Topological analysis of active networks
Computer programs for application to topological analysis of active networks
COMPUTER PROGRAM↗
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Topological analysis of passive networks
Application of network topology to analysis of passive networks
ELECTRIC NETWORK↗
Topological Analysis of Temporal Hypergraphs
In this work we study the topological properties of temporal hypergraphs. Hypergraphs provide a higher dimensional generalization of a graph that is capable of capturing multi-way connections. As such, they have become an integral part of network science. A common use of hypergraphs is to model events as hyperedges in which the event can involve many elements as nodes. This provides a more complete picture of the event in comparison to the standard dyadic connection limitation of a graph. However, a common attribution to events is temporal information as an interval for when the event occurred. Consequently, a temporal hypergraph is born which accurately captures both the temporal information of events as well as their multi-way connections. Common tools for studying these temporal hypergraphs typically use summary statistics of snapshots from a sliding window procedure to capture changes in the underlying dynamics. However, these do not provide insight into how the changing structure of the hypergraph evolves and which components of the temporal hypergraph persist and are influential to the underlying system. To alleviate this need we leverage zigzag persistence from the field of Topological Data Analysis (TDA) to study the change in topological structure of time-evolving hypergraphs. We apply our pipeline to both a cyber security and social network dataset and show how the topological structure of their temporal hypergraphs change and can be used to understand the underlying dynamics.
hypergraphs, topological data analysis, zigzag per↗
Topological analysis of the CfA redshift survey
We study the topology of large-scale structure in the Center for Astrophysics Redshift Survey, which now includes approximately 12,000 galaxies with limiting magnitude m(sub B) is less than or equal to 15.5. The dense sampling and large volume of this survey allow us to compute the topology on smoothing scales from 6 to 20/h Mpc; we thus examine the topology of structure in both 'nonlinear' and 'linear' regimes. On smoothing scales less than or equal to 10/h Mpc this sample has 3 times the number of resolution elements of samples examined in previous studies. Isodensity surface of the smoothed galaxy density field demonstrate that coherent high-density structures and large voids dominate the galaxy distribution. We compute the genus-threshold density relation for isodensity surfaces of the CfA survey. To quantify phase correlation in these data, we compare the CfA genus with the genus of realizations of Gaussian random fields with the power spectrum measured for the CfA survey. On scales less than or equal to 10/h Mpc the observed genus amplitude is smaller than random phase (96% confidence level). This decrement reflects the degree of phase coherence in the observed galaxy distribution. In other words the genus amplitude on these scales is not good measure of the power spectrum slope. On scales greater than 10/h Mpc, where the galaxy distribution is rougly in the 'linear' regime, the genus ampitude is consistent with the random phase amplitude. The shape of the genus curve reflects the strong coherence in the observed structure; the observed genus curve appears broader than random phase (94% confidence level for smoothing scales less than or equal to 10/h Mpc) because the topolgoy is spongelike over a very large range of density threshold. This departre from random phase consistent with a distribution like a filamentary net of 'walls with holes.' On smoothing scales approaching approximately 20/h Mpc the shape of the CfA genus curve is consistent with random phase. There is very weak evidence for a shift of the genus toward a 'bubble-like' topology. To test cosmological models, we compute the genus for mock CfA surveys drawn from large (L greater than or approximately 400/h Mpc) N-body simulations of three variants of the cold dark matter (CDM) cosmogony. The genus amplitude of the 'standard' CDM model (omega h = 0.5, b = 1.5) differs from the observations (96% confidence level) on smoothing scales is less than or approximately 10/h Mpc. An open CDM model (omega h = 0.2) and a CDM model with nonzero cosmological constant (omega h = 0.24, lambda (sub 0) = 0.6) are consistent with the observed genus amplitude over the full range of smoothing scales. All of these models fail (97% confidence level) to match the broadness of the observed genus curve on smoothing scales is less than or equal to 10/h Mpc.
Vogeley, Michael S.↗
Topological analysis of computed three-dimensional viscous flow fields
Computed solutions of the time-dependent, Reynolds-averaged Navier-Stokes equations for three dimensional flows having thin shear layers are analyzed using topological concepts. Specific examples include the transonic flow over a body of revolution with conical afterbody at moderate angles of incidence to the free stream. Experimental flow-visualization techniques are simulated graphically to visualize the computed flow. Scalar and vector fluid dynamics properties such as pressure, shear stress, and vorticity on the body surface are presented as topological maps, and their relationship to one another in terms of orientation and singular points is discussed. The extrapolation from these surface topologies toward the understanding of external flow-field behavior is and demonstrated.
