arXiv subjects

Debarati Das

Publications and source records attributed to Debarati Das.

33 records · Page 2Linked to original sources

arXiv2022

$\tilde{O}(n+\mathrm{poly}(k))$-time Algorithm for Bounded Tree Edit Distance

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 $O(n+k^2)$-time algorithm for edit distance has been known since the 1980s due to the works of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88). The existence of an $\tilde{O}(n+\mathrm{poly}(k))$-time algorithm for tree edit distance has been posed as an open question, e.g., by Akmal and Jin (ICALP'21), who gave a state-of-the-art $\tilde{O}(nk^2)$-time algorithm. In this paper, we answer this question positively.

cs.DS↗

arXiv2022

Fitting Distances by Tree Metrics Minimizing the Total Error within a Constant Factor

We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that their distances in $T$ match those in $D$. A nice application is in evolutionary biology where the tree $T$ aims to approximate the branching process leading to the observed distances in $D$ [Cavalli-Sforza and Edwards 1967]. We consider the total error, that is the sum of distance errors over all pairs of points. We present a deterministic polynomial time algorithm minimizing the total error within a constant factor. We can do this both for general trees, and for the special case of ultrametrics with a root having the same distance to all vertices in $S$. The problems are APX-hard, so a constant factor is the best we can hope for in polynomial time. The best previous approximation factor was $O((\log n)(\log \log n))$ by Ailon and Charikar [2005] who wrote "Determining whether an $O(1)$ approximation can be obtained is a fascinating question".

cs.DS↗

arXiv2021

Improved Approximation Algorithms for Dyck Edit Distance and RNA Folding

The Dyck language, which consists of well-balanced sequences of parentheses, is one of the most fundamental context-free languages. The Dyck edit distance quantifies the number of edits (character insertions, deletions, and substitutions) required to make a given parenthesis sequence well-balanced. RNA Folding involves a similar problem, where a closing parenthesis can match an opening parenthesis of the same type irrespective of their ordering. For example, in RNA Folding, both $\tt{()}$ and $\tt{)(}$ are valid matches, whereas the Dyck language only allows $\tt{()}$ as a match. Using fast matrix multiplication, it is possible to compute their exact solutions of both problems in time $O(n^{2.824})$. Whereas combinatorial algorithms would be more desirable, the two problems are known to be at least as hard as Boolean matrix multiplication. In terms of fast approximation algorithms that are combinatorial in nature, both problems admit an $εn$-additive approximation in $\tilde{O}(\frac{n^2}ε)$ time. Further, there is a $O(\log n)$-factor approximation algorithm for Dyck edit distance in near-linear time. In this paper, we design a constant-factor approximation algorithm for Dyck edit distance that runs in $O(n^{1.971})$ time. Moreover, we develop a $(1+ε)$-factor approximation algorithm running in $\tilde{O}(\frac{n^2}ε)$ time, which improves upon the earlier additive approximation. Finally, we design a $(3+ε)$-approximation that takes $\tilde{O}(\frac{nd}ε)$ time, where $d\ge 1$ is an upper bound on the sought distance. As for RNA folding, for any $s\ge1$, we design a factor-$s$ approximation algorithm that runs in $O(n+(\frac{n}{s})^3)$ time. To the best of our knowledge, this is the first nontrivial approximation algorithm for RNA Folding that can go below the $n^2$ barrier. All our algorithms are combinatorial.

cs.DS↗

arXiv2021

Approximating LCS and Alignment Distance over Multiple Sequences

We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the alignment distance (AD)). Multiple sequence alignment is a well-studied problem in bioinformatics and is used to identify regions of similarity among DNA, RNA, or protein sequences to detect functional, structural, or evolutionary relationships among them. It is known that exact computation of LCS or AD of $m$ sequences each of length $n$ requires $Θ(n^m)$ time unless the Strong Exponential Time Hypothesis is false. In this paper, we provide several results to approximate LCS and AD of multiple sequences. If the LCS of $m$ sequences each of length $n$ is $λn$ for some $λ\in [0,1]$, then in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+1})$ time, we can return a common subsequence of length at least $\frac{λ^2 n}{2+ε}$ for any arbitrary constant $ε>0$. It is possible to approximate the AD within a factor of two in time $\tilde{O}_m(n^{\lceil\frac{m}{2}\rceil})$. However, going below-2 approximation requires breaking the triangle inequality barrier which is a major challenge in this area. No such algorithm with a running time of $O(n^{αm})$ for any $α< 1$ is known. If the AD is $θn$, then we design an algorithm that approximates the AD within an approximation factor of $\left(2-\frac{3θ}{16}+ε\right)$ in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+2})$ time. Thus, if $θ$ is a constant, we get a below-two approximation in $\tilde{O}_m(n^{\lfloor\frac{m}{2}\rfloor+2})$ time. Moreover, we show if just one out of $m$ sequences is $(p,B)$-pseudorandom then, we get a below-2 approximation in $\tilde{O}_m(nB^{m-1}+n^{\lfloor \frac{m}{2}\rfloor+3})$ time irrespective of $θ$.

