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Frontiers in Immunology 2024Patients with resectable esophageal squamous cell carcinoma (ESCC) receiving neoadjuvant immunotherapy (NIT) display variable treatment responses. The purpose of this...
BACKGROUND
Patients with resectable esophageal squamous cell carcinoma (ESCC) receiving neoadjuvant immunotherapy (NIT) display variable treatment responses. The purpose of this study is to establish and validate a radiomics based on enhanced computed tomography (CT) and combined with clinical data to predict the major pathological response to NIT in ESCC patients.
METHODS
This retrospective study included 82 ESCC patients who were randomly divided into the training group (n = 57) and the validation group (n = 25). Radiomic features were derived from the tumor region in enhanced CT images obtained before treatment. After feature reduction and screening, radiomics was established. Logistic regression analysis was conducted to select clinical variables. The predictive model integrating radiomics and clinical data was constructed and presented as a nomogram. Area under curve (AUC) was applied to evaluate the predictive ability of the models, and decision curve analysis (DCA) and calibration curves were performed to test the application of the models.
RESULTS
One clinical data (radiotherapy) and 10 radiomic features were identified and applied for the predictive model. The radiomics integrated with clinical data could achieve excellent predictive performance, with AUC values of 0.93 (95% CI 0.87-0.99) and 0.85 (95% CI 0.69-1.00) in the training group and the validation group, respectively. DCA and calibration curves demonstrated a good clinical feasibility and utility of this model.
CONCLUSION
Enhanced CT image-based radiomics could predict the response of ESCC patients to NIT with high accuracy and robustness. The developed predictive model offers a valuable tool for assessing treatment efficacy prior to initiating therapy, thus providing individualized treatment regimens for patients.
PubMed: 38947338
DOI: 10.3389/fimmu.2024.1405146 -
Frontiers in Immunology 2024Monocytes play a critical role in tumor initiation and progression, with their impact on prostate adenocarcinoma (PRAD) not yet fully understood. This study aimed to...
BACKGROUND
Monocytes play a critical role in tumor initiation and progression, with their impact on prostate adenocarcinoma (PRAD) not yet fully understood. This study aimed to identify key monocyte-related genes and elucidate their mechanisms in PRAD.
METHOD
Utilizing the TCGA-PRAD dataset, immune cell infiltration levels were assessed using CIBERSORT, and their correlation with patient prognosis was analyzed. The WGCNA method pinpointed 14 crucial monocyte-related genes. A diagnostic model focused on monocytes was developed using a combination of machine learning algorithms, while a prognostic model was created using the LASSO algorithm, both of which were validated. Random forest and gradient boosting machine singled out CCNA2 as the most significant gene related to prognosis in monocytes, with its function further investigated through gene enrichment analysis. Mendelian randomization analysis of the association of HLA-DR high-expressing monocytes with PRAD. Molecular docking was employed to assess the binding affinity of CCNA2 with targeted drugs for PRAD, and experimental validation confirmed the expression and prognostic value of CCNA2 in PRAD.
RESULT
Based on the identification of 14 monocyte-related genes by WGCNA, we developed a diagnostic model for PRAD using a combination of multiple machine learning algorithms. Additionally, we constructed a prognostic model using the LASSO algorithm, both of which demonstrated excellent predictive capabilities. Analysis with random forest and gradient boosting machine algorithms further supported the potential prognostic value of CCNA2 in PRAD. Gene enrichment analysis revealed the association of CCNA2 with the regulation of cell cycle and cellular senescence in PRAD. Mendelian randomization analysis confirmed that monocytes expressing high levels of HLA-DR may promote PRAD. Molecular docking results suggested a strong affinity of CCNA2 for drugs targeting PRAD. Furthermore, immunohistochemistry experiments validated the upregulation of CCNA2 expression in PRAD and its correlation with patient prognosis.
CONCLUSION
Our findings offer new insights into monocyte heterogeneity and its role in PRAD. Furthermore, CCNA2 holds potential as a novel targeted drug for PRAD.
