Mikael Vejdemo-Johansson

Extracting insights from the shape of complex data using topology

This paper applies topological methods to study complex high dimensional data sets by extracting shapes (patterns) and obtaining insights about them. Our method combines the best features of existing standard methodologies such as principal component and cluster analyses to provide a geometric representation of complex data sets. Through this hybrid method, we often find subgroups in data sets that traditional methodologies fail to find. Our method also permits the analysis of individual data sets as well as the analysis of relationships between related data sets. We illustrate the use of our method by applying it to three very different kinds of data, namely gene expression from breast tumors, voting data from the United States House of Representatives and player performance data from the NBA, in each case finding stratifications of the data which are more refined than those produced by standard methods.

javaPlex: A Research Software Package for Persistent (Co)Homology

The computation of persistent homology has proven a fundamental component of the nascent field of topological data analysis and computational topology. We describe a new software package for topological computation, with design focus on needs of the research community. This tool, replacing previous jPlex and Plex, enables researchers to access state of the art algorithms for persistent homology, cohomology, hom complexes, filtered simplicial complexes, filtered cell complexes, witness complex constructions, and many more essential components of computational topology.

Dualities in persistent (co)homology

We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establish algebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existing algorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. We present experimental evidence for the practical efficiency of the latter algorithm.

Persistent cohomology and circular coordinates

Nonlinear dimensionality reduction (NLDR) algorithms such as Isomap, LLE and Laplacian Eigenmaps address the problem of representing high-dimensional nonlinear data in terms of low-dimensional coordinates which represent the intrinsic structure of the data. This paradigm incorporates the assumption that real-valued coordinates provide a rich enough class of functions to represent the data faithfully and efficiently. On the other hand, there are simple structures which challenge this assumption: the circle, for example, is one-dimensional but its faithful representation requires two real coordinates. In this work, we present a strategy for constructing circle-valued functions on a statistical data set. We develop a machinery of persistent cohomology to identify candidates for significant circle-structures in the data, and we use harmonic smoothing and integration to obtain the circle-valued coordinate functions themselves. We suggest that this enriched class of coordinate functions permits a precise NLDR analysis of a broader range of realistic data sets.

Branching and Circular Features in High Dimensional Data

Large observations and simulations in scientific research give rise to high-dimensional data sets that present many challenges and opportunities in data analysis and visualization. Researchers in application domains such as engineering, computational biology, climate study, imaging and motion capture are faced with the problem of how to discover compact representations of highdimensional data while preserving their intrinsic structure. In many applications, the original data is projected onto low-dimensional space via dimensionality reduction techniques prior to modeling. One problem with this approach is that the projection step in the process can fail to preserve structure in the data that is only apparent in high dimensions. Conversely, such techniques may create structural illusions in the projection, implying structure not present in the original high-dimensional data. Our solution is to utilize topological techniques to recover important structures in high-dimensional data that contains non-trivial topology. Specifically, we are interested in high-dimensional branching structures. We construct local circle-valued coordinate functions to represent such features. Subsequently, we perform dimensionality reduction on the data while ensuring such structures are visually preserved. Additionally, we study the effects of global circular structures on visualizations. Our results reveal never-before-seen structures on real-world data sets from a variety of applications.

Cohomological learning of periodic motion

This work develops a novel framework which can automatically detect, parameterize and interpolate periodic motion patterns obtained from a motion capture sequence. Using our framework, periodic motions such as walking and running gaits or any motion sequence with periodic structure such as cleaning, dancing etc. can be detected automatically and without manual marking of the period start and end points. Our approach constructs an intrinsic parameterization of the motion and is computationally fast. Using this parameterization, we are able generate prototypical periodic motions. Additionally, we are able to interpolate between various motions, yielding a rich class of ‘mixed’ periodic actions. Our approach is based on ideas from applied algebraic topology. In particular, we apply a novel persistent cohomology based method for the first time in a graphics application which enables us to recover circular coordinates of motions. We also develop a suitable notion of homotopy which can be used to interpolate between periodic motion patterns. Our framework is directly applicable to the construction of walk cycles for animating character motions with motion graphs or state machine driven animation engines and processed our examples at an average speed of 11.78 frames per secondGraphical abstract

Automatic Recognition and Tagging of Topologically Different Regimes in Dynamical Systems

Complex systems are commonly modeled using nonlinear dynamical systems. These models are often high-dimensional and chaotic. An important goal in studying physical systems through the lens of mathematical models is to determine when the system undergoes changes in qualitative behavior. A detailed description of the dynamics can be difficult or impossible to obtain for high-dimensional and chaotic systems. Therefore, a more sensible goal is to recognize and mark transitions of a system between qualitatively different regimes of behavior. In practice, one is interested in developing techniques for detection of such transitions from sparse observations, possibly contaminated by noise. In this paper we develop a framework to accurately tag different regimes of complex systems based on topological features. In particular, our framework works with a high degree of success in picking out a cyclically orbiting regime from a stationary equilibrium regime in high-dimensional stochastic dynamical systems.

Sketches of a platypus : persistent homology and its algebraic foundations

Let k be a regular F_p-algebra, let A = k[x,y]/(x^b - y^a) be the coordinate ring of a planar cuspical curve, and let I = (x,y) be the ideal that defines the cusp point. We give a formula for the relative K-groups K_q(A,I) in terms of the groups of de Rham-Witt forms of the ring k. At present, the validity of the formula depends on a conjecture that concerns the combinatorial structure of a new family of polytopes that we call stunted regular cyclic polytopes. The polytopes in question appear as the intersections of regular cyclic polytopes with (certain) linear subspaces. We verify low-dimensional cases of the conjecture. This leads to unconditional new results on K_2 and K_3 which extend earlier results by Krusemeyer for K_0 and K_1.

Comparing Distributions of Color Words : Pitfalls and Metric Choices

Computational methods have started playing a significant role in semantic analysis. One particularly accessible area for developing good computational methods for linguistic semantics is in color naming, where perceptual dissimilarity measures provide a geometric setting for the analyses. This setting has been studied first by Berlin & Kay in 1969, and then later on by a large data collection effort: the World Color Survey (WCS). From the WCS, a dataset on color naming by 2 616 speakers of 110 different languages is made available for further research. In the analysis of color naming from WCS, however, the choice of analysis method is an important factor of the analysis. We demonstrate concrete problems with the choice of metrics made in recent analyses of WCS data, and offer approaches for dealing with the problems we can identify. Picking a metric for the space of color naming distributions that ignores perceptual distances between colors assumes a decorrelated system, where strong spatial correlations in fact exist. We can demonstrate that the corresponding issues are significantly improved when using Earth Movers Distance, or Quadratic -square Distance, and we can approximate these solutions with a kernel-based analysis method.

More ties than we thought

We extend the existing enumeration of neck tie-knots to include tie-knots with a textured front, tied with the narrow end of a tie. These tie-knots have gained popularity in recent years, based on reconstructions of a costume detail from The Matrix Reloaded, and are explicitly ruled out in the enumeration by Fink and Mao (2000). We show that the relaxed tie-knot description language that comprehensively describes these extended tie-knot classes is context free. It has a regular sub-language that covers all the knots that originally inspired the work. From the full language, we enumerate 266682 distinct tie-knots that seem tie-able with a normal neck-tie. Out of these 266682, we also enumerate 24882 tie-knots that belong to the regular sub-language.