only a probability distribution for their possible measurement values is available. Incomplete statistics does not permit to compute classical correlation functions for arbitrary subsystem-observables. Bell's inequalities are not generally applicable.

We give a simple, fully correct, and assumption-light replacement for the contested "domain-extension" in Step 9 of a recent windowed-QFT lattice algorithm with complex-Gaussian windows~chen2024quantum. The published Step~9 suffers from a periodicity/support mismatch. We present a pair-shift difference construction that coherently cancels all unknown offsets, produces an exact uniform CRT-coset state over Z_{P}, and then uses the QFT to enforce the intended modular linear relation. The unitary is reversible, uses poly(log M_2) gates, and preserves the algorithm's asymptotics. Project Page: https://github.com/yifanzhang-pro/quantum-lattice.

Quantum computers can be used to address molecular structure, materials science and condensed matter physics problems, which currently stretch the limits of existing high-performance computing resources. Finding exact numerical solutions to these interacting fermion problems has exponential cost, while Monte Carlo methods are plagued by the fermionic sign problem. These limitations of classical computational methods have made even few-atom molecular structures problems of practical interest for medium-sized quantum computers. Yet, thus far experimental implementations have been restricted to molecules involving only Period I elements. Here, we demonstrate the experimental optimization of up to six-qubit Hamiltonian problems with over a hundred Pauli terms, determining the ground state energy for molecules of increasing size, up to BeH2. This is enabled by a hardware-efficient variational quantum eigensolver with trial states specifically tailored to the available interactions in our quantum processor, combined with a compact encoding of fermionic Hamiltonians and a robust stochastic optimization routine. We further demonstrate the flexibility of our approach by applying the technique to a problem of quantum magnetism. Across all studied problems, we find agreement between experiment and numerical simulations with a noisy model of the device. These results help elucidate the requirements for scaling the method to larger systems, and aim at bridging the gap between problems at the forefront of high-performance computing and their implementation on quantum hardware.

Recently, sophisticated deep learning-based approaches have been developed for generating efficient initial guesses to accelerate the convergence of density functional theory (DFT) calculations. While the actual initial guesses are often density matrices (DM), quantities that can convert into density matrices also qualify as alternative forms of initial guesses. Hence, existing works mostly rely on the prediction of the Hamiltonian matrix for obtaining high-quality initial guesses. However, the Hamiltonian matrix is both numerically difficult to predict and intrinsically non-transferable, hindering the application of such models in real scenarios. In light of this, we propose a method that constructs DFT initial guesses by predicting the electron density in a compact auxiliary basis representation using E(3)-equivariant neural networks. Trained on small molecules with up to 20 atoms, our model is able to achieve an average 33.3% self-consistent field (SCF) step reduction on systems up to 60 atoms, substantially outperforming Hamiltonian-centric and DM-centric models. Critically, this acceleration remains nearly constant with increasing system sizes and exhibits strong transferring behaviors across orbital basis sets and exchange-correlation (XC) functionals. To the best of our knowledge, this work represents the first and robust candidate for a universally transferable DFT acceleration method. We are also releasing the SCFbench dataset and its accompanying code to facilitate future research in this promising direction.

Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii) implicitly, using a property predictor. However, training property predictors or conditional diffusion models requires an abundance of labeled data and is inherently challenging in real-world applications. We propose a novel approach that attenuates the limitations of acquiring large labeled datasets by leveraging domain knowledge from quantum chemistry as a non-differentiable oracle to guide an unconditional diffusion model. Instead of relying on neural networks, the oracle provides accurate guidance in the form of estimated gradients, allowing the diffusion process to sample from a conditional distribution specified by quantum chemistry. We show that this results in more precise conditional generation of novel and stable molecular structures. Our experiments demonstrate that our method: (1) significantly reduces atomic forces, enhancing the validity of generated molecules when used for stability optimization; (2) is compatible with both explicit and implicit guidance in diffusion models, enabling joint optimization of molecular properties and stability; and (3) generalizes effectively to molecular optimization tasks beyond stability optimization.

Crystal structure determination from powder diffraction patterns is a complex challenge in materials science, often requiring extensive expertise and computational resources. This study introduces DiffractGPT, a generative pre-trained transformer model designed to predict atomic structures directly from X-ray diffraction (XRD) patterns. By capturing the intricate relationships between diffraction patterns and crystal structures, DiffractGPT enables fast and accurate inverse design. Trained on thousands of atomic structures and their simulated XRD patterns from the JARVIS-DFT dataset, we evaluate the model across three scenarios: (1) without chemical information, (2) with a list of elements, and (3) with an explicit chemical formula. The results demonstrate that incorporating chemical information significantly enhances prediction accuracy. Additionally, the training process is straightforward and fast, bridging gaps between computational, data science, and experimental communities. This work represents a significant advancement in automating crystal structure determination, offering a robust tool for data-driven materials discovery and design.

