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Mingzhou Song

Publications and source records attributed to Mingzhou Song.

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Fast Exact k-Means, k-Medians and Bregman Divergence Clustering in 1D

The $k$-Means clustering problem on $n$ points is NP-Hard for any dimension $d\ge 2$, however, for the 1D case there exists exact polynomial time algorithms. Previous literature reported an $O(kn^2)$ time dynamic programming algorithm that uses $O(kn)$ space. It turns out that the problem has been considered under a different name more than twenty years ago. We present all the existing work that had been overlooked and compare the various solutions theoretically. Moreover, we show how to reduce the space usage for some of them, as well as generalize them to data structures that can quickly report an optimal $k$-Means clustering for any $k$. Finally we also generalize all the algorithms to work for the absolute distance and to work for any Bregman Divergence. We complement our theoretical contributions by experiments that compare the practical performance of the various algorithms.

cs.DS

Deciphering Interactions in Causal Networks without Parametric Assumptions

With the assumption that the effect is a mathematical function of the cause in a causal relationship, FunChisq, a chi-square test defined on a non-parametric representation of interactions, infers network topology considering both interaction directionality and nonlinearity. Here we show that both experimental and in silico biological network data suggest the importance of directionality as evidence for causality. Counter-intuitively, patterns in those interactions effectively revealed by FunChisq enlist an experimental design principle essential to network inference -- perturbations to a biological system shall make it transits between linear and nonlinear working zones, instead of operating only in a linear working zone.

q-bio.MN