-
Sensors (Basel, Switzerland) Nov 2023Machine learning is an effective method for developing automatic algorithms for analysing sophisticated biomedical data [...].
Machine learning is an effective method for developing automatic algorithms for analysing sophisticated biomedical data [...].
Topics: Machine Learning; Algorithms
PubMed: 38067750
DOI: 10.3390/s23239377 -
The Journal of International Medical... Apr 2024Breast cancer (BC) is the most prominent form of cancer among females all over the world. The current methods of BC detection include X-ray mammography, ultrasound,... (Review)
Review
Breast cancer (BC) is the most prominent form of cancer among females all over the world. The current methods of BC detection include X-ray mammography, ultrasound, computed tomography, magnetic resonance imaging, positron emission tomography and breast thermographic techniques. More recently, machine learning (ML) tools have been increasingly employed in diagnostic medicine for its high efficiency in detection and intervention. The subsequent imaging features and mathematical analyses can then be used to generate ML models, which stratify, differentiate and detect benign and malignant breast lesions. Given its marked advantages, radiomics is a frequently used tool in recent research and clinics. Artificial neural networks and deep learning (DL) are novel forms of ML that evaluate data using computer simulation of the human brain. DL directly processes unstructured information, such as images, sounds and language, and performs precise clinical image stratification, medical record analyses and tumour diagnosis. Herein, this review thoroughly summarizes prior investigations on the application of medical images for the detection and intervention of BC using radiomics, namely DL and ML. The aim was to provide guidance to scientists regarding the use of artificial intelligence and ML in research and the clinic.
Topics: Humans; Breast Neoplasms; Female; Machine Learning; Neural Networks, Computer; Mammography; Deep Learning; Magnetic Resonance Imaging; Tomography, X-Ray Computed
PubMed: 38663911
DOI: 10.1177/03000605241237867 -
Biomedical Engineering Online Sep 2023Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However,... (Review)
Review
Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.
Topics: Diagnosis, Differential; Algorithms; Machine Learning; Precision Medicine; Technology
PubMed: 37658345
DOI: 10.1186/s12938-023-01148-1 -
Medical Image Analysis Aug 2023Image analysis and machine learning algorithms operating on multi-gigapixel whole-slide images (WSIs) often process a large number of tiles (sub-images) and require... (Review)
Review
Image analysis and machine learning algorithms operating on multi-gigapixel whole-slide images (WSIs) often process a large number of tiles (sub-images) and require aggregating predictions from the tiles in order to predict WSI-level labels. In this paper, we present a review of existing literature on various types of aggregation methods with a view to help guide future research in the area of computational pathology (CPath). We propose a general CPath workflow with three pathways that consider multiple levels and types of data and the nature of computation to analyse WSIs for predictive modelling. We categorize aggregation methods according to the context and representation of the data, features of computational modules and CPath use cases. We compare and contrast different methods based on the principle of multiple instance learning, perhaps the most commonly used aggregation method, covering a wide range of CPath literature. To provide a fair comparison, we consider a specific WSI-level prediction task and compare various aggregation methods for that task. Finally, we conclude with a list of objectives and desirable attributes of aggregation methods in general, pros and cons of the various approaches, some recommendations and possible future directions.
Topics: Humans; Algorithms; Machine Learning; Image Processing, Computer-Assisted
PubMed: 37423055
DOI: 10.1016/j.media.2023.102885 -
Bioinformatics (Oxford, England) Sep 2023The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning...
MOTIVATION
The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Because of this, previous approaches have typically been limited to inferring relationships among unrooted quartets of taxa, where there are only three possible topologies. Here, we explore the potential of generative adversarial networks (GANs) to address this limitation. GANs consist of a generator and a discriminator: at each step, the generator aims to create data that is similar to real data, while the discriminator attempts to distinguish generated and real data. By using an evolutionary model as the generator, we use GANs to make evolutionary inferences. Since a new model can be considered at each iteration, heuristic searches of complex model spaces are possible. Thus, GANs offer a potential solution to the challenges of applying machine learning in phylogenetics.