The neural operator has emerged as a powerful tool in learning mappings between function spaces in PDEs. However, when faced with real-world physical data, which are often highly non-uniformly distributed, it is challenging to use mesh-based techniques such as the FFT. To address this, we introduce the Non-Uniform Neural Operator (NUNO), a comprehensive framework designed for efficient operator learning with non-uniform data. Leveraging a K-D tree-based domain decomposition, we transform non-uniform data into uniform grids while effectively controlling interpolation error, thereby paralleling the speed and accuracy of learning from non-uniform data. We conduct extensive experiments on 2D elasticity, (2+1)D channel flow, and a 3D multi-physics heatsink, which, to our knowledge, marks a novel exploration into 3D PDE problems with complex geometries. Our framework has reduced error rates by up to 60% and enhanced training speeds by 2x to 30x. The code is now available at https://github.com/thu-ml/NUNO.

E(3)-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.

The development of efficient machine learning models for molecular systems representation is becoming crucial in scientific research. We introduce TensorNet, an innovative O(3)-equivariant message-passing neural network architecture that leverages Cartesian tensor representations. By using Cartesian tensor atomic embeddings, feature mixing is simplified through matrix product operations. Furthermore, the cost-effective decomposition of these tensors into rotation group irreducible representations allows for the separate processing of scalars, vectors, and tensors when necessary. Compared to higher-rank spherical tensor models, TensorNet demonstrates state-of-the-art performance with significantly fewer parameters. For small molecule potential energies, this can be achieved even with a single interaction layer. As a result of all these properties, the model's computational cost is substantially decreased. Moreover, the accurate prediction of vector and tensor molecular quantities on top of potential energies and forces is possible. In summary, TensorNet's framework opens up a new space for the design of state-of-the-art equivariant models.

We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias: treating lattice and atomic properties as a single, interdependent system. Combined with a periodic table-based atomic representation and a balanced training strategy, our approach achieves 9.62% SUN (Stable, Unique, Novel) rate on MP-20, substantially outperforming recent methods including FlowMM (4.38%) and MatterGen (3.42%). Notably, CrystalDiT generates 63.28% unique and novel structures while maintaining comparable stability rates, demonstrating that architectural simplicity can be more effective than complexity for materials discovery. Our results suggest that in data-limited scientific domains, carefully designed simple architectures outperform sophisticated alternatives that are prone to overfitting.

The dot product attention mechanism, originally designed for natural language processing tasks, is a cornerstone of modern Transformers. It adeptly captures semantic relationships between word pairs in sentences by computing a similarity overlap between queries and keys. In this work, we explore the suitability of Transformers, focusing on their attention mechanisms, in the specific domain of the parametrization of variational wave functions to approximate ground states of quantum many-body spin Hamiltonians. Specifically, we perform numerical simulations on the two-dimensional J_1-J_2 Heisenberg model, a common benchmark in the field of quantum many-body systems on lattice. By comparing the performance of standard attention mechanisms with a simplified version that excludes queries and keys, relying solely on positions, we achieve competitive results while reducing computational cost and parameter usage. Furthermore, through the analysis of the attention maps generated by standard attention mechanisms, we show that the attention weights become effectively input-independent at the end of the optimization. We support the numerical results with analytical calculations, providing physical insights of why queries and keys should be, in principle, omitted from the attention mechanism when studying large systems.

The study of high-speed rotating matter is a crucial research topic in physics due to the emergence of novel phenomena. In this paper, we combined cranking covariant density functional theory (CDFT) with a similar renormalization group approach to decompose the Hamiltonian from the cranking CDFT into different Hermit components, including the non-relativistic term, the dynamical term, the spin-orbit coupling, and the Darwin term. Especially, we obtained the rotational term, the term relating to Zeeman effect-like, and the spin-rotation coupling due to consideration of rotation and spatial component of vector potential. By exploring these operators, we aim to identify novel phenomena that may occur in rotating nuclei. Signature splitting, Zeeman effect-like, spin-rotation coupling, and spin current are among the potential novelties that may arise in rotating nuclei. Additionally, we investigated the observability of these phenomena and their dependence on various factors such as nuclear deformation, rotational angular velocity, and strength of magnetic field.

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.

Here we investigate the role of quantum interference in the quantum homogenizer, whose convergence properties model a thermalization process. In the original quantum homogenizer protocol, a system qubit converges to the state of identical reservoir qubits through partial-swap interactions, that allow interference between reservoir qubits. We design an alternative, incoherent quantum homogenizer, where each system-reservoir interaction is moderated by a control qubit using a controlled-swap interaction. We show that our incoherent homogenizer satisfies the essential conditions for homogenization, being able to transform a qubit from any state to any other state to arbitrary accuracy, with negligible impact on the reservoir qubits' states. Our results show that the convergence properties of homogenization machines that are important for modelling thermalization are not dependent on coherence between qubits in the homogenization protocol. We then derive bounds on the resources required to re-use the homogenizers for performing state transformations. This demonstrates that both homogenizers are universal for any number of homogenizations, for an increased resource cost.

