arXiv subjects

Weinan E

Publications and source records attributed to Weinan E.

At least 73 records · Page 4Linked to original sources

arXiv2024

Uni-Mol2: Exploring Molecular Pretraining Model at Scale

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining models remains unexplored. In this work, we present Uni-Mol2 , an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, characterizing the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale Uni-Mol2 to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show consistent improvement in the downstream tasks as the model size grows. The Uni-Mol2 with 1.1B parameters also outperforms existing methods, achieving an average 27% improvement on the QM9 and 14% on COMPAS-1D dataset.

cs.LG↗

arXiv2024

$\text{Memory}^3$: Language Modeling with Explicit Memory

The training and inference of large language models (LLMs) are together a costly process that transports knowledge from raw data to meaningful computation. Inspired by the memory hierarchy of the human brain, we reduce this cost by equipping LLMs with explicit memory, a memory format cheaper than model parameters and text retrieval-augmented generation (RAG). Conceptually, with most of its knowledge externalized to explicit memories, the LLM can enjoy a smaller parameter size, training cost, and inference cost, all proportional to the amount of remaining "abstract knowledge". As a preliminary proof of concept, we train from scratch a 2.4B LLM, which achieves better performance than much larger LLMs as well as RAG models, and maintains higher decoding speed than RAG. The model is named $\text{Memory}^3$, since explicit memory is the third form of memory in LLMs after implicit memory (model parameters) and working memory (context key-values). We introduce a memory circuitry theory to support the externalization of knowledge, and present novel techniques including a memory sparsification mechanism that makes storage tractable and a two-stage pretraining scheme that facilitates memory formation.

cs.CL↗

arXiv2024

Coarse-graining conformational dynamics with multi-dimensional generalized Langevin equation: how, when, and why

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained conformational dynamics. Constrained by the fluctuation-dissipation theorem, the approach can build coarse-grained models in dynamical consistency with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term dynamical consistency. Case studies of a toy polymer, with 20 coarse-grained sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling coarse-grained conformational dynamics in practice.

physics.bio-ph↗

arXiv2024

Ab Initio Generalized Langevin Equation

We introduce a machine learning-based approach called ab initio generalized Langevin equation (AIGLE) to model the dynamics of slow collective variables in materials and molecules. In this scheme, the parameters are learned from atomistic simulations based on ab initio quantum mechanical models. Force field, memory kernel, and noise generator are constructed in the context of the Mori-Zwanzig formalism, under the constraint of the fluctuation-dissipation theorem. Combined with deep potential molecular dynamics and electronic density functional theory, this approach opens the way to multi-scale modeling in a variety of situations. Here, we demonstrate this capability with a study of two mesoscale processes in crystalline lead titanate, namely the field-driven dynamics of a planar ferroelectric domain wall, and the dynamics of an extensive lattice of coarse-grained electric dipoles. In the first case, AIGLE extends the reach of ab initio simulations to a regime of noise-driven motions not accessible to molecular dynamics. In the second case, AIGLE deals with an extensive set of collective variables by adopting a local approximation for the memory kernel and retaining only short-range noise correlations. The scheme is computationally more efficient than molecular dynamics by several orders of magnitude, and mimics the microscopic dynamics at low frequencies where it reproduces accurately the dominant far-infrared absorption frequency.

physics.comp-ph↗

arXiv2024

Anchor function: a type of benchmark functions for studying language models

Understanding transformer-based language models is becoming increasingly crucial, particularly as they play pivotal roles in advancing towards artificial general intelligence. However, language model research faces significant challenges, especially for academic research groups with constrained resources. These challenges include complex data structures, unknown target functions, high computational costs and memory requirements, and a lack of interpretability in the inference process, etc. Drawing a parallel to the use of simple models in scientific research, we propose the concept of an anchor function. This is a type of benchmark function designed for studying language models in learning tasks that follow an "anchor-key" pattern. By utilizing the concept of an anchor function, we can construct a series of functions to simulate various language tasks. The anchor function plays a role analogous to that of mice in diabetes research, particularly suitable for academic research. We demonstrate the utility of the anchor function with an example, revealing two basic operations by attention structures in language models: shifting tokens and broadcasting one token from one position to many positions. These operations are also commonly observed in large language models. The anchor function framework, therefore, opens up a series of valuable and accessible research questions for further exploration, especially for theoretical study.

