arXiv subjects

Lipeng Wan

Publications and source records attributed to Lipeng Wan.

33 records · Page 2Linked to original sources

arXiv2024

Spatiotemporally adaptive compression for scientific dataset with feature preservation -- a case study on simulation data with extreme climate events analysis

Scientific discoveries are increasingly constrained by limited storage space and I/O capacities. For time-series simulations and experiments, their data often need to be decimated over timesteps to accommodate storage and I/O limitations. In this paper, we propose a technique that addresses storage costs while improving post-analysis accuracy through spatiotemporal adaptive, error-controlled lossy compression. We investigate the trade-off between data precision and temporal output rates, revealing that reducing data precision and increasing timestep frequency lead to more accurate analysis outcomes. Additionally, we integrate spatiotemporal feature detection with data compression and demonstrate that performing adaptive error-bounded compression in higher dimensional space enables greater compression ratios, leveraging the error propagation theory of a transformation-based compressor. To evaluate our approach, we conduct experiments using the well-known E3SM climate simulation code and apply our method to compress variables used for cyclone tracking. Our results show a significant reduction in storage size while enhancing the quality of cyclone tracking analysis, both quantitatively and qualitatively, in comparison to the prevalent timestep decimation approach. Compared to three state-of-the-art lossy compressors lacking feature preservation capabilities, our adaptive compression framework improves perfectly matched cases in TC tracking by 26.4-51.3% at medium compression ratios and by 77.3-571.1% at large compression ratios, with a merely 5-11% computational overhead.

cs.CV↗

arXiv2023

High-performance Data Management for Whole Slide Image Analysis in Digital Pathology

When dealing with giga-pixel digital pathology in whole-slide imaging, a notable proportion of data records holds relevance during each analysis operation. For instance, when deploying an image analysis algorithm on whole-slide images (WSI), the computational bottleneck often lies in the input-output (I/O) system. This is particularly notable as patch-level processing introduces a considerable I/O load onto the computer system. However, this data management process could be further paralleled, given the typical independence of patch-level image processes across different patches. This paper details our endeavors in tackling this data access challenge by implementing the Adaptable IO System version 2 (ADIOS2). Our focus has been constructing and releasing a digital pathology-centric pipeline using ADIOS2, which facilitates streamlined data management across WSIs. Additionally, we've developed strategies aimed at curtailing data retrieval times. The performance evaluation encompasses two key scenarios: (1) a pure CPU-based image analysis scenario ("CPU scenario"), and (2) a GPU-based deep learning framework scenario ("GPU scenario"). Our findings reveal noteworthy outcomes. Under the CPU scenario, ADIOS2 showcases an impressive two-fold speed-up compared to the brute-force approach. In the GPU scenario, its performance stands on par with the cutting-edge GPU I/O acceleration framework, NVIDIA Magnum IO GPU Direct Storage (GDS). From what we know, this appears to be among the initial instances, if any, of utilizing ADIOS2 within the field of digital pathology. The source code has been made publicly available at https://github.com/hrlblab/adios.

eess.IV↗

arXiv2023

An Accelerated Pipeline for Multi-label Renal Pathology Image Segmentation at the Whole Slide Image Level

Deep-learning techniques have been used widely to alleviate the labour-intensive and time-consuming manual annotation required for pixel-level tissue characterization. Our previous study introduced an efficient single dynamic network - Omni-Seg - that achieved multi-class multi-scale pathological segmentation with less computational complexity. However, the patch-wise segmentation paradigm still applies to Omni-Seg, and the pipeline is time-consuming when providing segmentation for Whole Slide Images (WSIs). In this paper, we propose an enhanced version of the Omni-Seg pipeline in order to reduce the repetitive computing processes and utilize a GPU to accelerate the model's prediction for both better model performance and faster speed. Our proposed method's innovative contribution is two-fold: (1) a Docker is released for an end-to-end slide-wise multi-tissue segmentation for WSIs; and (2) the pipeline is deployed on a GPU to accelerate the prediction, achieving better segmentation quality in less time. The proposed accelerated implementation reduced the average processing time (at the testing stage) on a standard needle biopsy WSI from 2.3 hours to 22 minutes, using 35 WSIs from the Kidney Tissue Atlas (KPMP) Datasets. The source code and the Docker have been made publicly available at https://github.com/ddrrnn123/Omni-Seg.

