Cross-validation Dataset Research Articles

M6A-TCPred: a web server to predict tissue-conserved human m6A sites using machine learning approach

BackgroundN6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotic cells that plays a crucial role in regulating various biological processes, and dysregulation of m6A status is involved in multiple human diseases including cancer contexts. A number of prediction frameworks have been proposed for high-accuracy identification of putative m6A sites, however, none have targeted for direct prediction of tissue-conserved m6A modified residues from non-conserved ones at base-resolution level.ResultsWe report here m6A-TCPred, a computational tool for predicting tissue-conserved m6A residues using m6A profiling data from 23 human tissues. By taking advantage of the traditional sequence-based characteristics and additional genome-derived information, m6A-TCPred successfully captured distinct patterns between potentially tissue-conserved m6A modifications and non-conserved ones, with an average AUROC of 0.871 and 0.879 tested on cross-validation and independent datasets, respectively.ConclusionOur results have been integrated into an online platform: a database holding 268,115 high confidence m6A sites with their conserved information across 23 human tissues; and a web server to predict the conserved status of user-provided m6A collections. The web interface of m6A-TCPred is freely accessible at: www.rnamd.org/m6ATCPred.

A causality-inspired generalized model for automated pancreatic cancer diagnosis

Pancreatic cancer (PC) is a severely malignant cancer variant with high mortality. Since PC has no obvious symptoms, most PC patients are belatedly diagnosed at advanced disease stages. Recently, artificial intelligence (AI) approaches have demonstrated promising prospects for early diagnosis of pancreatic cancer. However, certain non-causal factors (such as intensity and texture appearance variations, also called confounders) tend to induce spurious correlation with PC diagnosis. This undermines the generalization performance and the clinical applicability of the AI-based PC diagnosis approaches. Therefore, we propose a causal intervention based automated method for pancreatic cancer diagnosis with contrast-enhanced computerized tomography (CT) images, where a confounding effects reduction scheme is developed for alleviating spurious correlations to achieve unbiased learning, thereby improving the generalization performance. Specifically, a continuous image generation strategy was developed to simulate wide variations of intensity differences caused by imaging heterogeneities, where Monte Carlo sampling is added to further enhance the continuity of simulated images. Then, to enhance the pancreatic texture variability, a texture diversification method was introduced in conjunction with gradient-based data augmentation. Finally, a causal intervention strategy was proposed to alleviate the adverse confounding effects by decoupling the causal and non-causal factors and combining them randomly. Extensive experiments showed remarkable diagnosis performance on a cross-validation dataset. Also, promising generalization performance with an average accuracy of 0.87 was attained on three independent test sets of a total of 782 subjects. Therefore, the proposed method shows high clinical feasibility and applicability for pancreatic cancer diagnosis.

Combining radiomics with thyroid imaging reporting and data system to predict lateral cervical lymph node metastases in medullary thyroid cancer.

Medullary Thyroid Carcinoma (MTC) is a rare type of thyroid cancer. Accurate prediction of lateral cervical lymph node metastases (LCLNM) in MTC patients can help guide surgical decisions and ensure that patients receive the most appropriate and effective surgery. To our knowledge, no studies have been published that use radiomics analysis to forecast LCLNM in MTC patients. The purpose of this study is to develop a radiomics combined with thyroid imaging reporting and data system (TI-RADS) model that can use preoperative thyroid ultrasound images to noninvasively predict the LCLNM status of MTC. We retrospectively included 218 MTC patients who were confirmed from postoperative pathology as LCLNM negative (n=111) and positive (n=107). Ultrasound features were selected using the Student's t-test, while radiomics features are first extracted from preoperative thyroid ultrasound images, and then a two-step feature selection approach was used to select features. These features are then used to establish three regularized logistic regression models, namely the TI-RADS model (TM), the radiomics model (RM), and the radiomics-TI-RADS model (RTM), in 5-fold cross-validation to determine the likelihood of the LCLNM. The Delong's test and decision curve analysis (DCA) were used to evaluate and compare the performance of the models. The ultrasound features of margin and TI-RADS level, and a total of 12 selected radiomics features, were significantly different between the LCLNM negative and positive groups (p<0.05). The TM, RM, and RTM yielded an averaged AUC of 0.68±0.05, 0.78±0.06, and 0.82±0.05 in the 5-fold cross-validation dataset, respectively. RM and RTM are statistically better than TM (p<0.05 and p<0.001) according to Delong test. DCA demonstrates that RTM brings more benefit than TM and RM. We have developed a joint radiomics-based model for noninvasive prediction of the LCLNM in MTC patients solely using preoperative thyroid ultrasound imaging. It has the potential to be used as a complementary tool to help guide treatment decisions for this rare form of thyroid cancer.

