Validation Set Research Articles

Bayesian Estimate of Mean Proper Scores for Diversity-Enhanced Active Learning.

The effectiveness of active learning largely depends on the sampling efficiency of the acquisition function. Expected Loss Reduction (ELR) focuses on a Bayesian estimate of the reduction in classification error, and more general costs fit in the same framework. We propose Bayesian Estimate of Mean Proper Scores (BEMPS) to estimate the increase in strictly proper scores such as log probability or negative mean square error within this framework. We also prove convergence results for this general class of costs. To facilitate better experimentation with the new acquisition functions, we develop a complementary batch AL algorithm that encourages diversity in the vector of expected changes in scores for unlabeled data. To allow high-performance classifiers, we combine deep ensembles, and dynamic validation set construction on pretrained models, and further speed up the ensemble process with the idea of Monte Carlo Dropout. Extensive experiments on both texts and images show that the use of mean square error and log probability with BEMPS yields robust acquisition functions and well-calibrated classifiers, and consistently outperforms the others tested. The advantages of BEMPS over the others are further supported by a set of qualitative analyses, where we visualise their sampling behaviour using data maps and t-SNE plots.

Analysis of the sodium pump subunit ATP1A3 in glioma patients: Potential value in prognostic prediction and immunotherapy

The ATP1A3 gene is associated with the development and progression of neurological diseases. However, the pathological function and therapeutic value of ATP1A3 in glioblastoma (GBM) remains unknown. In this study, we tried to explore the correlation between the ATP1A3 gene expression and immune features in GBM samples. We found that ATP1A3 gene expression levels showed significant negative correlation with immune checkpoints such as PD-L1, CTLA-4 and IDO1. Next, ATP1A3 gene expression levels showed significant negative correlation with the anti-cancer immune cell process, the immune score and stromal score. By grouping ATP1A3 expression levels, we found that that immunomodulator-related genes and tumor-associated immune cell effector gene expression levels were associated with lower ATP1A3 expression. In addition, immunotherapy prediction pathway activity and a majority of the anti-cancer immune cell process activity levels were also showed to be correlated with lower ATP1A3 gene expression. Further, nine prognostic factors were identified by prognostic analysis, and a GBM prognostic model (risk score) was established. We applied the model to the TCGA GBM training set sample and the GSE4412 validation set sample and found that patients in the high risk score subgroup had significantly shorter survival time, demonstrating the prognostic value and prognostic efficacy of the risk score. Furthermore, ATP1A3 overexpression has also been found to sensitize cancer cells to anti-PD-1 therapy. In conclusion, we showed that ATP1A3 is a highly promising treatment target in GBM and the risk score is an independent prognostic factor for cancer and can be used to help guide the prediction of survival time in patients with GBM.

Permeability estimation for deformable porous media with convolutional neural network

Purpose Accurately evaluating fluid flow behaviors and determining permeability for deforming porous media is time-consuming and remains challenging. This paper aims to propose a novel machine-learning method for the rapid estimation of permeability of porous media at different deformation stages constrained by hydro-mechanical coupling analysis. Design/methodology/approach A convolutional neural network (CNN) is proposed in this paper, which is guided by the results of finite element coupling analysis of equilibrium equation for mechanical deformation and Boltzmann equation for fluid dynamics during the hydro-mechanical coupling process [denoted as Finite element lattice Boltzmann model (FELBM) in this paper]. The FELBM ensures the Lattice Boltzmann analysis of coupled fluid flow with an unstructured mesh, which varies with the corresponding nodal displacement resulting from mechanical deformation. It provides reliable label data for permeability estimation at different stages using CNN. Findings The proposed CNN can rapidly and accurately estimate the permeability of deformable porous media, significantly reducing processing time. The application studies demonstrate high accuracy in predicting the permeability of deformable porous media for both the test and validation sets. The corresponding correlation coefficients (R2) is 0.93 for the validation set, and the R2 for the test set A and test set B are 0.93 and 0.94, respectively. Originality/value This study proposes an innovative approach with the CNN to rapidly estimate permeability in porous media under dynamic deformations, guided by FELBM coupling analysis. The fast and accurate performance of CNN underscores its promising potential for future applications.

