arXiv subjects

Han-Wei Shen

Publications and source records attributed to Han-Wei Shen.

At least 37 records · Page 2Linked to original sources

arXiv2024

Compressing and Interpreting Word Embeddings with Latent Space Regularization and Interactive Semantics Probing

Word embedding, a high-dimensional (HD) numerical representation of words generated by machine learning models, has been used for different natural language processing tasks, e.g., translation between two languages. Recently, there has been an increasing trend of transforming the HD embeddings into a latent space (e.g., via autoencoders) for further tasks, exploiting various merits the latent representations could bring. To preserve the embeddings' quality, these works often map the embeddings into an even higher-dimensional latent space, making the already complicated embeddings even less interpretable and consuming more storage space. In this work, we borrow the idea of $β$VAE to regularize the HD latent space. Our regularization implicitly condenses information from the HD latent space into a much lower-dimensional space, thus compressing the embeddings. We also show that each dimension of our regularized latent space is more semantically salient, and validate our assertion by interactively probing the encoding-level of user-proposed semantics in the dimensions. To the end, we design a visual analytics system to monitor the regularization process, explore the HD latent space, and interpret latent dimensions' semantics. We validate the effectiveness of our embedding regularization and interpretation approach through both quantitative and qualitative evaluations.

cs.HC↗

arXiv2024

GNNInterpreter: A Probabilistic Generative Model-Level Explanation for Graph Neural Networks

Recently, Graph Neural Networks (GNNs) have significantly advanced the performance of machine learning tasks on graphs. However, this technological breakthrough makes people wonder: how does a GNN make such decisions, and can we trust its prediction with high confidence? When it comes to some critical fields, such as biomedicine, where making wrong decisions can have severe consequences, it is crucial to interpret the inner working mechanisms of GNNs before applying them. In this paper, we propose a model-agnostic model-level explanation method for different GNNs that follow the message passing scheme, GNNInterpreter, to explain the high-level decision-making process of the GNN model. More specifically, GNNInterpreter learns a probabilistic generative graph distribution that produces the most discriminative graph pattern the GNN tries to detect when making a certain prediction by optimizing a novel objective function specifically designed for the model-level explanation for GNNs. Compared to existing works, GNNInterpreter is more flexible and computationally efficient in generating explanation graphs with different types of node and edge features, without introducing another blackbox or requiring manually specified domain-specific rules. In addition, the experimental studies conducted on four different datasets demonstrate that the explanation graphs generated by GNNInterpreter match the desired graph pattern if the model is ideal; otherwise, potential model pitfalls can be revealed by the explanation. The official implementation can be found at https://github.com/yolandalalala/GNNInterpreter.

cs.LG↗

arXiv2024

Improving Efficiency of Iso-Surface Extraction on Implicit Neural Representations Using Uncertainty Propagation

Implicit Neural representations (INRs) are widely used for scientific data reduction and visualization by modeling the function that maps a spatial location to a data value. Without any prior knowledge about the spatial distribution of values, we are forced to sample densely from INRs to perform visualization tasks like iso-surface extraction which can be very computationally expensive. Recently, range analysis has shown promising results in improving the efficiency of geometric queries, such as ray casting and hierarchical mesh extraction, on INRs for 3D geometries by using arithmetic rules to bound the output range of the network within a spatial region. However, the analysis bounds are often too conservative for complex scientific data. In this paper, we present an improved technique for range analysis by revisiting the arithmetic rules and analyzing the probability distribution of the network output within a spatial region. We model this distribution efficiently as a Gaussian distribution by applying the central limit theorem. Excluding low probability values, we are able to tighten the output bounds, resulting in a more accurate estimation of the value range, and hence more accurate identification of iso-surface cells and more efficient iso-surface extraction on INRs. Our approach demonstrates superior performance in terms of the iso-surface extraction time on four datasets compared to the original range analysis method and can also be generalized to other geometric query tasks.