Deiwert, G. S.↗
Topological analysis of computed three-dimensional viscous flow fields
Computed solutions of the time-dependent, Reynolds-averaged Navier-Stokes equations for three-dimensional flows having thin shear layers are analyzed, using topological concepts. Specific examples include the transonic flow over a body of revolution with conical afterbody at moderate angles of incidence to the free stream. Experimental flow-visualization techniques are simulated graphically to visualize the computed flow. Scalar and vector fluid dynamic properties, such as pressure, shear stress, and vorticity on the body surface, are presented as topological maps, and their relationship to one another in terms of orientation and singular points is discussed. The extrapolation from these surface topologies toward the understanding of external flow-field behavior is discussed and demonstrated.
Deiwert, G. S.↗
Topological analysis of chaotic orbits: Revisiting Hyperion
There is emerging interest in the possibility of chaotic evolution in astrophysical systems. To mention just one example, recent well-sampled ground-based observations of the Saturian satellite Hyperion strongly suggest that it is exhibiting chaotic behavior. We present a general technique, the method of close returns, for the analysis of data from astronomical objects believed to be exhibiting chaotic motion. The method is based on the extraction of pieces of the evolution that exhibit nearly periodic behavior-episodes during which the object stays near in phase space to some unstable periodic orbit. Such orbits generally act as skeletal features, tracing the topological organization of the manifold on which the chaotic dynamics takes place. This method does not require data sets as lengthy as other nonlinear analysis techniques do and is therefore well suited to many astronomical observing programs. Well sampled data covering between twenty and forty characteristic periods of the system have been found to be sufficient for the application of this technique. Additional strengths of this method are its robustness in the presence of noise and the ability for a user to clearly distinguish between periodic, random, and chaotic behavior by inspection of the resulting two-dimensional image. As an example of its power, we analyze close returns in a numerically generated data set, based on a model for Hyperion extensively studied in the literature, corresponding to nightly observations of the satellite. We show that with a small data set, embedded unstable periodic orbits can be extracted and that these orbits can be responsible for nearly periodic behavior lasting a substantial fraction of the observing run.
Boyd, Patricia T.↗
Topological analysis of X-ray CT data for the recognition and trending of subtle changes in microstructure under material aging
X-ray computed tomography (CT) is an established non-destructive tool for 3D imaging of multiphasic composites. Numerous applications of X-ray CT in medical diagnosis and materials characterization have been reported, many involving field-specific innovations in the imaging technology itself. Yet, quantitative summarization to link image features to properties of interest has been rare. Here we address this issue by employing state-of-the-art technics in scalar field topology for the summarization of X-ray CT images of an example biphasic system. By varying processing-parameters we create different microstructures, evolve them through accelerated thermal aging, CT-image them pre- and post-aged, and demonstrate the ability of our image summarization method to systematically track process- and age-related changes, which can often be very subtle. A novel aspect of the algorithm involves recognition over multiple resolution levels, which provides deeper insight into the pattern relationship between grain-like features and their neighbors. The method is general, adaptable to diverse image reconstruction methods and materials systems, and particularly useful in applications where practical constraints on the sample-size limits the reliable use of more complex models, e.g., convolutional neural networks.
36 MATERIALS SCIENCE↗
Topological Analysis of The SPOKE Graph
The SPOKE graph [2, 6] is a sparse decorated semantic graph representing a collection of knowledge collected in many scientific databases from the fields of healthcare, biochemistry, chemistry, biology, et cetera. This knowledge graph is stored as a relational dataset decorated with metadata on each constituent vertex and edge. Formally, the graph is G(V, E, D), where V is a set of n vertices V := {1, ..., n} and edges of the form (i, j) ϵ E for i, j ϵ V, and table D that for any item in V υ E stores unstructured data such as vertex/edge type, nature of a relationship, et cetera. D(i) = {data involving vertex i ϵ V}, and D(i, j) = {data involving edge (i, j) ϵ E}. Here, we treat the graph as undirected in the sense that a direct relationship for (i, j) causes a (possibly opposite) reverse direct relationship for (j, i). The SPOKE graph G(V, E, D) is formed by processing a collection of relational datasets from medicine, chemistry, and biology, connecting many entities. Here, we analyze an instance from 2019, Spoke-20190707, where a graph file contains 6.16M edges and associated metadata and a vertex file contains 2.15M vertices and the associated metadata. There are 12 different types of vertex entities; all edge types used are implicit (see §2). There is other metadata in D on edges and vertices, but we just use the topology and the vertex labels in this report. SPOKE is growing as more knowledge is gained and more datasets are added. SPOKE is likely to grow 10x during the next phase of this project, and we therefore would like to consider topoligical analysis techniques that are scalable to several orders of magnitude larger than the current dataset (say >1B edges).