Interpretable machine learning model integrating clinical and elastosonographic features to detect renal fibrosis in Asian patients with chronic kidney disease

BackgroundNon-invasive renal fibrosis assessment is critical for tailoring personalized decision-making and managing follow-up in patients with chronic kidney disease (CKD). We aimed to exploit machine learning algorithms using clinical and elastosonographic features to distinguish moderate-severe fibrosis from mild fibrosis among CKD patients.MethodsA total of 162 patients with CKD who underwent shear wave elastography examinations and renal biopsies at our institution were prospectively enrolled. Four classifiers using machine learning algorithms, including eXtreme Gradient Boosting (XGBoost), Support Vector Machine (SVM), Light Gradient Boosting Machine (LightGBM), and K-Nearest Neighbor (KNN), which integrated elastosonographic features and clinical characteristics, were established to differentiate moderate-severe renal fibrosis from mild forms. The area under the receiver operating characteristic curve (AUC) and average precision were employed to compare the performance of constructed models, and the SHapley Additive exPlanations (SHAP) strategy was used to visualize and interpret the model output.ResultsThe XGBoost model outperformed the other developed machine learning models, demonstrating optimal diagnostic performance in both the primary (AUC = 0.97, 95% confidence level (CI) 0.94–0.99; average precision = 0.97, 95% CI 0.97–0.98) and five-fold cross-validation (AUC = 0.85, 95% CI 0.73–0.98; average precision = 0.90, 95% CI 0.86–0.93) datasets. The SHAP approach provided visual interpretation for XGBoost, highlighting the features’ impact on the diagnostic process, wherein the estimated glomerular filtration rate provided the largest contribution to the model output, followed by the elastic modulus, then renal length, renal resistive index, and hypertension.ConclusionThis study proposed an XGBoost model for distinguishing moderate-severe renal fibrosis from mild forms in CKD patients, which could be used to assist clinicians in decision-making and follow-up strategies. Moreover, the SHAP algorithm makes it feasible to visualize and interpret the feature processing and diagnostic processes of the model output.Graphical

Incorporation of Partial Least Squares-Discriminant Analysis with Ultra-High-Performance Liquid Chromatography Diode-Array Detector for Authentication of Skin Gelatine Sources

This research seeks to (1) authenticate sources of skin gelatine by combining putative 17 aminoacids (AAs) analysis with chemometrics by Ultra-High-Performance Liquid ChromatographyDiode-Array Detector (UHPLC-DAD) and (2) create AA profiles in skin gelatines. Theclassification capability of partial least square-discriminant analysis (PLS-DA) models wasassessed to determine the most effective discriminant model. Principal component analysis(PCA) with quartimax rotation was utilised to accurately organise gelatine clusters and assign thesignificantly contributing AAs to each cluster. The PLS-DA model with 13 AAs (PLS-DAVIPAA)outperformed the PLS-DA model with 17 AAs (PLS-DAAA) because its R2Y (0.938), R2X (0.881),and Q2 (0.929) values were greater. With 13 significant AAs, the PLS-DAVIPAA model obtainedcluster classification accuracy of 100% on training and cross-validation datasets and 93.3% ontesting and verification datasets. The chemical structure of gelatines may shed light on theinteractions between AAs. Following six quartimax rotations, the gelatines were groupedcorrectly. The PCA showed the dominant presence of these AAs: L-Valine, L-Phenylalanine andL-Tyrosine in porcine gelatine; Glycine, L-Threonine, L-Arginine, L-Methionine, L-Histidine andL-Serine in fish gelatine; and L-Hydroxyproline, L-Leucine and L-Proline in bovine gelatine. Theauthority could use this technique to set a standard for authenticating skin gelatine samples.