cs.GR↗

arXiv2023

SmartGD: A GAN-Based Graph Drawing Framework for Diverse Aesthetic Goals

While a multitude of studies have been conducted on graph drawing, many existing methods only focus on optimizing a single aesthetic aspect of graph layouts, which can lead to sub-optimal results. There are a few existing methods that have attempted to develop a flexible solution for optimizing different aesthetic aspects measured by different aesthetic criteria. Furthermore, thanks to the significant advance in deep learning techniques, several deep learning-based layout methods were proposed recently. These methods have demonstrated the advantages of deep learning approaches for graph drawing. However, none of these existing methods can be directly applied to optimizing non-differentiable criteria without special accommodation. In this work, we propose a novel Generative Adversarial Network (GAN) based deep learning framework for graph drawing, called SmartGD, which can optimize different quantitative aesthetic goals, regardless of their differentiability. To demonstrate the effectiveness and efficiency of SmartGD, we conducted experiments on minimizing stress, minimizing edge crossing, maximizing crossing angle, maximizing shape-based metrics, and a combination of multiple aesthetics. Compared with several popular graph drawing algorithms, the experimental results show that SmartGD achieves good performance both quantitatively and qualitatively.

cs.LG↗

arXiv2023

PSRFlow: Probabilistic Super Resolution with Flow-Based Models for Scientific Data

Although many deep-learning-based super-resolution approaches have been proposed in recent years, because no ground truth is available in the inference stage, few can quantify the errors and uncertainties of the super-resolved results. For scientific visualization applications, however, conveying uncertainties of the results to scientists is crucial to avoid generating misleading or incorrect information. In this paper, we propose PSRFlow, a novel normalizing flow-based generative model for scientific data super-resolution that incorporates uncertainty quantification into the super-resolution process. PSRFlow learns the conditional distribution of the high-resolution data based on the low-resolution counterpart. By sampling from a Gaussian latent space that captures the missing information in the high-resolution data, one can generate different plausible super-resolution outputs. The efficient sampling in the Gaussian latent space allows our model to perform uncertainty quantification for the super-resolved results. During model training, we augment the training data with samples across various scales to make the model adaptable to data of different scales, achieving flexible super-resolution for a given input. Our results demonstrate superior performance and robust uncertainty quantification compared with existing methods such as interpolation and GAN-based super-resolution networks.

eess.IV↗

arXiv2023

Neural Stream Functions

We present a neural network approach to compute stream functions, which are scalar functions with gradients orthogonal to a given vector field. As a result, isosurfaces of the stream function extract stream surfaces, which can be visualized to analyze flow features. Our approach takes a vector field as input and trains an implicit neural representation to learn a stream function for that vector field. The network learns to map input coordinates to a stream function value by minimizing the inner product of the gradient of the neural network's output and the vector field. Since stream function solutions may not be unique, we give optional constraints for the network to learn particular stream functions of interest. Specifically, we introduce regularizing loss functions that can optionally be used to generate stream function solutions whose stream surfaces follow the flow field's curvature, or that can learn a stream function that includes a stream surface passing through a seeding rake. We also discuss considerations for properly visualizing the trained implicit network and extracting artifact-free surfaces. We compare our results with other implicit solutions and present qualitative and quantitative results for several synthetic and simulated vector fields.

cs.GR↗

arXiv2023

SKG: A Versatile Information Retrieval and Analysis Framework for Academic Papers with Semantic Knowledge Graphs

The number of published research papers has experienced exponential growth in recent years, which makes it crucial to develop new methods for efficient and versatile information extraction and knowledge discovery. To address this need, we propose a Semantic Knowledge Graph (SKG) that integrates semantic concepts from abstracts and other meta-information to represent the corpus. The SKG can support various semantic queries in academic literature thanks to the high diversity and rich information content stored within. To extract knowledge from unstructured text, we develop a Knowledge Extraction Module that includes a semi-supervised pipeline for entity extraction and entity normalization. We also create an ontology to integrate the concepts with other meta information, enabling us to build the SKG. Furthermore, we design and develop a dataflow system that demonstrates how to conduct various semantic queries flexibly and interactively over the SKG. To demonstrate the effectiveness of our approach, we conduct the research based on the visualization literature and provide real-world use cases to show the usefulness of the SKG. The dataset and codes for this work are available at https://osf.io/aqv8p/?view_only=2c26b36e3e3941ce999df47e4616207f.