59 BASIC BIOLOGICAL SCIENCES↗
A topological study of computer efficiency in network analysis.
Topological study of digital computer programming efficiency in electric network analysis, considering cost of computation
Chan, S. P.↗
Topology property analysis and application of stable time-delay regions for linear multiple time-delay systems
This study examines the relationship between the topology of stable time-delay regions and the stability analysis of an linear multiple time delay system. To analyze the topology of stable time-delay regions, we construct a function with a value equal to zero for the time-delay points on the boundaries of stable time-delay regions. The function is continuous and differentiable in the whole defining field with a global minimum of zero so that we can locate the boundaries by minimizing the value of the function. Based on the topology analysis, we proposed a performance validation approach for controllers that are designed to stabilize the system using feedback signals with time delays. The method based on the topology analysis is simple and reliable so that can deal with a linear time-invariant system with high order and multiple time delays (more than 3). The example case study shows that the above method is reliable and enables ultra-low latency coordination and control for the future power grid with ubiquitous power electronics.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Topological Data Analysis for Particulate Gels
Soft gels, formed via the self-assembly of particulate materials, exhibit intricate multiscale structures that provide them with flexibility and resilience when subjected to external stresses. Here, this work combines particle simulations and topological data analysis (TDA) to characterize the complex multiscale structure of soft gels. Our TDA analysis focuses on the use of the Euler characteristic, which is an interpretable and computationally scalable topological descriptor that is combined with filtration operations to obtain information on the geometric (local) and topological (global) structure of soft gels. We reduce the topological information obtained with TDA using principal component analysis (PCA) and show that this provides an informative low-dimensional representation of the gel structure. We use the proposed computational framework to investigate the influence of gel preparation (e.g., quench rate, volume fraction) on soft gel structure and to explore dynamic deformations that emerge under oscillatory shear in various response regimes (linear, nonlinear, and flow). Our analysis provides evidence of the existence of hierarchical structures in soft gels, which are not easily identifiable otherwise. Moreover, our analysis reveals direct correlations between topological changes of the gel structure under deformation and mechanical phenomena distinctive of gel materials, such as stiffening and yielding. In summary, we show that TDA facilitates the mathematical representation, quantification, and analysis of soft gel structures, extending traditional network analysis methods to capture both local and global organization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Con Connections: Detecting Fraud from Abstracts using Topological Data Analysis
In this paper we present a novel approach for identifying fraudulent papers from their titles and abstracts. The premise of the approach is that there are holes in the presentation of the approach and findings of fraudulent research papers. As an abstract is intended to highlight key features of the approach as well as important conclusions the authors seek to determine if the assumed existence of holes can be identified from analysis of abstracts alone. The data set considered is derived from papers sharing a single author with labels determined based on a formal linguistic analysis of the complete documents. To detect these logical and literary holes we utilize techniques from topological data analysis which summarizes data based on the presence of multi-dimensional, topological holes. We find that, in fact, topological features derived through a combination of techniques in natural language processing and time-series analysis allow for superior detection of the fraudulent papers than the natural language processing tools alone. Thus we conclude that the connections and holes present in the abstracts of research cons contributes to an ability to infer the scientific validity of the corresponding work.
Tymochko, Sarah J.↗
Topological network analysis of patient similarity for precision management of acute blood pressure in spinal cord injury
Background: Predicting neurological recovery after spinal cord injury (SCI) is challenging. Using topological data analysis, we have previously shown that mean arterial pressure (MAP) during SCI surgery predicts long-term functional recovery in rodent models, motivating the present multicenter study in patients. Methods: Intra-operative monitoring records and neurological outcome data were extracted (n = 118 patients). We built a similarity network of patients from a low-dimensional space embedded using a non-linear algorithm, Isomap, and ensured topological extraction using persistent homology metrics. Confirmatory analysis was conducted through regression methods. Results: Network analysis suggested that time outside of an optimum MAP range (hypotension or hypertension) during surgery was associated with lower likelihood of neurological recovery at hospital discharge. Logistic and LASSO (least absolute shrinkage and selection operator) regression confirmed these findings, revealing an optimal MAP range of 76–[104-117] mmHg associated with neurological recovery. Conclusions: We show that deviation from this optimal MAP range during SCI surgery predicts lower probability of neurological recovery and suggest new targets for therapeutic intervention. Funding: NIH/NINDS: R01NS088475 (ARF); R01NS122888 (ARF); UH3NS106899 (ARF); Department of Veterans Affairs: 1I01RX002245 (ARF), I01RX002787 (ARF); Wings for Life Foundation (ATE, ARF); Craig H. Neilsen Foundation (ARF); and DOD: SC150198 (MSB); SC190233 (MSB); DOE: DE-AC02-05CH11231 (DM).
