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BioMedInformatics, Volume 4, Issue 1

2024 March - 48 articles

Cover Story: This Figure perfectly summarizes our young journal BioMedInformatics as it provides a bridge between medical science and new developments in bioinformatics in all its forms from biomedical informatics, as well as computational biology and medicine, linking patient diagnosis to new discoveries and personalized medicine. View this paper
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Articles (48)

  • Article
  • Open Access
17 Citations
5,850 Views
24 Pages

Background: Creating models to differentiate self-reported mental workload perceptions is challenging and requires machine learning to identify features from EEG signals. EEG band ratios quantify human activity, but limited research on mental workloa...

(This article belongs to the Special Issue Feature Papers in Medical Statistics and Data Science Section)
  • Review
  • Open Access
90 Citations
12,479 Views
16 Pages

This review explores the transformative integration of artificial intelligence (AI) and healthcare through conversational AI leveraging Natural Language Processing (NLP). Focusing on Large Language Models (LLMs), this paper navigates through various...

(This article belongs to the Special Issue Computational Biology and Artificial Intelligence in Medicine)
  • Article
  • Open Access
2 Citations
3,902 Views
14 Pages

Overall Survival Time Estimation for Epithelioid Peritoneal Mesothelioma Patients from Whole-Slide Images

  • Kleanthis Marios Papadopoulos,
  • Panagiotis Barmpoutis,
  • Tania Stathaki,
  • Vahan Kepenekian,
  • Peggy Dartigues,
  • Séverine Valmary-Degano,
  • Claire Illac-Vauquelin,
  • Gerlinde Avérous,
  • Anne Chevallier and
  • Nazim Benzerdjeb
  • + 6 authors

Background: The advent of Deep Learning initiated a new era in which neural networks relying solely on Whole-Slide Images can estimate the survival time of cancer patients. Remarkably, despite deep learning’s potential in this domain, no prior...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
2 Citations
2,382 Views
12 Pages

Genetic Optimization in Uncovering Biologically Meaningful Gene Biomarkers for Glioblastoma Subtypes

  • Petros Paplomatas,
  • Ioanna-Efstathia Douroumi,
  • Panagiotis Vlamos and
  • Aristidis Vrahatis

Background: Glioblastoma multiforme (GBM) is a highly aggressive brain cancer known for its challenging survival rates; it is characterized by distinct subtypes, such as the proneural and mesenchymal states. The development of targeted therapies is c...

(This article belongs to the Special Issue Editor's Choice Series for the Applied Biomedical Data Science Section)
  • Article
  • Open Access
9 Citations
4,609 Views
15 Pages

Background: Epilepsy, a prevalent neurological disorder characterized by recurrent seizures affecting an estimated 70 million people worldwide, poses a significant diagnostic challenge. EEG serves as an important tool in identifying these seizures, b...

  • Article
  • Open Access
4 Citations
3,939 Views
16 Pages

Electronic Health Records (EHR) provide a vast amount of patient data that are relevant to predicting clinical outcomes. The inherent presence of missing values poses challenges to building performant machine learning models. This paper aims to inves...

(This article belongs to the Special Issue Feature Papers in Medical Statistics and Data Science Section)
  • Review
  • Open Access
21 Citations
10,725 Views
26 Pages

Background: Over the past few years, clinical studies have utilized machine learning in telehealth and smart care for disease management, self-management, and managing health issues like pulmonary diseases, heart failure, diabetes screening, and intr...

(This article belongs to the Special Issue Feature Papers in Clinical Informatics Section)
  • Article
  • Open Access
1 Citations
3,590 Views
21 Pages

Background: Antibiotics can play a pivotal role in the treatment of colorectal cancer (CRC) at various stages of the disease, both directly and indirectly. Identifying novel patterns of antibiotic effects or responses in CRC within extensive medical...