In recent years, diffusion-based models have demonstrated exceptional performance in searching for simultaneously stable, unique, and novel (S.U.N.) crystalline materials. However, most of these models don't have the ability to change the number of atoms in the crystal during the generation process, which limits the variability of model sampling trajectories. In this paper, we demonstrate the severity of this restriction and introduce a simple yet powerful technique, mirage infusion, which enables diffusion models to change the state of the atoms that make up the crystal from existent to non-existent (mirage) and vice versa. We show that this technique improves model quality by up to times2.5 compared to the same model without this modification. The resulting model, Mirage Atom Diffusion (MiAD), is an equivariant joint diffusion model for de novo crystal generation that is capable of altering the number of atoms during the generation process. MiAD achieves an 8.2% S.U.N. rate on the MP-20 dataset, which substantially exceeds existing state-of-the-art approaches. The source code can be found at https://github.com/andrey-okhotin/miad.git{github.com/andrey-okhotin/miad}.

We present a compact design of dual-beam Zeeman slower optimized for efficient production of cold atom applications. Traditional single-beam configurations face challenges from substantial residual atomic flux impacting downstream optical windows, resulting in increased system size, atomic deposition contamination, and a reduced operational lifetime. Our approach employs two oblique laser beams and a capillary-array collimation system to address these challenges while maintaining efficient deceleration. For rubidium (^{87}Rb), simulations demonstrate a significant increase in the fraction of atoms captured by a two-dimensional magneto-optical trap (2D-MOT) and nearly eliminate atom-induced contamination probability at optical windows, all within a compact Zeeman slower length of 44 cm. Experimental validation with Rb and Yb demonstrates highly efficient atomic loading within the same compact design. This advancement represents a substantial improvement for high-flux cold atom applications, providing reliable performance for high-precision metrology, quantum computation and simulation.

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.

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.

The paper is a continuation of the study started in Yorzh1. Schrodinger operators on finite compact metric graphs are considered under the assumption that the matching conditions at the graph vertices are of delta type. Either an infinite series of trace formulae (provided that edge potentials are infinitely smooth) or a finite number of such formulae (in the cases of L_1 and C^M edge potentials) are obtained which link together two different quantum graphs under the assumption that their spectra coincide. Applications are given to the problem of recovering matching conditions for a quantum graph based on its spectrum.

We present and experimentally realize a quantum algorithm for efficiently solving the following problem: given an Ntimes N matrix M, an N-dimensional vector emph{b}, and an initial vector emph{x}(0), obtain a target vector emph{x}(t) as a function of time t according to the constraint demph{x}(t)/dt=Memph{x}(t)+emph{b}. We show that our algorithm exhibits an exponential speedup over its classical counterpart in certain circumstances. In addition, we demonstrate our quantum algorithm for a 4times4 linear differential equation using a 4-qubit nuclear magnetic resonance quantum information processor. Our algorithm provides a key technique for solving many important problems which rely on the solutions to linear differential equations.

The efficacy of deep residual networks is fundamentally predicated on the identity shortcut connection. While this mechanism effectively mitigates the vanishing gradient problem, it imposes a strictly additive inductive bias on feature transformations, thereby limiting the network's capacity to model complex state transitions. In this paper, we introduce Deep Delta Learning (DDL), a novel architecture that generalizes the standard residual connection by modulating the identity shortcut with a learnable, data-dependent geometric transformation. This transformation, termed the Delta Operator, constitutes a rank-1 perturbation of the identity matrix, parameterized by a reflection direction vector k(X) and a gating scalar β(X). We provide a spectral analysis of this operator, demonstrating that the gate β(X) enables dynamic interpolation between identity mapping, orthogonal projection, and geometric reflection. Furthermore, we restructure the residual update as a synchronous rank-1 injection, where the gate acts as a dynamic step size governing both the erasure of old information and the writing of new features. This unification empowers the network to explicitly control the spectrum of its layer-wise transition operator, enabling the modeling of complex, non-monotonic dynamics while preserving the stable training characteristics of gated residual architectures.

The study of the long-time dynamics of quantum systems can be a real challenge, especially in systems like ultracold gases, where the required timescales may be longer than the lifetime of the system itself. In this work, we show that it is possible to access the long-time dynamics of a strongly repulsive atomic gas mixture in shorter times. The shortcut-to-dynamics protocol that we propose does not modify the fate of the observables, but effectively jumps ahead in time without changing the system's inherent evolution. Just like the next-chapter button in a movie player that allows to quickly reach the part of the movie one wants to watch, it is a leap into the future.

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.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

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.