PubMed: 38947325
DOI: 10.3389/fimmu.2024.1426474 -
Frontiers in Medicine 2024As machine learning progresses, techniques such as neural networks, decision trees, and support vector machines are being increasingly applied in the medical domain,... (Review)
Review
As machine learning progresses, techniques such as neural networks, decision trees, and support vector machines are being increasingly applied in the medical domain, especially for tasks involving large datasets, such as cell detection, recognition, classification, and visualization. Within the domain of bone marrow cell morphology analysis, deep learning offers substantial benefits due to its robustness, ability for automatic feature learning, and strong image characterization capabilities. Deep neural networks are a machine learning paradigm specifically tailored for image processing applications. Artificial intelligence serves as a potent tool in supporting the diagnostic process of clinical bone marrow cell morphology. Despite the potential of artificial intelligence to augment clinical diagnostics in this domain, manual analysis of bone marrow cell morphology remains the gold standard and an indispensable tool for identifying, diagnosing, and assessing the efficacy of hematologic disorders. However, the traditional manual approach is not without limitations and shortcomings, necessitating, the exploration of automated solutions for examining and analyzing bone marrow cytomorphology. This review provides a multidimensional account of six bone marrow cell morphology processes: automated bone marrow cell morphology detection, automated bone marrow cell morphology segmentation, automated bone marrow cell morphology identification, automated bone marrow cell morphology classification, automated bone marrow cell morphology enumeration, and automated bone marrow cell morphology diagnosis. Highlighting the attractiveness and potential of machine learning systems based on bone marrow cell morphology, the review synthesizes current research and recent advances in the application of machine learning in this field. The objective of this review is to offer recommendations to hematologists for selecting the most suitable machine learning algorithms to automate bone marrow cell morphology examinations, enabling swift and precise analysis of bone marrow cytopathic trends for early disease identification and diagnosis. Furthermore, the review endeavors to delineate potential future research avenues for machine learning-based applications in bone marrow cell morphology analysis.
PubMed: 38947236
DOI: 10.3389/fmed.2024.1402768 -
Meta-radiology Sep 2024Fairness of artificial intelligence and machine learning models, often caused by imbalanced datasets, has long been a concern. While many efforts aim to minimize model...
Fairness of artificial intelligence and machine learning models, often caused by imbalanced datasets, has long been a concern. While many efforts aim to minimize model bias, this study suggests that traditional fairness evaluation methods may be biased, highlighting the need for a proper evaluation scheme with multiple evaluation metrics due to varying results under different criteria. Moreover, the limited data size of minority groups introduces significant data uncertainty, which can undermine the judgement of fairness. This paper introduces an innovative evaluation approach that estimates data uncertainty in minority groups through bootstrapping from majority groups for a more objective statistical assessment. Extensive experiments reveal that traditional evaluation methods might have drawn inaccurate conclusions about model fairness. The proposed method delivers an unbiased fairness assessment by adeptly addressing the inherent complications of model evaluation on imbalanced datasets. The results show that such comprehensive evaluation can provide more confidence when adopting those models.
PubMed: 38947177
DOI: 10.1016/j.metrad.2024.100084 -
Research Square Jun 2024Background Hospitalizations for exacerbations of congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD) and diabetic ketoacidosis (DKA) are costly...
Development and Optimization of Machine Learning Algorithms for Predicting In-hospital Patient Charges for Congestive Heart Failure Exacerbations, Chronic Obstructive Pulmonary Disease Exacerbations and Diabetic Ketoacidosis.
Background Hospitalizations for exacerbations of congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD) and diabetic ketoacidosis (DKA) are costly in the United States. The purpose of this study was to predict in-hospital charges for each condition using machine learning (ML) models. Results We conducted a retrospective cohort study on national discharge records of hospitalized adult patients from January 1st, 2016, to December 31st, 2019. We used numerous ML techniques to predict in-hospital total cost. We found that linear regression (LM), gradient boosting (GBM) and extreme gradient boosting (XGB) models had good predictive performance and were statistically equivalent, with training R-square values ranging from 0.49-0.95 for CHF, 0.56-0.95 for COPD, and 0.32-0.99 for DKA. We identified important key features driving costs, including patient age, length of stay, number of procedures. and elective/nonelective admission. Conclusions ML methods may be used to accurately predict costs and identify drivers of high cost for COPD exacerbations, CHF exacerbations and DKA. Overall, our findings may inform future studies that seek to decrease the underlying high patient costs for these conditions.
