Topological data analysis is an emerging mathematical concept for characterizing shapes in multi-scale data. In this field, persistence diagrams are widely used as a descriptor of the input data, and can distinguish robust and noisy topological properties. Nowadays, it is highly desired to develop a statistical framework on persistence diagrams to deal with practical data. This paper proposes a kernel method on persistence diagrams. A theoretical contribution of our method is that the proposed kernel allows one to control the effect of persistence, and, if necessary, noisy topological properties can be discounted in data analysis. Furthermore, the method provides a fast approximation technique. The method is applied into several problems including practical data in physics, and the results show the advantage compared to the existing kernel method on persistence diagrams.
This paper is an extended version of our ICML paper @cite_46 . The difference from this conference version is as follows: (i) Comparisons with other relevant methods, in particular, persistence landscapes and persistence images, have been added to this version. (ii) New experimental results in comparison with other relevant methods. (iii) Detailed proofs of the stability theorem has been added.
@cite_46
2963754066 2408772186 2605102252 2122101130
A standard way of approximating or discretizing a metric space is by taking its Rips complexes. These approximations for all parameters are often bound together into a filtration, to which we apply the fundamental group or the first homology. We call the resulting object persistence. Recent results demonstrate that persistence of a compact geodesic locally contractible space X carries a lot of geometric information. However, by definition the corresponding Rips complexes have uncountably many vertices. In this paper we show that nonetheless, the whole persistence of X may be obtained by an appropriate finite sample (subset of X), and that persistence of any subset of X is well interleaved with the persistence of X. It follows that the persistence of X is the minimum of persistences obtained by all finite samples. Furthermore, we prove a much improved Stability theorem for such approximations. As a special case we provide for each (r>0 ) a density (s>0 ), so that for each s-dense sample (S X ) the corresponding fundamental group (and the first homology) of the Rips complex of S is isomorphic to the one of X, leading to an improved reconstruction result. Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues. Furthermore, persistence landscapes can be applied to machine learning methods. A hyperplane from a support vector machine shows the clear separation between the closed and open proteins conformations. Moreover, because our approach captures dynamical properties of the protein our results may help in identifying residues susceptible to ligand binding; we show that the majority of active site residues and allosteric pathway residues are located in the vicinity of the most persistent loop in the corresponding filtered Vietoris-Rips complex. This finding was not observed in the classical anisotropic network model. We address the problem of distance metric learning (DML), defined as learning a distance consistent with a notion of semantic similarity. Traditionally, for this problem supervision is expressed in the form of sets of points that follow an ordinal relationship – an anchor point x is similar to a set of positive points Y , and dissimilar to a set of negative points Z, and a loss defined over these distances is minimized. While the specifics of the optimization differ, in this work we collectively call this type of supervision Triplets and all methods that follow this pattern Triplet-Based methods. These methods are challenging to optimize. A main issue is the need for finding informative triplets, which is usually achieved by a variety of tricks such as increasing the batch size, hard or semi-hard triplet mining, etc. Even with these tricks, the convergence rate of such methods is slow. In this paper we propose to optimize the triplet loss on a different space of triplets, consisting of an anchor data point and similar and dissimilar proxy points which are learned as well. These proxies approximate the original data points, so that a triplet loss over the proxies is a tight upper bound of the original loss. This proxy-based loss is empirically better behaved. As a result, the proxy-loss improves on state-of-art results for three standard zero-shot learning datasets, by up to 15 points, while converging three times as fast as other triplet-based losses. We prove two stability results for Lipschitz functions on triangulable, compact metric spaces and consider applications of both to problems in systems biology. Given two functions, the first result is formulated in terms of the Wasserstein distance between their persistence diagrams and the second in terms of their total persistence.