Recently, text-to-motion models have opened new possibilities for creating realistic human motion with greater efficiency and flexibility. However, aligning motion generation with event-level textual descriptions presents unique challenges due to the complex relationship between textual prompts and desired motion outcomes. To address this, we introduce AToM, a framework that enhances the alignment between generated motion and text prompts by leveraging reward from GPT-4Vision. AToM comprises three main stages: Firstly, we construct a dataset MotionPrefer that pairs three types of event-level textual prompts with generated motions, which cover the integrity, temporal relationship and frequency of motion. Secondly, we design a paradigm that utilizes GPT-4Vision for detailed motion annotation, including visual data formatting, task-specific instructions and scoring rules for each sub-task. Finally, we fine-tune an existing text-to-motion model using reinforcement learning guided by this paradigm. Experimental results demonstrate that AToM significantly improves the event-level alignment quality of text-to-motion generation.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

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.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

The intrinsic probabilistic nature of quantum systems makes error correction or mitigation indispensable for quantum computation. While current error-correcting strategies focus on correcting errors in quantum states or quantum gates, these fine-grained error-correction methods can incur significant overhead for quantum algorithms of increasing complexity. We present a first step in achieving error correction at the level of quantum algorithms by combining a unified perspective on modern quantum algorithms via quantum signal processing (QSP). An error model of under- or over-rotation of the signal processing operator parameterized by epsilon < 1 is introduced. It is shown that while Pauli Z-errors are not recoverable without additional resources, Pauli X and Y errors can be arbitrarily suppressed by coherently appending a noisy `recovery QSP.' Furthermore, it is found that a recovery QSP of length O(2^k c^{k^2} d) is sufficient to correct any length-d QSP with c unique phases to k^{th}-order in error epsilon. Allowing an additional assumption, a lower bound of Omega(cd) is shown, which is tight for k = 1, on the length of the recovery sequence. Our algorithmic-level error correction method is applied to Grover's fixed-point search algorithm as a demonstration.

Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory. However, previous methods learned from 1D SMILES sequences or 2D molecular graphs failed to achieve high accuracy as QC properties primarily depend on the 3D equilibrium conformations optimized by electronic structure methods, far different from the sequence-type and graph-type data. In this paper, we propose a novel approach called Uni-Mol+ to tackle this challenge. Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive methods such as RDKit. Then, the raw conformation is iteratively updated to its target DFT equilibrium conformation using neural networks, and the learned conformation will be used to predict the QC properties. To effectively learn this update process towards the equilibrium conformation, we introduce a two-track Transformer model backbone and train it with the QC property prediction task. We also design a novel approach to guide the model's training process. Our extensive benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets. We have made the code and model publicly available at https://github.com/dptech-corp/Uni-Mol.

This article provides an introduction to surface code quantum computing. We first estimate the size and speed of a surface code quantum computer. We then introduce the concept of the stabilizer, using two qubits, and extend this concept to stabilizers acting on a two-dimensional array of physical qubits, on which we implement the surface code. We next describe how logical qubits are formed in the surface code array and give numerical estimates of their fault-tolerance. We outline how logical qubits are physically moved on the array, how qubit braid transformations are constructed, and how a braid between two logical qubits is equivalent to a controlled-NOT. We then describe the single-qubit Hadamard, S and T operators, completing the set of required gates for a universal quantum computer. We conclude by briefly discussing physical implementations of the surface code. We include a number of appendices in which we provide supplementary information to the main text.

The independent atom ansatz of density functional theory yields an accurate analytical expression for dynamic correlation energy in the H_{2} molecule: E_{c} = 0.5(1 - 2)(ab|ba) for the atom-additive self-consistent density rho = |a|^{2} + |b|^{2}. Combined with exact atomic self-exchange, it recovers more than 99.5 % of nearly exact SCAN exchange-correlation energy at R > 0.5 A, differing by less than 0.12 eV. The total energy functional correctly dissociates the H-H bond and yields absolute errors of 0.002 A, 0.19 eV, and 13 cm^{-1} relative to experiment at the tight binding computational cost. The chemical bond formation is attributed to the asymptotic Heitler-London resonance of quasi-orthogonal atomic states (- (ab|ba)) with no contributions from kinetic energy or charge accumulation in the bond.

The theory of open quantum systems lays the foundations for a substantial part of modern research in quantum science and engineering. Rooted in the dimensionality of their extended Hilbert spaces, the high computational complexity of simulating open quantum systems calls for the development of strategies to approximate their dynamics. In this paper, we present an approach for tackling open quantum system dynamics. Using an exact probabilistic formulation of quantum physics based on positive operator-valued measure (POVM), we compactly represent quantum states with autoregressive transformer neural networks; such networks bring significant algorithmic flexibility due to efficient exact sampling and tractable density. We further introduce the concept of String States to partially restore the symmetry of the autoregressive transformer neural network and improve the description of local correlations. Efficient algorithms have been developed to simulate the dynamics of the Liouvillian superoperator using a forward-backward trapezoid method and find the steady state via a variational formulation. Our approach is benchmarked on prototypical one and two-dimensional systems, finding results which closely track the exact solution and achieve higher accuracy than alternative approaches based on using Markov chain Monte Carlo to sample restricted Boltzmann machines. Our work provides general methods for understanding quantum dynamics in various contexts, as well as techniques for solving high-dimensional probabilistic differential equations in classical setups.