cs.DS↗

arXiv2021

Approximate Trace Reconstruction via Median String (in Average-Case)

We consider an \emph{approximate} version of the trace reconstruction problem, where the goal is to recover an unknown string $s\in\{0,1\}^n$ from $m$ traces (each trace is generated independently by passing $s$ through a probabilistic insertion-deletion channel with rate $p$). We present a deterministic near-linear time algorithm for the average-case model, where $s$ is random, that uses only \emph{three} traces. It runs in near-linear time $\tilde O(n)$ and with high probability reports a string within edit distance $O(εp n)$ from $s$ for $ε=\tilde O(p)$, which significantly improves over the straightforward bound of $O(pn)$. Technically, our algorithm computes a $(1+ε)$-approximate median of the three input traces. To prove its correctness, our probabilistic analysis shows that an approximate median is indeed close to the unknown $s$. To achieve a near-linear time bound, we have to bypass the well-known dynamic programming algorithm that computes an optimal median in time $O(n^3)$.

cs.DS↗

arXiv2021

A Linear-Time $n^{0.4}$-Approximation for Longest Common Subsequence

We consider the classic problem of computing the Longest Common Subsequence (LCS) of two strings of length $n$. While a simple quadratic algorithm has been known for the problem for more than 40 years, no faster algorithm has been found despite an extensive effort. The lack of progress on the problem has recently been explained by Abboud, Backurs, and Vassilevska Williams [FOCS'15] and Bringmann and Künnemann [FOCS'15] who proved that there is no subquadratic algorithm unless the Strong Exponential Time Hypothesis fails. This has led the community to look for subquadratic approximation algorithms for the problem. Yet, unlike the edit distance problem for which a constant-factor approximation in almost-linear time is known, very little progress has been made on LCS, making it a notoriously difficult problem also in the realm of approximation. For the general setting, only a naive $O(n^{\varepsilon/2})$-approximation algorithm with running time $\tilde{O}(n^{2-\varepsilon})$ has been known, for any constant $0 < \varepsilon \le 1$. Recently, a breakthrough result by Hajiaghayi, Seddighin, Seddighin, and Sun [SODA'19] provided a linear-time algorithm that yields a $O(n^{0.497956})$-approximation in expectation; improving upon the naive $O(\sqrt{n})$-approximation for the first time. In this paper, we provide an algorithm that in time $O(n^{2-\varepsilon})$ computes an $\tilde{O}(n^{2\varepsilon/5})$-approximation with high probability, for any $0 < \varepsilon \le 1$. Our result (1) gives an $\tilde{O}(n^{0.4})$-approximation in linear time, improving upon the bound of Hajiaghayi, Seddighin, Seddighin, and Sun, (2) provides an algorithm whose approximation scales with any subquadratic running time $O(n^{2-\varepsilon})$, improving upon the naive bound of $O(n^{\varepsilon/2})$ for any $\varepsilon$, and (3) instead of only in expectation, succeeds with high probability.

cs.DS↗

arXiv2021

Approximating Edit Distance Within Constant Factor in Truly Sub-Quadratic Time

Edit distance is a measure of similarity of two strings based on the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. The edit distance can be computed exactly using a dynamic programming algorithm that runs in quadratic time. Andoni, Krauthgamer, and Onak (2010) gave a nearly linear time algorithm that approximates edit distance within an approximation factor $\text{poly}(\log n)$. In this paper, we provide an algorithm with running time $\tilde{O}(n^{2-2/7})$ that approximates the edit distance within a constant factor.