59 BASIC BIOLOGICAL SCIENCES↗
Analyzing Prospects for Quantum Advantage in Topological Data Analysis
Lloyd [Nat. Commun. , 10138 (2016)] were first to demonstrate the promise of quantum algorithms for computing Betti numbers, a way to characterize topological features of data sets. Here, we propose, analyze, and optimize an improved quantum algorithm for topological data analysis (TDA) with reduced scaling, including a method for preparing Dicke states based on inequality testing, a more efficient amplitude estimation algorithm using Kaiser windows, and an optimal implementation of eigenvalue projectors based on Chebyshev polynomials. We compile our approach to a fault-tolerant gate set and estimate constant factors in the Toffoli complexity. Our analysis reveals that superquadratic quantum speedups are only possible for this problem when targeting a multiplicative error approximation and the Betti number grows asymptotically. Further, we propose a dequantization of the quantum TDA algorithm that shows that having exponentially large dimension and Betti number are necessary, but insufficient conditions, for superpolynomial advantage. We then introduce and analyze specific problem examples which have parameters in the regime where superpolynomial advantages may be achieved, and argue that quantum circuits with tens of billions of Toffoli gates can solve seemingly classically intractable instances. Published by the American Physical Society 2024
97 MATHEMATICS AND COMPUTING↗
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction
Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.
Swenson, Nicolas↗
Topological data analysis of task-based fMRI data from experiments on schizophrenia
We use methods from computational algebraic topology to study functional brain networks, in which nodes represent brain regions and weighted edges represent similarity of fMRI time series from each region. With these tools, which allow one to characterize topological invariants such as loops in high-dimensional data, we are able to gain understanding into low-dimensional structures in networks in a way that complements traditional approaches based on pairwise interactions. In the present paper, we analyze networks constructed from task-based fMRI data from schizophrenia patients, healthy controls, and healthy siblings of schizophrenia patients using persistent homology, which allows us to explore the persistence of topological structures such as loops at different scales in the networks. We use persistence landscapes, persistence images, and Betti curves to create output summaries from our persistent-homology calculations, and we study the persistence landscapes and images using k-means clustering and community detection. Based on our analysis of persistence landscapes, we find that the members of the sibling cohort have topological features (specifically, their 1-dimensional loops) that are distinct from the other two cohorts. From the persistence images, we are able to distinguish all three subject groups and to determine the brain regions in the loops (with four or more edges) that allow us to make these distinctions.
60 APPLIED LIFE SCIENCES↗
Atomic and Electronic Structure in MgO–SiO 2
Understanding disordered structure is difficult due to insufficient information in experimental data. Here, we overcome this issue by using a combination of diffraction and simulation to investigate oxygen packing and network topology in glassy (g-) and liquid (l-) MgO–SiO 2 based on a comparison with the crystalline topology. We find that packing of oxygen atoms in Mg 2 SiO 4 is larger than that in MgSiO 3 , and that of the glasses is larger than that of the liquids. Moreover, topological analysis suggests that topological similarity between crystalline (c)- and g-(l-) Mg 2 SiO 4 is the signature of low glass-forming ability (GFA), and high GFA g-(l-) MgSiO 3 shows a unique glass topology, which is different from c-MgSiO 3 . We also find that the lowest unoccupied molecular orbital (LUMO) is a free electron-like state at a void site of magnesium atom arising from decreased oxygen coordination, which is far away from crystalline oxides in which LUMO is occupied by oxygen’s 3s orbital state in g- and l-MgO–SiO 2 , suggesting that electronic structure does not play an important role to determine GFA. We finally concluded the GFA of MgO–SiO 2 binary is dominated by the atomic structure in terms of network topology.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