The rapid development of universal machine learning interatomic potentials (uMLIPs) has demonstrated the possibility for generalizable learning of the universal potential energy surface. In principle, the accuracy of uMLIPs can be further improved by bridging the model from lower-fidelity datasets to high-fidelity ones. In this work, we analyze the challenge of this transfer learning problem within the CHGNet framework. We show that significant energy scale shifts and poor correlations between GGA and r^2SCAN pose challenges to cross-functional data transferability in uMLIPs. By benchmarking different transfer learning approaches on the MP-r^2SCAN dataset of 0.24 million structures, we demonstrate the importance of elemental energy referencing in the transfer learning of uMLIPs. By comparing the scaling law with and without the pre-training on a low-fidelity dataset, we show that significant data efficiency can still be achieved through transfer learning, even with a target dataset of sub-million structures. We highlight the importance of proper transfer learning and multi-fidelity learning in creating next-generation uMLIPs on high-fidelity data.

The classical development of neural networks has primarily focused on learning mappings between finite dimensional Euclidean spaces or finite sets. We propose a generalization of neural networks to learn operators, termed neural operators, that map between infinite dimensional function spaces. We formulate the neural operator as a composition of linear integral operators and nonlinear activation functions. We prove a universal approximation theorem for our proposed neural operator, showing that it can approximate any given nonlinear continuous operator. The proposed neural operators are also discretization-invariant, i.e., they share the same model parameters among different discretization of the underlying function spaces. Furthermore, we introduce four classes of efficient parameterization, viz., graph neural operators, multi-pole graph neural operators, low-rank neural operators, and Fourier neural operators. An important application for neural operators is learning surrogate maps for the solution operators of partial differential equations (PDEs). We consider standard PDEs such as the Burgers, Darcy subsurface flow, and the Navier-Stokes equations, and show that the proposed neural operators have superior performance compared to existing machine learning based methodologies, while being several orders of magnitude faster than conventional PDE solvers.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

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.

Isotopic substitution in molecular systems can affect fundamental molecular properties including the energy position and spacing of electronic, vibrational and rotational levels, thus modifying the dynamics associated to their coherent superposition. In extreme ultraviolet spectroscopy, the photoelectron leaving the molecule after the absorption of a single photon can trigger an ultrafast nuclear motion in the cation, which can lead, eventually, to molecular fragmentation. This dynamics depends on the mass of the constituents of the cation, thus showing, in general, a significant isotopic dependence. In time-resolved attosecond photoelectron interferometry, the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional quantum of energy (typically in the infrared spectral range) with the photoelectron-photoion system, offering the opportunity to investigate in time the influence of isotopic substitution on the characteristics of the photoionisation dynamics. Here we show that attosecond photoelectron interferometry is sensitive to isotopic substitution by investigating the two-color photoionisation spectra measured in a mixture of methane (CH_4) and deuteromethane (CD_4). The isotopic dependence manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks generated in the two-color field with the two isotopologues. The observed effects are interpreted considering the differences in the time evolution of the nuclear autocorrelation functions in the two molecules.

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose Unified Variational Auto-Encoder for 3D Molecular Latent Diffusion Modeling (UAE-3D), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both de novo and conditional 3D molecule generation, achieving leading efficiency and quality.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

In this paper, we construct a mixture of neural operators (MoNOs) between function spaces whose complexity is distributed over a network of expert neural operators (NOs), with each NO satisfying parameter scaling restrictions. Our main result is a distributed universal approximation theorem guaranteeing that any Lipschitz non-linear operator between L^2([0,1]^d) spaces can be approximated uniformly over the Sobolev unit ball therein, to any given varepsilon>0 accuracy, by an MoNO while satisfying the constraint that: each expert NO has a depth, width, and rank of O(varepsilon^{-1}). Naturally, our result implies that the required number of experts must be large, however, each NO is guaranteed to be small enough to be loadable into the active memory of most computers for reasonable accuracies varepsilon. During our analysis, we also obtain new quantitative expression rates for classical NOs approximating uniformly continuous non-linear operators uniformly on compact subsets of L^2([0,1]^d).

