Related papers: A linear-time algorithm for finding the longest se…
In this paper, we propose a methodology to compute the optimal finite-length coding rate for random linear network coding schemes over a line network. To do so, we first model the encoding, reencoding, and decoding process of different…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
We consider the problem of inferring an edge-labeled graph from the sequence of edge labels seen in a walk of that graph. It has been known that this problem is solvable in $O(n \log n)$ time when the targets are path or cycle graphs. This…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
We present a new algorithm for finding a near optimal low-rank approximation of a matrix $A$ in $O(nnz(A))$ time. Our method is based on a recursive sampling scheme for computing a representative subset of $A$'s columns, which is then used…
This paper proposes a thought experiment to search for efficient bounded algorithms of NPC problems by machine enumeration. The key contributions are: -- On Universal Turing Machines, a program's time complexity should be characterized as:…
Given an array A containing arbitrary (positive and negative) numbers, we consider the problem of supporting range maximum-sum segment queries on A: i.e., given an arbitrary range [i,j], return the subrange [i' ,j' ] \subseteq [i,j] such…
We present a general approach to the problem of determining tight asymptotic lower bounds for generalized central moments of the optimal alignment score of two independent sequences of i.i.d. random variables. At first, these are obtained…
In this paper we discuss a sequential algorithm for the computation of a minimum-time speed profile over a given path, under velocity, acceleration and jerk constraints. Such a problem arises in industrial contexts such as automated…
Algorithm selection, a critical process of automated machine learning, aims to identify the most suitable algorithm for solving a specific problem prior to execution. Mainstream algorithm selection techniques heavily rely on problem…
Anytime heuristic search algorithms try to find a (potentially suboptimal) solution as quickly as possible and then work to find better and better solutions until an optimal solution is obtained or time is exhausted. The most widely-known…
We study ranked enumeration of join-query results according to very general orders defined by selective dioids. Our main contribution is a framework for ranked enumeration over a class of dynamic programming problems that generalizes…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
In iterative supervised learning algorithms it is common to reach a point in the search where no further induction seems to be possible with the available data. If the search is continued beyond this point, the risk of overfitting increases…
We present algorithms that extend the path-based hierarchical drawing framework and give experimental results. Our algorithms run in $O(km)$ time, where $k$ is the number of paths and $m$ is the number of edges of the graph, and provide…
An algorithm is proposed for the segmentation of image into multiple levels using mean and standard deviation in the wavelet domain. The procedure provides for variable size segmentation with bigger block size around the mean, and having…
We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$…
In this paper we introduce an evolutionary algorithm for the solution of linear integer programs. The strategy is based on the separation of the variables into the integer subset and the continuous subset; the integer variables are fixed by…
We consider the Bayesian optimal filtering problem: i.e. estimating some conditional statistics of a latent time-series signal from an observation sequence. Classical approaches often rely on the use of assumed or estimated transition and…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…