Efficacy of Random Forest Models in Predicting Multidrug-Resistant Gram-Negative Bacterial Nosocomial Infections Compared to Traditional Logistic Regression Models.

This study evaluates whether random forest (RF) models are as effective as traditional Logistic Regression (LR) models in predicting multidrug-resistant Gram-negative bacterial nosocomial infections. Data were collected from 541 patients with hospital-acquired Gram-negative bacterial infections at two tertiary-level hospitals in Urumqi, Xinjiang, China, from August 2022 to November 2023. Relevant literature informed the selection of significant predictors based on patients' pre-infection clinical information and medication history. The data were split into a training set of 379 cases and a validation set of 162 cases, adhering to a 7:3 ratio. Both RF and LR models were developed using the training set and subsequently evaluated on the validation set. The LR model achieved an accuracy of 84.57%, sensitivity of 82.89%, specificity of 80.10%, positive predictive value of 84%, negative predictive value of 85.06%, and a Yoden index of 0.69. In contrast, the RF model demonstrated superior performance with an accuracy of 89.51%, sensitivity of 90.79%, specificity of 88.37%, positive predictive value of 87.34%, negative predictive value of 91.57%, and a Yoden index of 0.79. Receiver operating characteristic curve analysis revealed an area under the curve of 0.91 for the LR model and 0.94 for the RF model. These findings indicate that the RF model surpasses the LR model in specificity, sensitivity, and accuracy in predicting hospital-acquired multidrug-resistant Gram-negative infections, showcasing its greater potential for clinical application.

Generative adversarial network-based synthesis of contrast-enhanced MR images from precontrast images for predicting histological characteristics in breast cancer

Objective. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a sensitive tool for assessing breast cancer by analyzing tumor blood flow, but it requires gadolinium-based contrast agents, which carry risks such as brain retention and astrocyte migration. Contrast-free MRI is thus preferable for patients with renal impairment or who are pregnant. This study aimed to investigate the feasibility of generating contrast-enhanced MR images from precontrast images and to evaluate the potential use of synthetic images in diagnosing breast cancer. Approach. This retrospective study included 322 women with invasive breast cancer who underwent preoperative DCE-MRI. A generative adversarial network (GAN) based postcontrast image synthesis (GANPIS) model with perceptual loss was proposed to generate contrast-enhanced MR images from precontrast images. The quality of the synthesized images was evaluated using the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM). The diagnostic performance of the generated images was assessed using a convolutional neural network to predict Ki-67, luminal A and histological grade with the area under the receiver operating characteristic curve (AUC). The patients were divided into training (n = 200), validation (n = 60), and testing sets (n = 62). Main results. Quantitative analysis revealed strong agreement between the generated and real postcontrast images in the test set, with PSNR and SSIM values of 36.210 ± 2.670 and 0.988 ± 0.006, respectively. The generated postcontrast images achieved AUCs of 0.918 ± 0.018, 0.842 ± 0.028 and 0.815 ± 0.019 for predicting the Ki-67 expression level, histological grade, and luminal A subtype, respectively. These results showed a significant improvement compared to the use of precontrast images alone, which achieved AUCs of 0.764 ± 0.031, 0.741 ± 0.035, and 0.797 ± 0.021, respectively. Significance. This study proposed a GAN-based MR image synthesis method for breast cancer that aims to generate postcontrast images from precontrast images, allowing the use of contrast-free images to simulate kinetic features for improved diagnosis.

Multi-feature, Chinese-Western medicine-integrated prediction model for diabetic peripheral neuropathy based on machine learning and SHAP.

