Related papers: Speeding Hirschberg Algorithm for Sequence Alignme…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
Topic modeling is a very powerful technique in data analysis and data mining but it is generally slow. Many parallelization approaches have been proposed to speed up the learning process. However, they are usually not very efficient because…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
We consider a matching problem for time series with values in an arbitrary metric space, with the stretching penalty given by the Hellinger kernel. To optimize this matching, we introduce the Elastic Time Warping algorithm with a cubic…
The organization of latent token representations plays a crucial role in determining the stability, generalization, and contextual consistency of language models, yet conventional approaches to embedding refinement often rely on parameter…
Linear autoregressive models serve as basic representations of discrete time stochastic processes. Different attempts have been made to provide non-linear versions of the basic autoregressive process, including different versions based on…
Hierarchical clustering over graphs is a fundamental task in data mining and machine learning with applications in domains such as phylogenetics, social network analysis, and information retrieval. Specifically, we consider the recently…
It has been shown that the parallel Lattice Linear Predicate (LLP) algorithm solves many combinatorial optimization problems such as the shortest path problem, the stable marriage problem and the market clearing price problem. In this…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
We describe how to convert the heuristic search algorithm A* into an anytime algorithm that finds a sequence of improved solutions and eventually converges to an optimal solution. The approach we adopt uses weighted heuristic search to find…
This paper addresses a common problem with hierarchical time series. Time series analysis demands the series for a model to be the sum of multiple series at corresponding sub-levels. Hierarchical Time Series presents a two-fold problem.…
We present an algorithm which computes the $D^{th}$ term of a sequence satisfying a linear recurrence relation of order $d$ over a field $K$ in $O( \mathsf{M}(\bar d)\log(D) + \mathsf{M}(d)\log(d))$ operations in $K$, where $\bar d \leq d$…
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…
In two earlier papers, we designed a distributed deterministic asynchronous algorithm for minimizing the sum of subdifferentiable and proximable functions and a regularizing quadratic on time-varying graphs based on Dykstra's algorithm, or…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
For many applications involving a sequence of linear systems with slowly changing system matrices, subspace recycling, which exploits relationships among systems and reuses search space information, can achieve huge gains in iterations…
This paper proposes new algorithms for the assembly line balancing problem with hierarchical worker assignment (ALBHW). The ALBHW appears in real industrial contexts where companies deal with a multi-skilled workforce. It considers task…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
We present in this paper first-order alternating linearization algorithms based on an alternating direction augmented Lagrangian approach for minimizing the sum of two convex functions. Our basic methods require at most $O(1/\epsilon)$…
We revisit the complexity of the classical Interval Scheduling in the dynamic setting. In this problem, the goal is to maintain a set of intervals under insertions and deletions and report the size of the maximum size subset of pairwise…