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Information
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Multi-Modal Biomedical Data Science—Modeling and Analysis
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Multi-Modal Biomedical Data Science—Modeling and Analysis

A special issue of Information (ISSN 2078-2489). This special issue belongs to the section "Biomedical Information and Health".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 10010

Special Issue Editor

Dr. Vanathi Gopalakrishnan

E-Mail Website
Guest Editor
Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206-3701, USA
Interests: hybrid machine learning; multimodal intelligence; biomedical data science; biomarker discovery; rule learning; educational technologies; early detection; precision medicine; pattern recognition from multimodal signals; risk assessment for management
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We look forward to your submissions for this Special Issue, which will cover a broad range of topics that are of major interest to biomedical information mining for health and well-being. Our main focus is the use of multi-modal biomedical data in various applications related to pattern recognition of risk for developing disease, and early intervention to prevent adverse outcomes. Topics that include the use of multi-omics data and associated algorithms for modeling and analysis are highly welcomed. The development of trustworthy data and methods, including the use of human-in-the-loop architectures to enable efficient processing of existing knowledge and tools towards intelligent agent design in health-related applications, are also highly encouraged.

Dr. Vanathi Gopalakrishnan
Guest Editor

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. Information is an international peer-reviewed open access monthly 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 1600 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

  • multi-modal biomedical data mining
  • trustworthy data science and AI
  • multi-omics modeling and pattern recognition
  • human-in-the-loop intelligent agents
  • precision medicine

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Published Papers (3 papers)

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Research

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16 pages, 1931 KiB  
Article
Baseline Structural Connectomics Data of Healthy Brain Development Assessed with Multi-Modal Magnetic Resonance Imaging
by David Mattie, Zihang Fang, Emi Takahashi, Lourdes Peña Castillo and Jacob Levman
Information 2024, 15(1), 66; https://doi.org/10.3390/info15010066 - 22 Jan 2024
Cited by 1 | Viewed by 1788
Abstract
Diffusion magnetic resonance imaging (MRI) tractography is a powerful tool for non-invasively studying brain architecture and structural integrity by inferring fiber tracts based on water diffusion profiles. This study provided a thorough set of baseline data of structural connectomics biomarkers for 809 healthy [...] Read more.
Diffusion magnetic resonance imaging (MRI) tractography is a powerful tool for non-invasively studying brain architecture and structural integrity by inferring fiber tracts based on water diffusion profiles. This study provided a thorough set of baseline data of structural connectomics biomarkers for 809 healthy participants between the ages of 1 and 35 years. The data provided can help to identify potential biomarkers that may be helpful in characterizing physiological and anatomical neurodevelopmental changes linked with healthy brain maturation and can be used as a baseline for comparing abnormal and pathological development in future studies. Our results demonstrate statistically significant differences between the sexes, representing a potentially important baseline from which to establish healthy growth trajectories. Biomarkers that correlated with age, potentially representing useful methods for assessing brain development, are also presented. This baseline information may facilitate studies that identify abnormal brain development associated with a variety of pathological conditions as departures from healthy sex-specific age-dependent neural development. Our findings are the result of combining the use of mainstream analytic methods with in-house-developed open-source software to help facilitate reproducible analyses, inclusive of many potential biomarkers that cannot be derived from existing software packages. Assessing relationships between our identified regional tract measurements produced by our technology and participant characteristics/phenotypic data in future analyses has tremendous potential for the study of human neurodevelopment. Full article
(This article belongs to the Special Issue Multi-Modal Biomedical Data Science—Modeling and Analysis)
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14 pages, 339 KiB  
Article
Data Augmentation with Cross-Modal Variational Autoencoders (DACMVA) for Cancer Survival Prediction
by Sara Rajaram and Cassie S. Mitchell
Information 2024, 15(1), 7; https://doi.org/10.3390/info15010007 - 21 Dec 2023
Viewed by 1908
Abstract
The ability to translate Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) into different modalities and data types is essential to improve Deep Learning (DL) for predictive medicine. This work presents DACMVA, a novel framework to conduct data augmentation in a cross-modal dataset [...] Read more.
The ability to translate Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) into different modalities and data types is essential to improve Deep Learning (DL) for predictive medicine. This work presents DACMVA, a novel framework to conduct data augmentation in a cross-modal dataset by translating between modalities and oversampling imputations of missing data. DACMVA was inspired by previous work on the alignment of latent spaces in Autoencoders. DACMVA is a DL data augmentation pipeline that improves the performance in a downstream prediction task. The unique DACMVA framework leverages a cross-modal loss to improve the imputation quality and employs training strategies to enable regularized latent spaces. Oversampling of augmented data is integrated into the prediction training. It is empirically demonstrated that the new DACMVA framework is effective in the often-neglected scenario of DL training on tabular data with continuous labels. Specifically, DACMVA is applied towards cancer survival prediction on tabular gene expression data where there is a portion of missing data in a given modality. DACMVA significantly (p << 0.001, one-sided Wilcoxon signed-rank test) outperformed the non-augmented baseline and competing augmentation methods with varying percentages of missing data (4%, 90%, 95% missing). As such, DACMVA provides significant performance improvements, even in very-low-data regimes, over existing state-of-the-art methods, including TDImpute and oversampling alone. Full article
(This article belongs to the Special Issue Multi-Modal Biomedical Data Science—Modeling and Analysis)
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Review

