EE Systems Seminar

Wednesday April 18, 2018 4:15 PM

Recovering a hidden hamiltonian cycle via linear programming

Speaker: Yihong Wu, Department of Statistics and Data Science, Yale University
Location: Moore B280

Abstract: One of the most pressing challenges in genomics is to reconstruct a long and contiguous DNA sequence from short DNA subsequences (contigs). Enabled by very recent developments in sequencing technology one can now obtain linkage information that is statistically correlated with the true contig ordering, so that many links are observed between neighboring pairs of contigs, while relatively few links are observed for non-neighboring pairs.

Representing contigs as vertices and observed numbers of links between contigs as edge weights, the problem of contig assembly reduces to a Travelling Salesman Problem (TSP) in a weighted complete graph of size $n$ with a hidden Hamiltonian cycle corresponding to the true ordering. We assume a statistical model where the edge weights on the hidden Hamiltonian cycle are drawn independently from a distribution $P_n$, while the remaining edge weights are drawn independently from $Q_n$. Despite the worst-case intractability of solving the TSP, we show that a simple linear programming (LP) relaxation, namely the fractional $2$-factor (F2F) LP, recovers the hidden Hamiltonian cycle with probability tending to one as $n to infty$ provided that $alpha_n - log n \to \infty$, where $\alpha_n \triangleq -2 \log \int \sqrt{dP_n dQ_n}$. This condition is information-theoretically optimal in the sense that, under mild distributional assumptions, $\alpha_n \geq (1+o(1) \log n$ is necessary for any algorithm to succeed regardless of the computational cost.

The analysis relies on the combinatorial characterization (in particular, the half-integrality) of vertices of the F2F polytope and the representation of extremal solutions as bicolored multi-graphs, which can be further decomposed into simpler ``blossom-type'' structures whose statistical deviation can be controlled.

This is joint work with Vivek Bagaria (Stanford), Jian Ding (Penn), David Tse (Stanford), and Jiaming Xu (Purdue).

Bio: Yihong Wu is an assistant professor in the Department of Statistics and Data Science at Yale University. He received his Ph.D. degree from Princeton University in 2011. He was a postdoctoral fellow with the Statistics Department in The Wharton School at the University of Pennsylvania from 2011 to 2012 and an assistant professor in the Department of ECE at the University of Illinois at Urbana-Champaign from 2013 to 2016. His research interests are in the theoretical and algorithmic aspects of high-dimensional statistics and information theory. He was a recipient of the NSF CAREER award in 2017 and Sloan Research Fellowship in Mathematics in 2018.


Series Electrical Engineering Systems Seminar Series

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