cs.IR↗

arXiv2023

VMap: An Interactive Rectangular Space-filling Visualization for Map-like Vertex-centric Graph Exploration

We present VMap, a map-like rectangular space-filling visualization, to perform vertex-centric graph exploration. Existing visualizations have limited support for quality optimization among rectangular aspect ratios, vertex-edge intersection, and data encoding accuracy. To tackle this problem, VMap integrates three novel components: (1) a desired-aspect-ratio (DAR) rectangular partitioning algorithm, (2) a two-stage rectangle adjustment algorithm, and (3) a simulated annealing based heuristic optimizer. First, to generate a rectangular space-filling layout of an input graph, we subdivide the 2D embedding of the graph into rectangles with optimization of rectangles' aspect ratios toward a desired aspect ratio. Second, to route graph edges between rectangles without vertex-edge occlusion, we devise a two-stage algorithm to adjust a rectangular layout to insert border space between rectangles. Third, to produce and arrange rectangles by considering multiple visual criteria, we design a simulated annealing based heuristic optimization to adjust vertices' 2D embedding to support trade-offs among aspect ratio quality and the encoding accuracy of vertices' weights and adjacency. We evaluated the effectiveness of VMap on both synthetic and application datasets. The resulting rectangular layout has better aspect ratio quality on synthetic data compared with the existing method for the rectangular partitioning of 2D points. On three real-world datasets, VMap achieved better encoding accuracy and attained faster generation speed compared with existing methods on graphs' rectangular layout generation. We further illustrate the usefulness of VMap for vertex-centric graph exploration through three case studies on visualizing social networks, representing academic communities, and displaying geographic information.

cs.GR↗

arXiv2023

On the Importance and Applicability of Pre-Training for Federated Learning

Pre-training is prevalent in nowadays deep learning to improve the learned model's performance. However, in the literature on federated learning (FL), neural networks are mostly initialized with random weights. These attract our interest in conducting a systematic study to explore pre-training for FL. Across multiple visual recognition benchmarks, we found that pre-training can not only improve FL, but also close its accuracy gap to the counterpart centralized learning, especially in the challenging cases of non-IID clients' data. To make our findings applicable to situations where pre-trained models are not directly available, we explore pre-training with synthetic data or even with clients' data in a decentralized manner, and found that they can already improve FL notably. Interestingly, many of the techniques we explore are complementary to each other to further boost the performance, and we view this as a critical result toward scaling up deep FL for real-world applications. We conclude our paper with an attempt to understand the effect of pre-training on FL. We found that pre-training enables the learned global models under different clients' data conditions to converge to the same loss basin, and makes global aggregation in FL more stable. Nevertheless, pre-training seems to not alleviate local model drifting, a fundamental problem in FL under non-IID data.

cs.LG↗

arXiv2022

Deep Hierarchical Super Resolution for Scientific Data

We present a novel technique for hierarchical super resolution (SR) with neural networks (NNs), which upscales volumetric data represented with an octree data structure to a high-resolution uniform grid with minimal seam artifacts on octree node boundaries. Our method uses existing state-of-the-art SR models and adds flexibility to upscale input data with varying levels of detail across the domain, instead of only uniform grid data that are supported in previous approaches. The key is to use a hierarchy of SR NNs, each trained to perform 2x SR between two levels of detail, with a hierarchical SR algorithm that minimizes seam artifacts by starting from the coarsest level of detail and working up. We show that our hierarchical approach outperforms baseline interpolation and hierarchical upscaling methods, and demonstrate the usefulness of our proposed approach across three use cases including data reduction using hierarchical downsampling+SR instead of uniform downsampling+SR, computation savings for hierarchical finite-time Lyapunov exponent field calculation, and super-resolving low-resolution simulation results for a high-resolution approximation visualization.

eess.IV↗

arXiv2022

Not As Easy As You Think -- Experiences and Lessons Learnt from Trying to Create a Bottom-Up Visualization Image Typology