Convolution has been the core ingredient of modern neural networks, triggering the surge of deep learning in vision. In this work, we rethink the inherent principles of standard convolution for vision tasks, specifically spatial-agnostic and channel-specific. Instead, we present a novel atomic operation for deep neural networks by inverting the aforementioned design principles of convolution, coined as involution. We additionally demystify the recent popular self-attention operator and subsume it into our involution family as an over-complicated instantiation. The proposed involution operator could be leveraged as fundamental bricks to build the new generation of neural networks for visual recognition, powering different deep learning models on several prevalent benchmarks, including ImageNet classification, COCO detection and segmentation, together with Cityscapes segmentation. Our involution-based models improve the performance of convolutional baselines using ResNet-50 by up to 1.6% top-1 accuracy, 2.5% and 2.4% bounding box AP, and 4.7% mean IoU absolutely while compressing the computational cost to 66%, 65%, 72%, and 57% on the above benchmarks, respectively. Code and pre-trained models for all the tasks are available at https://github.com/d-li14/involution.

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

In this work, we propose a concise neural operator architecture for operator learning. Drawing an analogy with a conventional fully connected neural network, we define the neural operator as follows: the output of the i-th neuron in a nonlinear operator layer is defined by mathcal O_i(u) = sigmaleft( sum_j mathcal W_{ij} u + mathcal B_{ij}right). Here, mathcal W_{ij} denotes the bounded linear operator connecting j-th input neuron to i-th output neuron, and the bias mathcal B_{ij} takes the form of a function rather than a scalar. Given its new universal approximation property, the efficient parameterization of the bounded linear operators between two neurons (Banach spaces) plays a critical role. As a result, we introduce MgNO, utilizing multigrid structures to parameterize these linear operators between neurons. This approach offers both mathematical rigor and practical expressivity. Additionally, MgNO obviates the need for conventional lifting and projecting operators typically required in previous neural operators. Moreover, it seamlessly accommodates diverse boundary conditions. Our empirical observations reveal that MgNO exhibits superior ease of training compared to other CNN-based models, while also displaying a reduced susceptibility to overfitting when contrasted with spectral-type neural operators. We demonstrate the efficiency and accuracy of our method with consistently state-of-the-art performance on different types of partial differential equations (PDEs).

Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

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.

We report the measurement of the electric dipole moment of aluminum monochloride (AlCl) using a cryogenic buffer-gas beam source. Our measurements provide values for the dipole moments of the two lowest vibrational states of the X^1Sigma^+ and the A^1Pi electronic states. We also show that spin-orbit coupling with an extended number of spin states is essential in the ab initio calculation to correctly describe both the dipole moment and the Te energy of AlCl. We further lay out the implications of these results for astrophysical models of stellar and planetary evolution that have used a substitute value for the dipole moment of AlCl until now.

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Classical methods to simulate quantum systems are not only a key element of the physicist's toolkit for studying many-body models but are also increasingly important for verifying and challenging upcoming quantum computers. Pauli propagation has recently emerged as a promising new family of classical algorithms for simulating digital quantum systems. Here we provide a comprehensive account of Pauli propagation, tracing its algorithmic structure from its bit-level implementation and formulation as a tree-search problem, all the way to its high-level user applications for simulating quantum circuits and dynamics. Utilising these observations, we present PauliPropagation.jl, a Julia software package that can perform rapid Pauli propagation simulation straight out-of-the-box and can be used more generally as a building block for novel simulation algorithms.

SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks in which CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single shared parameter set without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS/tree/main/OpenMol/TDN{https://github.com/divelab/AIRS/}).

We introduce the framework of model space into quantum imaginary time evolution (QITE) to enable stable estimation of ground and excited states using a quantum computer. Model-space QITE (MSQITE) propagates a model space to the exact one by retaining its orthogonality, and hence is able to describe multiple states simultaneously. The quantum Lanczos (QLanczos) algorithm is extended to MSQITE to accelerate the convergence. The present scheme is found to outperform both the standard QLanczos and the recently proposed folded-spectrum QITE in simulating excited states. Moreover, we demonstrate that spin contamination can be effectively removed by shifting the imaginary time propagator, and thus excited states with a particular spin quantum number are efficiently captured without falling into the different spin states that have lower energies. We also investigate how different levels of the unitary approximation employed in MSQITE can affect the results. The effectiveness of the algorithm over QITE is demonstrated by noise simulations for the H4 model system.

Neural operators learn mappings between function spaces, which is practical for learning solution operators of PDEs and other scientific modeling applications. Among them, the Fourier neural operator (FNO) is a popular architecture that performs global convolutions in the Fourier space. However, such global operations are often prone to over-smoothing and may fail to capture local details. In contrast, convolutional neural networks (CNN) can capture local features but are limited to training and inference at a single resolution. In this work, we present a principled approach to operator learning that can capture local features under two frameworks by learning differential operators and integral operators with locally supported kernels. Specifically, inspired by stencil methods, we prove that we obtain differential operators under an appropriate scaling of the kernel values of CNNs. To obtain local integral operators, we utilize suitable basis representations for the kernels based on discrete-continuous convolutions. Both these approaches preserve the properties of operator learning and, hence, the ability to predict at any resolution. Adding our layers to FNOs significantly improves their performance, reducing the relative L2-error by 34-72% in our experiments, which include a turbulent 2D Navier-Stokes and the spherical shallow water equations.

