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Information networks are becoming increasingly popular to capture complex relationships across various disciplines, such as social networks, citation networks, and biological networks. The primary challenge in this domain is measuring…
The machinery of topological data analysis becomes increasingly popular in a broad range of machine learning tasks, ranging from anomaly detection and manifold learning to graph classification. Persistent homology is one of the key…
Topological data analysis uses tools from topology -- the mathematical area that studies shapes -- to create representations of data. In particular, in persistent homology, one studies one-parameter families of spaces associated with data,…
Persistent homology analysis provides means to capture the connectivity structure of data sets in various dimensions. On the mathematical level, by defining a metric between the objects that persistence attaches to data sets, we can…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Visualization in the emerging field of topological data analysis has progressed from persistence barcodes and persistence diagrams to display of two-parameter persistent homology. Although persistence barcodes and diagrams have permitted…
We introduce a new feature map for barcodes that arise in persistent homology computation. The main idea is to first realize each barcode as a path in a convenient vector space, and to then compute its path signature which takes values in…
Persistent homology (PH) is a recently developed theory in the field of algebraic topology to study shapes of datasets. It is an effective data analysis tool that is robust to noise and has been widely applied. We demonstrate a general…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
Persistent Homology (PH) is a fundamental tool in computational topology, designed to uncover the intrinsic geometric and topological features of data across multiple scales. Originating within the broader framework of Topological Data…
In this work, we develop a pipeline that associates Persistence Diagrams to digital data via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation…
Persistent homology is a method for computing the topological features present in a given data. Recently, there has been much interest in the integration of persistent homology as a computational step in neural networks or deep learning. In…
Popular network models such as the mixed membership and standard stochastic block model are known to exhibit distinct geometric structure when embedded into $\mathbb{R}^{d}$ using spectral methods. The resulting point cloud concentrates…
Persistent homology is a popular technique in topological data analysis that tracks the lifespans of homological features in a nested sequence of spaces. This data is typically presented in a multi-set called a persistence diagram or a…
This article studies the robust version of persistent homology based on trimming methodology to capture the geometric feature through support of the data in presence of outliers. Precisely speaking, the proposed methodology works when the…
Topological data analysis is a relatively new branch of machine learning that excels in studying high dimensional data, and is theoretically known to be robust against noise. Meanwhile, data objects with mixed numeric and categorical…
Persistent homology has been devised as a promising tool for the topological simplification of complex data. However, it is computationally intractable for large data sets. In this work, we introduce multiresolution persistent homology for…
Techniques from computational topology, in particular persistent homology, are becoming increasingly relevant for data analysis. Their stable metrics permit the use of many distance-based data analysis methods, such as multidimensional…
Persistent homology is a popular tool in Topological Data Analysis. It provides numerical characteristics of data sets which reflect global geometric properties. In order to be useful in practice, for example for feature generation in…
In Topological Data Analysis, a common way of quantifying the shape of data is to use a persistence diagram (PD). PDs are multisets of points in $\mathbb{R}^2$ computed using tools of algebraic topology. However, this multi-set structure…