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Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with machine learning based interatomic potentials. With recent advancements in high-performance computing, highly accurate and large-scale simulations become feasible. This study introduces TensorMD, a new machine learning interatomic potential (MLIP) model that integrates physical principles and tensor diagrams. The tensor formalism provides a more efficient computation and greater flexibility for use with other scientific codes. Additionally, we proposed several portable optimization strategies and developed a highly optimized version for the new Sunway supercomputer. Our optimized TensorMD can achieve unprecedented performance on the new Sunway, enabling simulations of up to 52 billion atoms with a time-to-solution of 31 ps/step/atom, setting new records for HPC + AI + MD.

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機器學習(Machine Learning)是一個研究計算學習方法的國際論壇。該雜志發表文章,報告廣泛的學習方法應用于各種學習問題的實質性結果。該雜志的特色論文描述研究的問題和方法,應用研究和研究方法的問題。有關學習問題或方法的論文通過實證研究、理論分析或與心理現象的比較提供了堅實的支持。應用論文展示了如何應用學習方法來解決重要的應用問題。研究方法論文改進了機器學習的研究方法。所有的論文都以其他研究人員可以驗證或復制的方式描述了支持證據。論文還詳細說明了學習的組成部分,并討論了關于知識表示和性能任務的假設。 官網地址:

Nature evolves creatures with a high complexity of morphological and behavioral intelligence, meanwhile computational methods lag in approaching that diversity and efficacy. Co-optimization of artificial creatures' morphology and control in silico shows promise for applications in physical soft robotics and virtual character creation; such approaches, however, require developing new learning algorithms that can reason about function atop pure structure. In this paper, we present DiffuseBot, a physics-augmented diffusion model that generates soft robot morphologies capable of excelling in a wide spectrum of tasks. DiffuseBot bridges the gap between virtually generated content and physical utility by (i) augmenting the diffusion process with a physical dynamical simulation which provides a certificate of performance, and (ii) introducing a co-design procedure that jointly optimizes physical design and control by leveraging information about physical sensitivities from differentiable simulation. We showcase a range of simulated and fabricated robots along with their capabilities. Check our website at //diffusebot.github.io/

Deep Operator Network (DeepONet) is a neural network framework for learning nonlinear operators such as those from ordinary differential equations (ODEs) describing complex systems. Multiple-input deep neural operators (MIONet) extended DeepONet to allow multiple input functions in different Banach spaces. MIONet offers flexibility in training dataset grid spacing, without constraints on output location. However, it requires offline inputs and cannot handle varying sequence lengths in testing datasets, limiting its real-time application in dynamic complex systems. This work redesigns MIONet, integrating Long Short Term Memory (LSTM) to learn neural operators from time-dependent data. This approach overcomes data discretization constraints and harnesses LSTM's capability with variable-length, real-time data. Factors affecting learning performance, like algorithm extrapolation ability are presented. The framework is enhanced with uncertainty quantification through a novel Bayesian method, sampling from MIONet parameter distributions. Consequently, we develop the B-LSTM-MIONet, incorporating LSTM's temporal strengths with Bayesian robustness, resulting in a more precise and reliable model for noisy datasets.

We formulate the predicted-updates dynamic model, one of the first beyond-worst-case models for dynamic algorithms, which generalizes a large set of well-studied dynamic models including the offline dynamic, incremental, and decremental models to the fully dynamic setting when given predictions about the update times of the elements. In the most basic form of our model, we receive a set of predicted update times for all of the updates that occur over the event horizon. We give a novel framework that "lifts" offline divide-and-conquer algorithms into the fully dynamic setting with little overhead. Using this, we are able to interpolate between the offline and fully dynamic settings; when the $\ell_1$ error of the prediction is linear in the number of updates, we achieve the offline runtime of the algorithm (up to $\mathrm{poly} \log n$ factors). Provided a fully dynamic backstop algorithm, our algorithm will never do worse than the backstop algorithm regardless of the prediction error. Furthermore, our framework achieves a smooth linear trade-off between $\ell_1$ error in the predictions and runtime. These correspond to the desiderata of consistency, robustness, and graceful degradation of the algorithms-with-predictions literature. We further extend our techniques to incremental and decremental settings, transforming algorithms in these settings when given predictions of only the deletion and insertion times, respectively. Our framework is general, and we apply it to obtain improved efficiency bounds over the state-of-the-art dynamic algorithms for a variety of problems including triconnectivity, planar digraph all pairs shortest paths, $k$-edge connectivity, and others, for prediction error of reasonable magnitude.