cs.DS↗

arXiv2020

Approximating the Median under the Ulam Metric

We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation is known for this NP-hard problem. This problem is motivated e.g.~by computational biology, and belongs to the class of median problems (over different metric spaces), which are fundamental tasks in data analysis. Our main result is for the Ulam metric, where all strings are permutations over $[n]$ and each edit operation moves a symbol (deletion plus insertion). We devise for this problem an algorithms that breaks the $2$-approximation barrier, i.e., computes a $(2-δ)$-approximate median permutation for some constant $δ>0$ in time $\tilde{O}(nm^2+n^3)$. We further use these techniques to achieve a $(2-δ)$ approximation for the median string problem in the special case where the median is restricted to length $n$ and the optimal objective is large $Ω(mn)$. We also design an approximation algorithm for the following probabilistic model of the Ulam median: the input consists of $m$ perturbations of an (unknown) permutation $x$, each generated by moving every symbol to a random position with probability (a parameter) $ε>0$. Our algorithm computes with high probability a $(1+o(1/ε))$-approximate median permutation in time $O(mn^2+n^3)$.

cs.DS↗

arXiv2020

No Repetition: Fast Streaming with Highly Concentrated Hashing

To get estimators that work within a certain error bound with high probability, a common strategy is to design one that works with constant probability, and then boost the probability using independent repetitions. Important examples of this approach are small space algorithms for estimating the number of distinct elements in a stream, or estimating the set similarity between large sets. Using standard strongly universal hashing to process each element, we get a sketch based estimator where the probability of a too large error is, say, 1/4. By performing $r$ independent repetitions and taking the median of the estimators, the error probability falls exponentially in $r$. However, running $r$ independent experiments increases the processing time by a factor $r$. Here we make the point that if we have a hash function with strong concentration bounds, then we get the same high probability bounds without any need for repetitions. Instead of $r$ independent sketches, we have a single sketch that is $r$ times bigger, so the total space is the same. However, we only apply a single hash function, so we save a factor $r$ in time, and the overall algorithms just get simpler. Fast practical hash functions with strong concentration bounds were recently proposed by Aamand em et al. (to appear in STOC 2020). Using their hashing schemes, the algorithms thus become very fast and practical, suitable for online processing of high volume data streams.

cs.DS↗

arXiv2018

Approximate Online Pattern Matching in Sub-linear Time

We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $Σ$, and a positive integer $k$. The goal is to find all the positions $j$ in $T$ such that there is a substring of $T$ ending at $j$ which has edit distance at most $k$ from the pattern $P$. Recall, the edit distance between two strings is the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. For a position $t$ in $\{1,...,n\}$, let $k_t$ be the smallest edit distance between $P$ and any substring of $T$ ending at $t$. In this paper we give a constant factor approximation to the sequence $k_1,k_2,...,k_{n}$. We consider both offline and online settings. In the offline setting, where both $P$ and $T$ are available, we present an algorithm that for all $t$ in $\{1,...,n\}$, computes the value of $k_t$ approximately within a constant factor. The worst case running time of our algorithm is $O(n w^{3/4})$. As a consequence we break the $O(nw)$-time barrier for this problem. In the online setting, we are given $P$ and then $T$ arrives one symbol at a time. We design an algorithm that upon arrival of the $t$-th symbol of $T$ computes $k_t$ approximately within $O(1)$-multiplicative factor and $w^{8/9}$-additive error. Our algorithm takes $O(w^{1-(7/54)})$ amortized time per symbol arrival and takes $O(w^{1-(1/54)})$ additional space apart from storing the pattern $P$. Both of our algorithms are randomized and produce correct answer with high probability. To the best of our knowledge this is the first worst-case sub-linear (in the length of the pattern) time and sub-linear succinct space algorithm for online approximate pattern matching problem.

cs.DS↗

arXiv2018

Optimal Quasi-Gray Codes: The Alphabet Matters

A quasi-Gray code of dimension $n$ and length $\ell$ over an alphabet $Σ$ is a sequence of distinct words $w_1,w_2,\dots,w_\ell$ from $Σ^n$ such that any two consecutive words differ in at most $c$ coordinates, for some fixed constant $c>0$. In this paper we are interested in the read and write complexity of quasi-Gray codes in the bit-probe model, where we measure the number of symbols read and written in order to transform any word $w_i$ into its successor $w_{i+1}$. We present construction of quasi-Gray codes of dimension $n$ and length $3^n$ over the ternary alphabet $\{0,1,2\}$ with worst-case read complexity $O(\log n)$ and write complexity $2$. This generalizes to arbitrary odd-size alphabets. For the binary alphabet, we present quasi-Gray codes of dimension $n$ and length at least $2^n - 20n$ with worst-case read complexity $6+\log n$ and write complexity $2$. This complements a recent result by Raskin [Raskin '17] who shows that any quasi-Gray code over binary alphabet of length $2^n$ has read complexity $Ω(n)$. Our results significantly improve on previously known constructions and for the odd-size alphabets we break the $Ω(n)$ worst-case barrier for space-optimal (non-redundant) quasi-Gray codes with constant number of writes. We obtain our results via a novel application of algebraic tools together with the principles of catalytic computation [Buhrman et al. '14, Ben-Or and Cleve '92, Barrington '89, Coppersmith and Grossman '75].