cs.CL↗

arXiv2023

Hybrid Auxiliary Field Quantum Monte Carlo for Molecular Systems

We propose a quantum Monte Carlo approach to solve the ground state many-body Schrodinger equation for the electronic ground state. The method combines optimization from variational Monte Carlo and propagation from auxiliary field quantum Monte Carlo, in a way that significantly alleviates the sign problem. In application to molecular systems, we obtain highly accurate results for configurations dominated by either dynamic or static electronic correlation.

physics.comp-ph↗

arXiv2023

DeePMD-kit v2: A software package for Deep Potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments.

physics.chem-ph↗

arXiv2023

The Random Feature Method for Time-dependent Problems

We present a framework for solving time-dependent partial differential equations (PDEs) in the spirit of the random feature method. The numerical solution is constructed using a space-time partition of unity and random feature functions. Two different ways of constructing the random feature functions are investigated: feature functions that treat the spatial and temporal variables (STC) on the same footing, or functions that are the product of two random feature functions depending on spatial and temporal variables separately (SoV). Boundary and initial conditions are enforced by penalty terms. We also study two ways of solving the resulting least-squares problem: the problem is solved as a whole or solved using the block time-marching strategy. The former is termed ``the space-time random feature method'' (ST-RFM). Numerical results for a series of problems show that the proposed method, i.e. ST-RFM with STC and ST-RFM with SoV, have spectral accuracy in both space and time. In addition, ST-RFM only requires collocation points, not a mesh. This is important for solving problems with complex geometry. We demonstrate this by using ST-RFM to solve a two-dimensional wave equation over a complex domain. The two strategies differ significantly in terms of the behavior in time. In the case when block time-marching is used, we prove a lower error bound that shows an exponentially growing factor with respect to the number of blocks in time. For ST-RFM, we prove an upper bound with a sublinearly growing factor with respect to the number of subdomains in time. These estimates are also confirmed by numerical results.

math.NA↗

arXiv2023

MAC: A unified framework boosting low resource automatic speech recognition

We propose a unified framework for low resource automatic speech recognition tasks named meta audio concatenation (MAC). It is easy to implement and can be carried out in extremely low resource environments. Mathematically, we give a clear description of MAC framework from the perspective of bayesian sampling. In this framework, we leverage a novel concatenative synthesis text-to-speech system to boost the low resource ASR task. By the concatenative synthesis text-to-speech system, we can integrate language pronunciation rules and adjust the TTS process. Furthermore, we propose a broad notion of meta audio set to meet the modeling needs of different languages and different scenes when using the system. Extensive experiments have demonstrated the great effectiveness of MAC on low resource ASR tasks. For CTC greedy search, CTC prefix, attention, and attention rescoring decode mode in Cantonese ASR task, Taiwanese ASR task, and Japanese ASR task the MAC method can reduce the CER by more than 15\%. Furthermore, in the ASR task, MAC beats wav2vec2 (with fine-tuning) on common voice datasets of Cantonese and gets really competitive results on common voice datasets of Taiwanese and Japanese. Among them, it is worth mentioning that we achieve a \textbf{10.9\%} character error rate (CER) on the common voice Cantonese ASR task, bringing about \textbf{30\%} relative improvement compared to the wav2vec2 (with fine-tuning).

cs.CL↗

arXiv2022

A deep learning-based model reduction (DeePMR) method for simplifying chemical kinetics

A deep learning-based model reduction (DeePMR) method for simplifying chemical kinetics is proposed and validated using high-temperature auto-ignitions, perfectly stirred reactors (PSR), and one-dimensional freely propagating flames of n-heptane/air mixtures. The mechanism reduction is modeled as an optimization problem on Boolean space, where a Boolean vector, each entry corresponding to a species, represents a reduced mechanism. The optimization goal is to minimize the reduced mechanism size given the error tolerance of a group of pre-selected benchmark quantities. The key idea of the DeePMR is to employ a deep neural network (DNN) to formulate the objective function in the optimization problem. In order to explore high dimensional Boolean space efficiently, an iterative DNN-assisted data sampling and DNN training procedure are implemented. The results show that DNN-assistance improves sampling efficiency significantly, selecting only $10^5$ samples out of $10^{34}$ possible samples for DNN to achieve sufficient accuracy. The results demonstrate the capability of the DNN to recognize key species and reasonably predict reduced mechanism performance. The well-trained DNN guarantees the optimal reduced mechanism by solving an inverse optimization problem. By comparing ignition delay times, laminar flame speeds, temperatures in PSRs, the resulting skeletal mechanism has fewer species (45 species) but the same level of accuracy as the skeletal mechanism (56 species) obtained by the Path Flux Analysis (PFA) method. In addition, the skeletal mechanism can be further reduced to 28 species if only considering atmospheric, near-stoichiometric conditions (equivalence ratio between 0.6 and 1.2). The DeePMR provides an innovative way to perform model reduction and demonstrates the great potential of data-driven methods in the combustion area.

