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Water Research Oct 2023Modeling wastewater processes supports tasks such as process prediction, soft sensing, data analysis and computer assisted design of wastewater systems. Wastewater... (Review)
Review
Modeling wastewater processes supports tasks such as process prediction, soft sensing, data analysis and computer assisted design of wastewater systems. Wastewater treatment processes are large, complex processes, with multiple controlling mechanisms, a high degree of disturbance variability and non-linear (generally stable) behavior with multiple internal recycle loops. Semi-mechanistic biochemical models currently dominate research and application, with data-driven deep learning models emerging as an alternative and supplementary approach. But these modeling approaches have grown in separate communities of research and practice, and so there is limited appreciation of the strengths, weaknesses, contrasts and similarities between the methods. This review addresses that gap by providing a detailed guide to deep learning methods and their application to wastewater process modeling. The review is aimed at wastewater modeling experts who are familiar with established mechanistic modeling approach, and are curious about the opportunities and challenges afforded by deep learning methods. We conclude with a discussion and needs analysis on the value of different ways of modeling wastewater processes and open research problems.
Topics: Deep Learning; Wastewater
PubMed: 37716298
DOI: 10.1016/j.watres.2023.120518 -
Biochemical Society Transactions Oct 2023Dynamic pathway engineering aims to build metabolic production systems embedded with intracellular control mechanisms for improved performance. These control systems... (Review)
Review
Dynamic pathway engineering aims to build metabolic production systems embedded with intracellular control mechanisms for improved performance. These control systems enable host cells to self-regulate the temporal activity of a production pathway in response to perturbations, using a combination of biosensors and feedback circuits for controlling expression of heterologous enzymes. Pathway design, however, requires assembling together multiple biological parts into suitable circuit architectures, as well as careful calibration of the function of each component. This results in a large design space that is costly to navigate through experimentation alone. Methods from artificial intelligence (AI) and machine learning are gaining increasing attention as tools to accelerate the design cycle, owing to their ability to identify hidden patterns in data and rapidly screen through large collections of designs. In this review, we discuss recent developments in the application of machine learning methods to the design of dynamic pathways and their components. We cover recent successes and offer perspectives for future developments in the field. The integration of AI into metabolic engineering pipelines offers great opportunities to streamline design and discover control systems for improved production of high-value chemicals.
Topics: Artificial Intelligence; Machine Learning; Metabolic Engineering; Biosensing Techniques
PubMed: 37656433
DOI: 10.1042/BST20221542 -
International Journal of Medical... Dec 2023Medication prescription is a complex process that could benefit from current research and development in machine learning through decision support systems. Particularly... (Review)
Review
BACKGROUND
Medication prescription is a complex process that could benefit from current research and development in machine learning through decision support systems. Particularly pediatricians are forced to prescribe medications "off-label" as children are still underrepresented in clinical studies, which leads to a high risk of an incorrect dose and adverse drug effects.
METHODS
PubMed, IEEE Xplore and PROSPERO were searched for relevant studies that developed and evaluated well-performing machine learning algorithms following the PRISMA statement. Quality assessment was conducted in accordance with the IJMEDI checklist. Identified studies were reviewed in detail, including the required variables for predicting the correct dose, especially of pediatric medication prescription.
RESULTS
The search identified 656 studies, of which 64 were reviewed in detail and 36 met the inclusion criteria. According to the IJMEDI checklist, five studies were considered to be of high quality. 19 of the 36 studies dealt with the active substance warfarin. Overall, machine learning algorithms based on decision trees or regression methods performed superior regarding their predictive power than algorithms based on neural networks, support vector machines or other methods. The use of ensemble methods like bagging or boosting generally enhanced the accuracy of the dose predictions. The required input and output variables of the algorithms were considerably heterogeneous and differ strongly among the respective substance.
CONCLUSIONS
By using machine learning algorithms, the prescription process could be simplified and dosing correctness could be enhanced. Despite the heterogenous results among the different substances and cases and the lack of pediatric use cases, the identified approaches and required variables can serve as an excellent starting point for further development of algorithms predicting drug doses, particularly for children. Especially the combination of physiologically-based pharmacokinetic models with machine learning algorithms represents a great opportunity to enhance the predictive power and accuracy of the developed algorithms.
