arXiv subjects

Matheus Henrique Pimenta-Zanon

Publications and source records attributed to Matheus Henrique Pimenta-Zanon.

3 recordsLinked to original sources

arXiv2024

GRAMEP: an alignment-free method based on the Maximum Entropy Principle for identifying SNPs

Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating genomic mutations is critical because of their impact on chromosomal evolution, genetic disorders, and diseases. It is common to adopt aligning sequences for analyzing genomic variations. However, this approach can be computationally expensive and restrictive in scenarios with large datasets. Results: We present a novel method for identifying single nucleotide polymorphisms (SNPs) in DNA sequences from assembled genomes. This study proposes GRAMEP, an alignment-free approach that adopts the principle of maximum entropy to discover the most informative k-mers specific to a genome or set of sequences under investigation. The informative k-mers enable the detection of variant-specific mutations in comparison to a reference genome or other set of sequences. In addition, our method offers the possibility of classifying novel sequences with no need for organism-specific information. GRAMEP demonstrated high accuracy in both in silico simulations and analyses of viral genomes, including Dengue, HIV, and SARS-CoV-2. Our approach maintained accurate SARS-CoV-2 variant identification while demonstrating a lower computational cost compared to methods with the same purpose. Conclusions: GRAMEP is an open and user-friendly software based on maximum entropy that provides an efficient alignment-free approach to identifying and classifying unique genomic subsequences and SNPs with high accuracy, offering advantages over comparative methods. The instructions for use, applicability, and usability of GRAMEP are open access at https://github.com/omatheuspimenta/GRAMEP

q-bio.GN↗

arXiv2022

BASiNETEntropy: an alignment-free method for classification of biological sequences through complex networks and entropy maximization

The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which computational methods have become essential for analysis and knowledge discovery. In particular, RNAs have received much attention because of the diversity of their functionalities in the organism and the discoveries of different classes with different functions in many biological processes. Therefore, the correct identification of RNA sequences is increasingly important to provide relevant information to understand the functioning of organisms. This work addresses this context by presenting a new method for the classification of biological sequences through complex networks and entropy maximization. The maximum entropy principle is proposed to identify the most informative edges about the RNA class, generating a filtered complex network. The proposed method was evaluated in the classification of different RNA classes from 13 species. The proposed method was compared to PLEK, CPC2 and BASiNET methods, outperforming all compared methods. BASiNETEntropy classified all RNA sequences with high accuracy and low standard deviation in results, showing assertiveness and robustness. The proposed method is implemented in an open source in R language and is freely available at https://cran.r-project.org/web/packages/BASiNETEntropy.

q-bio.MN↗

arXiv2021

Complex Network-Based Approach for Feature Extraction and Classification of Musical Genres

Musical genre's classification has been a relevant research topic. The association between music and genres is fundamental for the media industry, which manages musical recommendation systems, and for music streaming services, which may appear classified by genres. In this context, this work presents a feature extraction method for the automatic classification of musical genres, based on complex networks and their topological measurements. The proposed method initially converts the musics into sequences of musical notes and then maps the sequences as complex networks. Topological measurements are extracted to characterize the network topology, which composes a feature vector that applies to the classification of musical genres. The method was evaluated in the classification of 10 musical genres by adopting the GTZAN dataset and 8 musical genres by adopting the FMA dataset. The results were compared with methods in the literature. The proposed method outperformed all compared methods by presenting high accuracy and low standard deviation, showing its suitability for the musical genre's classification, which contributes to the media industry in the automatic classification with assertiveness and robustness. The proposed method is implemented in an open source in the Python language and freely available at https://github.com/omatheuspimenta/examinner.

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