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The distribution of frequency counts of distinct words by length in a language's vocabulary will be analyzed using two methods. The first, will look at the empirical distributions of several languages and derive a distribution that…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
The Chapter starts with introductory information about quantitative linguistics notions, like rank--frequency dependence, Zipf's law, frequency spectra, etc. Similarities in distributions of words in texts with level occupation in quantum…
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
$n$-gram profiles have been successfully and widely used to analyse long sequences of potentially differing lengths for clustering or classification. Mainly, machine learning algorithms have been used for this purpose but, despite their…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
As a research community grows, more and more papers are published each year. As a result there is increasing demand for improved methods for finding relevant papers, automatically understanding the key ideas and recommending potential…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
Today's probabilistic language generators fall short when it comes to producing coherent and fluent text despite the fact that the underlying models perform well under standard metrics, e.g., perplexity. This discrepancy has puzzled the…
Recent empirical and modeling research has focused on the semantic fluency task because it is informative about semantic memory. An interesting interplay arises between the richness of representations in semantic memory and the complexity…
The article, after a brief introduction on genetic algorithms and their functioning, presents a kind of genetic algorithm called Viral Search. We present the key concepts, we formally derive the algorithm and we perform numerical tests…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
The biological literature is rich with sentences that describe causal relations. Methods that automatically extract such sentences can help biologists to synthesize the literature and even discover latent relations that had not been…
All living organisms use the same genetic languages in their molecular biology machinery. They can be understood as the optimal solutions to the replication tasks involving DNA and proteins. These solutions perfectly fit the pattern…
Search engines perform the task of retrieving information related to the user-supplied query words. This task has two parts; one is finding "featured words" which describe an article best and the other is finding a match among these words…
In recent years, topological data analysis has been utilized for a wide range of problems to deal with high dimensional noisy data. While text representations are often high dimensional and noisy, there are only a few work on the…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…