Topics: Humans; Child; Algorithms; Neural Networks, Computer; Machine Learning; Prescriptions
PubMed: 37939541
DOI: 10.1016/j.ijmedinf.2023.105241 -
Molecules (Basel, Switzerland) Aug 2023With the advancement of computer technology, machine learning-based artificial intelligence technology has been increasingly integrated and applied in the fields of... (Review)
Review
With the advancement of computer technology, machine learning-based artificial intelligence technology has been increasingly integrated and applied in the fields of medicine, biology, and pharmacy, thereby facilitating their development. Transporters have important roles in influencing drug resistance, drug-drug interactions, and tissue-specific drug targeting. The investigation of drug transporter substrates and inhibitors is a crucial aspect of pharmaceutical development. However, long duration and high expenses pose significant challenges in the investigation of drug transporters. In this review, we discuss the present situation and challenges encountered in applying machine learning techniques to investigate drug transporters. The transporters involved include ABC transporters (P-gp, BCRP, MRPs, and BSEP) and SLC transporters (OAT, OATP, OCT, MATE1,2-K, and NET). The aim is to offer a point of reference for and assistance with the progression of drug transporter research, as well as the advancement of more efficient computer technology. Machine learning methods are valuable and attractive for helping with the study of drug transporter substrates and inhibitors, but continuous efforts are still needed to develop more accurate and reliable predictive models and to apply them in the screening process of drug development to improve efficiency and success rates.
Topics: Artificial Intelligence; ATP Binding Cassette Transporter, Subfamily G, Member 2; Neoplasm Proteins; Membrane Transport Proteins; Machine Learning
PubMed: 37630188
DOI: 10.3390/molecules28165936 -
BMC Medical Informatics and Decision... Jul 2023Esophageal cancer (EC) is a significant global health problem, with an estimated 7th highest incidence and 6th highest mortality rate. Timely diagnosis and treatment are...
INTRODUCTION
Esophageal cancer (EC) is a significant global health problem, with an estimated 7th highest incidence and 6th highest mortality rate. Timely diagnosis and treatment are critical for improving patients' outcomes, as over 40% of patients with EC are diagnosed after metastasis. Recent advances in machine learning (ML) techniques, particularly in computer vision, have demonstrated promising applications in medical image processing, assisting clinicians in making more accurate and faster diagnostic decisions. Given the significance of early detection of EC, this systematic review aims to summarize and discuss the current state of research on ML-based methods for the early detection of EC.
METHODS
We conducted a comprehensive systematic search of five databases (PubMed, Scopus, Web of Science, Wiley, and IEEE) using search terms such as "ML", "Deep Learning (DL (", "Neural Networks (NN)", "Esophagus", "EC" and "Early Detection". After applying inclusion and exclusion criteria, 31 articles were retained for full review.
RESULTS
The results of this review highlight the potential of ML-based methods in the early detection of EC. The average accuracy of the reviewed methods in the analysis of endoscopic and computed tomography (CT (images of the esophagus was over 89%, indicating a high impact on early detection of EC. Additionally, the highest percentage of clinical images used in the early detection of EC with the use of ML was related to white light imaging (WLI) images. Among all ML techniques, methods based on convolutional neural networks (CNN) achieved higher accuracy and sensitivity in the early detection of EC compared to other methods.
CONCLUSION
Our findings suggest that ML methods may improve accuracy in the early detection of EC, potentially supporting radiologists, endoscopists, and pathologists in diagnosis and treatment planning. However, the current literature is limited, and more studies are needed to investigate the clinical applications of these methods in early detection of EC. Furthermore, many studies suffer from class imbalance and biases, highlighting the need for validation of detection algorithms across organizations in longitudinal studies.
Topics: Humans; Deep Learning; Early Detection of Cancer; Machine Learning; Neural Networks, Computer; Esophageal Neoplasms
PubMed: 37460991
DOI: 10.1186/s12911-023-02235-y -
Scientific Reports Sep 2023For many machine learning applications in drug discovery, only limited amounts of training data are available. This typically applies to compound design and activity...
For many machine learning applications in drug discovery, only limited amounts of training data are available. This typically applies to compound design and activity prediction and often restricts machine learning, especially deep learning. For low-data applications, specialized learning strategies can be considered to limit required training data. Among these is meta-learning that attempts to enable learning in low-data regimes by combining outputs of different models and utilizing meta-data from these predictions. However, in drug discovery settings, meta-learning is still in its infancy. In this study, we have explored meta-learning for the prediction of potent compounds via generative design using transformer models. For different activity classes, meta-learning models were derived to predict highly potent compounds from weakly potent templates in the presence of varying amounts of fine-tuning data and compared to other transformers developed for this task. Meta-learning consistently led to statistically significant improvements in model performance, in particular, when fine-tuning data were limited. Moreover, meta-learning models generated target compounds with higher potency and larger potency differences between templates and targets than other transformers, indicating their potential for low-data compound design.