Clinical studies have shown that diabetic peripheral neuropathy (DPN) has been on the rise, with most patients presenting with severe and progressive symptoms. Currently, most of the available prediction models for DPN are derived from general clinical information and laboratory indicators. Several Traditional Chinese medicine (TCM) indicators have been utilised to construct prediction models. In this study, we established a novel machine learning-based multi-featured Chinese-Western medicine-integrated prediction model for DPN using clinical features of TCM. The clinical data of 1581 patients with Type 2 diabetes mellitus (T2DM) treated at the Department of Endocrinology of the First Affiliated Hospital of Anhui University of Chinese Medicine were collected. The data (including general information, laboratory parameters and TCM features) of 1142 patients with T2DM were selected after data cleaning. After baseline description analysis of the variables, the data were divided into training and validation sets. Four prediction models were established and their performance was evaluated using validation sets. Meanwhile, the accuracy, precision, recall, F1 score and area under the curve (AUC) of ROC were calculated using ten-fold cross-validation to further assess the performance of the models. An explanatory analysis of the results of the DPN prediction model was carried out using the SHAP framework based on machine learning-based prediction models. Of the 1142 patients with T2DM, 681 had a comorbidity of DPN, while 461 did not. There was a significant difference between the two groups in terms of age, cause of disease, systolic pressure, HbA1c, ALT, RBC, Cr, BUN, red blood cells in the urine, glucose in the urine, and protein in the urine (p<0.05). T2DM patients with a comorbidity of DPN exhibited diverse TCM symptoms, including limb numbness, limb pain, hypodynamia, thirst with desire for drinks, dry mouth and throat, blurred vision, gloomy complexion, and unsmooth pulse, with statistically significant differences (p<0.05). Our results showed that the proposed multi-featured Chinese-Western medicine-integrated prediction model was superior to conventional models without characteristic TCM indicators. The model showed the best performance (accuracy=0.8109, precision=0.8029, recall=0.9060, F1 score=0.8511, and AUC=0.9002). SHAP analysis revealed that the dominant risk factors that caused DPN were TCM symptoms (limb numbness, thirst with desire for drinks, blurred vision), age, cause of disease, and glycosylated haemoglobin. These risk factors were exerted positive effects on the DPN prediction models. A multi-feature, Chinese-Western medicine-integrated prediction model for DPN was established and validated. The model improves early-stage identification of high-risk groups for DPN in the diagnosis and treatment of T2DM, while also providing informative support for the intelligent management of chronic conditions such as diabetes.

Predictive Modeling and Experimental Validation for Assessing the Mechanical Properties of Cementitious Composites Made with Silica Fume and Ground Granulated Blast Furnace Slag

Using sustainable cement-based alternatives, such as secondary cementitious raw materials (SCMs), could be a viable option to decrease CO2 emissions resulting from cement production. Previously conducted studies to determine the optimal mix designs of concrete primarily focused on either experimental approaches or empirical modeling techniques. However, in these experimental approaches, few tests could be performed for optimization due to time restrictions and lack of resources, and empirical modeling methods cannot be relied on without external validation. The machine learning-based approaches are further characterized by certain shortcomings, including a smaller number of data points, a less robust connection among the controlling factors, and a lack of comparative analyses among machine learning models. Furthermore, the literature on predicting the performance of concrete utilizing binary SCMs (silica fume (SF) and ground granulated blast furnace slag (GGBS)) is not available. Therefore, to address these drawbacks, this research aimed to integrate ML-based models with experimental validations for accurate predictions of the compressive strength (CS) and tensile strength (TS) of concrete that includes SF and GGBS as SCMs. Three soft computing techniques, namely the ANN, ANFIS, and GEP methods, were used for prediction purposes. Eight major input parameters, including the W/B ratio, cement, GGBS, SF, coarse aggregates, fine aggregates, superplasticizer, and the age of the specimens, were considered for modeling. The validity of the established models was assessed by using external experimental validation criteria, statistical metrics, and performance measures. In addition, sensitivity and parametric analyses were performed. Based on statistical measures, the ANFIS models outperformed other models with higher correlation and lower statistical error values. However, the GEP models exhibited superior performance compared to ANFIS and ANN with respect to the closeness of the RMSE, MAE, RSE, and R2 values between the training, validation, and testing sets for both the CS and TS models. Experimental validation showed strong evidence for the applicability of the proposed models with an R2 of 0.88 and error percentages of less than 10%. Sensitivity and parametric investigations demonstrated that the input variables exhibited the patterns described in the experimental dataset and the available literature. Hence, the proposed models are accurate, have better prediction performance, and can be used for design purposes.

A novel electronic health record-based, machine-learning model to predict severe hypoglycemia leading to hospitalizations in older adults with diabetes: A territory-wide cohort and modeling study.