cs.LG↗

arXiv2022

A multi-scale sampling method for accurate and robust deep neural network to predict combustion chemical kinetics

Machine learning has long been considered as a black box for predicting combustion chemical kinetics due to the extremely large number of parameters and the lack of evaluation standards and reproducibility. The current work aims to understand two basic questions regarding the deep neural network (DNN) method: what data the DNN needs and how general the DNN method can be. Sampling and preprocessing determine the DNN training dataset, further affect DNN prediction ability. The current work proposes using Box-Cox transformation (BCT) to preprocess the combustion data. In addition, this work compares different sampling methods with or without preprocessing, including the Monte Carlo method, manifold sampling, generative neural network method (cycle-GAN), and newly-proposed multi-scale sampling. Our results reveal that the DNN trained by the manifold data can capture the chemical kinetics in limited configurations but cannot remain robust toward perturbation, which is inevitable for the DNN coupled with the flow field. The Monte Carlo and cycle-GAN samplings can cover a wider phase space but fail to capture small-scale intermediate species, producing poor prediction results. A three-hidden-layer DNN, based on the multi-scale method without specific flame simulation data, allows predicting chemical kinetics in various scenarios and being stable during the temporal evolutions. This single DNN is readily implemented with several CFD codes and validated in various combustors, including (1). zero-dimensional autoignition, (2). one-dimensional freely propagating flame, (3). two-dimensional jet flame with triple-flame structure, and (4). three-dimensional turbulent lifted flames. The results demonstrate the satisfying accuracy and generalization ability of the pre-trained DNN. The Fortran and Python versions of DNN and example code are attached in the supplementary for reproducibility.

physics.chem-ph↗

arXiv2022

Bridging Traditional and Machine Learning-based Algorithms for Solving PDEs: The Random Feature Method

One of the oldest and most studied subject in scientific computing is algorithms for solving partial differential equations (PDEs). A long list of numerical methods have been proposed and successfully used for various applications. In recent years, deep learning methods have shown their superiority for high-dimensional PDEs where traditional methods fail. However, for low dimensional problems, it remains unclear whether these methods have a real advantage over traditional algorithms as a direct solver. In this work, we propose the random feature method (RFM) for solving PDEs, a natural bridge between traditional and machine learning-based algorithms. RFM is based on a combination of well-known ideas: 1. representation of the approximate solution using random feature functions; 2. collocation method to take care of the PDE; 3. the penalty method to treat the boundary conditions, which allows us to treat the boundary condition and the PDE in the same footing. We find it crucial to add several additional components including multi-scale representation and rescaling the weights in the loss function. We demonstrate that the method exhibits spectral accuracy and can compete with traditional solvers in terms of both accuracy and efficiency. In addition, we find that RFM is particularly suited for complex problems with complex geometry, where both traditional and machine learning-based algorithms encounter difficulties.

math.NA↗

arXiv2022

Empowering Optimal Control with Machine Learning: A Perspective from Model Predictive Control

Solving complex optimal control problems have confronted computational challenges for a long time. Recent advances in machine learning have provided us with new opportunities to address these challenges. This paper takes model predictive control, a popular optimal control method, as the primary example to survey recent progress that leverages machine learning techniques to empower optimal control solvers. We also discuss some of the main challenges encountered when applying machine learning to develop more robust optimal control algorithms.