PubMed: 38947079
DOI: 10.21203/rs.3.rs-4490027/v1 -
Research Square Jun 2024Accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD) is crucial for disease management. Machine learning techniques...
Accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD) is crucial for disease management. Machine learning techniques have demonstrated success in classifying AD and MCI cases, particularly with the use of resting-state functional magnetic resonance imaging (rs-fMRI) data.This study utilized three years of rs-fMRI data from the ADNI, involving 142 patients with stable MCI (sMCI) and 136 with progressive MCI (pMCI). Graph signal processing was applied to filter rs-fMRI data into low, middle, and high frequency bands. Connectivity-based features were derived from both filtered and unfiltered data, resulting in a comprehensive set of 100 features, including global graph metrics, minimum spanning tree (MST) metrics, triadic interaction metrics, hub tendency metrics, and the number of links. Feature selection was enhanced using particle swarm optimization (PSO) and simulated annealing (SA). A support vector machine (SVM) with a radial basis function (RBF) kernel and a 10-fold cross-validation setup were employed for classification. The proposed approach demonstrated superior performance, achieving optimal accuracy with minimal feature utilization. When PSO selected five features, SVM exhibited accuracy, specificity, and sensitivity rates of 77%, 70%, and 83%, respectively. The identified features were as follows: (Mean of clustering coefficient, Mean of strength)/Radius/(Mean Eccentricity, and Modularity) from low/middle/high frequency bands of graph. The study highlights the efficacy of the proposed framework in identifying individuals at risk of AD development using a parsimonious feature set. This approach holds promise for advancing the precision of MCI to AD progression prediction, aiding in early diagnosis and intervention strategies.
PubMed: 38947050
DOI: 10.21203/rs.3.rs-4549428/v1 -
Research Square Jun 2024Effective prevention of cardiac malformations, a leading cause of infant morbidity, is constrained by limited understanding of etiology. The study objective was to...
Effective prevention of cardiac malformations, a leading cause of infant morbidity, is constrained by limited understanding of etiology. The study objective was to screen for associations between maternal and paternal characteristics and cardiac malformations. We selected 720,381 pregnancies linked to live-born infants (n=9,076 cardiac malformations) in 2011-2021 MarketScan US insurance claims data. Odds ratios were estimated with clinical diagnostic and medication codes using logistic regression. Screening of 2,000 associations selected 81 associated codes at the 5% false discovery rate. Grouping of selected codes, using latent semantic analysis and the Apriori-SD algorithm, identified elevated risk with known risk factors, including maternal diabetes and chronic hypertension. Less recognized potential signals included maternal fingolimod or azathioprine use. Signals identified might be explained by confounding, measurement error, and selection bias and warrant further investigation. The screening methods employed identified known risk factors, suggesting potential utility for identifying novel risk factors for other pregnancy outcomes.
PubMed: 38947037
DOI: 10.21203/rs.3.rs-4490534/v1 -
MedRxiv : the Preprint Server For... Jun 2024Heart disease is the leading cause of death worldwide, and cardiac function as measured by ejection fraction (EF) is an important determinant of outcomes, making...
Heart disease is the leading cause of death worldwide, and cardiac function as measured by ejection fraction (EF) is an important determinant of outcomes, making accurate measurement a critical parameter in PT evaluation. Echocardiograms are commonly used for measuring EF, but human interpretation has limitations in terms of intra- and inter-observer (or reader) variance. Deep learning (DL) has driven a resurgence in machine learning, leading to advancements in medical applications. We introduce the ViViEchoformer DL approach, which uses a video vision transformer to directly regress the left ventricular function (LVEF) from echocardiogram videos. The study used a dataset of 10,030 apical-4-chamber echocardiography videos from patients at Stanford University Hospital. The model accurately captures spatial information and preserves inter-frame relationships by extracting spatiotemporal tokens from video input, allowing for accurate, fully automatic EF predictions that aid human assessment and analysis. The ViViEchoformer's prediction of ejection fraction has a mean absolute error of 6.14%, a root mean squared error of 8.4%, a mean squared log error of 0.04, and an of 0.55. ViViEchoformer predicted heart failure with reduced ejection fraction (HFrEF) with an area under the curve of 0.83 and a classification accuracy of 87 using a standard threshold of less than 50% ejection fraction. Our video-based method provides precise left ventricular function quantification, offering a reliable alternative to human evaluation and establishing a fundamental basis for echocardiogram interpretation.
