arXiv subjects

Jiaqing Chen

Publications and source records attributed to Jiaqing Chen.

8 recordsLinked to original sources

arXiv2026

LatentFlow: Visual Analytics for Latent Space Analysis in Molecular Graph Neural Networks

Chemists and materials scientists increasingly use machine learning models, such as graph neural networks (GNNs), to predict properties of molecules and the outcomes of their reactions. Beyond predictive performance, understanding how these models organize chemical information internally in their latent spaces, i.e., the embeddings of the molecules, is critical. Analyzing latent spaces helps diagnose model behavior and assess whether the learned embeddings are organized in ways that reflect meaningful chemical relationships. Unfortunately, existing methods provide limited support for analyzing latent spaces across layers and across different model states (e.g., training epochs, model configurations, and input data), making it difficult to understand how these latent spaces evolve throughout a model or relate to chemical concepts. We present LatentFlow, a visual analytics system developed in collaboration with a domain expert for analyzing latent spaces in molecular GNNs. LatentFlow groups embeddings into clusters and supports exploration of latent spaces by tracking how these clusters change across layers and model states using a modified Sankey diagram. To support interpretation, LatentFlow links these clusters to representative molecules and their shared substructures, and it allows scientists to introduce their own domain knowledge and compare it with the patterns found in the latent spaces. We evaluate LatentFlow through two case studies. The results show that LatentFlow helps scientists understand how latent spaces evolve, identify meaningful molecular patterns, and better interpret model behavior.

cs.LG↗

arXiv2026

Boundary Embedding Shaping with Adaptive Contrastive Learning for Graph Structural Disentanglement

Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction.

cs.LG↗

arXiv2026

Landscaper: Understanding Loss Landscapes Through Multi-Dimensional Topological Analysis

Loss landscapes are a powerful tool for understanding neural network optimization and generalization, yet traditional low-dimensional analyses often miss complex topological features. We present Landscaper, an open-source Python package for arbitrary-dimensional loss landscape analysis. Landscaper combines Hessian-based subspace construction with topological data analysis to reveal geometric structures such as basin hierarchy and connectivity. A key component is the Saddle-Minimum Average Distance (SMAD) for quantifying landscape smoothness. We demonstrate Landscaper's effectiveness across various architectures and tasks, including those involving pre-trained language models, showing that SMAD captures training transitions, such as landscape simplification, that conventional metrics miss. We also illustrate Landscaper's performance in challenging chemical property prediction tasks, where SMAD can serve as a metric for out-of-distribution generalization, offering valuable insights for model diagnostics and architecture design in data-scarce scientific machine learning scenarios.

cs.LG↗

arXiv2024

LossLens: Diagnostics for Machine Learning through Loss Landscape Visual Analytics

Modern machine learning often relies on optimizing a neural network's parameters using a loss function to learn complex features. Beyond training, examining the loss function with respect to a network's parameters (i.e., as a loss landscape) can reveal insights into the architecture and learning process. While the local structure of the loss landscape surrounding an individual solution can be characterized using a variety of approaches, the global structure of a loss landscape, which includes potentially many local minima corresponding to different solutions, remains far more difficult to conceptualize and visualize. To address this difficulty, we introduce LossLens, a visual analytics framework that explores loss landscapes at multiple scales. LossLens integrates metrics from global and local scales into a comprehensive visual representation, enhancing model diagnostics. We demonstrate LossLens through two case studies: visualizing how residual connections influence a ResNet-20, and visualizing how physical parameters influence a physics-informed neural network (PINN) solving a simple convection problem.

cs.LG↗

arXiv2024

Visualizing Loss Functions as Topological Landscape Profiles

In machine learning, a loss function measures the difference between model predictions and ground-truth (or target) values. For neural network models, visualizing how this loss changes as model parameters are varied can provide insights into the local structure of the so-called loss landscape (e.g., smoothness) as well as global properties of the underlying model (e.g., generalization performance). While various methods for visualizing the loss landscape have been proposed, many approaches limit sampling to just one or two directions, ignoring potentially relevant information in this extremely high-dimensional space. This paper introduces a new representation based on topological data analysis that enables the visualization of higher-dimensional loss landscapes. After describing this new topological landscape profile representation, we show how the shape of loss landscapes can reveal new details about model performance and learning dynamics, highlighting several use cases, including image segmentation (e.g., UNet) and scientific machine learning (e.g., physics-informed neural networks). Through these examples, we provide new insights into how loss landscapes vary across distinct hyperparameter spaces: we find that the topology of the loss landscape is simpler for better-performing models; and we observe greater variation in the shape of loss landscapes near transitions from low to high model performance.

