Quantifying Homology Classes

We develop a method for measuring homology classes. This involves three problems. First, we define the size of a homology class, using ideas from relative homology. Second, we define an optimal basis of a homology group to be the basis whose elements' size have the minimal sum. We provide a greedy algorithm to compute the optimal basis and measure classes in it. The algorithm runs in $O(\beta^4 n^3 \log^2 n)$ time, where $n$ is the size of the simplicial complex and $\beta$ is the Betti number of the homology group. Third, we discuss different ways of localizing homology classes and prove some hardness results

A topological approach for protein classification

Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity be- tween proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics. Persistent homology is a new branch of algebraic topology that has found its success in the topological data analysis in a variety of disciplines, including molecular biology. The present work explores the potential of using persistent homology as an indepen- dent tool for protein classification. To this end, we propose a molecular topological fingerprint based support vector machine (MTF-SVM) classifier. Specifically, we construct machine learning feature vectors solely from protein topological fingerprints, which are topological invariants generated during the filtration process. To validate the present MTF-SVM approach, we consider four types of problems. First, we study protein-drug binding by using the M2 channel protein of influenza A virus. We achieve 96% accuracy in discriminating drug bound and unbound M2 channels. Additionally, we examine the use of MTF-SVM for the classification of hemoglobin molecules in their relaxed and taut forms and obtain about 80% accuracy. The identification of all alpha, all beta, and alpha-beta protein domains is carried out in our next study using 900 proteins. We have found a 85% success in this identifica- tion. Finally, we apply the present technique to 55 classification tasks of protein superfamilies over 1357 samples. An average accuracy of 82% is attained. The present study establishes computational topology as an independent and effective alternative for protein classification

Parametrized Homology via Zigzag Persistence

This paper develops the idea of homology for 1-parameter families of topological spaces. We express parametrized homology as a collection of real intervals with each corresponding to a homological feature supported over that interval or, equivalently, as a persistence diagram. By defining persistence in terms of finite rectangle measures, we classify barcode intervals into four classes. Each of these conveys how the homological features perish at both ends of the interval over which they are defined

Topological Machine Learning with Persistence Indicator Functions

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 scaling, while providing a firm theoretical ground. Many modern machine learning algorithms, however, are based on kernels. This paper presents persistence indicator functions (PIFs), which summarize persistence diagrams, i.e., feature descriptors in topological data analysis. PIFs can be calculated and compared in linear time and have many beneficial properties, such as the availability of a kernel-based similarity measure. We demonstrate their usage in common data analysis scenarios, such as confidence set estimation and classification of complex structured data.Comment: Topology-based Methods in Visualization 201