We present and discuss the results of a two-year qualitative analysis of images published in IEEE Visualization (VIS) papers. Specifically, we derive a typology of 13 visualization image types, coded to distinguish visualizations and several image characteristics. The categorization process required much more time and was more difficult than we initially thought. The resulting typology and image analysis may serve a number of purposes: to study the evolution of the community and its research output over time, to facilitate the categorization of visualization images for the purpose of teaching, to identify visual designs for evaluation purposes, or to enable progress towards standardization in visualization. In addition to the typology and image characterization, we provide a dataset of 6,833 tagged images and an online tool that can be used to explore and analyze the large set of tagged images. We thus facilitate a discussion of the diverse visualizations used and how they are published and communicated in our community.

cs.GR↗

arXiv2022

IDLat: An Importance-Driven Latent Generation Method for Scientific Data

Deep learning based latent representations have been widely used for numerous scientific visualization applications such as isosurface similarity analysis, volume rendering, flow field synthesis, and data reduction, just to name a few. However, existing latent representations are mostly generated from raw data in an unsupervised manner, which makes it difficult to incorporate domain interest to control the size of the latent representations and the quality of the reconstructed data. In this paper, we present a novel importance-driven latent representation to facilitate domain-interest-guided scientific data visualization and analysis. We utilize spatial importance maps to represent various scientific interests and take them as the input to a feature transformation network to guide latent generation. We further reduced the latent size by a lossless entropy encoding algorithm trained together with the autoencoder, improving the storage and memory efficiency. We qualitatively and quantitatively evaluate the effectiveness and efficiency of latent representations generated by our method with data from multiple scientific visualization applications.

cs.LG↗

arXiv2022

VDL-Surrogate: A View-Dependent Latent-based Model for Parameter Space Exploration of Ensemble Simulations

We propose VDL-Surrogate, a view-dependent neural-network-latent-based surrogate model for parameter space exploration of ensemble simulations that allows high-resolution visualizations and user-specified visual mappings. Surrogate-enabled parameter space exploration allows domain scientists to preview simulation results without having to run a large number of computationally costly simulations. Limited by computational resources, however, existing surrogate models may not produce previews with sufficient resolution for visualization and analysis. To improve the efficient use of computational resources and support high-resolution exploration, we perform ray casting from different viewpoints to collect samples and produce compact latent representations. This latent encoding process reduces the cost of surrogate model training while maintaining the output quality. In the model training stage, we select viewpoints to cover the whole viewing sphere and train corresponding VDL-Surrogate models for the selected viewpoints. In the model inference stage, we predict the latent representations at previously selected viewpoints and decode the latent representations to data space. For any given viewpoint, we make interpolations over decoded data at selected viewpoints and generate visualizations with user-specified visual mappings. We show the effectiveness and efficiency of VDL-Surrogate in cosmological and ocean simulations with quantitative and qualitative evaluations. Source code is publicly available at https://github.com/trainsn/VDL-Surrogate.

cs.GR↗

arXiv2022

Efficient Interpolation-based Pathline Tracing with B-spline Curves in Particle Dataset

Particle tracing through numerical integration is a well-known approach to generating pathlines for visualization. However, for particle simulations, the computation of pathlines is expensive, since the interpolation method is complicated due to the lack of connectivity information. Previous studies utilize the k-d tree to reduce the time for neighborhood search. However, the efficiency is still limited by the number of tracing time steps. Therefore, we propose a novel interpolation-based particle tracing method that first represents particle data as B-spline curves and interpolates B-spline control points to reduce the number of interpolation time steps. We demonstrate our approach achieves good tracing accuracy with much less computation time.

cs.GR↗

arXiv2022

Local Latent Representation based on Geometric Convolution for Particle Data Feature Exploration

Feature related particle data analysis plays an important role in many scientific applications such as fluid simulations, cosmology simulations and molecular dynamics. Compared to conventional methods that use hand-crafted feature descriptors, some recent studies focus on transforming the data into a new latent space, where features are easier to be identified, compared and extracted. However, it is challenging to transform particle data into latent representations, since the convolution neural networks used in prior studies require the data presented in regular grids. In this paper, we adopt Geometric Convolution, a neural network building block designed for 3D point clouds, to create latent representations for scientific particle data. These latent representations capture both the particle positions and their physical attributes in the local neighborhood so that features can be extracted by clustering in the latent space, and tracked by applying tracking algorithms such as mean-shift. We validate the extracted features and tracking results from our approach using datasets from three applications and show that they are comparable to the methods that define hand-crafted features for each specific dataset.

