Towards Data-Driven Large Scale Scientific Visualization and Exploration

Technological advances have enabled us to acquire extremely large datasets but it remains a challenge to store, process, and extract information from them. This dissertation builds upon recent advances in machine learning, visualization, and user interactions to facilitate exploration of large-scale scientific datasets. First, we use data-driven approaches to computationally identify regions of interest in the datasets. Second, we use visual presentation for effective user comprehension. Third, we provide interactions for human users to integrate domain knowledge and semantic information into this exploration process. Our research shows how to extract, visualize, and explore informative regions on very large 2D landscape images, 3D volumetric datasets, high-dimensional volumetric mouse brain datasets with thousands of spatially-mapped gene expression profiles, and geospatial trajectories that evolve over time. The contribution of this dissertation include: (1) We introduce a sliding-window saliency model that discovers regions of user interest in very large images; (2) We develop visual segmentation of intensity-gradient histograms to identify meaningful components from volumetric datasets; (3) We extract boundary surfaces from a wealth of volumetric gene expression mouse brain profiles to personalize the reference brain atlas; (4) We show how to efficiently cluster geospatial trajectories by mapping each sequence of locations to a high-dimensional point with the kernel distance framework. We aim to discover patterns, relationships, and anomalies that would lead to new scientific, engineering, and medical advances. This work represents one of the first steps toward better visual understanding of large-scale scientific data by combining machine learning and human intelligence

Lagrangian Based Methods for Coherent Structure Detection

There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows. (C) 2015 AIP Publishing LLC.ONR N000141210665Center for Nonlinear Dynamic

voxel2vec: A Natural Language Processing Approach to Learning Distributed Representations for Scientific Data

Relationships in scientific data, such as the numerical and spatial distribution relations of features in univariate data, the scalar-value combinations' relations in multivariate data, and the association of volumes in time-varying and ensemble data, are intricate and complex. This paper presents voxel2vec, a novel unsupervised representation learning model, which is used to learn distributed representations of scalar values/scalar-value combinations in a low-dimensional vector space. Its basic assumption is that if two scalar values/scalar-value combinations have similar contexts, they usually have high similarity in terms of features. By representing scalar values/scalar-value combinations as symbols, voxel2vec learns the similarity between them in the context of spatial distribution and then allows us to explore the overall association between volumes by transfer prediction. We demonstrate the usefulness and effectiveness of voxel2vec by comparing it with the isosurface similarity map of univariate data and applying the learned distributed representations to feature classification for multivariate data and to association analysis for time-varying and ensemble data.Comment: Accepted by IEEE Transaction on Visualization and Computer Graphics (TVCG

Lifted Wasserstein Matcher for Fast and Robust Topology Tracking

This paper presents a robust and efficient method for tracking topological features in time-varying scalar data. Structures are tracked based on the optimal matching between persistence diagrams with respect to the Wasserstein metric. This fundamentally relies on solving the assignment problem, a special case of optimal transport, for all consecutive timesteps. Our approach relies on two main contributions. First, we revisit the seminal assignment algorithm by Kuhn and Munkres which we specifically adapt to the problem of matching persistence diagrams in an efficient way. Second, we propose an extension of the Wasserstein metric that significantly improves the geometrical stability of the matching of domain-embedded persistence pairs. We show that this geometrical lifting has the additional positive side-effect of improving the assignment matrix sparsity and therefore computing time. The global framework implements a coarse-grained parallelism by computing persistence diagrams and finding optimal matchings in parallel for every couple of consecutive timesteps. Critical trajectories are constructed by associating successively matched persistence pairs over time. Merging and splitting events are detected with a geometrical threshold in a post-processing stage. Extensive experiments on real-life datasets show that our matching approach is an order of magnitude faster than the seminal Munkres algorithm. Moreover, compared to a modern approximation method, our method provides competitive runtimes while yielding exact results. We demonstrate the utility of our global framework by extracting critical point trajectories from various simulated time-varying datasets and compare it to the existing methods based on associated overlaps of volumes. Robustness to noise and temporal resolution downsampling is empirically demonstrated

An Ensemble Machine Learning Approach for Tropical Cyclone Detection Using ERA5 Reanalysis Data

Tropical Cyclones (TCs) are counted among the most destructive phenomena that can be found in nature. Every year, globally an average of 90 TCs occur over tropical waters, and global warming is making them stronger, larger and more destructive. The accurate detection and tracking of such phenomena have become a relevant and interesting area of research in weather and climate science. Traditionally, TCs have been identified in large climate datasets through the use of deterministic tracking schemes that rely on subjective thresholds. Machine Learning (ML) models can complement deterministic approaches due to their ability to capture the mapping between the input climatic drivers and the geographical position of the TC center from the available data. This study presents a ML ensemble approach for locating TC center coordinates, embedding both TC classification and localization in a single end-to-end learning task. The ensemble combines TC center estimates of different ML models that agree about the presence of a TC in input data. ERA5 reanalysis were used for model training and testing jointly with the International Best Track Archive for Climate Stewardship records. Results showed that the ML approach is well-suited for TC detection providing good generalization capabilities on out of sample data. In particular, it was able to accurately detect lower TC categories than those used for training the models. On top of this, the ensemble approach was able to further improve TC localization performance with respect to single model TC center estimates, demonstrating the good capabilities of the proposed approach.Comment: 27 pages, 8 figures, 1 table, submitted to Journal of Advances in Modeling Earth System