Text-to-motion generation is a crucial task in computer vision, which generates the target 3D motion by the given text. The existing annotated datasets are limited in scale, resulting in most existing methods overfitting to the small datasets and unable to generalize to the motions of the open domain. Some methods attempt to solve the open-vocabulary motion generation problem by aligning to the CLIP space or using the Pretrain-then-Finetuning paradigm. However, the current annotated dataset's limited scale only allows them to achieve mapping from sub-text-space to sub-motion-space, instead of mapping between full-text-space and full-motion-space (full mapping), which is the key to attaining open-vocabulary motion generation. To this end, this paper proposes to leverage the atomic motion (simple body part motions over a short time period) as an intermediate representation, and leverage two orderly coupled steps, i.e., Textual Decomposition and Sub-motion-space Scattering, to address the full mapping problem. For Textual Decomposition, we design a fine-grained description conversion algorithm, and combine it with the generalization ability of a large language model to convert any given motion text into atomic texts. Sub-motion-space Scattering learns the compositional process from atomic motions to the target motions, to make the learned sub-motion-space scattered to form the full-motion-space. For a given motion of the open domain, it transforms the extrapolation into interpolation and thereby significantly improves generalization. Our network, DSO-Net, combines textual decomposition and sub-motion-space scattering to solve the open-vocabulary motion generation. Extensive experiments demonstrate that our DSO-Net achieves significant improvements over the state-of-the-art methods on open-vocabulary motion generation. Code is available at https://vankouf.github.io/DSONet/.

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.

Modularization is a cornerstone of computer science, abstracting complex functions into atomic building blocks. In this paper, we introduce a new level of modularization by abstracting generative models into atomic generative modules. Analogous to fractals in mathematics, our method constructs a new type of generative model by recursively invoking atomic generative modules, resulting in self-similar fractal architectures that we call fractal generative models. As a running example, we instantiate our fractal framework using autoregressive models as the atomic generative modules and examine it on the challenging task of pixel-by-pixel image generation, demonstrating strong performance in both likelihood estimation and generation quality. We hope this work could open a new paradigm in generative modeling and provide a fertile ground for future research. Code is available at https://github.com/LTH14/fractalgen.

In today's rapidly expanding data landscape, knowledge extraction from unstructured text is vital for real-time analytics, temporal inference, and dynamic memory frameworks. However, traditional static knowledge graph (KG) construction often overlooks the dynamic and time-sensitive nature of real-world data, limiting adaptability to continuous changes. Moreover, recent zero- or few-shot approaches that avoid domain-specific fine-tuning or reliance on prebuilt ontologies often suffer from instability across multiple runs, as well as incomplete coverage of key facts. To address these challenges, we introduce ATOM (AdapTive and OptiMized), a few-shot and scalable approach that builds and continuously updates Temporal Knowledge Graphs (TKGs) from unstructured texts. ATOM splits input documents into minimal, self-contained "atomic" facts, improving extraction exhaustivity and stability. Then, it constructs atomic TKGs from these facts while employing a dual-time modeling that distinguishes when information is observed from when it is valid. The resulting atomic TKGs are subsequently merged in parallel. Empirical evaluations demonstrate that ATOM achieves ~18% higher exhaustivity, ~17% better stability, and over 90% latency reduction compared to baseline methods, demonstrating a strong scalability potential for dynamic TKG construction.

Elliptic partial differential equations (PDEs) are a major class of time-independent PDEs that play a key role in many scientific and engineering domains such as fluid dynamics, plasma physics, and solid mechanics. Recently, neural operators have emerged as a promising technique to solve elliptic PDEs more efficiently by directly mapping the input to solutions. However, existing networks typically cannot handle complex geometries and inhomogeneous boundary values present in the real world. Here we introduce Boundary-Embedded Neural Operators (BENO), a novel neural operator architecture that embeds the complex geometries and inhomogeneous boundary values into the solving of elliptic PDEs. Inspired by classical Green's function, BENO consists of two branches of Graph Neural Networks (GNNs) for interior source term and boundary values, respectively. Furthermore, a Transformer encoder maps the global boundary geometry into a latent vector which influences each message passing layer of the GNNs. We test our model extensively in elliptic PDEs with various boundary conditions. We show that all existing baseline methods fail to learn the solution operator. In contrast, our model, endowed with boundary-embedded architecture, outperforms state-of-the-art neural operators and strong baselines by an average of 60.96\%. Our source code can be found https://github.com/AI4Science-WestlakeU/beno.git.

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own merit, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, from low-level libraries, training utilities, to interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

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.