SynergyX: a multi-modality mutual attention network for interpretable drug synergy prediction.

Discovering effective anti-tumor drug combinations is crucial for advancing cancer therapy. Taking full account of intricate biological interactions is highly important in accurately predicting drug synergy. However, the extremely limited prior knowledge poses great challenges in developing current computational methods. To address this, we introduce SynergyX, a multi-modality mutual attention network to improve anti-tumor drug synergy prediction. It dynamically captures cross-modal interactions, allowing for the modeling of complex biological networks and drug interactions. A convolution-augmented attention structure is adopted to integrate multi-omic data in this framework effectively. Compared with other state-of-the-art models, SynergyX demonstrates superior predictive accuracy in both the General Test and Blind Test and cross-dataset validation. By exhaustively screening combinations of approved drugs, SynergyX reveals its ability to identify promising drug combination candidates for potential lung cancer treatment. Another notable advantage lies in its multidimensional interpretability. Taking Sorafenib and Vorinostat as an example, SynergyX serves as a powerful tool for uncovering drug-gene interactions and deciphering cell selectivity mechanisms. In summary, SynergyX provides an illuminating and interpretable framework, poised to catalyze the expedition of drug synergy discovery and deepen our comprehension of rational combination therapy.

An Interactive Spreadsheet Model for Teaching Classification Using Logistic Regression

We present an interactive spreadsheet that supports teaching essential concepts in classification using the logistic regression (LoR) model for binary classification. The interactive spreadsheet demonstrates the capabilities of LoR by integrating computation with visualization. Students will reinforce concepts like probabilities, maximum likelihood estimation (MLE), and the use of likelihoods to optimize parameters for the LoR. We then discuss using LoR for classifications while adjusting its decision boundary (DB), demonstrating how to convert assigned likelihoods into classification using the DB; impact classification outcome by varying DBs; designate predictions as true positive, true negative, false positive, or false negative; and determine the classification accuracy. We use a variety of performance measures, including sensitivity, specificity, precision, negative predictive value, F1 and F2 scores, the receiver operating characteristics curve, and lift/decile charts. These measures are dynamically adjusted when the DB changes. We also reiterate the usage of these measures in the context of crossvalidation and imbalanced data sets. We provide a case study that implements LoR and an option for teaching the details behind MLE. We discuss the pedagogical aspects of this spreadsheet based on a survey of the 2022 student cohort in the Master of Management Analytics Program at the Rotman School of Management.

Directional statistics-inspired end-to-end atrial fibrillation detection model based on ECG rhythm

Numerous algorithms designed for detecting atrial fibrillation (AF) often exhibit limitations in extracting essential rhythm features, leading to challenges in accurately discerning ectopic beats and consequently yielding suboptimal detection performance. In this study, we explored the distribution patterns of R-R intervals (RRIs) in both AF and specific rhythms, such as atrial premature beats (APBs) and normal sinus rhythm (NSR). For the first time, we employed the Sobolev test statistics, a method used in directional statistics to assess spherical uniformity, to quantify the irregularity and variability characteristics of RRIs. We developed an end-to-end learnable model for detecting AF by leveraging this approach. A cross-dataset validation method is employed to train and test the proposed model. This involved the use of a simulated dataset and eight distinct real-world databases. Notably, when trained on the Computing in Cardiology Challenge 2017 (C2017) and tested on the MIT-BIH Atrial Fibrillation Database (AFDB), our model, designed to take only a sequence of 32 RRIs as input, achieved a sensitivity of 96.2%, specificity of 98.2%, and accuracy of 97.3%. The results illustrate its competitive standing against the existing methods for AF detection and its enhanced resilience to ectopic beats. Unlike existing deep learning-based AF detection models, our model prioritizes interpretability, boasts lower computational complexity (with fewer than 2000 learnable parameters), and demonstrates superior generalization capabilities. This will help improve the quality of long-term real-time monitoring and management of AF, reduce the burden on clinicians, and ultimately improve patient outcomes.

