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Jacob Gilbert

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4 papers
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4

FOCS Conference 2025 Conference Paper

Dynamic Dyck and Tree Edit Distance: Decompositions and Reductions to String Edit Distance

  • Debarati Das 0001
  • Jacob Gilbert
  • MohammadTaghi Hajiaghayi
  • Tomasz Kociumaka
  • Barna Saha

In this paper, we present the first dynamic algorithms for Dyck edit distance and tree edit distance that achieve subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a wellparenthesized expression (i. e. , the Dyck language), while tree edit distance quantifies the minimum number of node insertions, deletions, and substitutions required to transform one rooted, ordered, and labeled tree into another. These problems have been studied extensively since the 1970s, with recent advances in both algorithmic efficiency and fine-grained complexity lower bounds. Despite this progress, no prior work has addressed efficient dynamic algorithms for these problems, even though many real-world applications involve evolving structured data such as LaTeX, JSON, XML, HTML, hierarchical datasets, and RNA secondary structures. We take the first step in this direction by designing new approximation algorithms for Dyck and tree edit distances in the dynamic setting. Our key technical contribution is a set of novel reduction and decomposition techniques that transform instances of Dyck and tree edit distance into efficiently maintainable instances of string edit distance. Leveraging existing dynamic algorithms for string edit distance, we obtain an $n^{o(1)}$ approximation for Dyck edit distance with $n^{o(1)}$ update time. This builds upon and significantly extends prior work on Dyck language decomposition ([Saha, FOCS’14] and [Koucký & Saks; SODA’23]). For tree edit distance, we introduce a new static reduction that improves the best-known approximation bound from $O\left(n^{3 / 4}\right)$ [Akutsu, Fukagawa, and Takasu; Algorithmica, 2010] to $\tilde{O}(\sqrt{n})$. Moreover, while the previous result was restricted to constant-degree trees, ours holds for arbitrary trees. We then extend our reduction dynamically, yielding a dynamic tree edit distance algorithm with an approximation factor of $n^{1 / 2+o(1)}$ and update time $n^{o(1)}$. A core component of our approach is a new dynamic maintenance algorithm for heavy-light decomposition, a widely used technique in tree algorithms. Given its broad applicability, we believe this result is of independent interest. Finally, we introduce a novel static and dynamic decomposition method that achieves an $\tilde{O}(k)$-approximation for tree edit distance when the tree edit distance is at most k; combined with the trivial bound $k \leq n$, this yields a deterministic $\tilde{O}(\sqrt{n})$-approximation. While similar decompositions exist for strings, no prior work has successfully extended them to trees. Our approach breaks this barrier, improving the best-known approximations for tree edit distance both in the static and dynamic setting. In the static setting, our algorithm runs in $\tilde{O}(n)$ time; in the dynamic setting, it only requires a polylogarithmic worst-case update time. The state-of-the-art near-lineartime static algorithm for tree edit distance previously achieved an $O(\sqrt{n})$-approximation [Boroujeni, Ghodsi, Hajiaghayi, and Seddighin; STOC’19].

STOC Conference 2023 Conference Paper

Weighted Edit Distance Computation: Strings, Trees, and Dyck

  • Debarati Das 0001
  • Jacob Gilbert
  • MohammadTaghi Hajiaghayi
  • Tomasz Kociumaka
  • Barna Saha

Given two strings of length n over alphabet Σ, and an upper bound k on their edit distance, the algorithm of Myers (Algorithmica’86) and Landau and Vishkin (JCSS’88) from almost forty years back computes the unweighted string edit distance in O ( n + k 2 ) time. To date, it remains the fastest algorithm for exact edit distance computation, and it is optimal under the Strong Exponential Hypothesis (Backurs and Indyk; STOC’15). Over the years, this result has inspired many developments, including fast approximation algorithms for string edit distance as well as similar Õ( n + poly ( k ))-time algorithms for generalizations to tree and Dyck edit distances. Surprisingly, all these results hold only for unweighted instances.

AAAI Conference 2022 Conference Paper

Generalized Stochastic Matching

  • Alireza Farhadi
  • Jacob Gilbert
  • MohammadTaghi Hajiaghayi

In this paper, we generalize the recently studied stochastic matching problem to more accurately model a significant medical process, kidney exchange, and several other applications. Up until now the stochastic matching problem that has been studied was as follows: given a graph G = (V, E), each edge is included in the realized sub-graph G of G mutually independently with probability pe, and the goal is to find a degree-bounded sub-graph Q of G that has an expected maximum matching that approximates the expected maximum matching of G. This model does not account for possibilities of vertex dropouts, which can be found in several applications, e. g. in kidney exchange when donors or patients opt out of the exchange process as well as in online freelancing and online dating when online profiles are found to be faked. Thus, we will study a more generalized model of stochastic matching in which vertices and edges are both realized independently with some probabilities pv, pe, respectively, which more accurately fits important applications than the previously studied model. We will discuss the first algorithms and analysis for this generalization of the stochastic matching model and prove that they achieve good approximation ratios. In particular, we show that the approximation factor of a natural algorithm for this problem is at least 0. 6568 in unweighted graphs, and 1/2 + ϵ in weighted graphs for some constant ϵ > 0. We further improve our result for unweighted graphs to 2/3 using edge degree constrained subgraphs (EDCS).

FOCS Conference 2022 Conference Paper

Õ(n+poly(k))-time Algorithm for Bounded Tree Edit Distance

  • Debarati Das 0001
  • Jacob Gilbert
  • MohammadTaghi Hajiaghayi
  • Tomasz Kociumaka
  • Barna Saha
  • Hamed Saleh

Computing the edit distance of two strings is one of the most basic problems in computer science and combinatorial optimization. Tree edit distance is a natural generalization of edit distance in which the task is to compute a measure of dissimilarity between two (unweighted) rooted trees with node labels. Perhaps the most notable recent application of tree edit distance is in NoSQL big databases, such as MongoDB, where each row of the database is a JSON document represented as a labeled rooted tree and finding dissimilarity between two rows is a basic operation. Until recently, the fastest algorithm for tree edit distance ran in cubic time (Demaine, Mozes, Rossman, Weimann; TALG’10); however, Mao (FOCS’21) broke the cubic barrier for the tree edit distance problem using fast matrix multiplication. Given a parameter k as an upper bound on the distance, an $\mathcal{O}(n+k^{2})$-time algorithm for edit distance has been known since the 1980s due to works of Myers (Algorithmica’86) and Landau and Vishkin (JCSS’88). The existence of an $\tilde{\mathcal{O}}(n+poly(k))$-time algorithm for tree edit distance has been posed as open question, e. g. , by Akmal and Jin (ICALP’21), who give a stateof-the-art $O(nk^{2})$-time algorithm. In this paper, we answer this question positively.

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