(This article belongs to the Special Issue Feature Papers in Computational Biology and Medicine)
  • Article
  • Open Access
2 Citations
2,412 Views
12 Pages

Predictive Analysis of Endoscope Demand in Otolaryngology Outpatient Settings

  • David Lanier,
  • Cristie Roush,
  • Gwendolyn Young and
  • Sara Masoud

Background: There has been a trend to transit reprocessing of flexible endoscopes from a high-level disinfectant (HLD) centralized manner to sterilization performed by nursing staff in some Ear, Nose, and Throat (ENT) clinics. In doing so, the clinic...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
5 Citations
4,008 Views
12 Pages

The Development and Usability Assessment of an Augmented Reality Decision Support System to Address Burn Patient Management

  • Sena Veazey,
  • Nicole Caldwell,
  • David Luellen,
  • Angela Samosorn,
  • Allison McGlasson,
  • Patricia Colston,
  • Craig Fenrich,
  • Jose Salinas,
  • Jared Mike and
  • Maria Serio-Melvin
  • + 1 author

Critical care injuries, such as burn trauma, require specialized skillsets and knowledge. A clinical decision support system to aid clinicians in providing burn patient management can increase proficiency and provide knowledge content for specific in...

(This article belongs to the Special Issue Feature Papers in Computational Biology and Medicine)
  • Article
  • Open Access
5 Citations
3,006 Views
19 Pages

Reliability and Agreement of Free Web-Based 3D Software for Computing Facial Area and Volume Measurements

  • Oguzhan Topsakal,
  • Philip Sawyer,
  • Tahir Cetin Akinci,
  • Elif Topsakal and
  • M. Mazhar Celikoyar

Background: Facial surgeries require meticulous planning and outcome assessments, where facial analysis plays a critical role. This study introduces a new approach by utilizing three-dimensional (3D) imaging techniques, which are known for their abil...

(This article belongs to the Section Computational Biology and Medicine)
  • Review
  • Open Access
19 Citations
9,618 Views
17 Pages

This review explores the integration of artificial intelligence (AI) and machine learning (ML) into kidney transplantation (KT), set against the backdrop of a significant donor organ shortage and the evolution of ‘Next-Generation Healthcare&rsq...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
42 Citations
14,039 Views
12 Pages

Background: Currently, discriminating Iron Deficiency Anemia (IDA) from other anemia requires an expensive test (serum ferritin). Complete Blood Count (CBC) tests are less costly and more widely available. Machine learning models have not yet been ap...

(This article belongs to the Special Issue Editor's Choice Series for the Applied Biomedical Data Science Section)
  • Article
  • Open Access
20 Citations
5,714 Views
23 Pages

Naturalize Revolution: Unprecedented AI-Driven Precision in Skin Cancer Classification Using Deep Learning

  • Mohamad Abou Ali,
  • Fadi Dornaika,
  • Ignacio Arganda-Carreras,
  • Hussein Ali and
  • Malak Karaouni

Background: In response to the escalating global concerns surrounding skin cancer, this study aims to address the imperative for precise and efficient diagnostic methodologies. Focusing on the intricate task of eight-class skin cancer classification,...

(This article belongs to the Special Issue Computational Biology and Artificial Intelligence in Medicine)
  • Article
  • Open Access
38 Citations
9,924 Views
15 Pages

Real-Time Jaundice Detection in Neonates Based on Machine Learning Models

  • Ahmad Yaseen Abdulrazzak,
  • Saleem Latif Mohammed,
  • Ali Al-Naji and
  • Javaan Chahl

Introduction: Despite the many attempts made by researchers to diagnose jaundice non-invasively using machine learning techniques, the low amount of data used to build their models remains the key factor limiting the performance of their models. Obje...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
13 Citations
5,702 Views
23 Pages

Machine Learning Approach to Identify Case-Control Studies on ApoE Gene Mutations Linked to Alzheimer’s Disease in Italy

  • Giorgia Francesca Saraceno,
  • Diana Marisol Abrego-Guandique,
  • Roberto Cannataro,
  • Maria Cristina Caroleo and
  • Erika Cione

Background: An application of artificial intelligence is machine learning, which allows computer programs to learn and create data. Methods: In this work, we aimed to evaluate the performance of the MySLR machine learning platform, which implements t...