Predictive modeling for cardiovascular disease risk assessment

Cardiovascular diseases (CVDs) continue to be the world's leading cause of death. It is imperative that accurate risk assessment and early intervention be implemented. This study proposes a predictive modeling framework, termed "HeartGuard," designed to assess an individual's risk of developing cardiovascular disease. Leveraging a diverse dataset comprising demographic information, lifestyle factors, medical history, and biomarker data, advanced machine learning techniques are employed to construct robust predictive models. The developed models incorporate features such as age, gender, blood pressure, cholesterol levels, smoking status, physical activity, and family history to estimate the probability of CVD occurrence within a specified timeframe. The evaluation of the models using cross-validation and independent validation datasets demonstrates their high accuracy, sensitivity, and specificity. HeartGuard offers a reliable tool for clinicians to identify individuals at heightened risk of cardiovascular disease, enabling targeted preventive measures and personalized healthcare interventions to mitigate the burden of CVD morbidity and mortality.

A Lumped-Parameter Model of the Cardiovascular System Response for Evaluating Automated Fluid Resuscitation Systems.

Physiological closed-loop controlled (PCLC) medical devices, such as those designed for blood pressure regulation, can be tested for safety and efficacy in real-world clinical settings. However, relying solely on limited animal and clinical studies may not capture the diverse range of physiological conditions. Credible mathematical models can complement these studies by allowing the testing of the device against simulated patient scenarios. This research involves the development and validation of a low-order lumped-parameter mathematical model of the cardiovascular system's response to fluid perturbation. The model takes rates of hemorrhage and fluid infusion as inputs and provides hematocrit and blood volume, heart rate, stroke volume, cardiac output and mean arterial blood pressure as outputs. The model was calibrated using data from 27 sheep subjects, and its predictive capability was evaluated through a leave-one-out cross-validation procedure, followed by independent validation using 12 swine subjects. Our findings showed small model calibration error against the training dataset, with the normalized root-mean-square error (NRMSE) less than 10% across all variables. The mathematical model and virtual patient cohort generation tool demonstrated a high level of predictive capability and successfully generated a sufficient number of subjects that closely resembled the test dataset. The average NRMSE for the best virtual subject, across two distinct samples of virtual subjects, was below 12.7% and 11.9% for the leave-one-out cross-validation and independent validation dataset. These findings suggest that the model and virtual cohort generator are suitable for simulating patient populations under fluid perturbation, indicating their potential value in PCLC medical device evaluation.

Fusion of Brain Imaging Data with Artificial Intelligence to detect Autism Spectrum Disorder

Autism, a developmental and neurological disorder, impacts communication, interaction, and behavior, setting individuals with it apart from those without. This spectrum disorder affects various aspects of an individual's life, including social, cognitive, emotional, and physical health. Early detection and intervention are crucial for symptom reduction and facilitating learning and development. Recent advancements in machine learning and deep learning have facilitated the diagnosis of Autism by analyzing brain signals. This current study introduces an approach for Autism detection utilizing functional Magnetic Resonance Imaging (fMRI) data. The Autism Brain Imaging Data Exchange (ABIDE) dataset serves as the foundation, employing hierarchical graph pooling to abstract brain images into a graph structure. Graph Convolutional Networks are then used to learn node embeddings derived from sparse feature vectors. The model attains an accuracy of 87% on the 10-fold cross-validation dataset. This study proves to be cost-effective and efficient in identifying Autism through fMRI, making it suitable for near real-time applications.

A three-path network with multi-scale selective feature fusion, edge-inspiring and edge-guiding for liver tumor segmentation

Automatic liver tumor segmentation is one of the most important tasks in computer-aided diagnosis and treatment. Deep learning techniques have gained increasing popularity for medical image segmentation in recent years. However, due to the various shapes, sizes, and obscure boundaries of tumors, it is still difficult to automatically extract tumor regions from CT images. Based on the complementarity of edge detection and region segmentation, a three-path structure with multi-scale selective feature fusion (MSFF) module, multi-channel feature fusion (MFF) module, edge-inspiring (EI) module, and edge-guiding (EG) module is proposed in this paper. The MSFF module includes the process of generation, fusion, and selection of multi-scale features, which can adaptively correct the response weights in multiple branches to filter redundant information. The MFF module integrates richer hierarchical features to capture targets at different scales. The EI module aggregates high-level semantic information at different levels to obtain fine edge semantics, which is injected into the EG module for representation learning of segmentation features. Experiments on the LiTs2017 dataset show that our proposed method achieves a Dice index of 85.55% and a Jaccard index of 81.11%, which are higher than what can be obtained by the current state-of-the-art methods. Cross-dataset validation experiments conducted on 3Dircadb and Clinical datasets show the generalization and robustness of the proposed method by achieving dice indices of 80.14% and 81.68%, respectively.