cs.GR↗

arXiv2022

GNN-Surrogate: A Hierarchical and Adaptive Graph Neural Network for Parameter Space Exploration of Unstructured-Mesh Ocean Simulations

We propose GNN-Surrogate, a graph neural network-based surrogate model to explore the parameter space of ocean climate simulations. Parameter space exploration is important for domain scientists to understand the influence of input parameters (e.g., wind stress) on the simulation output (e.g., temperature). The exploration requires scientists to exhaust the complicated parameter space by running a batch of computationally expensive simulations. Our approach improves the efficiency of parameter space exploration with a surrogate model that predicts the simulation outputs accurately and efficiently. Specifically, GNN-Surrogate predicts the output field with given simulation parameters so scientists can explore the simulation parameter space with visualizations from user-specified visual mappings. Moreover, our graph-based techniques are designed for unstructured meshes, making the exploration of simulation outputs on irregular grids efficient. For efficient training, we generate hierarchical graphs and use adaptive resolutions. We give quantitative and qualitative evaluations on the MPAS-Ocean simulation to demonstrate the effectiveness and efficiency of GNN-Surrogate. Source code is publicly available at https://github.com/trainsn/GNN-Surrogate.

physics.ao-ph↗

arXiv2022

Reinforcement Learning for Load-balanced Parallel Particle Tracing

We explore an online reinforcement learning (RL) paradigm to dynamically optimize parallel particle tracing performance in distributed-memory systems. Our method combines three novel components: (1) a work donation algorithm, (2) a high-order workload estimation model, and (3) a communication cost model. First, we design an RL-based work donation algorithm. Our algorithm monitors workloads of processes and creates RL agents to donate data blocks and particles from high-workload processes to low-workload processes to minimize program execution time. The agents learn the donation strategy on the fly based on reward and cost functions designed to consider processes' workload changes and data transfer costs of donation actions. Second, we propose a workload estimation model, helping RL agents estimate the workload distribution of processes in future computations. Third, we design a communication cost model that considers both block and particle data exchange costs, helping RL agents make effective decisions with minimized communication costs. We demonstrate that our algorithm adapts to different flow behaviors in large-scale fluid dynamics, ocean, and weather simulation data. Our algorithm improves parallel particle tracing performance in terms of parallel efficiency, load balance, and costs of I/O and communication for evaluations with up to 16,384 processors.

cs.GR↗

arXiv2022

SQRQuerier: A Visual Querying Framework for Cross-national Survey Data Recycling

Public opinion surveys constitute a powerful tool to study peoples' attitudes and behaviors in comparative perspectives. However, even worldwide surveys provide only partial geographic and time coverage, which hinders comprehensive knowledge production. To broaden the scope of comparison, social scientists turn to ex-post harmonization of variables from datasets that cover similar topics but in different populations and/or years. The resulting new datasets can be analyzed as a single source, which can be flexibly accessed through many data portals. However, such portals offer little guidance to explore the data in-depth or query data with user-customized needs. As a result, it is still challenging for social scientists to efficiently identify related data for their studies and evaluate their theoretical models based on the sliced data. To overcome them, in the Survey Data Recycling (SDR) international cooperation research project, we propose SDRQuerier and apply it to the harmonized SDR database, which features over two million respondents interviewed in a total of 1,721 national surveys that are part of 22 well-known international projects. We design the SDRQuerier to solve three practical challenges that social scientists routinely face. First, a BERT-based model provides customized data queries through research questions or keywords. Second, we propose a new visual design to showcase the availability of the harmonized data at different levels, thus helping users decide if empirical data exist to address a given research question. Lastly, SDRQuerier discloses the underlying relational patterns among substantive and methodological variables in the database, to help social scientists rigorously evaluate or even improve their regression models. Through case studies with multiple social scientists in solving their daily challenges, we demonstrated the novelty, effectiveness of SDRQuerier.

cs.HC↗