Related papers: Arc-preserving subsequences of arc-annotated seque…
In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…
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…
Series-parallel (SP) graphs are binary edge-labeled graphs with a designated source and target vertex, built using serial and parallel composition. A set of graphs is recognizable if membership depends only on its image under a homomorphism…
Sequence alignments are used to capture patterns composed of elements representing multiple conceptual levels through the alignment of sequences that contain overlapping and variable length annotations. The alignments also determine the…
In this paper, we propose an encoding scheme for partitioned linear block codes (PLBC) which mask the stuck-at defects in memories. In addition, we derive an upper bound and the estimate of the probability that masking fails. Numerical…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
The expected length of longest common subsequences is a problem that has been in the literature for at least twenty five years. Determining the limiting constants \gamma_k appears to be quite difficult, and the current best bounds leave…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
We study several variations of line segment covering problem with axis-parallel unit squares in $I\!\!R^2$. A set $S$ of $n$ line segments is given. The objective is to find the minimum number of axis-parallel unit squares which cover at…
Efficient numerical solvers for sparse linear systems are crucial in science and engineering. One of the fastest methods for solving large-scale sparse linear systems is algebraic multigrid (AMG). The main challenge in the construction of…
Structured learning is appropriate when predicting structured outputs such as trees, graphs, or sequences. Most prior work requires the training set to consist of complete trees, graphs or sequences. Specifying such detailed ground truth…
It has been proved that to implement a linearizable shared memory in synchronous message-passing systems it is necessary to wait for a time proportional to the uncertainty in the latency of the network for both read and write operations,…
We revisit several maximization problems for geometric networks design under the non-crossing constraint, first studied by Alon, Rajagopalan and Suri (ACM Symposium on Computational Geometry, 1993). Given a set of $n$ points in the plane in…
Unconstrained handwriting recognition is an essential task in document analysis. It is usually carried out in two steps. First, the document is segmented into text lines. Second, an Optical Character Recognition model is applied on these…
Transformer architectures have facilitated the development of large-scale and general-purpose sequence models for prediction tasks in natural language processing and computer vision, e.g., GPT-3 and Swin Transformer. Although originally…
Signatures are iterated path integrals of continuous and discrete-time processes, and their universal nonlinearity linearizes the problem of feature selection in time series data analysis. This paper studies the consistency of signature…
Encoding long sequences in Natural Language Processing (NLP) is a challenging problem. Though recent pretraining language models achieve satisfying performances in many NLP tasks, they are still restricted by a pre-defined maximum length,…
An arc is a set of vectors of the $k$-dimensional vector space over the finite field with $q$ elements ${\mathbb F}_q$, in which every subset of size $k$ is a basis of the space, i.e. every $k$-subset is a set of linearly independent…
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…