arXiv subjects

Duo Zhang

Publications and source records attributed to Duo Zhang.

At least 55 records · Page 3Linked to original sources

arXiv2024

Efficient and Precise Force Field Optimization for Biomolecules Using DPA-2

Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant challenges in accurately representing novel molecules and complex chemical environments due to the labor-intensive process of manually setting optimization parameters and the high computational cost of quantum mechanical calculations. To overcome these difficulties, we fine-tuned a high-accuracy DPA-2 pre-trained model and applied it to optimize force field parameters on-the-fly, significantly reducing computational costs. Our method combines this fine-tuned DPA-2 model with a node-embedding-based similarity metric, allowing seamless augmentation to new chemical species without manual intervention. We applied this process to the TYK2 inhibitor and PTP1B systems and demonstrated its effectiveness through the improvement of free energy perturbation calculation results. This advancement contributes valuable insights and tools for the computational chemistry community.

physics.chem-ph↗

arXiv2024

Machine-Learning-Based Interatomic Potentials for Group IIB to VIA Semiconductors: Towards a Universal Model

Rapid advancements in machine-learning methods have led to the emergence of machine-learning-based interatomic potentials as a new cutting-edge tool for simulating large systems with ab initio accuracy. Still, the community awaits universal inter-atomic models that can be applied to a wide range of materials without tuning neural network parameters. We develop a unified deep-learning inter-atomic potential (the DPA-Semi model) for 19 semiconductors ranging from group IIB to VIA, including Si, Ge, SiC, BAs, BN, AlN, AlP, AlAs, InP, InAs, InSb, GaN, GaP, GaAs, CdTe, InTe, CdSe, ZnS, and CdS. In addition, independent deep potential models for each semiconductor are prepared for detailed comparison. The training data are obtained by performing density functional theory calculations with numerical atomic orbitals basis sets to reduce the computational costs. We systematically compare various properties of the solid and liquid phases of semiconductors between different machine-learning models. We conclude that the DPA-Semi model achieves GGA exchange-correlation functional quality accuracy and can be regarded as a pre-trained model towards a universal model to study group IIB to VIA semiconductors.

cond-mat.mtrl-sci↗

arXiv2024

Toward Holistic Planning and Control Optimization for Dual-Arm Rearrangement

Long-horizon task and motion planning (TAMP) is notoriously difficult to solve, let alone optimally, due to the tight coupling between the interleaved (discrete) task and (continuous) motion planning phases, where each phase on its own is frequently an NP-hard or even PSPACE-hard computational challenge. In this study, we tackle the even more challenging goal of jointly optimizing task and motion plans for a real dual-arm system in which the two arms operate in close vicinity to solve highly constrained tabletop multi-object rearrangement problems. Toward that, we construct a tightly integrated planning and control optimization pipeline, Makespan-Optimized Dual-Arm Planner (MODAP) that combines novel sampling techniques for task planning with state-of-the-art trajectory optimization techniques. Compared to previous state-of-the-art, MODAP produces task and motion plans that better coordinate a dual-arm system, delivering significantly improved execution time improvements while simultaneously ensuring that the resulting time-parameterized trajectory conforms to specified acceleration and jerk limits.

cs.RO↗

arXiv2023

Universal interatomic potential for perovskite oxides

With their celebrated structural and chemical flexibility, perovskite oxides have served as a highly adaptable material platform for exploring emergent phenomena arising from the interplay between different degrees of freedom. Molecular dynamics (MD) simulations leveraging classical force fields, commonly depicted as parameterized analytical functions, have made significant contributions in elucidating the atomistic dynamics and structural properties of crystalline solids including perovskite oxides. However, the force fields currently available for solids are rather specific and offer limited transferability, making it time-consuming to use MD to study new materials systems since a new force field must be parameterized and tested first. The lack of a generalized force field applicable to a broad spectrum of solid materials hinders the facile deployment of MD in computer-aided materials discovery (CAMD). Here, by utilizing a deep-neural network with a self-attention scheme, we have developed a unified force field that enables MD simulations of perovskite oxides involving 14 metal elements and conceivably their solid solutions with arbitrary compositions. Notably, isobaric-isothermal ensemble MD simulations with this model potential accurately predict the experimental phase transition sequences for several markedly different ferroelectric oxides, including a 6-element ternary solid solution, Pb(In$_{1/2}$Nb$_{1/2}$)O$_3$--Pb(Mg$_{1/3}$Nb$_{2/3}$)O$_3$--PbTiO$_3$. We believe the universal interatomic potential along with the training database, proposed regression tests, and the auto-testing workflow, all released publicly, will pave the way for a systematic improvement and extension of a unified force field for solids, potentially heralding a new era in CAMD.