eess.IV↗

arXiv2023

MMRDN: Consistent Representation for Multi-View Manipulation Relationship Detection in Object-Stacked Scenes

Manipulation relationship detection (MRD) aims to guide the robot to grasp objects in the right order, which is important to ensure the safety and reliability of grasping in object stacked scenes. Previous works infer manipulation relationship by deep neural network trained with data collected from a predefined view, which has limitation in visual dislocation in unstructured environments. Multi-view data provide more comprehensive information in space, while a challenge of multi-view MRD is domain shift. In this paper, we propose a novel multi-view fusion framework, namely multi-view MRD network (MMRDN), which is trained by 2D and 3D multi-view data. We project the 2D data from different views into a common hidden space and fit the embeddings with a set of Von-Mises-Fisher distributions to learn the consistent representations. Besides, taking advantage of position information within the 3D data, we select a set of $K$ Maximum Vertical Neighbors (KMVN) points from the point cloud of each object pair, which encodes the relative position of these two objects. Finally, the features of multi-view 2D and 3D data are concatenated to predict the pairwise relationship of objects. Experimental results on the challenging REGRAD dataset show that MMRDN outperforms the state-of-the-art methods in multi-view MRD tasks. The results also demonstrate that our model trained by synthetic data is capable to transfer to real-world scenarios.

cs.CV↗

arXiv2022

Pixel super-resolution interference pattern sensing via the aliasing effect for laser frequency metrology

The superposition of several optical beams with large mutual angles results in sub-micrometer periodic patterns with a complex intensity, phase and polarization structure. For high-resolution imaging thereof, one often employs optical super-resolution methods such as scanning nano-particle imaging. Here, we report that by using a conventional arrayed image sensor in combination with 2D Fourier analysis, the periodicities of light fields much smaller than the pixel size can be resolved in a simple and compact setup, with a resolution far beyond the Nyquist limit set by the pixel size. We demonstrate the ability to resolve periodicities with spatial frequencies of ~3/$μ$m, 15 times higher than the pixel sampling frequency of 0.188/$μ$m. This is possible by analyzing high-quality Fourier aliases in the first Brillouin zone. In order to obtain the absolute spatial frequencies of the interference patterns, we show that simple rotation of the image sensor is sufficient, which modulates the effective pixel size and allows determination of the original Brillouin zone. Based on this method, we demonstrate wavelength sensing with a resolving power beyond 100,000 without any special equipment

physics.optics↗

arXiv2022

Greedy based Value Representation for Optimal Coordination in Multi-agent Reinforcement Learning

Due to the representation limitation of the joint Q value function, multi-agent reinforcement learning methods with linear value decomposition (LVD) or monotonic value decomposition (MVD) suffer from relative overgeneralization. As a result, they can not ensure optimal consistency (i.e., the correspondence between individual greedy actions and the maximal true Q value). In this paper, we derive the expression of the joint Q value function of LVD and MVD. According to the expression, we draw a transition diagram, where each self-transition node (STN) is a possible convergence. To ensure optimal consistency, the optimal node is required to be the unique STN. Therefore, we propose the greedy-based value representation (GVR), which turns the optimal node into an STN via inferior target shaping and further eliminates the non-optimal STNs via superior experience replay. In addition, GVR achieves an adaptive trade-off between optimality and stability. Our method outperforms state-of-the-art baselines in experiments on various benchmarks. Theoretical proofs and empirical results on matrix games demonstrate that GVR ensures optimal consistency under sufficient exploration.

cs.MA↗

arXiv2022

Transitioning from file-based HPC workflows to streaming data pipelines with openPMD and ADIOS2