RESULTS
We developed phyloGAN, a GAN that infers phylogenetic relationships among species. phyloGAN takes as input a concatenated alignment, or a set of gene alignments, and infers a phylogenetic tree either considering or ignoring gene tree heterogeneity. We explored the performance of phyloGAN for up to 15 taxa in the concatenation case and 6 taxa when considering gene tree heterogeneity. Error rates are relatively low in these simple cases. However, run times are slow and performance metrics suggest issues during training. Future work should explore novel architectures that may result in more stable and efficient GANs for phylogenetics.
AVAILABILITY AND IMPLEMENTATION
phyloGAN is available on github: https://github.com/meganlsmith/phyloGAN/.
Topics: Phylogeny; Biological Evolution; Benchmarking; Genetic Heterogeneity; Machine Learning
PubMed: 37669126
DOI: 10.1093/bioinformatics/btad543 -
Cells Feb 2024Cell segmentation is an important task in the field of image processing, widely used in the life sciences and medical fields. Traditional methods are mainly based on... (Review)
Review
Cell segmentation is an important task in the field of image processing, widely used in the life sciences and medical fields. Traditional methods are mainly based on pixel intensity and spatial relationships, but have limitations. In recent years, machine learning and deep learning methods have been widely used, providing more-accurate and efficient solutions for cell segmentation. The effort to develop efficient and accurate segmentation software tools has been one of the major focal points in the field of cell segmentation for years. However, each software tool has unique characteristics and adaptations, and no universal cell-segmentation software can achieve perfect results. In this review, we used three publicly available datasets containing multiple 2D cell-imaging modalities. Common segmentation metrics were used to evaluate the performance of eight segmentation tools to compare their generality and, thus, find the best-performing tool.
Topics: Software; Image Processing, Computer-Assisted; Machine Learning
PubMed: 38391965
DOI: 10.3390/cells13040352 -
Journal of Medical Internet Research Jul 2023Normal voice production depends on the synchronized cooperation of multiple physiological systems, which makes the voice sensitive to changes. Any systematic,... (Review)
Review
BACKGROUND
Normal voice production depends on the synchronized cooperation of multiple physiological systems, which makes the voice sensitive to changes. Any systematic, neurological, and aerodigestive distortion is prone to affect voice production through reduced cognitive, pulmonary, and muscular functionality. This sensitivity inspired using voice as a biomarker to examine disorders that affect the voice. Technological improvements and emerging machine learning (ML) technologies have enabled possibilities of extracting digital vocal features from the voice for automated diagnosis and monitoring systems.
OBJECTIVE
This study aims to summarize a comprehensive view of research on voice-affecting disorders that uses ML techniques for diagnosis and monitoring through voice samples where systematic conditions, nonlaryngeal aerodigestive disorders, and neurological disorders are specifically of interest.
METHODS
This systematic literature review (SLR) investigated the state of the art of voice-based diagnostic and monitoring systems with ML technologies, targeting voice-affecting disorders without direct relation to the voice box from the point of view of applied health technology. Through a comprehensive search string, studies published from 2012 to 2022 from the databases Scopus, PubMed, and Web of Science were scanned and collected for assessment. To minimize bias, retrieval of the relevant references in other studies in the field was ensured, and 2 authors assessed the collected studies. Low-quality studies were removed through a quality assessment and relevant data were extracted through summary tables for analysis. The articles were checked for similarities between author groups to prevent cumulative redundancy bias during the screening process, where only 1 article was included from the same author group.
RESULTS
In the analysis of the 145 included studies, support vector machines were the most utilized ML technique (51/145, 35.2%), with the most studied disease being Parkinson disease (PD; reported in 87/145, 60%, studies). After 2017, 16 additional voice-affecting disorders were examined, in contrast to the 3 investigated previously. Furthermore, an upsurge in the use of artificial neural network-based architectures was observed after 2017. Almost half of the included studies were published in last 2 years (2021 and 2022). A broad interest from many countries was observed. Notably, nearly one-half (n=75) of the studies relied on 10 distinct data sets, and 11/145 (7.6%) used demographic data as an input for ML models.
