Principal manifolds and graphs in practice: from molecular biology to dynamical systems

We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.Comment: 12 pages, 9 figure

Representing complex data using localized principal components with application to astronomical data

Often the relation between the variables constituting a multivariate data space might be characterized by one or more of the terms: ``nonlinear'', ``branched'', ``disconnected'', ``bended'', ``curved'', ``heterogeneous'', or, more general, ``complex''. In these cases, simple principal component analysis (PCA) as a tool for dimension reduction can fail badly. Of the many alternative approaches proposed so far, local approximations of PCA are among the most promising. This paper will give a short review of localized versions of PCA, focusing on local principal curves and local partitioning algorithms. Furthermore we discuss projections other than the local principal components. When performing local dimension reduction for regression or classification problems it is important to focus not only on the manifold structure of the covariates, but also on the response variable(s). Local principal components only achieve the former, whereas localized regression approaches concentrate on the latter. Local projection directions derived from the partial least squares (PLS) algorithm offer an interesting trade-off between these two objectives. We apply these methods to several real data sets. In particular, we consider simulated astrophysical data from the future Galactic survey mission Gaia.Comment: 25 pages. In "Principal Manifolds for Data Visualization and Dimension Reduction", A. Gorban, B. Kegl, D. Wunsch, and A. Zinovyev (eds), Lecture Notes in Computational Science and Engineering, Springer, 2007, pp. 180--204, http://www.springer.com/dal/home/generic/search/results?SGWID=1-40109-22-173750210-

PHom-GeM: Persistent Homology for Generative Models

Generative neural network models, including Generative Adversarial Network (GAN) and Auto-Encoders (AE), are among the most popular neural network models to generate adversarial data. The GAN model is composed of a generator that produces synthetic data and of a discriminator that discriminates between the generator's output and the true data. AE consist of an encoder which maps the model distribution to a latent manifold and of a decoder which maps the latent manifold to a reconstructed distribution. However, generative models are known to provoke chaotically scattered reconstructed distribution during their training, and consequently, incomplete generated adversarial distributions. Current distance measures fail to address this problem because they are not able to acknowledge the shape of the data manifold, i.e. its topological features, and the scale at which the manifold should be analyzed. We propose Persistent Homology for Generative Models, PHom-GeM, a new methodology to assess and measure the distribution of a generative model. PHom-GeM minimizes an objective function between the true and the reconstructed distributions and uses persistent homology, the study of the topological features of a space at different spatial resolutions, to compare the nature of the true and the generated distributions. Our experiments underline the potential of persistent homology for Wasserstein GAN in comparison to Wasserstein AE and Variational AE. The experiments are conducted on a real-world data set particularly challenging for traditional distance measures and generative neural network models. PHom-GeM is the first methodology to propose a topological distance measure, the bottleneck distance, for generative models used to compare adversarial samples in the context of credit card transactions

Dimension reduction for linear separation with curvilinear distances

Any high dimensional data in its original raw form may contain obviously classifiable clusters which are difficult to identify given the high-dimension representation. In reducing the dimensions it may be possible to perform a simple classification technique to extract this cluster information whilst retaining the overall topology of the data set. The supervised method presented here takes a high dimension data set consisting of multiple clusters and employs curvilinear distance as a relation between points, projecting in a lower dimension according to this relationship. This representation allows for linear separation of the non-separable high dimensional cluster data and the classification to a cluster of any successive unseen data point extracted from the same higher dimension

Visualization of AE's Training on Credit Card Transactions with Persistent Homology

Auto-encoders are among the most popular neural network architecture for dimension reduction. They are composed of two parts: the encoder which maps the model distribution to a latent manifold and the decoder which maps the latent manifold to a reconstructed distribution. However, auto-encoders are known to provoke chaotically scattered data distribution in the latent manifold resulting in an incomplete reconstructed distribution. Current distance measures fail to detect this problem because they are not able to acknowledge the shape of the data manifolds, i.e. their topological features, and the scale at which the manifolds should be analyzed. We propose Persistent Homology for Wasserstein Auto-Encoders, called PHom-WAE, a new methodology to assess and measure the data distribution of a generative model. PHom-WAE minimizes the Wasserstein distance between the true distribution and the reconstructed distribution and uses persistent homology, the study of the topological features of a space at different spatial resolutions, to compare the nature of the latent manifold and the reconstructed distribution. Our experiments underline the potential of persistent homology for Wasserstein Auto-Encoders in comparison to Variational Auto-Encoders, another type of generative model. The experiments are conducted on a real-world data set particularly challenging for traditional distance measures and auto-encoders. PHom-WAE is the first methodology to propose a topological distance measure, the bottleneck distance, for Wasserstein Auto-Encoders used to compare decoded samples of high quality in the context of credit card transactions.Comment: arXiv admin note: substantial text overlap with arXiv:1905.0989