cs.LG↗

arXiv2024

Evaluating Loss Landscapes from a Topology Perspective

Characterizing the loss of a neural network with respect to model parameters, i.e., the loss landscape, can provide valuable insights into properties of that model. Various methods for visualizing loss landscapes have been proposed, but less emphasis has been placed on quantifying and extracting actionable and reproducible insights from these complex representations. Inspired by powerful tools from topological data analysis (TDA) for summarizing the structure of high-dimensional data, here we characterize the underlying shape (or topology) of loss landscapes, quantifying the topology to reveal new insights about neural networks. To relate our findings to the machine learning (ML) literature, we compute simple performance metrics (e.g., accuracy, error), and we characterize the local structure of loss landscapes using Hessian-based metrics (e.g., largest eigenvalue, trace, eigenvalue spectral density). Following this approach, we study established models from image pattern recognition (e.g., ResNets) and scientific ML (e.g., physics-informed neural networks), and we show how quantifying the shape of loss landscapes can provide new insights into model performance and learning dynamics.

cs.LG↗

arXiv2022

Serving Deep Learning Models with Deduplication from Relational Databases

There are significant benefits to serve deep learning models from relational databases. First, features extracted from databases do not need to be transferred to any decoupled deep learning systems for inferences, and thus the system management overhead can be significantly reduced. Second, in a relational database, data management along the storage hierarchy is fully integrated with query processing, and thus it can continue model serving even if the working set size exceeds the available memory. Applying model deduplication can greatly reduce the storage space, memory footprint, cache misses, and inference latency. However, existing data deduplication techniques are not applicable to the deep learning model serving applications in relational databases. They do not consider the impacts on model inference accuracy as well as the inconsistency between tensor blocks and database pages. This work proposed synergistic storage optimization techniques for duplication detection, page packing, and caching, to enhance database systems for model serving. We implemented the proposed approach in netsDB, an object-oriented relational database. Evaluation results show that our proposed techniques significantly improved the storage efficiency and the model inference latency, and serving models from relational databases outperformed existing deep learning frameworks when the working set size exceeds available memory.

cs.DB↗

arXiv2019

A Time-driven Data Placement Strategy for a Scientific Workflow Combining Edge Computing and Cloud Computing

Compared to traditional distributed computing environments such as grids, cloud computing provides a more cost-effective way to deploy scientific workflows. Each task of a scientific workflow requires several large datasets that are located in different datacenters from the cloud computing environment, resulting in serious data transmission delays. Edge computing reduces the data transmission delays and supports the fixed storing manner for scientific workflow private datasets, but there is a bottleneck in its storage capacity. It is a challenge to combine the advantages of both edge computing and cloud computing to rationalize the data placement of scientific workflow, and optimize the data transmission time across different datacenters. Traditional data placement strategies maintain load balancing with a given number of datacenters, which results in a large data transmission time. In this study, a self-adaptive discrete particle swarm optimization algorithm with genetic algorithm operators (GA-DPSO) was proposed to optimize the data transmission time when placing data for a scientific workflow. This approach considered the characteristics of data placement combining edge computing and cloud computing. In addition, it considered the impact factors impacting transmission delay, such as the band-width between datacenters, the number of edge datacenters, and the storage capacity of edge datacenters. The crossover operator and mutation operator of the genetic algorithm were adopted to avoid the premature convergence of the traditional particle swarm optimization algorithm, which enhanced the diversity of population evolution and effectively reduced the data transmission time. The experimental results show that the data placement strategy based on GA-DPSO can effectively reduce the data transmission time during workflow execution combining edge computing and cloud computing.

cs.DC↗