Older adults with diabetes are at high risk of severe hypoglycemia (SH). Many machine-learning (ML) models predict short-term hypoglycemia are not specific for older adults and show poor precision-recall. We aimed to develop a multidimensional, electronic health record (EHR)-based ML model to predict one-year risk of SH requiring hospitalization in older adults with diabetes. We adopted a case-control design for a retrospective territory-wide cohort of 1,456,618 records from 364,863 unique older adults (age ≥65 years) with diabetes and at least 1 Hong Kong Hospital Authority attendance from 2013 to 2018. We used 258 predictors including demographics, admissions, diagnoses, medications, and routine laboratory tests in a one-year period to predict SH events requiring hospitalization in the following 12 months. The cohort was randomly split into training, testing, and internal validation sets in a 7:2:1 ratio. Six ML algorithms were evaluated including logistic-regression, random forest, gradient boost machine, deep neural network (DNN), XGBoost, and Rulefit. We tested our model in a temporal validation cohort in the Hong Kong Diabetes Register with predictors defined in 2018 and outcome events defined in 2019. Predictive performance was assessed using area under the receiver operating characteristic curve (AUROC), area under the precision-recall curve (AUPRC) statistics, and positive predictive value (PPV). We identified 11,128 SH events requiring hospitalization during the observation periods. The XGBoost model yielded the best performance (AUROC = 0.978 [95% CI 0.972 to 0.984]; AUPRC = 0.670 [95% CI 0.652 to 0.688]; PPV = 0.721 [95% CI 0.703 to 0.739]). This was superior to an 11-variable conventional logistic-regression model comprised of age, sex, history of SH, hypertension, blood glucose, kidney function measurements, and use of oral glucose-lowering drugs (GLDs) (AUROC = 0.906; AUPRC = 0.085; PPV = 0.468). Top impactful predictors included non-use of lipid-regulating drugs, in-patient admission, urgent emergency triage, insulin use, and history of SH. External validation in the HKDR cohort yielded AUROC of 0.856 [95% CI 0.838 to 0.873]. Main limitations of this study included limited transportability of the model and lack of geographically independent validation. Our novel-ML model demonstrated good discrimination and high precision in predicting one-year risk of SH requiring hospitalization. This may be integrated into EHR decision support systems for preemptive intervention in older adults at highest risk.

Science lab safety goes immersive: An ecological media-comparison study with gender analyses assessing iVR’s learning effectiveness

We conducted a media-comparison study in ecologically valid settings to understand immersive virtual reality’s (iVR’s) instructional effectiveness in a university science course. We tested how complementing regular science lab safety instruction with interactive iVR simulation, desktop simulation, or the re-viewing of a text-heavy manual compare with each other in terms of knowledge-related and affective learning outcomes. We also explored gender differences in the outcomes across these instructional conditions. 102 undergraduates (51 females) were randomly assigned to one of the instructional conditions. Throughout the one-day course, all students received the same set of instructions, demonstrations, and hands-on lab safety training except for the following: the iVR group engaged with HMD-based interactive lab safety iVR training simulation; the desktop group interacted with the same simulation on a laptop, whereas the remaining group re-viewed the text-heavy course material in detail. Topic knowledge-related and self-report affective data were collected before and immediately after the course. Statistical analyses revealed that: (i) all three instructional modes helped students gain significant lab safety knowledge, (ii) there were several significant between-group differences in multiple affective measures, and (iii) the instructional modes affected/benefited the two genders considerably differently. Besides extending previous findings, the strong ecological grounding of our results adds important insights into real-life implications of integrating different media in undergraduate education. Our gender-related findings merely scratch the surface on the complex issue of “designing for diversity”, inviting scaled-up efforts to develop more equitable technology-enhanced science learning settings to address the cognitive-affective needs of different genders and other diversities.

Acute Pancreatitis in Pregnancy: A Propensity Score Matching Analysis and Dynamic Nomogram for Risk Assessment.