PubMed: 38947006
DOI: 10.1101/2024.06.21.24309327 -
MedRxiv : the Preprint Server For... Jun 2024There is a growing focus on better understanding the complexity of dietary patterns and how they relate to health and other factors. Approaches that have not...
There is a growing focus on better understanding the complexity of dietary patterns and how they relate to health and other factors. Approaches that have not traditionally been applied to characterize dietary patterns, such as machine learning algorithms and latent class analysis methods, may offer opportunities to measure and characterize dietary patterns in greater depth than previously considered. However, there has not been a formal examination of how this wide range of approaches has been applied to characterize dietary patterns. This scoping review synthesized literature from 2005-2022 applying methods not traditionally used to characterize dietary patterns, referred to as novel methods. MEDLINE, CINAHL, and Scopus were searched using keywords including machine learning, latent class analysis, and least absolute shrinkage and selection operator (LASSO). Of 5274 records identified, 24 met the inclusion criteria. Twelve of 24 articles were published since 2020. Studies were conducted across 17 countries. Nine studies used approaches that have applications in machine learning to identify dietary patterns. Fourteen studies assessed associations between dietary patterns that were characterized using novel methods and health outcomes, including cancer, cardiovascular disease, and asthma. There was wide variation in the methods applied to characterize dietary patterns and in how these methods were described. The extension of reporting guidelines and quality appraisal tools relevant to nutrition research to consider specific features of novel methods may facilitate complete and consistent reporting and enable evidence synthesis to inform policies and programs aimed at supporting healthy dietary patterns.
PubMed: 38947003
DOI: 10.1101/2024.06.20.24309251 -
MedRxiv : the Preprint Server For... Jun 2024ANCA-associated vasculitis (AAV) is a rare but serious disease. Traditional case-identification methods using claims data can be time-intensive and may miss important...
BACKGROUND
ANCA-associated vasculitis (AAV) is a rare but serious disease. Traditional case-identification methods using claims data can be time-intensive and may miss important subgroups. We hypothesized that a deep learning model analyzing electronic health records (EHR) can more accurately identify AAV cases.
METHODS
We examined the Mass General Brigham (MGB) repository of clinical documentation from 12/1/1979 to 5/11/2021, using expert-curated keywords and ICD codes to identify a large cohort of potential AAV cases. Three labeled datasets (I, II, III) were created, each containing note sections. We trained and evaluated a range of machine learning and deep learning algorithms for note-level classification, using metrics like positive predictive value (PPV), sensitivity, F-score, area under the receiver operating characteristic curve (AUROC), and area under the precision and recall curve (AUPRC). The deep learning model was further evaluated for its ability to classify AAV cases at the patient-level, compared with rule-based algorithms in 2,000 randomly chosen samples.
RESULTS
Datasets I, II, and III comprised 6,000, 3,008, and 7,500 note sections, respectively. Deep learning achieved the highest AUROC in all three datasets, with scores of 0.983, 0.991, and 0.991. The deep learning approach also had among the highest PPVs across the three datasets (0.941, 0.954, and 0.800, respectively). In a test cohort of 2,000 cases, the deep learning model achieved a PPV of 0.262 and an estimated sensitivity of 0.975. Compared to the best rule-based algorithm, the deep learning model identified six additional AAV cases, representing 13% of the total.
CONCLUSION
The deep learning model effectively classifies clinical note sections for AAV diagnosis. Its application to EHR notes can potentially uncover additional cases missed by traditional rule-based methods.
SIGNIFICANCE AND INNOVATIONS
Traditional approaches to identifying AAV cases for research have relied on registries assembled through clinical care and/or on billing codes which may miss important subgroups.Unstructured data entered as free text by clinicians document a patient's diagnosis, symptoms, manifestations, and other features of their condition which may be useful for identifying AAV casesWe found that a deep learning approach can classify notes as being indicative of AAV and, when applied at the case level, identifies more cases with AAV than rule-based algorithms.
PubMed: 38946986
DOI: 10.1101/2024.06.09.24308603