arXiv subjects

Gunther H. Weber

Publications and source records attributed to Gunther H. Weber.

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

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↗

arXiv2025

Extremely Scalable Distributed Computation of Contour Trees via Pre-Simplification

Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains challenging due to scalability limitations. Recent developments in distributed hierarchical contour trees have addressed these challenges by enabling scalable computation across distributed systems. Building on these structures, advanced analytical tasks -- such as volumetric branch decomposition and contour extraction -- have been introduced to facilitate large-scale scientific analysis. Despite these advancements, such analytical tasks substantially increase memory usage, which hampers scalability. In this paper, we propose a pre-simplification strategy to significantly reduce the memory overhead associated with analytical tasks on distributed hierarchical contour trees. We demonstrate enhanced scalability through strong scaling experiments, constructing the largest known contour tree -- comprising over half a trillion nodes with complex topology -- in under 15 minutes on a dataset containing 550 billion elements.

cs.CG↗

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↗

arXiv2024

Distributed Augmentation, Hypersweeps, and Branch Decomposition of Contour Trees for Scientific Exploration

Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale using high-performance computing. To address this challenge, recent work has introduced distributed hierarchical contour trees for distributed computation and storage of contour trees. However, effective use of these distributed structures in analysis and visualization requires subsequent computation of geometric properties and branch decomposition to support contour extraction and exploration. In this work, we introduce distributed algorithms for augmentation, hypersweeps, and branch decomposition that enable parallel computation of geometric properties, and support the use of distributed contour trees as query structures for scientific exploration. We evaluate the parallel performance of these algorithms and apply them to identify and extract important contours for scientific visualization.

cs.CG↗

arXiv2023

Extensions to the SENSEI In situ Framework for Heterogeneous Architectures

The proliferation of GPUs and accelerators in recent supercomputing systems, so called heterogeneous architectures, has led to increased complexity in execution environments and programming models as well as to deeper memory hierarchies on these systems. In this work, we discuss challenges that arise in in situ code coupling on these heterogeneous architectures. In particular, we present data and execution model extensions to the SENSEI in situ framework that are targeted at the effective use of systems with heterogeneous architectures. We then use these new data and execution model extensions to investigate several in situ placement and execution configurations and to analyze the impact these choices have on overall performance.

cs.DC↗