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The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
In the dynamic metric $k$-median problem, we wish to maintain a set of $k$ centers $S \subseteq V$ in an input metric space $(V, d)$ that gets updated via point insertions/deletions, so as to minimize the objective $\sum_{x \in V} \min_{y…
Matrix completion is the problem of recovering a low rank matrix by observing a small fraction of its entries. A series of recent works [KOM12,JNS13,HW14] have proposed fast non-convex optimization based iterative algorithms to solve this…
Estimating the density of a distribution from its samples is a fundamental problem in statistics. Hypothesis selection addresses the setting where, in addition to a sample set, we are given $n$ candidate distributions -- referred to as…
In the $k$-mismatch problem we are given a pattern of length $n$ and a text and must find all locations where the Hamming distance between the pattern and the text is at most $k$. A series of recent breakthroughs have resulted in an…
Algorithms often carry out equally many computations for "easy" and "hard" problem instances. In particular, algorithms for finding nearest neighbors typically have the same running time regardless of the particular problem instance. In…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
A distance matrix $A \in \mathbb R^{n \times m}$ represents all pairwise distances, $A_{ij}=\mathrm{d}(x_i,y_j)$, between two point sets $x_1,...,x_n$ and $y_1,...,y_m$ in an arbitrary metric space $(\mathcal Z, \mathrm{d})$. Such matrices…
Capacitated k-median is one of the few outstanding optimization problems for which the existence of a polynomial time constant factor approximation algorithm remains an open problem. In a series of recent papers algorithms producing…
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…
We present deterministic algorithms for maintaining a $(3/2 + \epsilon)$ and $(2 + \epsilon)$-approximate maximum matching in a fully dynamic graph with worst-case update times $\hat{O}(\sqrt{n})$ and $\tilde{O}(1)$ respectively. The…
The min-distance between two nodes $u, v$ is defined as the minimum of the distance from $v$ to $u$ or from $u$ to $v$, and is a natural distance metric in DAGs. As with the standard distance problems, the Strong Exponential Time Hypothesis…
In this paper we study the adaptivity of submodular maximization. Adaptivity quantifies the number of sequential rounds that an algorithm makes when function evaluations can be executed in parallel. Adaptivity is a fundamental concept that…
The metric $k$-median problem is a textbook clustering problem. As input, we are given a metric space $V$ of size $n$ and an integer $k$, and our task is to find a subset $S \subseteq V$ of at most $k$ `centers' that minimizes the total…
The Fr\'echet distance is a popular measure of dissimilarity for polygonal curves. It is defined as a min-max formulation that considers all direction-preserving continuous bijections of the two curves. Because of its susceptibility to…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
Clustering is an important task with applications in many fields of computer science. We study the fully dynamic setting in which we want to maintain good clusters efficiently when input points (from a metric space) can be inserted and…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We engineer an algorithm to solve the approximate dictionary matching problem. Given a list of words $\mathcal{W}$, maximum distance $d$ fixed at preprocessing time and a query word $q$, we would like to retrieve all words from…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…