cond-mat.mtrl-sci↗

arXiv2023

Provably Robust Semi-Infinite Program Under Collision Constraints via Subdivision

We present a semi-infinite program (SIP) solver for trajectory optimizations of general articulated robots. These problems are more challenging than standard Nonlinear Program (NLP) by involving an infinite number of non-convex, collision constraints. Prior SIP solvers based on constraint sampling cannot guarantee the satisfaction of all constraints. Instead, our method uses a conservative bound on articulated body motions to ensure the solution feasibility throughout the optimization procedure. We further use subdivision to adaptively reduce the error in conservative motion estimation. Combined, we prove that our SIP solver guarantees feasibility while approaches the critical point of SIP problems up to arbitrary user-provided precision. We have verified our method on a row of trajectory optimization problems involving industrial robot arms and UAVs, where our method can generate collision-free, locally optimal trajectories within a couple minutes.

cs.RO↗

arXiv2023

A Multi-Scale Spatial Transformer U-Net for Simultaneously Automatic Reorientation and Segmentation of 3D Nuclear Cardiac Images

Accurate reorientation and segmentation of the left ventricular (LV) is essential for the quantitative analysis of myocardial perfusion imaging (MPI), in which one critical step is to reorient the reconstructed transaxial nuclear cardiac images into standard short-axis slices for subsequent image processing. Small-scale LV myocardium (LV-MY) region detection and the diverse cardiac structures of individual patients pose challenges to LV segmentation operation. To mitigate these issues, we propose an end-to-end model, named as multi-scale spatial transformer UNet (MS-ST-UNet), that involves the multi-scale spatial transformer network (MSSTN) and multi-scale UNet (MSUNet) modules to perform simultaneous reorientation and segmentation of LV region from nuclear cardiac images. The proposed method is trained and tested using two different nuclear cardiac image modalities: 13N-ammonia PET and 99mTc-sestamibi SPECT. We use a multi-scale strategy to generate and extract image features with different scales. Our experimental results demonstrate that the proposed method significantly improves the reorientation and segmentation performance. This joint learning framework promotes mutual enhancement between reorientation and segmentation tasks, leading to cutting edge performance and an efficient image processing workflow. The proposed end-to-end deep network has the potential to reduce the burden of manual delineation for cardiac images, thereby providing multimodal quantitative analysis assistance for physicists.

eess.IV↗

arXiv2023

Deep learning-based flow disaggregation for short-term hydropower plant operations

High temporal resolution data plays a vital role in effective short-term hydropower plant operations. In the majority of the Norwegian hydropower system, inflow data is predominantly collected at daily resolutions through measurement installations. However, for enhanced precision in managerial decision-making within hydropower plants, hydrological data with intraday resolutions, such as hourly data, are often indispensable. To address this gap, time series disaggregation utilizing deep learning emerges as a promising tool. In this study, we propose a deep learning-based time series disaggregation model to derive hourly inflow data from daily inflow data for short-term hydropower plant operations. Our preliminary results demonstrate the applicability of our method, with scope for further improvements.

eess.SP↗

arXiv2023

DPA-1: Pretraining of Attention-based Deep Potential Model for Molecular Simulation

Machine learning assisted modeling of the inter-atomic potential energy surface (PES) is revolutionizing the field of molecular simulation. With the accumulation of high-quality electronic structure data, a model that can be pretrained on all available data and finetuned on downstream tasks with a small additional effort would bring the field to a new stage. Here we propose DPA-1, a Deep Potential model with a novel attention mechanism, which is highly effective for representing the conformation and chemical spaces of atomic systems and learning the PES. We tested DPA-1 on a number of systems and observed superior performance compared with existing benchmarks. When pretrained on large-scale datasets containing 56 elements, DPA-1 can be successfully applied to various downstream tasks with a great improvement of sample efficiency. Surprisingly, for different elements, the learned type embedding parameters form a $spiral$ in the latent space and have a natural correspondence with their positions on the periodic table, showing interesting interpretability of the pretrained DPA-1 model.