Ensemble Quantitative Read-Across Structure-Activity Relationship Algorithm for Predicting Skin Cytotoxicity.

Read-across (RA) and quantitative structure-activity relationship (QSAR) are two alternative methods commonly used to fill data gaps in chemical registrations. These approaches use physicochemical properties or molecular fingerprints of source substances to predict the properties of unknown substances that have similar chemical structures or physicochemical properties. Research on RA and QSAR is essential to minimize the time, money, and animal testing needed to determine biological properties that are not currently known. This study developed a stacked ensemble quantitative read-across structure-activity relationship algorithm (enQRASAR) for predicting skin irritation toxicity based on negative log cell viability inhibition concentration at 50% (pIC50) against skin keratinocytes as the end point. The goodness-of-fit and predictability of this algorithm were validated using leave-one-out cross-validation and external test data sets. The results obtained were statistically reliable in terms of goodness-of-fit, robustness, and predictability metrics. Additionally, the developed model demonstrated a low prediction error when predicting FDA-approved drugs. These results confirm that the enQRASAR algorithm can be used to predict skin cytotoxicity of chemicals. Therefore, this model was publicly available to further facilitate toxicity predictions of unknown compounds in chemical registrations.

An Ensemble Machine Learning Model Using Gradient Boosting Identifies Patients with Disease Progression in Newly Diagnosed Multiple Myeloma

Introduction: In many cases, treatment decisions for multiple myeloma patients must be made in the absence of high quality randomized controlled clinical trials. As a result, many clinicians lean on prognostic models to drive treatment selection. The most widely used of these models incorporate a limited number of patient related factors that reflect tumor burden, cytogenetic features, or gene expression profiling. These prediction scores are derived from regression models that incorporate these variables at the time of diagnosis. They do not account for variables that change dynamically over time, do not explore the relationship between treatment selection and progression, and imperfectly predict survival outcomes. We designed a prognostic model based on an ensemble machine learning platform to predict progression in NDMM using Extreme Gradient Boosting Machine (XGBoost) combined with accelerated failure time modeling for survival analysis. Methods: We utilized a large retrospective data set containing treatment and response information for 1127 patients with newly diagnosed multiple myeloma (NDMM) treated at the Cleveland Clinic Foundation between 2000 and 2023. Following data preprocessing based on data completeness, 953 patient records were included in our training, testing, and cross validation datasets. For the purposes of our analysis, the initial dataset was randomly split into training (70%), testing (15%) and validation (15%) subsets at the patient level. We also defined the lower and upper bounds for each subset, which is critical due to the right-censored nature of survival data. Hyperparameters for XGBoost were optimized using Bayesian search, minimizing the negative log-likelihood. A random forest method was applied for the imputation of missing data (MissForest). We then trained the XGBoost model using GPU acceleration for enhanced computational efficiency. Finally, a log-rank test on predicted survival times was used to test the model's performance on patients with and without known progression. Results: Our preprocessed data set had 953 patients with a mean age at disease onset of 65 years and a slight male predominance (55%). Approximately 27% of patients harbored high cytogenetic risk disease and 3.5% of the cohort presented with extramedullary disease a diagnosis. At a median follow up of 35 months, 47% of patients had experienced disease progression or death. Induction therapy included an immunomodulatory drug in 40% of patients and proteasome inhibitors in 22%. Frontline autologous stem cell transplantation followed induction in 28% of patients. Median progression free survival in the overall data set was 44 months. These features were consistent across the randomly assigned training, testing, and validation cohorts. Following data preprocessing, 34 independent clinical and genomic variables including selection of first line treatment were assessed as model inputs each available record. Under optimized parameters, the model was trained with a maximum tree depth = 7 and a learning rate ~ 0.22 for the desired output of progression free survival (PFS). We then queried PFS for both the training and validation sets and divided patients into those known to have progressed and those without a progression event. Survival analysis was undertaken using predicted PFS values for patients known to have progressed and those who remained progression free. For the validation data set, our model successfully discerned between progressed and non-progressed cases (log-rank test statistic = 22.07, p &amp;lt; 0.005) (Figure 1). Discussion: We present a machine learning approach based on regularized gradient boosting that accurately discerns between patients who experience progression and those who remain progression free at a median ~35 months of follow-up in a large retrospective data set in patients presenting with NDMM. Further elaboration of our model will allow for the incorporation of large amounts data to predict survival outcomes on the basis of dynamic variables such as depth of response and treatment selection. With the ability to parse outcomes among multiple myeloma patients at high resolution, future clinicians and clinical trialists may be able to overcome limitations in trial design and patient-level therapy selection for both newly diagnosed and relapsed patients.

MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases

Recent advances in next-generation sequencing (NGS) technology have greatly accelerated the need for efficient annotation to accurately interpret clinically relevant genetic variants in human diseases. Therefore, it is crucial to develop appropriate analytical tools to improve the interpretation of disease variants. Given the unique genetic characteristics of mitochondria, including haplogroup, heteroplasmy, and maternal inheritance, we developed a suite of variant analysis toolkits specifically designed for primary mitochondrial diseases: the Mitochondrial Missense Variant Annotation Tool (MmisAT) and the Mitochondrial Missense Variant Pathogenicity Predictor (MmisP). MmisAT can handle protein-coding variants from both nuclear DNA and mtDNA and generate 349 annotation types across six categories. It processes 4.78 million variant data in 76 min, making it a valuable resource for clinical and research applications. Additionally, MmisP provides pathogenicity scores to predict the pathogenicity of genetic variations in mitochondrial disease. It has been validated using cross-validation and external datasets and demonstrated higher overall discriminant accuracy with a receiver operating characteristic (ROC) curve area under the curve (AUC) of 0.94, outperforming existing pathogenicity predictors. In conclusion, the MmisAT is an efficient tool that greatly facilitates the process of variant annotation, expanding the scope of variant annotation information. Furthermore, the development of MmisP provides valuable insights into the creation of disease-specific, phenotype-specific, and even gene-specific predictors of pathogenicity, further advancing our understanding of specific fields.

Machine Learning Pipeline for Predicting Bone Marrow Edema Along the Sacroiliac Joints on Magnetic Resonance Imaging.

We aimed to develop and validate a fully automated machine learning (ML) algorithm that predicts bone marrow edema (BME) on a quadrant level in sacroiliac (SI) joint magnetic resonance imaging (MRI). A computer vision workflow automatically locates the SI joints, segments regions of interest (ilium and sacrum), performs objective quadrant extraction, and predicts presence of BME, suggestive of inflammatory lesions, on a quadrant level in semicoronal slices of T1/T2-weighted MRI scans. Ground truth was determined by consensus among human readers. The inflammation classifier was trained using a ResNet18 backbone and five-fold cross-validated on scans of patients with spondyloarthritis (SpA) (n=279), postpartum individuals (n=71), and healthy subjects (n=114). Independent SpA patient MRI scans (n=243) served as test data set. Patient-level predictions were derived from aggregating quadrant-level predictions, ie, at least one positive quadrant. The algorithm automatically detects the SI joints with a precision of 98.4% and segments ilium/sacrum with an intersection over union of 85.6% and 67.9%, respectively. The inflammation classifier performed well in cross-validation: area under the curve (AUC) 94.5%, balanced accuracy (B-ACC) 80.5%, and F1 score 64.1%. In the test data set, AUC was 88.2%, B-ACC 72.1%, and F1 score 50.8%. On a patient level, the model achieved a B-ACC of 81.6% and 81.4% in the cross-validation and test data set, respectively. We propose a fully automated ML pipeline that enables objective and standardized evaluation of BME along the SI joints on MRI. This method has the potential to screen large numbers of patients with (suspected) SpA and is a step closer towards artificial intelligence-assisted diagnosis and follow-up.