(This article belongs to the Special Issue Feature Papers in Computational Biology and Medicine)
  • Review
  • Open Access
5 Citations
3,885 Views
34 Pages

Computational intelligence (CI) uses applied computational methods for problem-solving inspired by the behavior of humans and animals. Biological systems are used to construct software to solve complex problems, and one type of such system is an arti...

(This article belongs to the Special Issue Computational Biology and Artificial Intelligence in Medicine)
  • Article
  • Open Access
27 Citations
8,248 Views
17 Pages

Assessment of Voice Disorders Using Machine Learning and Vocal Analysis of Voice Samples Recorded through Smartphones

  • Michele Giuseppe Di Cesare,
  • David Perpetuini,
  • Daniela Cardone and
  • Arcangelo Merla

Background: The integration of edge computing into smart healthcare systems requires the development of computationally efficient models and methodologies for monitoring and detecting patients’ healthcare statuses. In this context, mobile devic...

(This article belongs to the Special Issue Editor's Choice Series for the Applied Biomedical Data Science Section)
  • Editorial
  • Open Access
3 Citations
4,261 Views
7 Pages

Artificial intelligence (AI), a branch of computer science, involves developing intelligent computer programs to mimic human intelligence and automate various processes [...]

  • Article
  • Open Access
22 Citations
6,041 Views
23 Pages

Early detection of dyslexia and learning disorders is vital for avoiding a learning disability, as well as supporting dyslexic students by tailoring academic programs to their needs. Several studies have investigated using supervised algorithms to sc...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
14 Citations
8,893 Views
30 Pages

Background: In recent years, there has been increasing research in the applications of Artificial Intelligence in the medical industry. Digital pathology has seen great success in introducing the use of technology in the digitisation and analysis of...

(This article belongs to the Special Issue Feature Papers in Medical Statistics and Data Science Section)
  • Article
  • Open Access
7 Citations
3,910 Views
12 Pages

Weighted Rank Difference Ensemble: A New Form of Ensemble Feature Selection Method for Medical Datasets

  • Arju Manara Begum,
  • M. Rubaiyat Hossain Mondal,
  • Prajoy Podder and
  • Joarder Kamruzzaman

Background: Feature selection (FS), a crucial preprocessing step in machine learning, greatly reduces the dimension of data and improves model performance. This paper focuses on selecting features for medical data classification. Methods: In this wor...

(This article belongs to the Special Issue Feature Papers in Clinical Informatics Section)
  • Article
  • Open Access
1 Citations
5,116 Views
23 Pages

An Interactive Dashboard for Statistical Analysis of Intensive Care Unit COVID-19 Data

  • Rúben Dias,
  • Artur Ferreira,
  • Iola Pinto,
  • Carlos Geraldes,
  • Cristiana Von Rekowski and
  • Luís Bento

Background: COVID-19 caused a pandemic, due to its ease of transmission and high number of infections. The evolution of the pandemic and its consequences for the mortality and morbidity of populations, especially the elderly, generated several scient...

(This article belongs to the Section Applied Biomedical Data Science)
  • Article
  • Open Access
5 Citations
5,259 Views
17 Pages

This study investigates the potential of low-cost infrared cameras for non-contact monitoring of blood pressure (BP) in individuals with fragile health, particularly the elderly. Previous research has shown success in developing non-contact BP monito...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
3 Citations
3,767 Views
14 Pages

Ensemble Methods to Optimize Automated Text Classification in Avatar Therapy

  • Alexandre Hudon,
  • Kingsada Phraxayavong,
  • Stéphane Potvin and
  • Alexandre Dumais

