Related papers: Pairwise sequence alignment with block and charact…
Post-editing in Automatic Speech Recognition (ASR) entails automatically correcting common and systematic errors produced by the ASR system. The outputs of an ASR system are largely prone to phonetic and spelling errors. In this paper, we…
Recent state-of-the-art natural language understanding models, such as BERT and XLNet, score a pair of sentences (A and B) using multiple cross-attention operations - a process in which each word in sentence A attends to all words in…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
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…
Graph Edit Distance (GED) is a widely used measure of graph similarity, valued for its flexibility in encoding domain knowledge through operation costs. However, existing learning-based approximation methods follow a modeling paradigm that…
We target the problem of automatically synthesizing proofs of semantic equivalence between two programs made of sequences of statements. We represent programs using abstract syntax trees (AST), where a given set of semantics-preserving…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Sequence comparison is a basic task to capture similarities and differences between two or more sequences of symbols, with countless applications such as in computational biology. An alignment is a way to compare sequences, where a giving…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
The tree edit distance problem is a natural generalization of the classic string edit distance problem. Given two ordered, edge-labeled trees $T_1$ and $T_2$, the edit distance between $T_1$ and $T_2$ is defined as the minimum total cost of…
In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e., the minimum number of substitutions, insertions, and deletions between a pair of sequences) for billions of genomic sequences is the…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
Node similarity is a fundamental problem in graph analytics. However, node similarity between nodes in different graphs (inter-graph nodes) has not received a lot of attention yet. The inter-graph node similarity is important in learning a…
Edit-distance-based string similarity search has many applications such as spell correction, data de-duplication, and sequence alignment. However, computing edit distance is known to have high complexity, which makes string similarity…
Graph Edit Distance (GED) is a fundamental graph similarity metric widely used in various applications. However, computing GED is an NP-hard problem. Recent state-of-the-art hybrid GED solver has shown promising performance by formulating…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Graph edit distance (GED) is an important similarity measure adopted in a similarity-based analysis between two graphs, and computing GED is a primitive operator in graph database analysis. Partially due to the NP-hardness, the existing…
Dynamic Time Warping (DTW) and Geometric Edit Distance (GED) are basic similarity measures between curves or general temporal sequences (e.g., time series) that are represented as sequences of points in some metric space $(X,…