Related papers: Characterising the D2 statistic: word matches in b…
Language modeling, a central task in natural language processing, involves estimating a probability distribution over strings. In most cases, the estimated distribution sums to 1 over all finite strings. However, in some pathological cases,…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
A set of words, also called a language, is letter-balanced if the number of occurrences of each letter only depends on the length of the word, up to a constant. Similarly, a language is factor-balanced if the difference of the number of…
The distributions of the number of occurrences of words (the distributions of words for short) play key roles in information theory, statistics, probability theory, ergodic theory, computer science, and DNA analysis. Bassino et al. 2010 and…
The concept of matching dependencies (mds) is recently pro- posed for specifying matching rules for object identification. Similar to the functional dependencies (with conditions), mds can also be applied to various data quality…
We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…
From a grammar point of view, the role of punctuation marks in a sentence is formally defined and well understood. In semantic analysis punctuation plays also a crucial role as a method of avoiding ambiguity of the meaning. A different…
The meanings and relationships of words shift over time. This phenomenon is referred to as semantic shift. Research focused on understanding how semantic shifts occur over multiple time periods is essential for gaining a detailed…
This paper describes Difference-aware Deep continuous prompt for Contrastive Sentence Embeddings (D2CSE) that learns sentence embeddings. Compared to state-of-the-art approaches, D2CSE computes sentence vectors that are exceptional to…
We present a theoretical and empirical investigation of the statistical behaviour of the words in a text produced by human language. To this aim, we analyse the word distribution of various texts of Italian language selected from a specific…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
A similarity join aims to find all similar pairs between two collections of records. Established approaches usually deal with synthetic differences like typos and abbreviations, but neglect the semantic relations between words. Such…
Zipf's law of abbreviation, namely the tendency of more frequent words to be shorter, has been viewed as a manifestation of compression, i.e. the minimization of the length of forms -- a universal principle of natural communication.…
We engineer an algorithm to solve the approximate dictionary matching problem. Given a list of words $\mathcal{W}$, maximum distance $d$ fixed at preprocessing time and a query word $q$, we would like to retrieve all words from…
Given a set of points $P \subset \mathbb{R}^d$, the $k$-means clustering problem is to find a set of $k$ {\em centers} $C = \{c_1,...,c_k\}, c_i \in \mathbb{R}^d,$ such that the objective function $\sum_{x \in P} d(x,C)^2$, where $d(x,C)$…
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…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al. We introduce a formalism, called search schemes, to specify search strategies of this type, then…