Related papers: Signal processing and statistical methods in analy…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
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…
The sequential data observed in earth science can be regarded as paths in multidimensional space. To read the path effectively, it is useful to convert it into a sequence of numbers called the signature, which can faithfully describe the…
This thesis develops the translation between category theory and computational linguistics as a foundation for natural language processing. The three chapters deal with syntax, semantics and pragmatics. First, string diagrams provide a…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
Deep Learning has impacted various fields especially in bio-medical applications. Deep learning algorithms work well with both structured and unstructured data. Especially, convolutional neural network work well with signal-based data like…
Classification is valuable and necessary in spectral analysis, especially for data-driven mining. Along with the rapid development of spectral surveys, a variety of classification techniques have been successfully applied to astronomical…
Natural language processing (NLP) has recently gained much attention for representing and analysing human language computationally. It has spread its applications in various fields such as machine translation, email spam detection,…
In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types, the resulting measurements thus give only…
Despite their growing capabilities, language models still frequently reproduce content from their training data, generate repetitive text, and favor common grammatical patterns and vocabulary. A possible cause is the decoding strategy: the…
Syllables play an important role in speech synthesis, speech recognition, and spoken document retrieval. A novel, low cost, and language agnostic approach to dividing words into their corresponding syllables is presented. A hybrid genetic…
Natural Language Processing (NLP) helps empower intelligent machines by enhancing a better understanding of the human language for linguistic-based human-computer communication. Recent developments in computational power and the advent of…
Brain signals constitute the information that are processed by millions of brain neurons (nerve cells and brain cells). These brain signals can be recorded and analyzed using various of non-invasive techniques such as the…
Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq)…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
In textual knowledge management, statistical methods prevail. Nonetheless, some difficulties cannot be overcome by these methodologies. I propose a symbolic approach using a complete textual analysis to identify which analysis level can…
Several methods have recently been proposed to analyze speech and automatically infer the personality of the speaker. These methods often rely on prosodic and other hand crafted speech processing features extracted with off-the-shelf…
In the next decade, high energy physicists will use very sophisticated equipment to record unprecedented amounts of data in the hope of making major advances in our understanding of particle phenomena. Some of the signals of new physics…
In this paper we present a general method for information extraction that exploits the features of data compression techniques. We first define and focus our attention on the so-called "dictionary" of a sequence. Dictionaries are…
Drilling activities in the oil and gas industry have been reported over decades for thousands of wells on a daily basis, yet the analysis of this text at large-scale for information retrieval, sequence mining, and pattern analysis is very…