Background: Psychotherapeutic approaches such as Avatar Therapy (AT) are novel therapeutic attempts to help patients diagnosed with treatment-resistant schizophrenia. Qualitative analyses of immersive sessions of AT have been undertaken to enhance an...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
25 Citations
8,852 Views
13 Pages

Lip-Reading Advancements: A 3D Convolutional Neural Network/Long Short-Term Memory Fusion for Precise Word Recognition

  • Themis Exarchos,
  • Georgios N. Dimitrakopoulos,
  • Aristidis G. Vrahatis,
  • Georgios Chrysovitsiotis,
  • Zoi Zachou and
  • Efthymios Kyrodimos

Lip reading, the art of deciphering spoken words from the visual cues of lip movements, has garnered significant interest for its potential applications in diverse fields, including assistive technologies, human–computer interaction, and securi...

(This article belongs to the Special Issue Feature Papers on Methods in Biomedical Informatics)
  • Review
  • Open Access
2 Citations
4,997 Views
25 Pages

Unravelling Insights into the Evolution and Management of SARS-CoV-2

  • Aganze Gloire-Aimé Mushebenge,
  • Samuel Chima Ugbaja,
  • Nonkululeko Avril Mbatha,
  • Rene B. Khan and
  • Hezekiel M. Kumalo

Worldwide, the COVID-19 pandemic, caused by the brand-new coronavirus SARS-CoV-2, has claimed a sizable number of lives. The virus’ rapid spread and impact on every facet of human existence necessitate a continuous and dynamic examination of it...

(This article belongs to the Section Clinical Informatics)
  • Article
  • Open Access
3 Citations
3,146 Views
25 Pages

Toward Cancer Chemoprevention: Mathematical Modeling of Chemically Induced Carcinogenesis and Chemoprevention

  • Dimitrios G. Boucharas,
  • Chryssa Anastasiadou,
  • Spyridon Karkabounas,
  • Efthimia Antonopoulou and
  • George Manis

Cancer, which is currently rated as the second-leading cause of mortality across the globe, is one of the most hazardous disease groups that has plagued humanity for centuries. The experiments presented here span over two decades and were conducted o...

(This article belongs to the Special Issue Computational Biology and Artificial Intelligence in Medicine)
  • Article
  • Open Access
34 Citations
4,885 Views
13 Pages

Identifying Potent Fat Mass and Obesity-Associated Protein Inhibitors Using Deep Learning-Based Hybrid Procedures

  • Kannan Mayuri,
  • Durairaj Varalakshmi,
  • Mayakrishnan Tharaheswari,
  • Chaitanya Sree Somala,
  • Selvaraj Sathya Priya,
  • Nagaraj Bharathkumar,
  • Renganathan Senthil,
  • Raja Babu Singh Kushwah,
  • Sundaram Vickram and
  • Konda Mani Saravanan
  • + 1 author

The fat mass and obesity-associated (FTO) protein catalyzes metal-dependent modifications of nucleic acids, namely the demethylation of methyl adenosine inside mRNA molecules. The FTO protein has been identified as a potential target for developing a...

(This article belongs to the Topic Machine Learning Empowered Drug Screen)
  • Article
  • Open Access
11 Citations
5,232 Views
21 Pages

Uterine corpus endometrial carcinoma (UCEC) poses significant clinical challenges due to its high incidence and poor prognosis, exacerbated by the lack of effective screening methods. The standard treatment for UCEC typically involves surgical interv...

