Mathematical Modelling and Machine Learning Methods for Bioinformatics and Data Science Applications, 2nd Edition

A special issue of Mathematics (ISSN 2227-7390). This special issue belongs to the section "Mathematics and Computer Science".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 6643

Special Issue Editors


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Guest Editor
Department of Information Engineering and Mathematics, University of Siena, 53100 Siena, Italy
Interests: artificial intelligence; machine learning; deep learning; approximation theory; bioinformatics; image processing
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Information Engineering and Mathematics, University of Siena, 53100 Siena, Italy
Interests: numerical analysis; scientific computing; geometric modeling; constrained interpolation and approximation; isogeometric analysis
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
1. Department of Information Engineering and Mathematics (DIISM), University of Siena, 53100 Siena, Italy
2. Department of Social, Political and Cognitive Sciences, University of Siena, 53100 Siena, Italy
Interests: medical image processing; computer vision; deep learning; machine learning

E-Mail Website
Guest Editor
1. Department of Information Engineering and Mathematics (DIISM), University of Siena, 53100 Siena, Italy
2. Department of Information Engineering, University of Florence, Via S. Marta 3, 50139 Florence, Italy
Interests: deep Learning for biological data; bioinformatics; graph neural networks; data mining

Special Issue Information

Dear Colleagues,

Although statistics has historically been used to solve problems in data science, mathematical methods and machine learning (ML) can be extremely helpful, especially for building concise decision models, making fast approximations, and predicting evolving phenomena based on known samples. In particular, mathematical modeling and machine learning methods are increasingly used to help interpret biomedical data produced by high-throughput genomics and proteomics projects. Indeed, as the study of biological systems becomes more quantitative, the role played by mathematical analysis increases. This ranges from the macroscopic (e.g., how to model the spread of a disease across a community) to the microscopic (e.g., how to determine the three-dimensional structure of proteins from the knowledge of their amino acid sequence).

The revolution in biological and information technologies has produced huge amounts of data and is accelerating the process of knowledge discovery from biological systems. Furthermore, clinical data complement biological data, allowing for detailed descriptions of both healthy and diseased states, as well as disease progression and response to therapies. With medical imaging playing an increasingly prominent role in disease diagnosis, interest in medical image processing has also increased significantly over the past several decades, with deep learning methods attracting more and more attention.

However, although advances in machine learning algorithms have been deemed critical for improving performance in analyzing huge datasets, their opacity, if not supported by preventive mathematical modeling of the problem, could prevent human experts—and especially doctors—from trusting their abilities and results.

This Special Issue provides a platform for researchers from academia and industry to present their new and unpublished work, and to promote future studies in an emerging field such as applying mathematically founded ML models to highly sensitive data. Topics include but are not limited to:

  • Mathematical and numerical methods in understanding biological systems and biomolecular dynamics, e.g., from disease diffusion to intracellular pattern formation.
  • Mathematical and computational models in therapy and diagnosis.
  • Machine learning algorithms and models for bio-information and bio-data understanding.
  • Deep learning techniques and evolutionary computing in biomedical image and signal processing.
  • Statistical and artificial intelligence-based models for complex biological data.
  • Big data analytics on biomedical pattern recognition.
  • Machine learning and artificial intelligence methods in data science with applications in other areas, etc.

Dr. Monica Bianchini
Dr. Maria Lucia Sampoli
Dr. Simone Bonechi
Dr. Pietro Bongini
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Mathematics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Mathematical modeling
  • Numerical methods
  • Machine learning
  • Statistical techniques
  • Statistical learning
  • Data science
  • Bioinformatics
  • Medical image processing
  • Biosignal processing

Published Papers (4 papers)