physics.chem-ph↗

arXiv2023

Dynamic Grouping for Climate Change Negotiation: Facilitating Cooperation and Balancing Interests through Effective Strategies

The current framework for climate change negotiation models presents several limitations that warrant further research and development. In this track, we discuss mainly two key areas for improvement, focusing on the geographical impacts and utility framework. In the aspects of geographical impacts, We explore five critical aspects: (1) the shift from local to global impact, (2) variability in climate change effects across regions, (3) heterogeneity in geographical location and political structures, and (4) collaborations between adjacent nations, (5) the importance of including historical and cultural factors influencing climate negotiations. Furthermore, we emphasize the need to refine the utility and rewards framework to reduce the homogeneity and the level of overestimating the climate mitigation by integrating the positive effects of saving rates into the reward function and heterogeneity among all regions. By addressing these limitations, we hope to enhance the accuracy and effectiveness of climate change negotiation models, enabling policymakers and stakeholders to devise targeted and appropriate strategies to tackle climate change at both regional and global levels.

cs.CY↗

arXiv2023

Dynamic Grouping for Climate Change Negotiation: Facilitating Cooperation and Balancing Interests through Effective Strategies

In this paper, we propose a dynamic grouping negotiation model for climate mitigation based on real-world business and political negotiation protocols. Within the AI4GCC competition framework, we develop a three-stage process: group formation and updates, intra-group negotiation, and inter-group negotiation. Our model promotes efficient and effective cooperation between various stakeholders to achieve global climate change objectives. By implementing a group-forming method and group updating strategy, we address the complexities and imbalances in multi-region climate negotiations. Intra-group negotiations ensure that all members contribute to mitigation efforts, while inter-group negotiations use the proposal-evaluation framework to set mitigation and savings rates. We demonstrate our negotiation model within the RICE-N framework, illustrating a promising approach for facilitating international cooperation on climate change mitigation.

cs.CY↗

arXiv2023

Understanding Persistent-Memory Related Issues in the Linux Kernel

Persistent memory (PM) technologies have inspired a wide range of PM-based system optimizations. However, building correct PM-based systems is difficult due to the unique characteristics of PM hardware. To better understand the challenges as well as the opportunities to address them, this paper presents a comprehensive study of PM-related issues in the Linux kernel. By analyzing 1,553 PM-related kernel patches in-depth and conducting experiments on reproducibility and tool extension, we derive multiple insights in terms of PM patch categories, PM bug patterns, consequences, fix strategies, triggering conditions, and remedy solutions. We hope our results could contribute to the development of robust PM-based storage systems

cs.OS↗

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↗

arXiv2021

Planning of Power Grasps Using Infinite Program Under Complementary Constraints

We propose an optimization-based approach to plan power grasps. Central to our method is a reformulation of grasp planning as an infinite program under complementary constraints (IPCC), which allows contacts to happen between arbitrary pairs of points on the object and the robot gripper. We show that IPCC can be reduced to a conventional finite-dimensional nonlinear program (NLP) using a kernel-integral relaxation. Moreover, the values and Jacobian matrices of the kernel-integral can be evaluated efficiently using a modified Fast Multipole Method (FMM). We further guarantee that the planned grasps are collision-free using primal barrier penalties. We demonstrate the effectiveness, robustness, and efficiency of our grasp planner on a row of challenging 3D objects and high-DOF grippers, such as Barrett Hand and Shadow Hand, where our method achieves superior grasp qualities over competitors.

cs.RO↗

arXiv2021

On Failure Diagnosis of the Storage Stack

Diagnosing storage system failures is challenging even for professionals. One example is the "When Solid State Drives Are Not That Solid" incident occurred at Algolia data center, where Samsung SSDs were mistakenly blamed for failures caused by a Linux kernel bug. With the system complexity keeps increasing, such obscure failures will likely occur more often. As one step to address the challenge, we present our on-going efforts called X-Ray. Different from traditional methods that focus on either the software or the hardware, X-Ray leverages virtualization to collects events across layers, and correlates them to generate a correlation tree. Moreover, by applying simple rules, X-Ray can highlight critical nodes automatically. Preliminary results based on 5 failure cases shows that X-Ray can effectively narrow down the search space for failures.