This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely-coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightly-coupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

cs.DC↗

arXiv2021

Multi-Agent Intention Sharing via Leader-Follower Forest

Intention sharing is crucial for efficient cooperation under partially observable environments in multi-agent reinforcement learning (MARL). However, message deceiving, i.e., a mismatch between the propagated intentions and the final decisions, may happen when agents change strategies simultaneously according to received intentions. Message deceiving leads to potential miscoordination and difficulty for policy learning. This paper proposes the leader-follower forest (LFF) to learn the hierarchical relationship between agents based on interdependencies, achieving one-sided intention sharing in multi-agent communication. By limiting the flowings of intentions through directed edges, intention sharing via LFF (IS-LFF) can eliminate message deceiving effectively and achieve better coordination. In addition, a twostage learning algorithm is proposed to train the forest and the agent network. We evaluate IS-LFF on multiple partially observable MARL benchmarks, and the experimental results show that our method outperforms state-of-the-art communication algorithms.

cs.MA↗

arXiv2021

Improving I/O Performance for Exascale Applications through Online Data Layout Reorganization

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based on particle-mesh methods and use advanced algorithms, especially dynamic load-balancing and mesh-refinement, to achieve high performance on Exascale machines. Yet, as such algorithms improve parallel application efficiency, they raise new challenges for I/O logic due to their irregular and dynamic data distributions. Thus, while the enormous data rates of Exascale simulations already challenge existing file system write strategies, the need for efficient read and processing of generated data introduces additional constraints on the data layout strategies that can be used when writing data to secondary storage. We review these I/O challenges and introduce two online data layout reorganization approaches for achieving good tradeoffs between read and write performance. We demonstrate the benefits of using these two approaches for the ECP particle-in-cell simulation WarpX, which serves as a motif for a large class of important Exascale applications. We show that by understanding application I/O patterns and carefully designing data layouts we can increase read performance by more than 80%.

cs.DC↗

arXiv2021

Scalable Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth makes it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data volumes: ideally, methods that can scale data volumes adaptively so as to enable negotiation of performance and fidelity tradeoffs in different situations. Multigrid-based hierarchical data representations hold promise as a solution to this problem, allowing for flexible conversion between different fidelities so that, for example, data can be created at high fidelity and then transferred or stored at lower fidelity via logically simple and mathematically sound operations. However, the effective use of such representations has been hindered until now by the relatively high costs of creating, accessing, reducing, and otherwise operating on such representations. We describe here highly optimized data refactoring kernels for GPU accelerators that enable efficient creation and manipulation of data in multigrid-based hierarchical forms. We demonstrate that our optimized design can achieve up to 264 TB/s aggregated data refactoring throughput -- 92% of theoretical peak -- on 1024 nodes of the Summit supercomputer. We showcase our optimized design by applying it to a large-scale scientific visualization workflow and the MGARD lossy compression software.

cs.DC↗

arXiv2021

Multi-agent Policy Optimization with Approximatively Synchronous Advantage Estimation

Cooperative multi-agent tasks require agents to deduce their own contributions with shared global rewards, known as the challenge of credit assignment. General methods for policy based multi-agent reinforcement learning to solve the challenge introduce differentiate value functions or advantage functions for individual agents. In multi-agent system, polices of different agents need to be evaluated jointly. In order to update polices synchronously, such value functions or advantage functions also need synchronous evaluation. However, in current methods, value functions or advantage functions use counter-factual joint actions which are evaluated asynchronously, thus suffer from natural estimation bias. In this work, we propose the approximatively synchronous advantage estimation. We first derive the marginal advantage function, an expansion from single-agent advantage function to multi-agent system. Further more, we introduce a policy approximation for synchronous advantage estimation, and break down the multi-agent policy optimization problem into multiple sub-problems of single-agent policy optimization. Our method is compared with baseline algorithms on StarCraft multi-agent challenges, and shows the best performance on most of the tasks.