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Research

13 pages, 2922 KiB  
Article
A Deep Learning Approach to Analyze NMR Spectra of SH-SY5Y Cells for Alzheimer’s Disease Diagnosis
by Filippo Costanti, Arian Kola, Franco Scarselli, Daniela Valensin and Monica Bianchini
Mathematics 2023, 11(12), 2664; https://doi.org/10.3390/math11122664 - 12 Jun 2023
Cited by 1 | Viewed by 1230
Abstract
The SH-SY5Y neuroblastoma cell line is often used as an in vitro model of neuronal function and is widely applied to study the molecular events leading to Alzheimer’s disease (AD). Indeed, recently, basic research on SH-SY5Y cells has provided interesting insights for the [...] Read more.
The SH-SY5Y neuroblastoma cell line is often used as an in vitro model of neuronal function and is widely applied to study the molecular events leading to Alzheimer’s disease (AD). Indeed, recently, basic research on SH-SY5Y cells has provided interesting insights for the discovery of new drugs and biomarkers for improved AD treatment and diagnosis. At the same time, untargeted NMR metabolomics is widely applied to metabolic profile analysis and screening for differential metabolites, to discover new biomarkers. In this paper, a compression technique based on convolutional autoencoders is proposed, which can perform a high dimensionality reduction in the spectral signal (up to more than 300 times), maintaining informative features (guaranteed by a reconstruction error always smaller than 5%). Moreover, before compression, an ad hoc preprocessing method was devised to remedy the scarcity of available data. The compressed spectral data were then used to train some SVM classifiers to distinguish diseased from healthy cells, achieving an accuracy close to 78%, a significantly better performance with respect to using standard PCA-compressed data. Full article
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0 pages, 910 KiB  
Article
Half Logistic Inverted Nadarajah–Haghighi Distribution under Ranked Set Sampling with Applications
by Naif Alotaibi, A. S. Al-Moisheer, Ibrahim Elbatal, Mansour Shrahili, Mohammed Elgarhy and Ehab M. Almetwally
Mathematics 2023, 11(7), 1693; https://doi.org/10.3390/math11071693 - 01 Apr 2023
Cited by 6 | Viewed by 909
Abstract
In this paper, we present the half logistic inverted Nadarajah–Haghigh (HL-INH) distribution, a novel extension of the inverted Nadarajah–Haghigh (INH) distribution. The probability density function (PDF) for the HL-INH distribution might have a unimodal, right skewness, or heavy-tailed shape for numerous parameter values; [...] Read more.
In this paper, we present the half logistic inverted Nadarajah–Haghigh (HL-INH) distribution, a novel extension of the inverted Nadarajah–Haghigh (INH) distribution. The probability density function (PDF) for the HL-INH distribution might have a unimodal, right skewness, or heavy-tailed shape for numerous parameter values; however, the shape forms of the hazard rate function (HRF) for the HL-INH distribution may be decreasing. Four specific entropy measurements were investigated. Some useful expansions for the HL-INH distribution were investigated. Several statistical and computational features of the HL-INH distribution were calculated. Using simple (SRS) and ranked set sampling (RSS), the parameters for the HL-INH distribution were estimated using the maximum likelihood (ML) technique. A simulation analysis was executed in order to determine the model parameters of the HL-INH distribution using the SRS and RSS methods, and RSS was shown to be more efficient than SRS. We demonstrate that the HL-INH distribution is more adaptable than the INH distribution and other statistical distributions when utilizing three real-world datasets. Full article
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24 pages, 5943 KiB  
Article
Multi-Method Diagnosis of Histopathological Images for Early Detection of Breast Cancer Based on Hybrid and Deep Learning
by Mohammed Al-Jabbar, Mohammed Alshahrani, Ebrahim Mohammed Senan and Ibrahim Abdulrab Ahmed
Mathematics 2023, 11(6), 1429; https://doi.org/10.3390/math11061429 - 15 Mar 2023
Cited by 4 | Viewed by 1859
Abstract
Breast cancer (BC) is a type of cancer suffered by adult females worldwide. A late diagnosis of BC leads to death, so early diagnosis is essential for saving lives. There are many methods of diagnosing BC, including surgical open biopsy (SOB), which however [...] Read more.
Breast cancer (BC) is a type of cancer suffered by adult females worldwide. A late diagnosis of BC leads to death, so early diagnosis is essential for saving lives. There are many methods of diagnosing BC, including surgical open biopsy (SOB), which however constitutes an intense workload for pathologists to follow SOB and additionally takes a long time. Therefore, artificial intelligence systems can help by accurately diagnosing BC earlier; it is a tool that can assist doctors in making sound diagnostic decisions. In this study, two proposed approaches were applied, each with two systems, to diagnose BC in a dataset with magnification factors (MF): 40×, 100×, 200×, and 400×. The first proposed method is a hybrid technology between CNN (AlexNet and GoogLeNet) models that extracts features and classify them using the support vector machine (SVM). Thus, all BC datasets were diagnosed using AlexNet + SVM and GoogLeNet + SVM. The second proposed method diagnoses all BC datasets by ANN based on combining CNN features with handcrafted features extracted using the fuzzy color histogram (FCH), local binary pattern (LBP), and gray level co-occurrence matrix (GLCM), which collectively is called fusion features. Finally, the fusion features were fed into an artificial neural network (ANN) for classification. This method has proven its superior ability to diagnose histopathological images (HI) of BC accurately. The ANN algorithm based on fusion features achieved results of 100% for all metrics with the 400× dataset. Full article
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15 pages, 1841 KiB  
Article
Drug Side Effect Prediction with Deep Learning Molecular Embedding in a Graph-of-Graphs Domain
by Niccolò Pancino, Yohann Perron, Pietro Bongini and Franco Scarselli
Mathematics 2022, 10(23), 4550; https://doi.org/10.3390/math10234550 - 01 Dec 2022
Cited by 2 | Viewed by 2036
Abstract
Drug side effects (DSEs), or adverse drug reactions (ADRs), constitute an important health risk, given the approximately 197,000 annual DSE deaths in Europe alone. Therefore, during the drug development process, DSE detection is of utmost importance, and the occurrence of ADRs prevents many [...] Read more.
Drug side effects (DSEs), or adverse drug reactions (ADRs), constitute an important health risk, given the approximately 197,000 annual DSE deaths in Europe alone. Therefore, during the drug development process, DSE detection is of utmost importance, and the occurrence of ADRs prevents many candidate molecules from going through clinical trials. Thus, early prediction of DSEs has the potential to massively reduce drug development times and costs. In this work, data are represented in a non-euclidean manner, in the form of a graph-of-graphs domain. In such a domain, structures of molecule are represented by molecular graphs, each of which becomes a node in the higher-level graph. In the latter, nodes stand for drugs and genes, and arcs represent their relationships. This relational nature represents an important novelty for the DSE prediction task, and it is directly used during the prediction. For this purpose, the MolecularGNN model is proposed. This new classifier is based on graph neural networks, a connectionist model capable of processing data in the form of graphs. The approach represents an improvement over a previous method, called DruGNN, as it is also capable of extracting information from the graph-based molecular structures, producing a task-based neural fingerprint (NF) of the molecule which is adapted to the specific task. The architecture has been compared with other GNN models in terms of performance, showing that the proposed approach is very promising. Full article
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