In the context of deep learning research, where model introductions continually occur, the need for effective and efficient evaluation remains paramount. Existing methods often emphasize accuracy metrics, overlooking stability. To address this, the paper introduces the Accuracy-Stability Index (ASI), a quantitative measure incorporating both accuracy and stability for assessing deep learning models. Experimental results demonstrate the application of ASI, and a 3D surface model is presented for visualizing ASI, mean accuracy, and coefficient of variation. This paper addresses the important issue of quantitative benchmarking metrics for deep learning models, providing a new approach for accurately evaluating accuracy and stability of deep learning models. The paper concludes with discussions on potential weaknesses and outlines future research directions.

Effectively modeling phenomena present in highly nonlinear dynamical systems whilst also accurately quantifying uncertainty is a challenging task, which often requires problem-specific techniques. We outline the deep latent force model (DLFM), a domain-agnostic approach to tackling this problem, which consists of a deep Gaussian process architecture where the kernel at each layer is derived from an ordinary differential equation using the framework of process convolutions. Two distinct formulations of the DLFM are presented which utilise weight-space and variational inducing points-based Gaussian process approximations, both of which are amenable to doubly stochastic variational inference. We provide evidence that our model is capable of capturing highly nonlinear behaviour in real-world multivariate time series data. In addition, we find that our approach achieves comparable performance to a number of other probabilistic models on benchmark regression tasks. We also empirically assess the negative impact of the inducing points framework on the extrapolation capabilities of LFM-based models.

Computational fluid dynamics (CFD) simulation is an irreplaceable modelling step in many engineering designs, but it is often computationally expensive. Some graph neural network (GNN)-based CFD methods have been proposed. However, the current methods inherit the weakness of traditional numerical simulators, as well as ignore the cell characteristics in the mesh used in the finite volume method, a common method in practical CFD applications. Specifically, the input nodes in these GNN methods have very limited information about any object immersed in the simulation domain and its surrounding environment. Also, the cell characteristics of the mesh such as cell volume, face surface area, and face centroid are not included in the message-passing operations in the GNN methods. To address these weaknesses, this work proposes two novel geometric representations: Shortest Vector (SV) and Directional Integrated Distance (DID). Extracted from the mesh, the SV and DID provide global geometry perspective to each input node, thus removing the need to collect this information through message-passing. This work also introduces the use of Finite Volume Features (FVF) in the graph convolutions as node and edge attributes, enabling its message-passing operations to adjust to different nodes. Finally, this work is the first to demonstrate how residual training, with the availability of low-resolution data, can be adopted to improve the flow field prediction accuracy. Experimental results on two datasets with five different state-of-the-art GNN methods for CFD indicate that SV, DID, FVF and residual training can effectively reduce the predictive error of current GNN-based methods by as much as 41%.

Automatic differentiation (AD) is a critical step in physics-informed machine learning, required for computing the high-order derivatives of network output w.r.t. coordinates of collocation points. In this paper, we present a novel and lightweight algorithm to conduct AD for physics-informed operator learning, which we call the trick of Zero Coordinate Shift (ZCS). Instead of making all sampled coordinates as leaf variables, ZCS introduces only one scalar-valued leaf variable for each spatial or temporal dimension, simplifying the wanted derivatives from "many-roots-many-leaves" to "one-root-many-leaves" whereby reverse-mode AD becomes directly utilisable. It has led to an outstanding performance leap by avoiding the duplication of the computational graph along the dimension of functions (physical parameters). ZCS is easy to implement with current deep learning libraries; our own implementation is achieved by extending the DeepXDE package. We carry out a comprehensive benchmark analysis and several case studies, training physics-informed DeepONets to solve partial differential equations (PDEs) without data. The results show that ZCS has persistently reduced GPU memory consumption and wall time for training by an order of magnitude, and such reduction factor scales with the number of functions. As a low-level optimisation technique, ZCS imposes no restrictions on data, physics (PDE) or network architecture and does not compromise training results from any aspect.

The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.

Deep learning has shown great potential for modeling the physical dynamics of complex particle systems such as fluids (in Lagrangian descriptions). Existing approaches, however, require the supervision of consecutive particle properties, including positions and velocities. In this paper, we consider a partially observable scenario known as fluid dynamics grounding, that is, inferring the state transitions and interactions within the fluid particle systems from sequential visual observations of the fluid surface. We propose a differentiable two-stage network named NeuroFluid. Our approach consists of (i) a particle-driven neural renderer, which involves fluid physical properties into the volume rendering function, and (ii) a particle transition model optimized to reduce the differences between the rendered and the observed images. NeuroFluid provides the first solution to unsupervised learning of particle-based fluid dynamics by training these two models jointly. It is shown to reasonably estimate the underlying physics of fluids with different initial shapes, viscosity, and densities. It is a potential alternative approach to understanding complex fluid mechanics, such as turbulence, that are difficult to model using traditional methods of mathematical physics.

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.

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