cs.OS↗

arXiv2021

Nonreciprocal high-order sidebands induced by magnon Kerr nonlinearity

We propose an effective approach for creating robust nonreciprocity of high-order sidebands, including the first-, second- and third-order sidebands, at microwave frequencies. This approach relies on magnon Kerr nonlinearity in a cavity magnonics system composed of two microwave cavities and one yttrium iron garnet (YIG) sphere. By manipulating the driving power applied on YIG and the frequency detuning between the magnon mode in YIG and the driving field, the effective Kerr nonlinearity can be strengthened, thereby inducing strong transmission non-reciprocity. More interestingly, we find the higher the sideband order, the stronger the transmission nonreciprocity marked by the higher isolation ratio in the optimal detuning regime. Such a series of equally-spaced high-order sidebands have potential applications in frequency comb-like precision measurement, besides structuring high-performance on-chip nonreciprocal devices.

physics.app-ph↗

arXiv2018

Exploiting Capacity of Sewer System Using Unsupervised Learning Algorithms Combined with Dimensionality Reduction

Exploiting capacity of sewer system using decentralized control is a cost effective mean of minimizing the overflow. Given the size of the real sewer system, exploiting all the installed control structures in the sewer pipes can be challenging. This paper presents a divide and conquer solution to implement decentralized control measures based on unsupervised learning algorithms. A sewer system is first divided into a number of subcatchments. A series of natural and built factors that have the impact on sewer system performance is then collected. Clustering algorithms are then applied to grouping subcatchments with similar hydraulic hydrologic characteristics. Following which, principal component analysis is performed to interpret the main features of sub-catchment groups and identify priority control locations. Overflows under different control scenarios are compared based on the hydraulic model. Simulation results indicate that priority control applied to the most suitable cluster could bring the most profitable result.

cs.LG↗

arXiv2018

Enhancing Operation of a Sewage Pumping Station for Inter Catchment Wastewater Transfer by Using Deep Learning and Hydraulic Model

This paper presents a novel Inter Catchment Wastewater Transfer (ICWT) method for mitigating sewer overflow. The ICWT aims at balancing the spatial mismatch of sewer flow and treatment capacity of Wastewater Treatment Plant (WWTP), through collaborative operation of sewer system facilities. Using a hydraulic model, the effectiveness of ICWT is investigated in a sewer system in Drammen, Norway. Concerning the whole system performance, we found that the Søren Lemmich pump station plays a vital role in the ICWT framework. To enhance the operation of this pump station, it is imperative to construct a multi-step ahead water level prediction model. Hence, one of the most promising artificial intelligence techniques, Long Short Term Memory (LSTM), is employed to undertake this task. Experiments demonstrated that LSTM is superior to Gated Recurrent Unit (GRU), Recurrent Neural Network (RNN), Feed-forward Neural Network (FFNN) and Support Vector Regression (SVR).

cs.CY↗

arXiv2018

DeepCSO: Forecasting of Combined Sewer Overflow at a Citywide Level using Multi-task Deep Learning

Combined Sewer Overflow (CSO) is a major problem to be addressed by many cities. Understanding the behavior of sewer system through proper urban hydrological models is an effective method of enhancing sewer system management. Conventional deterministic methods, which heavily rely on physical principles, is inappropriate for real-time purpose due to their expensive computation. On the other hand, data-driven methods have gained huge interests, but most studies only focus on modeling a single component of the sewer system and supply information at a very abstract level. In this paper, we proposed the DeepCSO model, which aims at forecasting CSO events from multiple CSO structures simultaneously in near real time at a citywide level. The proposed model provided an intermediate methodology that combines the flexibility of data-driven methods and the rich information contained in deterministic methods while avoiding the drawbacks of these two methods. A comparison of the results demonstrated that the deep learning based multi-task model is superior to the traditional methods.

cs.CY↗