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David N. Tse

Publications and source records attributed to David N. Tse.

3 recordsLinked to original sources

Bandit-Based Monte Carlo Optimization for Nearest Neighbors

The celebrated Monte Carlo method estimates an expensive-to-compute quantity by random sampling. Bandit-based Monte Carlo optimization is a general technique for computing the minimum of many such expensive-to-compute quantities by adaptive random sampling. The technique converts an optimization problem into a statistical estimation problem which is then solved via multi-armed bandits. We apply this technique to solve the problem of high-dimensional $k$-nearest neighbors, developing an algorithm which we prove is able to identify exact nearest neighbors with high probability. We show that under regularity assumptions on a dataset of $n$ points in $d$-dimensional space, the complexity of our algorithm scales logarithmically with the dimension of the data as $O\left((n+d)\log^2 \left(\frac{nd}δ\right)\right)$ for error probability $δ$, rather than linearly as in exact computation requiring $O(nd)$. We corroborate our theoretical results with numerical simulations, showing that our algorithm outperforms both exact computation and state-of-the-art algorithms such as kGraph, NGT, and LSH on real datasets.

cs.LG

Ultra Fast Medoid Identification via Correlated Sequential Halving

The medoid of a set of n points is the point in the set that minimizes the sum of distances to other points. It can be determined exactly in O(n^2) time by computing the distances between all pairs of points. Previous works show that one can significantly reduce the number of distance computations needed by adaptively querying distances. The resulting randomized algorithm is obtained by a direct conversion of the computation problem to a multi-armed bandit statistical inference problem. In this work, we show that we can better exploit the structure of the underlying computation problem by modifying the traditional bandit sampling strategy and using it in conjunction with a suitably chosen multi-armed bandit algorithm. Four to five orders of magnitude gains over exact computation are obtained on real data, in terms of both number of distance computations needed and wall clock time. Theoretical results are obtained to quantify such gains in terms of data parameters. Our code is publicly available online at https://github.com/TavorB/Correlated-Sequential-Halving.

cs.LG

Partial DNA Assembly: A Rate-Distortion Perspective

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the assembly graph, each of which correspond to a candidate assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an assembly graph and analyze its performance on real genomes.

cs.IT