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24 pages, 813 KiB  
Review
Revolutionizing Vaccine Development for COVID-19: A Review of AI-Based Approaches
by Aritra Ghosh, Maria M. Larrondo-Petrie and Mirjana Pavlovic
Information 2023, 14(12), 665; https://doi.org/10.3390/info14120665 - 18 Dec 2023
Cited by 7 | Viewed by 5663
Abstract
The evolvement of COVID-19 vaccines is rapidly being revolutionized using artificial intelligence-based technologies. Small compounds, peptides, and epitopes are collected to develop new therapeutics. These substances can also guide artificial intelligence-based modeling, screening, or creation. Machine learning techniques are used to leverage pre-existing [...] Read more.
The evolvement of COVID-19 vaccines is rapidly being revolutionized using artificial intelligence-based technologies. Small compounds, peptides, and epitopes are collected to develop new therapeutics. These substances can also guide artificial intelligence-based modeling, screening, or creation. Machine learning techniques are used to leverage pre-existing data for COVID-19 drug detection and vaccine advancement, while artificial intelligence-based models are used for these purposes. Models based on artificial intelligence are used to evaluate and recognize the best candidate targets for future therapeutic development. Artificial intelligence-based strategies can be used to address issues with the safety and efficacy of COVID-19 vaccine candidates, as well as issues with manufacturing, storage, and logistics. Because antigenic peptides are effective at eliciting immune responses, artificial intelligence algorithms can assist in identifying the most promising COVID-19 vaccine candidates. Following COVID-19 vaccination, the first phase of the vaccine-induced immune response occurs when major histocompatibility complex (MHC) class II molecules (typically bind peptides of 12–25 amino acids) recognize antigenic peptides. Therefore, AI-based models are used to identify the best COVID-19 vaccine candidates and ensure the efficacy and safety of vaccine-induced immune responses. This study explores the use of artificial intelligence-based approaches to address logistics, manufacturing, storage, safety, and effectiveness issues associated with several COVID-19 vaccine candidates. Additionally, we will evaluate potential targets for next-generation treatments and examine the role that artificial intelligence-based models can play in identifying the most promising COVID-19 vaccine candidates, while also considering the effectiveness of antigenic peptides in triggering immune responses. The aim of this project is to gain insights into how artificial intelligence-based approaches could revolutionize the development of COVID-19 vaccines and how they can be leveraged to address challenges associated with vaccine development. In this work, we highlight potential barriers and solutions and focus on recent improvements in using artificial intelligence to produce COVID-19 drugs and vaccines, as well as the prospects for intelligent training in COVID-19 treatment discovery. Full article
(This article belongs to the Special Issue Multi-Modal Biomedical Data Science—Modeling and Analysis)
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