Topics: Drug Discovery; Electric Power Supplies; Machine Learning
PubMed: 37752164
DOI: 10.1038/s41598-023-43046-5 -
Biomedicine & Pharmacotherapy =... Sep 2023Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The... (Review)
Review
Traditional bulk sequencing methods are limited to measuring the average signal in a group of cells, potentially masking heterogeneity, and rare populations. The single-cell resolution, however, enhances our understanding of complex biological systems and diseases, such as cancer, the immune system, and chronic diseases. However, the single-cell technologies generate massive amounts of data that are often high-dimensional, sparse, and complex, thus making analysis with traditional computational approaches difficult and unfeasible. To tackle these challenges, many are turning to deep learning (DL) methods as potential alternatives to the conventional machine learning (ML) algorithms for single-cell studies. DL is a branch of ML capable of extracting high-level features from raw inputs in multiple stages. Compared to traditional ML, DL models have provided significant improvements across many domains and applications. In this work, we examine DL applications in genomics, transcriptomics, spatial transcriptomics, and multi-omics integration, and address whether DL techniques will prove to be advantageous or if the single-cell omics domain poses unique challenges. Through a systematic literature review, we have found that DL has not yet revolutionized the most pressing challenges of the single-cell omics field. However, using DL models for single-cell omics has shown promising results (in many cases outperforming the previous state-of-the-art models) in data preprocessing and downstream analysis. Although developments of DL algorithms for single-cell omics have generally been gradual, recent advances reveal that DL can offer valuable resources in fast-tracking and advancing research in single-cell.
Topics: Deep Learning; Transcriptome; Genomics; Machine Learning; Gene Expression Profiling
PubMed: 37393865
DOI: 10.1016/j.biopha.2023.115077 -
Neurotherapeutics : the Journal of the... Jul 2023We reviewed foundational concepts in artificial intelligence (AI) and machine learning (ML) and discussed ways in which these methodologies may be employed to enhance... (Review)
Review
We reviewed foundational concepts in artificial intelligence (AI) and machine learning (ML) and discussed ways in which these methodologies may be employed to enhance progress in clinical trials and research, with particular attention to applications in the design, conduct, and interpretation of clinical trials for neurologic diseases. We discussed ways in which ML may help to accelerate the pace of subject recruitment, provide realistic simulation of medical interventions, and enhance remote trial administration via novel digital biomarkers and therapeutics. Lastly, we provide a brief overview of the technical, administrative, and regulatory challenges that must be addressed as ML achieves greater integration into clinical trial workflows.
Topics: Artificial Intelligence; Machine Learning; Neurology; Clinical Trials as Topic
PubMed: 37249836
DOI: 10.1007/s13311-023-01384-2 -
Human Vaccines & Immunotherapeutics Aug 2023Immunoprofiling has become a crucial tool for understanding the complex interactions between the immune system and diseases or interventions, such as therapies and... (Review)
Review
Immunoprofiling has become a crucial tool for understanding the complex interactions between the immune system and diseases or interventions, such as therapies and vaccinations. Immune response biomarkers are critical for understanding those relationships and potentially developing personalized intervention strategies. Single-cell data have emerged as a promising source for identifying immune response biomarkers. In this review, we discuss the current state-of-the-art methods for immunoprofiling, including those for reducing the dimensionality of high-dimensional single-cell data and methods for clustering, classification, and prediction. We also draw attention to recent developments in data integration.
Topics: Machine Learning; Cluster Analysis
PubMed: 37485833
DOI: 10.1080/21645515.2023.2234792 -
PloS One 2023The democratization of machine learning is a popular and growing movement. In a world with a wealth of publicly available data, it is important that algorithms for...
The democratization of machine learning is a popular and growing movement. In a world with a wealth of publicly available data, it is important that algorithms for analysis of data are accessible and usable by everyone. We present MLpronto, a system for machine learning analysis that is designed to be easy to use so as to facilitate engagement with machine learning algorithms. With its web interface, MLpronto requires no computer programming or machine learning background, and it normally returns results in a matter of seconds. As input, MLpronto takes a file of data to be analyzed. MLpronto then executes some of the more commonly used supervised machine learning algorithms on the data and reports the results of the analyses. As part of its execution, MLpronto generates computer programming code corresponding to its machine learning analysis, which it also supplies as output. Thus, MLpronto can be used as a no-code solution for citizen data scientists with no machine learning or programming background, as an educational tool for those learning about machine learning, and as a first step for those who prefer to engage with programming code in order to facilitate rapid development of machine learning projects. MLpronto is freely available for use at https://mlpronto.org/.
Topics: Algorithms; Machine Learning; Supervised Machine Learning
PubMed: 38032968
DOI: 10.1371/journal.pone.0294924