Acute pancreatitis is easily confused with abdominal pain symptoms, and it could lead to serious complications for pregnant women and fetus, the mortality was as high as 3.3% and 11.6-18.7%, respectively. However, there is still lack of sensitive laboratory markers for early diagnosis of APIP and authoritative guidelines to guide treatment. The purpose of this study was to explore the risk factors of acute pancreatitis in pregnancy, establish, and evaluate the dynamic prediction model of risk factors in acute pancreatitis in pregnancy patients. Clinical data of APIP patients and non-pregnant acute pancreases patients who underwent regular antenatal check-ups during the same period were collected. The dataset after propensity matching was randomly divided into training set and verification set at a ratio of 7:3. The model was constructed using Logistic regression, least absolute shrinkage and selection operator regression, R language and other methods. The training set model was used to construct the diagnostic nomogram model and the validation set was used to validate the model. Finally, the accuracy and clinical practicability of the model were evaluated. A total of 111 APIP were included. In all APIP patients, hyperlipidemic pancreatitis was the most important reason. The levels of serum amylase, creatinine, albumin, triglyceride, high-density lipoprotein cholesterol, and apolipoprotein A1 were significantly different between the two groups. The propensity matching method was used to match pregnant pancreatitis patients and pregnant non-pancreatic patients 1:1 according to age and gestational age, and the matching tolerance was 0.02. The multivariate logistic regression analysis of training set showed that diabetes, triglyceride, Body Mass Index, white blood cell, and C-reactive protein were identified and entered the dynamic nomogram. The area under the ROC curve of the training set was 0.942 and in validation set was 0.842. The calibration curve showed good predictive in training set, and the calibration performance in the validation set was acceptable. The calibration curve showed the consistency between the nomogram model and the actual probability. The dynamic nomogram model we constructed to predict the risk factors of acute pancreatitis in pregnancy has high accuracy, discrimination, and clinical practicability.

Identification of Multiclass Pediatric Low-Grade Neuroepithelial Tumor Molecular Subtype with ADC MR Imaging and Machine Learning.

Molecular biomarker identification increasingly influences the treatment planning of pediatric low-grade neuroepithelial tumors (PLGNTs). We aimed to develop and validate a radiomics-based ADC signature predictive of the molecular status of PLGNTs. In this retrospective bi-institutional study, we searched the PACS for baseline brain MRIs from children with PLGNTs. Semiautomated tumor segmentation on ADC maps was performed using the semiautomated level tracing effect tool with 3D Slicer. Clinical variables, including age, sex, and tumor location, were collected from chart review. The molecular status of tumors was derived from biopsy. Multiclass random forests were used to predict the molecular status and fine-tuned using a grid search on the validation sets. Models were evaluated using independent and unseen test sets based on the combined data, and the area under the receiver operating characteristic curve (AUC) was calculated for the prediction of 3 classes: KIAA1549-BRAF fusion, BRAF V600E mutation, and non-BRAF cohorts. Experiments were repeated 100 times using different random data splits and model initializations to ensure reproducible results. Two hundred ninety-nine children from the first institution and 23 children from the second institution were included (53.6% male; mean, age 8.01 years; 51.8% supratentorial; 52.2% with KIAA1549-BRAF fusion). For the 3-class prediction using radiomics features only, the average test AUC was 0.74 (95% CI, 0.73-0.75), and using clinical features only, the average test AUC was 0.67 (95% CI, 0.66-0.68). The combination of both radiomics and clinical features improved the AUC to 0.77 (95% CI, 0.75-0.77). The diagnostic performance of the per-class test AUC was higher in identifying KIAA1549-BRAF fusion tumors among the other subgroups (AUC = 0.81 for the combined radiomics and clinical features versus 0.75 and 0.74 for BRAF V600E mutation and non-BRAF, respectively). ADC values of tumor segmentations have differentiative signals that can be used for training machine learning classifiers for molecular biomarker identification of PLGNTs. ADC-based pretherapeutic differentiation of the BRAF status of PLGNTs has the potential to avoid invasive tumor biopsy and enable earlier initiation of targeted therapy.

A CT-based radiomics nomogram for predicting histologic grade and outcome in chondrosarcoma