math.OC↗

arXiv2022

DeePN$^2$: A deep learning-based non-Newtonian hydrodynamic model

A long standing problem in the modeling of non-Newtonian hydrodynamics of polymeric flows is the availability of reliable and interpretable hydrodynamic models that faithfully encode the underlying micro-scale polymer dynamics. The main complication arises from the long polymer relaxation time, the complex molecular structure and heterogeneous interaction. DeePN$^2$, a deep learning-based non-Newtonian hydrodynamic model, has been proposed and has shown some success in systematically passing the micro-scale structural mechanics information to the macro-scale hydrodynamics for suspensions with simple polymer conformation and bond potential. The model retains a multi-scaled nature by mapping the polymer configurations into a set of symmetry-preserving macro-scale features. The extended constitutive laws for these macro-scale features can be directly learned from the kinetics of their micro-scale counterparts. In this paper, we develop DeePN$^2$ using more complex micro-structural models. We show that DeePN$^2$ can faithfully capture the broadly overlooked viscoelastic differences arising from the specific molecular structural mechanics without human intervention.

physics.comp-ph↗

arXiv2022

A Machine Learning Enhanced Algorithm for the Optimal Landing Problem

We propose a machine learning enhanced algorithm for solving the optimal landing problem. Using Pontryagin's minimum principle, we derive a two-point boundary value problem for the landing problem. The proposed algorithm uses deep learning to predict the optimal landing time and a space-marching technique to provide good initial guesses for the boundary value problem solver. The performance of the proposed method is studied using the quadrotor example, a reasonably high dimensional and strongly nonlinear system. Drastic improvement in reliability and efficiency is observed.

math.OC↗

arXiv2022

Deep Potentials for Materials Science

To fill the gap between accurate (and expensive) ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials, a new class of descriptions of atomic interactions has emerged and been widely applied; i.e., machine learning potentials (MLPs). One recently developed type of MLP is the Deep Potential (DP) method. In this review, we provide an introduction to DP methods in computational materials science. The theory underlying the DP method is presented along with a step-by-step introduction to their development and use. We also review materials applications of DPs in a wide range of materials systems. The DP Library provides a platform for the development of DPs and a database of extant DPs. We discuss the accuracy and efficiency of DPs compared with ab initio methods and empirical potentials.

cond-mat.mtrl-sci↗

arXiv2022

DeepHAM: A Global Solution Method for Heterogeneous Agent Models with Aggregate Shocks

An efficient, reliable, and interpretable global solution method, the Deep learning-based algorithm for Heterogeneous Agent Models (DeepHAM), is proposed for solving high dimensional heterogeneous agent models with aggregate shocks. The state distribution is approximately represented by a set of optimal generalized moments. Deep neural networks are used to approximate the value and policy functions, and the objective is optimized over directly simulated paths. In addition to being an accurate global solver, this method has three additional features. First, it is computationally efficient in solving complex heterogeneous agent models, and it does not suffer from the curse of dimensionality. Second, it provides a general and interpretable representation of the distribution over individual states, which is crucial in addressing the classical question of whether and how heterogeneity matters in macroeconomics. Third, it solves the constrained efficiency problem as easily as it solves the competitive equilibrium, which opens up new possibilities for studying optimal monetary and fiscal policies in heterogeneous agent models with aggregate shocks.

econ.GN↗

arXiv2022

A deep potential model with long-range electrostatic interactions

Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make possible molecular simulations with the accuracy of quantum mechanical density functional theory, at a cost only moderately higher than that of empirical force fields. However, the majority of these models lack explicit long-range interactions and fail to describe properties that derive from the Coulombic tail of the forces. To overcome this limitation we extend the DP model by approximating the long-range electrostatic interaction between ions (nuclei+core electrons) and valence electrons with that of distributions of spherical Gaussian charges located at ionic and electronic sites. The latter are rigorously defined in terms of the centers of the maximally localized Wannier distributions, whose dependence on the local atomic environment is modeled accurately by a deep neural network. In the deep potential long-range (DPLR) model, the electrostatic energy of the Gaussian charge system is added to short-range interactions that are represented as in the standard DP model. The resulting potential energy surface is smooth and possesses analytical forces and virial. Missing effects in the standard DP scheme are recovered, improving on accuracy and predictive power. By including long-range electrostatics, DPLR correctly extrapolates to large systems the potential energy surface learned from quantum mechanical calculations on smaller systems. We illustrate the approach with three examples, the potential energy profile of the water dimer, the free energy of interaction of a water molecule with a liquid water slab, and the phonon dispersion curves of the NaCl crystal.

physics.chem-ph↗