Polytope of Correct (Linear Programming) Decoding and Low-Weight Pseudo-Codewords

We analyze Linear Programming (LP) decoding of graphical binary codes operating over soft-output, symmetric and log-concave channels. We show that the error-surface, separating domain of the correct decoding from domain of the erroneous decoding, is a polytope. We formulate the problem of finding the lowest-weight pseudo-codeword as a non-convex optimization (maximization of a convex function) over a polytope, with the cost function defined by the channel and the polytope defined by the structure of the code. This formulation suggests new provably convergent heuristics for finding the lowest weight pseudo-codewords improving in quality upon previously discussed. The algorithm performance is tested on the example of the Tanner [155, 64, 20] code over the Additive White Gaussian Noise (AWGN) channel.Comment: 6 pages, 2 figures, accepted for IEEE ISIT 201

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.Comment: 17 pages, 8 figure

Practical and Optimal LSH for Angular Distance

We show the existence of a Locality-Sensitive Hashing (LSH) family for the angular distance that yields an approximate Near Neighbor Search algorithm with the asymptotically optimal running time exponent. Unlike earlier algorithms with this property (e.g., Spherical LSH [Andoni, Indyk, Nguyen, Razenshteyn 2014], [Andoni, Razenshteyn 2015]), our algorithm is also practical, improving upon the well-studied hyperplane LSH [Charikar, 2002] in practice. We also introduce a multiprobe version of this algorithm, and conduct experimental evaluation on real and synthetic data sets. We complement the above positive results with a fine-grained lower bound for the quality of any LSH family for angular distance. Our lower bound implies that the above LSH family exhibits a trade-off between evaluation time and quality that is close to optimal for a natural class of LSH functions.Comment: 22 pages, an extended abstract is to appear in the proceedings of the 29th Annual Conference on Neural Information Processing Systems (NIPS 2015

Tradeoffs for nearest neighbors on the sphere

We consider tradeoffs between the query and update complexities for the (approximate) nearest neighbor problem on the sphere, extending the recent spherical filters to sparse regimes and generalizing the scheme and analysis to account for different tradeoffs. In a nutshell, for the sparse regime the tradeoff between the query complexity $n^{\rho_q}$ and update complexity $n^{\rho_u}$ for data sets of size $n$ is given by the following equation in terms of the approximation factor $c$ and the exponents $\rho_q$ and $\rho_u$: $$c^2\sqrt{\rho_q}+(c^2-1)\sqrt{\rho_u}=\sqrt{2c^2-1}.$$ For small $c=1+\epsilon$, minimizing the time for updates leads to a linear space complexity at the cost of a query time complexity $n^{1-4\epsilon^2}$. Balancing the query and update costs leads to optimal complexities $n^{1/(2c^2-1)}$, matching bounds from [Andoni-Razenshteyn, 2015] and [Dubiner, IEEE-TIT'10] and matching the asymptotic complexities of [Andoni-Razenshteyn, STOC'15] and [Andoni-Indyk-Laarhoven-Razenshteyn-Schmidt, NIPS'15]. A subpolynomial query time complexity $n^{o(1)}$ can be achieved at the cost of a space complexity of the order $n^{1/(4\epsilon^2)}$, matching the bound $n^{\Omega(1/\epsilon^2)}$ of [Andoni-Indyk-Patrascu, FOCS'06] and [Panigrahy-Talwar-Wieder, FOCS'10] and improving upon results of [Indyk-Motwani, STOC'98] and [Kushilevitz-Ostrovsky-Rabani, STOC'98]. For large $c$, minimizing the update complexity results in a query complexity of $n^{2/c^2+O(1/c^4)}$, improving upon the related exponent for large $c$ of [Kapralov, PODS'15] by a factor $2$, and matching the bound $n^{\Omega(1/c^2)}$ of [Panigrahy-Talwar-Wieder, FOCS'08]. Balancing the costs leads to optimal complexities $n^{1/(2c^2-1)}$, while a minimum query time complexity can be achieved with update complexity $n^{2/c^2+O(1/c^4)}$, improving upon the previous best exponents of Kapralov by a factor $2$.Comment: 16 pages, 1 table, 2 figures. Mostly subsumed by arXiv:1608.03580 [cs.DS] (along with arXiv:1605.02701 [cs.DS]

A Novel Symmetric Four Dimensional Polytope Found Using Optimization Strategies Inspired by Thomson's Problem of Charges on a Sphere

Inspired by, and using methods of optimization derived from classical three dimensional electrostatics, we note a novel beautiful symmetric four dimensional polytope we have found with 80 vertices. We also describe how the method used to find this symmetric polytope, and related methods can potentially be used to find good examples for the kissing and packing problems in D dimensions