ObjectiveThe preoperative identification of tumor grade in chondrosarcoma (CS) is crucial for devising effective treatment strategies and predicting outcomes. The study aims to build and validate a CT-based radiomics nomogram (RN) for the preoperative identification of tumor grade in CS, and to evaluate the correlation between the RN-predicted tumor grade and postoperative outcome.MethodsA total of 196 patients (139 in the training cohort and 57 in the external validation cohort) were derived from three different centers. A clinical model, radiomics signature (RS) and RN (which combines significant clinical factors and RS) were developed and validated to assess their ability to distinguish low-grade from high-grade CS with area under the curve (AUC). Additionally, Kaplan-Meier survival analysis was applied to examine the association between RN-predicted tumor grade and recurrence-free survival (RFS) of CS. The predictive accuracy of the RN was evaluated using Harrell’s concordance index (C-index), hazard ratio (HR) and AUC.ResultsSize, endosteal scalloping and active periostitis were selected to build the clinical model. Three radiomics features, based on CT images, were selected to construct the RS. Both the RN (AUC, 0.842) and RS (AUC, 0.835) were superior to the clinical model (AUC, 0.776) in the validation set (P = 0.003, 0.040, respectively). A correlation between Nomogram score (Nomo-score, derived from RN) and RFS was observed through Kaplan-Meier survival analysis in the training and test cohorts (log-rank P < 0.050). Patients with high Nomo-score tumors were 2.669 times more likely to suffer recurrence than those with low Nomo-score tumors (HR, 2.669, P < 0.001).ConclusionsThe CT-based RN performed well in predicting both the histologic grade and outcome of CS.

Interpretable detection of epiretinal membrane from optical coherence tomography with deep neural networks

This study aimed to automatically detect epiretinal membranes (ERM) in various OCT-scans of the central and paracentral macula region and classify them by size using deep-neural-networks (DNNs). To this end, 11,061 OCT-images were included and graded according to the presence of an ERM and its size (small 100–1000 µm, large > 1000 µm). The data set was divided into training, validation and test sets (75%, 10%, 15% of the data, respectively). An ensemble of DNNs was trained and saliency maps were generated using Guided-Backprob. OCT-scans were also transformed into a one-dimensional-value using t-SNE analysis. The DNNs’ receiver-operating-characteristics on the test set showed a high performance for no-ERM, small-ERM and large-ERM cases (AUC: 0.99, 0.92, 0.99, respectively; 3-way accuracy: 89%), with small-ERMs being the most difficult ones to detect. t-SNE analysis sorted cases by size and, in particular, revealed increased classification uncertainty at the transitions between groups. Saliency maps reliably highlighted ERM, regardless of the presence of other OCT features (i.e. retinal-thickening, intraretinal pseudo-cysts, epiretinal-proliferation) and entities such as ERM-retinoschisis, macular-pseudohole and lamellar-macular-hole. This study showed therefore that DNNs can reliably detect and grade ERMs according to their size not only in the fovea but also in the paracentral region. This is also achieved in cases of hard-to-detect, small-ERMs. In addition, the generated saliency maps can be used to highlight small-ERMs that might otherwise be missed. The proposed model could be used for screening-programs or decision-support-systems in the future.

Some combinatorics of data leakage induced by clusters

AbstractData leakage is a common issue that can lead to misleading generalisation error estimation and incorrect hyperparameter tuning. However, its mechanisms are not always well understood. In this work, we consider the case of clustered data and investigate the distribution of the number of elements in leakage when the data set is uniformly split. For both the validation and test sets, the first and second moments of the number of elements in leakage are derived analytically. Modelling consequences are investigated and exemplified on simulated data. In addition, the case of an actual agronomic feasibility study is presented. We demonstrate how data leakage can distort model performance estimation when an inadequate data splitting strategy is used. We provide an understanding of data leakage in the context of clustered data by quantifying its role in predictive modelling. This sheds light on related challenges that may impact the practice in agronomy and beyond.

An Efficient Deep Learning Approach for DNA-Binding Proteins Classification from Primary Sequences

As the number of identified proteins has expanded, the accurate identification of proteins has become a significant challenge in the field of biology. Various computational methods, such as Support Vector Machine (SVM), K-nearest neighbors (KNN), and convolutional neural network (CNN), have been proposed to recognize deoxyribonucleic acid (DNA)-binding proteins solely based on amino acid sequences. However, these methods do not consider the contextual information within amino acid sequences, limiting their ability to adequately capture sequence features. In this study, we propose a novel approach to identify DNA-binding proteins by integrating a CNN with bidirectional long-short-term memory (LSTM) and gated recurrent unit (GRU) as (CNN-BiLG). The CNN-BiLG model can explore the potential contextual relationships of amino acid sequences and obtain more features than traditional models. Our experimental results demonstrate a validation set prediction accuracy of 94% for the proposed CNN-BiLG, surpassing the accuracy of machine learning models and deep learning models. Furthermore, our model is both effective and efficient, exhibiting commendable classification accuracy based on comparative analysis.

