Engineering topics

Praggastis, Brenda L.

Publications and source records attributed to Praggastis, Brenda L..

13 records

DOE OSTI2023

Comparing Mapper Graphs of Artificial Neuron Activations

The mapper graph is a popular tool from topological data analysis that provides a graphical summary of point cloud data. It has been used to study data from cancer research, sports analytics, neurosciences, and machine learning. In particular, mapper graphs have been used recently to visualize the topology of high-dimensional artificial neural activations from convolutional neural networks and large language models. However, a key question that arises from using mapper graphs across applications is how to compare mapper graphs to study their structural differences. In this paper, we introduce a distance between mapper graphs using tools from optimal transport. We demonstrate the utility of such a distance by studying the topological changes of neural activations across convolutional layers in deep learning, as well as by capturing the loss of structural information for multiscale mapper.

mapper graphs, computational topology, machine lea↗

DOE OSTI2023

DeepDataProfiler: A Platform and Methodology for the Analysis and Interpretation of Neural Networks

The DeepDataProfiler is a methodology and framework for providing interpretability to trained neural networks. Its approach is to decompose a network into a weighted graph of neurons and synapses and link the components of the graph to human identifiable concepts. By identifying concepts important to the network and tracking the decision process employed by the network, the network becomes more transparent and less like a black box. Spurious decisions and poor generalization strategies can be identified and a measure of trustworthiness can be established.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗

DOE OSTI2021

Parallel Algorithms for Efficient Computation of High-Order Line Graphs of Hypergraphs

This paper considers structures of systems beyond dyadic (pairwise) interactions and investigates mathematical modeling of multi-way interactions and connections as hypergraphs, where captured relationships among system entities are set-valued. To date, in most situations, entities in a hypergraph are considered connected as long as there is at least one common ``neighbor''. However, minimal commonality sometimes discards the ``strength'' of connections and interactions among groups. To this end, considering the ``width'' of a connection, referred to as the \emph{$s$-overlap} of neighbors, provides more meaningful insights into how closely the communities or entities interact with each other. In addition, $s$-overlap computation is the fundamental kernel to construct the line graph of a hypergraph, a low-order approximation of the hypergraph which can carry significant information about the original hypergraph. Subsequent stages of a data analytics pipeline then can apply highly-tuned graph algorithms on the line graph to reveal important features. Given a hypergraph, computing the $s$-overlaps by exhaustively considering all pairwise entities can be computationally prohibitive. To tackle this challenge, we develop efficient algorithms to compute $s$-overlaps and the corresponding line graph of a hypergraph. We propose several heuristics to avoid execution of redundant work and improve performance of the $s$-overlap computation. Our parallel algorithm, combined with these heuristics, is orders of magnitude (more than $10\times$) faster than the naive algorithm in all cases and the SpGEMM algorithm with filtration in most cases (especially with large $s$ value).

hypergraph algorithms, graph algorithms, parallel ↗

DOE OSTI2021

Hypernetwork Science: From Multidimensional Networks to Computational Topology

As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra, lattice theory, and topology. They are able to represent complex systems interactions more faithfully than graphs and networks, while also being some of the simplest classes of systems representing topological structures as collections of multidimensional objects connected in a particular pattern. In this paper we discuss the role of (undirected) hypergraphs in the science of complex networks, and provide a mathematical overview of the core concepts needed for hypernetwork modeling, including duality and the relationship to bicolored graphs, quantitative adjacency and incidence, the nature of walks in hypergraphs, and available topological relationships and properties. We close with a brief discussion of two example applications: biomedical databases for disease analysis, and domain-name system (DNS) analysis of cyber data.

Joslyn, Cliff A.↗

DOE OSTI2021

Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

systems biology, hypergraph, viral infection, biol↗

DOE OSTI2020

Systematic Evaluation of Backdoor Data Poisoning Attacks on Image Classifiers

Backdoor data poisoning attacks have recently been demonstrated in computer vision research as a potential safety risk for machine learning (ML) systems. Traditional data poisoning attacks manipulate training data to induce unreliability of an ML model, whereas backdoor data poisoning attacks maintain system performance unless the MLmodel is presented with an input containing an embedded“trigger” that provides a predetermined response advantageous to the adversary. Our work builds upon prior back-door data-poisoning research for ML image classifiers and systematically assesses different experimental conditions including types of trigger patterns, persistence of trigger patterns during retraining, poisoning strategies, architectures (ResNet-50, NasNet, NasNet-Mobile), datasets (Flowers, CIFAR-10), and potential defensive regularization techniques (Contrastive Loss, Logit Squeezing, Manifold Mixup,Soft-Nearest-Neighbors Loss). Experiments yield four key findings. First, the success rate of backdoor poisoning at-tacks varies widely, depending on several factors, including model architecture, trigger pattern and regularization technique. Second, we find that poisoned models are hard to detect through performance inspection alone. Third, regularization typically reduces backdoor success rate, although it can have no effect or even slightly increase it, depending on the form of regularization. Finally, backdoors inserted through data poisoning can be rendered ineffective after just a few epochs of additional training on a small set of clean data without affecting the model’s performance.

