results for au:Krishnamoorthy_B in:cs

- Phenomics is an emerging branch of modern biology, which uses high throughput phenotyping tools to capture multiple environment and phenotypic trait measurements, at a massive scale. The resulting high dimensional data sets represent a treasure trove of information for providing an indepth understanding of how multiple factors interact and contribute to control the growth and behavior of different plant crop genotypes. However, computational tools that can parse through such high dimensional data sets and aid in extracting plausible hypothesis are currently lacking. In this paper, we present a new algorithmic approach to effectively decode and characterize the role of environment on phenotypic traits, from complex phenomic data. To the best of our knowledge, this effort represents the first application of topological data analysis on phenomics data. We applied this novel algorithmic approach on a real-world maize data set. Our results demonstrate the ability of our approach to delineate emergent behavior among subpopulations, as dictated by one or more environmental factors; notably, our approach shows how the environment plays a key role in determining the phenotypic behavior of one of the two genotypes. Source code for our implementation and test data are freely available with detailed instructions at https://xperthut.github.io/HYPPO-X.
- We had recently shown that every positive integer can be represented uniquely using a recurrence sequence, when certain restrictions on the digit strings are satisfied. We present the details of how such representations can be used to build a knapsack-like public key cryptosystem. We also present new disguising methods, and provide arguments for the security of the code against known methods of attack.
- Currents represent generalized surfaces studied in geometric measure theory. They range from relatively tame integral currents representing oriented compact manifolds with boundary and integer multiplicities, to arbitrary elements of the dual space of differential forms. The flat norm provides a natural distance in the space of currents, and works by decomposing a $d$-dimensional current into $d$- and (the boundary of) $(d+1)$-dimensional pieces in an optimal way. Given an integral current, can we expect its flat norm decomposition to be integral as well? This is not known in general, except in the case of $d$-currents that are boundaries of $(d+1)$-currents in $\mathbb{R}^{d+1}$ (following results from a corresponding problem on the $L^1$ total variation ($L^1$TV) of functionals). On the other hand, for a discretized flat norm on a finite simplicial complex, the analogous statement holds even when the inputs are not boundaries. This simplicial version relies on the total unimodularity of the boundary matrix of the simplicial complex -- a result distinct from the $L^1$TV approach. We develop an analysis framework that extends the result in the simplicial setting to one for $d$-currents in $\mathbb{R}^{d+1}$, provided a suitable triangulation result holds. In $\mathbb{R}^2$, we use a triangulation result of Shewchuk (bounding both the size and location of small angles), and apply the framework to show that the discrete result implies the continuous result for $1$-currents in $\mathbb{R}^2$.
- Given a simplicial complex K with weights on its simplices and a chain on it, the Optimal Homologous Chain Problem (OHCP) is to find a chain with minimal weight that is homologous (over the integers) to the given chain. The OHCP is NP-complete, but if the boundary matrix of K is totally unimodular (TU), it becomes solvable in polynomial time when modeled as a linear program (LP). We define a condition on the simplicial complex called non total-unimodularity neutralized, or NTU neutralized, which ensures that even when the boundary matrix is not TU, the OHCP LP must contain an integral optimal vertex for every input chain. This condition is a property of K, and is independent of the input chain and the weights on the simplices. This condition is strictly weaker than the boundary matrix being TU. More interestingly, the polytope of the OHCP LP may not be integral under this condition. Still, an integral optimal vertex exists for every right-hand side, i.e., for every input chain. Hence a much larger class of OHCP instances can be solved in polynomial time than previously considered possible. As a special case, we show that 2-complexes with trivial first homology group are guaranteed to be NTU neutralized.
- We study the effect of edge contractions on simplicial homology because these contractions have turned to be useful in various applications involving topology. It was observed previously that contracting edges that satisfy the so called link condition preserves homeomorphism in low dimensional complexes, and homotopy in general. But, checking the link condition involves computation in all dimensions, and hence can be costly, especially in high dimensional complexes. We define a weaker and more local condition called the p-link condition for each dimension p, and study its effect on edge contractions. We prove the following: (i) For homology groups, edges satisfying the p- and (p-1)-link conditions can be contracted without disturbing the p-dimensional homology group. (ii) For relative homology groups, the (p-1)-, and the (p-2)-link conditions suffice to guarantee that the contraction does not introduce any new class in any of the resulting relative homology groups, though some of the existing classes can be destroyed. Unfortunately, the surjection in relative homolgy groups does not guarantee that no new relative torsion is created. (iii) For torsions, edges satisfying the p-link condition alone can be contracted without creating any new relative torsion and the p-link condition cannot be avoided. The results on relative homology and relative torsion are motivated by recent results on computing optimal homologous chains, which state that such problems can be solved by linear programming if the complex has no relative torsion. Edge contractions that do not introduce new relative torsions, can safely be availed in these contexts.
- We study the multiscale simplicial flat norm (MSFN) problem, which computes flat norm at various scales of sets defined as oriented subcomplexes of finite simplicial complexes in arbitrary dimensions. We show that the multiscale simplicial flat norm is NP-complete when homology is defined over integers. We cast the multiscale simplicial flat norm as an instance of integer linear optimization. Following recent results on related problems, the multiscale simplicial flat norm integer program can be solved in polynomial time by solving its linear programming relaxation, when the simplicial complex satisfies a simple topological condition (absence of relative torsion). Our most significant contribution is the simplicial deformation theorem, which states that one may approximate a general current with a simplicial current while bounding the expansion of its mass. We present explicit bounds on the quality of this approximation, which indicate that the simplicial current gets closer to the original current as we make the simplicial complex finer. The multiscale simplicial flat norm opens up the possibilities of using flat norm to denoise or extract scale information of large data sets in arbitrary dimensions. On the other hand, it allows one to employ the large body of algorithmic results on simplicial complexes to address more general problems related to currents.
- Given a simplicial complex with weights on its simplices, and a nontrivial cycle on it, we are interested in finding the cycle with minimal weight which is homologous to the given one. Assuming that the homology is defined with integer coefficients, we show the following : For a finite simplicial complex $K$ of dimension greater than $p$, the boundary matrix $[\partial_{p+1}]$ is totally unimodular if and only if $H_p(L, L_0)$ is torsion-free, for all pure subcomplexes $L_0, L$ in $K$ of dimensions $p$ and $p+1$ respectively, where $L_0$ is a subset of $L$. Because of the total unimodularity of the boundary matrix, we can solve the optimization problem, which is inherently an integer programming problem, as a linear program and obtain integer solution. Thus the problem of finding optimal cycles in a given homology class can be solved in polynomial time. This result is surprising in the backdrop of a recent result which says that the problem is NP-hard under $\mathbb{Z}_2$ coefficients which, being a field, is in general easier to deal with. One consequence of our result, among others, is that one can compute in polynomial time an optimal 2-cycle in a given homology class for any finite simplicial complex embedded in $\mathbb{R}^3$. Our optimization approach can also be used for various related problems, such as finding an optimal chain homologous to a given one when these are not cycles.