Machine Learning Exploration of the Relationship Between Drugs and the Blood-Brain Barrier: Guiding Molecular Modification.

This study aimed to improve the efficiency of pharmacotherapy for CNS diseases by optimizing the ability of drug molecules to penetrate the Blood-Brain Barrier (BBB). We established qualitative and quantitative databases of the ADME properties of drugs and derived characteristic features of compounds with efficient BBB penetration. Using these insights, we developed four machine learning models to predict a drug's BBB permeability by assessing ADME properties and molecular topology. We then validated the models using the B3DB database. For acyclovir and ceftriaxone, we modified the Hydrogen Bond Donors and Acceptors, and evaluated the BBB permeability using the predictive model. The machine learning models performed well in predicting BBB permeability on both internal and external validation sets. Reducing the number of Hydrogen Bond Donors and Acceptors generally improves BBB permeability. Modification only enhanced BBB penetration in the case of acyclovir and not ceftriaxone. The machine learning models developed can accurately predict BBB permeability, and many drug molecules are likely to have increased BBB penetration if the number of Hydrogen Bond Donors and Acceptors are reduced. These findings suggest that molecular modifications can enhance the efficacy of CNS drugs and provide practical strategies for drug design and development. This is particularly relevant for improving drug penetration of the BBB.

Experimental validation and comprehensive analysis of m6A methylation regulators in intervertebral disc degeneration subpopulation classification

Intervertebral disc degeneration (IVDD) is one of the most prevalent causes of chronic low back pain. The role of m6A methylation modification in disc degeneration (IVDD) remains unclear. We investigated immune-related m6A methylation regulators as IVDD biomarkers through comprehensive analysis and experimental validation of m6A methylation regulators in disc degeneration. The training dataset was downloaded from the GEO database and analysed for differentially expressed m6A methylation regulators and immunological features, the differentially regulators were subsequently validated by a rat IVDD model and RT-qPCR. Further screening of key m6A methylation regulators based on machine learning and LASSO regression analysis. Thereafter, a predictive model based on key m6A methylation regulators was constructed for training sets, which was validated by validation set. IVDD patients were then clustered based on the expression of key m6A regulators, and the expression of key m6A regulators and immune infiltrates between clusters was investigated to determine immune markers in IVDD. Finally, we investigated the potential role of the immune marker in IVDD through enrichment analysis, protein-to-protein network analysis, and molecular prediction. By analysising of the training set, we revealed significant differences in gene expression of five methylation regulators including RBM15, YTHDC1, YTHDF3, HNRNPA2B1 and ALKBH5, while finding characteristic immune infiltration of differentially expressed genes, the result was validated by PCR. We then screen the differential m6A regulators in the training set and identified RBM15 and YTHDC1 as key m6A regulators. We then used RBM15 and YTHDC1 to construct a predictive model for IVDD and successfully validated it in the training set. Next, we clustered IVDD patients based on the expression of RBM15 and YTHDC1 and explored the immune infiltration characteristics between clusters as well as the expression of RBM15 and YTHDC1 in the clusters. YTHDC1 was finally identified as an immune biomarker for IVDD. We finally found that YTHDC1 may influence the immune microenvironment of IVDD through ABL1 and TXK. In summary, our results suggest that YTHDC1 is a potential biomarker for the development of IVDD and may provide new insights for the precise prevention and treatment of IVDD.

Navigating the future of diabetes: innovative nomogram models for predicting all-cause mortality risk in diabetic nephropathy.