(This article belongs to the Special Issue Feature Papers in Computational Biology and Medicine)
  • Article
  • Open Access
6 Citations
4,142 Views
26 Pages

Artificial Intelligence Analysis and Reverse Engineering of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using Gene Expression Data

  • Joaquim Carreras,
  • Yara Yukie Kikuti,
  • Masashi Miyaoka,
  • Saya Miyahara,
  • Giovanna Roncador,
  • Rifat Hamoudi and
  • Naoya Nakamura

Diffuse large B-cell lymphoma is one of the most frequent mature B-cell hematological neoplasms and non-Hodgkin lymphomas. Despite advances in diagnosis and treatment, clinical evolution is unfavorable in a subset of patients. Using molecular techniq...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
3,180 Views
10 Pages

Tetanus Severity Classification in Low-Middle Income Countries through ECG Wearable Sensors and a 1D-Vision Transformer

  • Ping Lu,
  • Zihao Wang,
  • Hai Duong Ha Thi,
  • Ho Bich Hai,
  • VITAL Consortium,
  • Louise Thwaites and
  • David A. Clifton

Tetanus, a life-threatening bacterial infection prevalent in low- and middle-income countries like Vietnam, impacts the nervous system, causing muscle stiffness and spasms. Severe tetanus often involves dysfunction of the autonomic nervous system (AN...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Review
  • Open Access
131 Citations
22,847 Views
49 Pages

Deep learning has emerged as a powerful tool for medical image analysis and diagnosis, demonstrating high performance on tasks such as cancer detection. This literature review synthesizes current research on deep learning techniques applied to lung c...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
5 Citations
5,536 Views
17 Pages

Hospital readmission involves the unplanned emergency admission of patients within 30 days from discharge after the previous admission. According to the Canadian Health Institute (CIHI), 1 in 11 patients were readmitted within 30 days of leaving the...

(This article belongs to the Special Issue Feature Papers in Computational Biology and Medicine)
  • Article
  • Open Access
11 Citations
5,208 Views
22 Pages

An Explainable AI System for the Diagnosis of High-Dimensional Biomedical Data

  • Alfred Ultsch,
  • Jörg Hoffmann,
  • Maximilian A. Röhnert,
  • Malte von Bonin,
  • Uta Oelschlägel,
  • Cornelia Brendel and
  • Michael C. Thrun

Typical state-of-the-art flow cytometry data samples typically consist of measures of 10 to 30 features of more than 100,000 cell “events”. Artificial intelligence (AI) systems are able to diagnose such data with almost the same accuracy...

(This article belongs to the Section Computational Biology and Medicine)
  • Review
  • Open Access
13 Citations
14,282 Views
24 Pages

Digital Pathology: A Comprehensive Review of Open-Source Histological Segmentation Software

  • Anna Maria Pavone,
  • Antonino Giulio Giannone,
  • Daniela Cabibi,
  • Simona D’Aprile,
  • Simona Denaro,
  • Giuseppe Salvaggio,
  • Rosalba Parenti,
  • Anthony Yezzi and
  • Albert Comelli

In the era of digitalization, the biomedical sector has been affected by the spread of artificial intelligence. In recent years, the possibility of using deep and machine learning methods for clinical diagnostic and therapeutic interventions has been...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Review
  • Open Access
3 Citations
11,513 Views
15 Pages

Radiation-induced gastrointestinal (GI) dose constraints are still a matter of concern with the ongoing evolution of patient outcomes and treatment-related toxicity in the era of image-guided intensity-modulated radiation therapy (IMRT), stereotactic...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
6 Citations
6,389 Views
19 Pages

Blood Pressure Estimation from Photoplythmography Using Hybrid Scattering–LSTM Networks

  • Osama A. Omer,
  • Mostafa Salah,
  • Ammar M. Hassan,
  • Mohamed Abdel-Nasser,
  • Norihiro Sugita and
  • Yoshifumi Saijo

One of the most significant indicators of heart and cardiovascular health is blood pressure (BP). Blood pressure (BP) has gained great attention in the last decade. Uncontrolled high blood pressure increases the risk of serious health problems, inclu...