CONCLUSIONS
This SLR revealed considerable interest across multiple countries in using ML techniques for diagnosing and monitoring voice-affecting disorders, with PD being the most studied disorder. However, the review identified several gaps, including limited and unbalanced data set usage in studies, and a focus on diagnostic test rather than disorder-specific monitoring. Despite the limitations of being constrained by only peer-reviewed publications written in English, the SLR provides valuable insights into the current state of research on ML-based voice-affecting disorder diagnosis and monitoring and highlighting areas to address in future research.
Topics: Humans; Monitoring, Physiologic; Machine Learning
PubMed: 37467031
DOI: 10.2196/46105 -
Scientific Reports Jan 2024Shannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and...
Shannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and quantitatively applied Shannon entropy in a systematic way to quantify the entropy of clinical situations using diagnostic variables (true and false positives and negatives, respectively). Decision tree representations of medical decision-making tools can be generated using diagnostic variables found in literature and entropy removal can be calculated for these tools. This concept of clinical entropy removal has significant potential for further use to bring forth healthcare innovation, such as quantifying the impact of clinical guidelines and value of care and applications to Emergency Medicine scenarios where diagnostic accuracy in a limited time window is paramount. This analysis was done for 623 diagnostic tools and provided unique insights into their utility. For studies that provided detailed data on medical decision-making algorithms, bootstrapped datasets were generated from source data to perform comprehensive machine learning analysis on these algorithms and their constituent steps, which revealed a novel and thorough evaluation of medical diagnostic algorithms.
Topics: Entropy; Algorithms; Clinical Decision-Making; Machine Learning; Information Theory
PubMed: 38216607
DOI: 10.1038/s41598-024-51268-4 -
Sensors (Basel, Switzerland) Sep 2023The integration of wearable sensor technology and machine learning algorithms has significantly transformed the field of intelligent medical rehabilitation. These... (Review)
Review
The integration of wearable sensor technology and machine learning algorithms has significantly transformed the field of intelligent medical rehabilitation. These innovative technologies enable the collection of valuable movement, muscle, or nerve data during the rehabilitation process, empowering medical professionals to evaluate patient recovery and predict disease development more efficiently. This systematic review aims to study the application of wearable sensor technology and machine learning algorithms in different disease rehabilitation training programs, obtain the best sensors and algorithms that meet different disease rehabilitation conditions, and provide ideas for future research and development. A total of 1490 studies were retrieved from two databases, the Web of Science and IEEE Xplore, and finally 32 articles were selected. In this review, the selected papers employ different wearable sensors and machine learning algorithms to address different disease rehabilitation problems. Our analysis focuses on the types of wearable sensors employed, the application of machine learning algorithms, and the approach to rehabilitation training for different medical conditions. It summarizes the usage of different sensors and compares different machine learning algorithms. It can be observed that the combination of these two technologies can optimize the disease rehabilitation process and provide more possibilities for future home rehabilitation scenarios. Finally, the present limitations and suggestions for future developments are presented in the study.
Topics: Humans; Algorithms; Databases, Factual; Intelligence; Machine Learning; Wearable Electronic Devices
PubMed: 37765724
DOI: 10.3390/s23187667 -
Current Opinion in Structural Biology Apr 2024Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional... (Review)
Review
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked the development of numerous computational approaches, such as the identification of allosteric binding sites, to facilitate allosteric drug discovery. Building on the success of machine learning (ML) models for solving complex problems in biology and chemistry, several ML models for predicting allosteric sites have been developed. In this review, we provide an overview of these models and discuss future perspectives powered by the field of artificial intelligence such as protein language models.
Topics: Allosteric Site; Artificial Intelligence; Allosteric Regulation; Binding Sites; Proteins; Machine Learning; Ligands
PubMed: 38354652
DOI: 10.1016/j.sbi.2024.102774