cs.IT↗

arXiv2018

Lower bounds for Combinatorial Algorithms for Boolean Matrix Multiplication

In this paper we propose models of combinatorial algorithms for the Boolean Matrix Multiplication (BMM), and prove lower bounds on computing BMM in these models. First, we give a relatively relaxed combinatorial model which is an extension of the model by Angluin (1976), and we prove that the time required by any algorithm for the BMM is at least $Ω(n^3 / 2^{O( \sqrt{ \log n })})$. Subsequently, we propose a more general model capable of simulating the "Four Russians Algorithm". We prove a lower bound of $Ω(n^{7/3} / 2^{O(\sqrt{ \log n })})$ for the BMM under this model. We use a special class of graphs, called $(r,t)$-graphs, originally discovered by Rusza and Szemeredi (1978), along with randomization, to construct matrices that are hard instances for our combinatorial models.

cs.CC↗

arXiv2017

Near Optimal Sized Weight Tolerant Subgraph for Single Source Shortest Path

In this paper we address the problem of computing a sparse subgraph of a weighted directed graph such that the exact distances from a designated source vertex to all other vertices are preserved under bounded weight increment. Finding a small sized subgraph that preserves distances between any pair of vertices is a well studied problem. Since in the real world any network is prone to failures, it is natural to study the fault tolerant version of the above problem. Unfortunately, it turns out that there may not always exist such a sparse subgraph even under single edge failure [Demetrescu \emph{et al.} '08]. However in real applications it is not always the case that a link (edge) in a network becomes completely faulty. Instead, it can happen that some links become more congested which can easily be captured by increasing weight on the corresponding edges. Thus it makes sense to try to construct a sparse distance preserving subgraph under the above weight increment model. To the best of our knowledge this problem has not been studied so far. In this paper we show that given any weighted directed graph with $n$ vertices and a source vertex, one can construct a subgraph that contains at most $e \cdot (k-1)!2^kn$ many edges such that it preserves distances between the source and all other vertices as long as the total weight increment is bounded by $k$ and we are allowed to have only integer valued (can be negative) weight on each edge and also weight of an edge can only be increased by some positive integer. Next we show a lower bound of $c\cdot 2^kn$, for some constant $c \ge 5/4$, on the size of the subgraph. We also argue that restriction of integer valued weight and integer valued weight increment are actually essential by showing that if we remove any one of these two restrictions we may need to store $Ω(n^2)$ edges to preserve distances.

cs.DS↗

arXiv2015

Modeling Memetics using Edge Diversity

The study of meme propagation and the prediction of meme trajectory are emerging areas of interest in the field of complex networks research. In addition to the properties of the meme itself, the structural properties of the underlying network decides the speed and the trajectory of the propagating meme. In this paper, we provide an artificial framework for studying the meme propagation patterns. Firstly, the framework includes a synthetic network which simulates a real world network and acts as a testbed for meme simulation. Secondly, we propose a meme spreading model based on the diversity of edges in the network. Through the experiments conducted, we show that the generated synthetic network combined with the proposed spreading model is able to simulate a real world meme spread. Our proposed model is validated by the propagation of the Higgs boson meme on Twitter as well as many real world social networks.

cs.SI↗

arXiv2015

Pseudo-Cores: The Terminus of an Intelligent Viral Meme's Trajectory

Comprehending the virality of a meme can help us in addressing the problems pertaining to disciplines like epidemiology and digital marketing. Therefore, it is not surprising that memetics remains a highly analyzed research topic ever since the mid 1990s. Some scientists choose to investigate the intrinsic contagiousness of a meme while others study the problem from a network theory perspective. In this paper, we revisit the idea of a core-periphery structure and apply it to understand the trajectory of a viral meme in a social network. We have proposed shell-based hill climbing algorithms to determine the path from a periphery shell(where the meme originates) to the core of the network. Further simulations and analysis on the networks behavioral characteristics helped us unearth specialized shells which we term Pseudo-Cores. These shells emulate the behavior of the core in terms of size of the cascade triggered. In our experiments, we have considered two sets for the target nodes, one being core and the other being any of the pseudo-core. We compare our algorithms against already existing path finding algorithms and validate the better performance experimentally.

cs.SI↗