(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
  • Article
  • Open Access
2 Citations
3,249 Views
12 Pages

Machine Learning Analysis of Genomic Factors Influencing Hyperbaric Oxygen Therapy in Parkinson’s Disease

  • Eirini Banou,
  • Aristidis G. Vrahatis,
  • Marios G. Krokidis and
  • Panagiotis Vlamos

(1) Background: Parkinson’s disease (PD) is a progressively worsening neurodegenerative disorder affecting movement, mental well-being, sleep, and pain. While no cure exists, treatments like hyperbaric oxygen therapy (HBOT) offer potential reli...

(This article belongs to the Special Issue Feature Papers in Medical Statistics and Data Science Section)
  • Review
  • Open Access
68 Citations
12,379 Views
14 Pages

Recent advancements in artificial intelligence (AI) have facilitated its widespread adoption in primary medical services, addressing the demand–supply imbalance in healthcare. Vision Transformers (ViT) have emerged as state-of-the-art computer...

(This article belongs to the Special Issue Explainable Artificial Intelligence (XAI) in Biomedical Research and Clinical Practice)
  • Article
  • Open Access
16 Citations
11,426 Views
15 Pages

The three-dimensional protein structure is pivotal in comprehending biological phenomena. It directly governs protein function and hence aids in drug discovery. The development of protein prediction algorithms, such as AlphaFold2, ESMFold, and trRose...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Editorial
  • Open Access
15 Citations
8,037 Views
9 Pages

Biomedical informatics can be considered as a multidisciplinary research and educational field situated at the intersection of computational sciences (including computer science, data science, mathematics, and statistics), biology, and medicine. In r...

  • Article
  • Open Access
9 Citations
4,306 Views
14 Pages

The Bioinformatics Identification of Potential Protein Glycosylation Genes Associated with a Glioma Stem Cell Signature

  • Kazuya Tokumura,
  • Koki Sadamori,
  • Makoto Yoshimoto,
  • Akane Tomizawa,
  • Yuki Tanaka,
  • Kazuya Fukasawa and
  • Eiichi Hinoi

Glioma stem cells (GSCs) contribute to the pathogenesis of glioblastoma (GBM), which is the most malignant form of glioma. The implications and underlying mechanisms of protein glycosylation in GSC phenotypes and GBM malignancy are not fully understo...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
  • Article
  • Open Access
29 Citations
10,287 Views
25 Pages

Survey of Multimodal Medical Question Answering

  • Hilmi Demirhan and
  • Wlodek Zadrozny

Multimodal medical question answering (MMQA) is a vital area bridging healthcare and Artificial Intelligence (AI). This survey methodically examines the MMQA research published in recent years. We collect academic literature through Google Scholar, a...

(This article belongs to the Topic Computational Intelligence and Bioinformatics (CIB))
  • Article
  • Open Access
5 Citations
8,286 Views
16 Pages

An Open-Access Dataset of Hospitalized Cardiac-Arrest Patients: Machine-Learning-Based Predictions Using Clinical Documentation

  • Lahiru Theekshana Weerasinghe Rajapaksha,
  • Sugandima Mihirani Vidanagamachchi,
  • Sampath Gunawardena and
  • Vajira Thambawita

Cardiac arrest is a sudden loss of heart function with serious consequences. In developing countries, healthcare professionals use clinical documentation to track patient information. These data are used to predict the development of cardiac arrest....

(This article belongs to the Section Methods in Biomedical Informatics)
  • Article
  • Open Access
47 Citations
11,297 Views
26 Pages

Supporting the Demand on Mental Health Services with AI-Based Conversational Large Language Models (LLMs)

  • Tin Lai,
  • Yukun Shi,
  • Zicong Du,
  • Jiajie Wu,
  • Ken Fu,
  • Yichao Dou and
  • Ziqi Wang

The demand for psychological counselling has grown significantly in recent years, particularly with the global outbreak of COVID-19, which heightened the need for timely and professional mental health support. Online psychological counselling emerged...

(This article belongs to the Special Issue Deep Learning Methods and Application for Bioinformatics and Healthcare)
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BioMedInformatics - ISSN 2673-7426