cs.LG↗

arXiv2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data volumes: ideally, methods that can scale data volumes adaptively so as to enable negotiation of performance and fidelity tradeoffs in different situations. Multigrid-based hierarchical data representations hold promise as a solution to this problem, allowing for flexible conversion between different fidelities so that, for example, data can be created at high fidelity and then transferred or stored at lower fidelity via logically simple and mathematically sound operations. However, the effective use of such representations has been hindered until now by the relatively high costs of creating, accessing, reducing, and otherwise operating on such representations. We describe here highly optimized data refactoring kernels for GPU accelerators that enable efficient creation and manipulation of data in multigrid-based hierarchical forms. We demonstrate that our optimized design can achieve up to 250 TB/s aggregated data refactoring throughput -- 83% of theoretical peak -- on 1024 nodes of the Summit supercomputer. We showcase our optimized design by applying it to a large-scale scientific visualization workflow and the MGARD lossy compression software.

cs.DC↗

arXiv2020

MGARD+: Optimizing Multilevel Methods for Error-bounded Scientific Data Reduction

Data management is becoming increasingly important in dealing with the large amounts of data produced by large-scale scientific simulations and instruments. Existing multilevel compression algorithms offer a promising way to manage scientific data at scale, but may suffer from relatively low performance and reduction quality. In this paper, we propose MGARD+, a multilevel data reduction and refactoring framework drawing on previous multilevel methods, to achieve high-performance data decomposition and high-quality error-bounded lossy compression. Our contributions are four-fold: 1) We propose a level-wise coefficient quantization method, which uses different error tolerances to quantize the multilevel coefficients. 2) We propose an adaptive decomposition method which treats the multilevel decomposition as a preconditioner and terminates the decomposition process at an appropriate level. 3) We leverage a set of algorithmic optimization strategies to significantly improve the performance of multilevel decomposition/recomposition. 4) We evaluate our proposed method using four real-world scientific datasets and compare with several state-of-the-art lossy compressors. Experiments demonstrate that our optimizations improve the decomposition/recomposition performance of the existing multilevel method by up to 70X, and the proposed compression method can improve compression ratio by up to 2X compared with other state-of-the-art error-bounded lossy compressors under the same level of data distortion.

cs.DC↗

arXiv2020

FTRANS: Energy-Efficient Acceleration of Transformers using FPGA

In natural language processing (NLP), the "Transformer" architecture was proposed as the first transduction model replying entirely on self-attention mechanisms without using sequence-aligned recurrent neural networks (RNNs) or convolution, and it achieved significant improvements for sequence to sequence tasks. The introduced intensive computation and storage of these pre-trained language representations has impeded their popularity into computation and memory-constrained devices. The field-programmable gate array (FPGA) is widely used to accelerate deep learning algorithms for its high parallelism and low latency. However, the trained models are still too large to accommodate to an FPGA fabric. In this paper, we propose an efficient acceleration framework, Ftrans, for transformer-based large scale language representations. Our framework includes enhanced block-circulant matrix (BCM)-based weight representation to enable model compression on large-scale language representations at the algorithm level with few accuracy degradation, and an acceleration design at the architecture level. Experimental results show that our proposed framework significantly reduces the model size of NLP models by up to 16 times. Our FPGA design achieves 27.07x and 81x improvement in performance and energy efficiency compared to CPU, and up to 8.80x improvement in energy efficiency compared to GPU.

cs.DC↗

arXiv2019

A Multi-task Convolutional Neural Network for Autonomous Robotic Grasping in Object Stacking Scenes

Autonomous robotic grasping plays an important role in intelligent robotics. However, how to help the robot grasp specific objects in object stacking scenes is still an open problem, because there are two main challenges for autonomous robots: (1)it is a comprehensive task to know what and how to grasp; (2)it is hard to deal with the situations in which the target is hidden or covered by other objects. In this paper, we propose a multi-task convolutional neural network for autonomous robotic grasping, which can help the robot find the target, make the plan for grasping and finally grasp the target step by step in object stacking scenes. We integrate vision-based robotic grasping detection and visual manipulation relationship reasoning in one single deep network and build the autonomous robotic grasping system. Experimental results demonstrate that with our model, Baxter robot can autonomously grasp the target with a success rate of 90.6%, 71.9% and 59.4% in object cluttered scenes, familiar stacking scenes and complex stacking scenes respectively.

cs.RO↗