Related papers: Approximating LCS and Alignment Distance over Mult…
We show that for every $\varepsilon > 0$, the degree-$n^\varepsilon$ Sherali-Adams linear program (with $\exp(\tilde{O}(n^\varepsilon))$ variables and constraints) approximates the maximum cut problem within a factor of…
An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of…
Given a sequence $S$ of length $n$, a letter-duplicated subsequence is a subsequence of $S$ in the form of $x_1^{d_1}x_2^{d_2}\cdots x_k^{d_k}$ with $x_i\in\Sigma$, $x_j\neq x_{j+1}$ and $d_i\geq 2$ for all $i$ in $[k]$ and $j$ in $[k-1]$.…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Approximate Logic Synthesis (ALS) is the process of synthesizing and mapping a given Boolean network to a library of logic cells so that the magnitude/rate of error between outputs of the approximate and initial (exact) Boolean netlists is…
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
We consider how to assign labels to any undirected graph with n nodes such that, given the labels of two nodes and no other information regarding the graph, it is possible to determine the distance between the two nodes. The challenge in…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions…
In this paper we address the problem of finding well approximating lattices for a given finite set $A$ of points in ${\mathbb R}^n$. More precisely, we search for $\v{o},\v{d_1}, \dots,\v{d_n}\in \mathbb{R}^n$ such that $\v{a}-\v{o}$ is…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
We seek tight bounds on the viable parallelism in asynchronous implementations of coordinate descent that achieves linear speedup. We focus on asynchronous coordinate descent (ACD) algorithms on convex functions which consist of the sum of…
We provide a randomized linear time approximation scheme for a generic problem about clustering of binary vectors subject to additional constrains. The new constrained clustering problem encompasses a number of problems and by solving it,…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
We study local computation algorithms (LCA) for maximum matching. An LCA does not return its output entirely, but reveals parts of it upon query. For matchings, each query is a vertex $v$; the LCA should return whether $v$ is matched -- and…
The error-correcting pair is a general algebraic decoding method for linear codes. The near maximal distance separable (NMDS) linear code is a subclass of linear codes and has applications in secret sharing scheme and communication systems…
In this paper, we study parallel algorithms for the correlation clustering problem, where every pair of two different entities is labeled with similar or dissimilar. The goal is to partition the entities into clusters to minimize the number…
We consider linear network error correction (LNEC) coding when errors may occur on edges of a communication network of which the topology is known. In this paper, we first revisit and explore the framework of LNEC coding, and then unify two…
We consider the canonical generalization of the well-studied Longest Increasing Subsequence problem to multiple sequences, called $k$-LCIS: Given $k$ integer sequences $X_1,\dots,X_k$ of length at most $n$, the task is to determine the…