Truong, Loc T.↗

DOE OSTI2020

Computing Hypergraph Homology in Chapel

In this paper, we discuss our experience in implementing homology computation, in particular Betti number calculation in Chapel hypergraph Library (CHGL). Given a dataset represented as a hypergraph, a Betti number for a particular dimension $k$ indicates how many $k$-dimensional `voids' are present in the dataset. Computing Betti number involves various array-centric and linear algebra operations. We demonstrate that implementing these operations in Chapel is both concise and intuitive. In addition, we show that Chapel provides language constructs for implementing parallel and distributed execution of the linear algebra kernels with minimal effort. Syntactically, Chapel provides succinctness of Python, while delivering comparable and better performance than C++-based and Julia-based packages for calculating Betti numbers respectively.

hypergraph, topological data analysis↗

DOE OSTI2020

A Sheaf Theoretical Approach to Uncertainty Quantification of Heterogeneous Geolocation Information

Integration of multiple, heterogeneous sensors is a challenging problem across a range of applications. Prominent among these are multi-target tracking, where one must combine observations from different sensor types in a meaningful and efficient way to track multiple targets. Because different sensors have differing error models, we seek a theoretically justified quantification of the agreement among ensembles of sensors, both overall for a sensor collection, and also at a fine-grained level specifying pairwise and multi-way interactions among sensors. We demonstrate that the theory of mathematical sheaves provides a unified answer to this need, supporting both quantitative and qualitative data. Furthermore, the theory provides algorithms to globalize data across the network of deployed sensors, and to diagnose issues when the data do not globalize cleanly. We demonstrate and illustrate the utility of sheaf-based tracking models based on experimental data of a wild population of black bears in Asheville, North Carolina. A measurement model involving four sensors deployed among the bears and the team of scientists charged with tracking their location is deployed. This provides a sheaf-based integration model which is small enough to fully interpret, but of sufficient complexity to demonstrate the sheaf’s ability to recover a holistic picture of the locations and behaviors of both individual bears and the bear-human tracking system. A statistical approach was developed in parallel for comparison, a dynamic linear model which was estimated using a Kalman filter. This approach also recovered bear and human locations and sensor accuracies. When the observations are normalized into a common coordinate system, the structure of the dynamic linear observation model recapitulates the structure of the sheaf model, demonstrating the canonicity of the sheaf-based approach. However, when the observations are not so normalized, the sheaf model still remains valid.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗

DOE OSTI2019

ReLVis: Visual Analytics for Situational Awareness During Reinforcement Learning Experimentation

Reinforcement learning (RL) is a branch of machine learning where an agent learns to maximize reward through trial and error. RL is challenging and data/compute intensive, and RL practitioners can easily become overwhelmed and make poor modeling decisions. Our contribution is a visual analytics tool designed to help data scientists maintain situation awareness during RL experimentation. Our tool allows the user to under- stand which hyper-parameter values lead to better or worse outcomes, what behaviors are associated with high and low reward, and how behaviors evolve and progress over training time. We evaluated our tool by applying state of the art deep RL models to six different RL tasks. We present three tasks as use cases that show how our tool leads to insightful findings and improves situation awareness.

Saldanha, Emily G.↗

DOE OSTI2018

A Topological Approach to Representational Data Models

As data accumulate faster and bigger, building representa- tional models has turned into an art form. Despite sharing common data types, each scientific discipline often takes a different approach. In this work, we propose representational models grounded in the mathematics of algebraic topology to understand foundational data types. We present hypergraphs for multi-relational data, point clouds for vector data, and sheaf models when both data types are present and interrelated. These three models use similar principles from algebraic topology and provide a domain-agnostic framework. We will discuss each method, provide ref- erences to their foundational mathematical papers, and give examples of their use.

relational data, relational data, vector data, vec↗

DOE OSTI2016

Towards Cache-Enabled, Order-Aware, Ontology-Based Stream Reasoning Framework

While streaming data have become increasingly more popular in business and research communities, semantic models and processing software for streaming data have not kept pace. Traditional semantic solutions have not addressed transient data streams. Semantic web languages (e.g., RDF, OWL) have typically addressed static data settings and linked data approaches have predominantly addressed static or growing data repositories. Streaming data settings have some fundamental differences; in particular, data are consumed on the fly and data may expire. Stream reasoning, a combination of stream processing and semantic reasoning, has emerged with the vision of providing "smart" processing of streaming data. C-SPARQL is a prominent stream reasoning system that handles semantic (RDF) data streams. Many stream reasoning systems including C-SPARQL use a sliding window and use data arrival time to evict data. For data streams that include expiration times, a simple arrival time scheme is inadequate if the window size does not match the expiration period. In this paper, we propose a cache-enabled, order-aware, ontology-based stream reasoning framework. This framework consumes RDF streams with expiration timestamps assigned by the streaming source. Our framework utilizes both arrival and expiration timestamps in its cache eviction policies. In addition, we introduce the notion of "semantic importance" which aims to address the relevance of data to the expected reasoning, thus enabling the eviction algorithms to be more context- and reasoning-aware when choosing what data to maintain for question answering. We evaluate this framework by implementing three different prototypes and utilizing five metrics. The trade-offs of deploying the proposed framework are also discussed.

Data Discovery↗