Large language models (LLMs) exhibit remarkable problem-solving abilities, but struggle with complex tasks due to static internal knowledge. Retrieval-Augmented Generation (RAG) enhances access to external information, yet remains limited in multi-hop reasoning and strategic search due to rigid workflows. Recent advancements in agentic deep research empower LLMs to autonomously reason, search, and synthesize information. However, current approaches relying on outcome-based reinforcement learning (RL) face critical issues such as conflicting gradients and reward sparsity, limiting performance gains and training efficiency. To address these, we first propose Atomic Thought, a novel LLM thinking paradigm that decomposes reasoning into fine-grained functional units. These units are supervised by Reasoning Reward Models (RRMs), which provide Atomic Thought Rewards (ATR) for fine-grained guidance. Building on this, we propose Atom-Searcher, a novel RL framework for agentic deep research that integrates Atomic Thought and ATR. Atom-Searcher uses a curriculum-inspired reward schedule, prioritizing process-level ATR early and transitioning to outcome rewards, accelerating convergence on effective reasoning paths. Experiments on seven benchmarks show consistent improvements over the state-of-the-art. Key advantages include: (1) Atom-Searcher scales computation at test-time. (2) Atomic Thought provides supervision anchors for RRMs, bridging deep research tasks and RRMs. (3) Atom-Searcher exhibits more interpretable, human-like reasoning patterns.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

This paper establishes a robust link between quantum dynamics and classical ones by deriving probabilistic representation for both continuous time and discrete time quantum walks. We first adapt Molchanov formula, originally employed in the study of Schrodinger operators on multidimensional integer lattice, to characterize the evolution of continuous time quantum walks. Extending this framework, we develop a probabilistic method to represent discrete time quantum walks on an infinite integer line, bypassing the locality constraints that typically inhibit direct application of Molchanov formula. The validity of our representation is empirically confirmed through a benchmark analysis of the Hadamard walk, demonstrating high fidelity with traditional unitary evolution. Our results suggest that this probabilistic lens offer a powerful alternative for learning multidimensional quantum walks and provides new analytical pathways for investigating quantum systems via classical stochastic processes.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

Accurate prediction of bond dissociation energies (BDEs) underpins mechanistic insight and the rational design of molecules and materials. We present a systematic, reproducible benchmark comparing quantum and classical machine learning models for BDE prediction using a chemically curated feature set encompassing atomic properties (atomic numbers, hybridization), bond characteristics (bond order, type), and local environmental descriptors. Our quantum framework, implemented in Qiskit Aer on six qubits, employs ZZFeatureMap encodings with variational ansatz (RealAmplitudes) across multiple architectures Variational Quantum Regressors (VQR), Quantum Support Vector Regressors (QSVR), Quantum Neural Networks (QNN), Quantum Convolutional Neural Networks (QCNN), and Quantum Random Forests (QRF). These are rigorously benchmarked against strong classical baselines, including Support Vector Regression (SVR), Random Forests (RF), and Multi-Layer Perceptrons (MLP). Comprehensive evaluation spanning absolute and relative error metrics, threshold accuracies, and error distributions shows that top-performing quantum models (QCNN, QRF) match the predictive accuracy and robustness of classical ensembles and deep networks, particularly within the chemically prevalent mid-range BDE regime. These findings establish a transparent baseline for quantum-enhanced molecular property prediction and outline a practical foundation for advancing quantum computational chemistry toward near chemical accuracy.

We present QuantumLLMInstruct (QLMMI), an innovative dataset featuring over 500,000 meticulously curated instruction-following problem-solution pairs designed specifically for quantum computing - the largest and most comprehensive dataset of its kind. Originating from over 90 primary seed domains and encompassing hundreds of subdomains autonomously generated by LLMs, QLMMI marks a transformative step in the diversity and richness of quantum computing datasets. Designed for instruction fine-tuning, QLMMI seeks to significantly improve LLM performance in addressing complex quantum computing challenges across a wide range of quantum physics topics. While Large Language Models (LLMs) have propelled advancements in computational science with datasets like Omni-MATH and OpenMathInstruct, these primarily target Olympiad-level mathematics, leaving quantum computing largely unexplored. The creation of QLMMI follows a rigorous four-stage methodology. Initially, foundational problems are developed using predefined templates, focusing on critical areas such as synthetic Hamiltonians, QASM code generation, Jordan-Wigner transformations, and Trotter-Suzuki quantum circuit decompositions. Next, detailed and domain-specific solutions are crafted to ensure accuracy and relevance. In the third stage, the dataset is enriched through advanced reasoning techniques, including Chain-of-Thought (CoT) and Task-Oriented Reasoning and Action (ToRA), which enhance problem-solution diversity while adhering to strict mathematical standards. Lastly, a zero-shot Judge LLM performs self-assessments to validate the dataset's quality and reliability, minimizing human oversight requirements.

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.