This study aims to establish and validate a nomogram model for the all-cause mortality rate in patients with diabetic nephropathy (DN). We analyzed data from the National Health and Nutrition Examination Survey (NHANES) spanning from 2007 to 2016. A random split of 7:3 was performed between the training and validation sets. Utilizing follow-up data until December 31, 2019, we examined the all-cause mortality rate. Cox regression models and Least Absolute Shrinkage and Selection Operator (LASSO) regression models were employed in the training cohort to develop a nomogram for predicting all-cause mortality in the studied population. Finally, various validation methods were employed to assess the predictive performance of the nomogram, and Decision Curve Analysis (DCA) was conducted to evaluate the clinical utility of the nomogram. After the results of LASSO regression models and Cox multivariate analyses, a total of 8 variables were selected, gender, age, poverty income ratio, heart failure, body mass index, albumin, blood urea nitrogen and serum uric acid. A nomogram model was built based on these predictors. The C-index values in training cohort of 3-year, 5-year, 10-year mortality rates were 0.820, 0.807, and 0.798. In the validation cohort, the C-index values of 3-year, 5-year, 10-year mortality rates were 0.773, 0.788, and 0.817, respectively. The calibration curve demonstrates satisfactory consistency between the two cohorts. The newly developed nomogram proves to be effective in predicting the all-cause mortality risk in patients with diabetic nephropathy, and it has undergone robust internal validation.

Automatic measurement of lower limb alignment in portable devices based on deep learning for knee osteoarthritis

BackgroundFor knee osteoarthritis patients, analyzing alignment of lower limbs is essential for therapy, which is currently measured from standing long-leg radiographs of anteroposterior X-ray (LLR) manually. To address the time wasting, poor reproducibility and inconvenience of use caused by existing methods, we present an automated measurement model in portable devices for assessing knee alignment from LLRs.MethodWe created a model and trained it with 837 conforming LLRs, and tested it using 204 LLRs without duplicates in a portable device. Both manual and model measurements were conducted independently, then we recorded knee alignment parameters such as Hip knee ankle angle (HKA), Joint line convergence angle (JCLA), Anatomical mechanical angle (AMA), mechanical Lateral distal femoral angle (mLDFA), mechanical Medial proximal tibial angle (mMPTA), and the time required. We evaluated the model’s performance compared with manual results in various metrics.ResultIn both the validation and test sets, the average mean radial errors were 2.778 and 2.447 (P<0.05). The test results for native knee joints showed that 92.22%, 79.38%, 87.94%, 79.82%, and 80.16% of the joints reached angle deviation<1° for HKA, JCLA, AMA, mLDFA, and mMPTA. Additionally, for joints with prostheses, 90.14%, 93.66%, 86.62%, 83.80%, and 85.92% of the joints reached that. The Chi-square test did not reveal any significant differences between the manual and model measurements in subgroups (P>0.05). Furthermore, the Bland-Altman 95% limits of agreement were less than ± 2° for HKA, JCLA, AMA, and mLDFA, and slightly more than ± 2 degrees for mMPTA.ConclusionThe automatic measurement tool can assess the alignment of lower limbs in portable devices for knee osteoarthritis patients. The results are reliable, reproducible, and time-saving.

Automated Sparse and Low-Rank Shallow Autoencoders for Recommendation

Collaborative filtering (CF) works have demonstrated the robust capabilities of Shallow Autoencoders on implicit feedback, showcasing highly competitive performance with other reasonable approaches (e.g., iALS and VAE-CF). However, despite their dual advantages of high performance and simple construction, EASE still exhibits several major shortcomings that must be addressed. To be more precise, the scalability of EASE is limited by the number of items, which determines the storage and inversion cost of a large dense matrix; the square-loss optimization objective does not consistently meet the recommendation task’s requirement for predicting personalized rankings, resulting in sub-optimal outcomes; the regularization coefficients are sensitive and require re-calibration with different datasets, leading to an exhaustive and time-consuming fine-tuning process. In order to address these obstacles, we propose a novel approach called Similarity-Structure Aware Shallow Autoencoder (AutoS 2 AE) that aims to enhance both recommendation accuracy and model efficiency. Our method introduces three similarity structures: Co-Occurrence, KNN, and NSW graphs, which replace the large dense matrix in EASE with a sparse structure, thus facilitating model compression. Additionally, we optimize the model by incorporating a low-rank training component into the matrix and applying a weighted square loss for improved ranking-oriented approximations. To automatically tune the hyperparameters, we further design two validation losses on the validation set for guidance and update the hyperparameters using the gradients of these validation losses. Both theoretical analyses regarding the introduction of similarity structures and empirical evaluations on multiple real-world datasets demonstrate the effectiveness of our proposed method, which significantly outperforms competing baselines.