Robust and novel attention guided MultiResUnet model for 3D ground reaction force and moment prediction from foot kinematics

Ground reaction force and moment (GRF&M) measurements are vital for biomechanical analysis and significantly impact the clinical domain for early abnormality detection for different neurodegenerative diseases. Force platforms have become the de facto standard for measuring GRF&M signals in recent years. Although the signal quality achieved from these devices is unparalleled, they are expensive and require laboratory setup, making them unsuitable for many clinical applications. For these reasons, predicting GRF&M from cheaper and more feasible alternatives has become a topic of interest. Several works have been done on predicting GRF&M from kinematic data captured from the subject’s body with the help of motion capture cameras. The problem with these solutions is that they rely on markers placed on the whole body to capture the movements, which can be very infeasible in many practical scenarios. This paper proposes a novel deep learning-based approach to predict 3D GRF&M from only 5 markers placed on the shoe. The proposed network “Attention Guided MultiResUNet” can predict the force and moment signals accurately and reliably compared to the techniques relying on full-body markers. The proposed deep learning model is tested on two publicly available datasets containing data from 66 healthy subjects to validate the approach. The framework has achieved an average correlation coefficient of 0.96 for 3D ground reaction force prediction and 0.86 for 3D ground reaction momentum prediction in cross-dataset validation. The framework can provide a cheaper and more feasible alternative for predicting GRF&M in many practical applications.

Stacked ensemble learning on HaCaT cytotoxicity for skin irritation prediction: A case study on dipterocarpol

Skin irritation is an adverse effect associated with various substances, including chemicals, drugs, or natural products. Dipterocarpol, extracted from Dipterocarpus alatus, contains several skin benefits notably anticancer, wound healing, and antibacterial properties. However, the skin irritation of dipterocarpol remains unassessed. Quantitative structure-activity relationship (QSAR) is a recommended tool for toxicity assessment involving less time, money, and animal testing to access unavailable acute toxicity data. Therefore, our study aimed to develop a highly accurate machine learning-based QSAR model for predicting skin irritation. We utilized a stacked ensemble learning model with 1064 chemicals. We also adhered to the recommendations from the OECD for QSAR validation. Subsequently, we used the proposed model to explore the cytotoxicity of dipterocarpol on keratinocytes. Our findings indicate that the model displayed promising statistical quality in terms of accuracy, precision, and recall in both 10-fold cross-validation and test datasets. Moreover, the model predicted that dipterocarpol does not have skin irritation, which was confirmed by the cell-based assay. In conclusion, our proposed model can be applied for the risk assessment of skin irritation in untested compounds that fall within its applicability domain. The web application of this model is available at https://qsarlabs.com/#stackhacat.

LncRNA-Top: Controlled deep learning approaches for lncRNA gene regulatory relationship annotations across different platforms

By soaking microRNAs (miRNAs), long non-coding RNAs (lncRNAs) have the potential to regulate gene expression. Few methods have been created based on this mechanism to anticipate the lncRNA-gene relationship prediction. Hence, we present lncRNA-Top to forecast potential lncRNA-gene regulation relationships. Specifically, we constructed controlled deep-learning methods using 12417 lncRNAs and 16127 genes. We have provided retrospective and innovative views among negative sampling, random seeds, cross-validation, metrics, and independent datasets. The AUC, AUPR, and our defined precision@k were leveraged to evaluate performance. In-depth case studies demonstrate that 47 out of 100 projected top unknown pairings were recorded in publications, supporting the predictive power. Our additional software can annotate the scores with target candidates. The lncRNA-Top will be a helpful tool to uncover prospective lncRNA targets and better comprehend the regulatory processes of lncRNAs.

Radiomics Analysis in Characterization of Salivary Gland Tumors on MRI: A Systematic Review.

Radiomics analysis can potentially characterize salivary gland tumors (SGTs) on magnetic resonance imaging (MRI). The procedures for radiomics analysis were various, and no consistent performances were reported. This review evaluated the methodologies and performances of studies using radiomics analysis to characterize SGTs on MRI. We systematically reviewed studies published until July 2023, which employed radiomics analysis to characterize SGTs on MRI. In total, 14 of 98 studies were eligible. Each study examined 23-334 benign and 8-56 malignant SGTs. Least absolute shrinkage and selection operator (LASSO) was the most common feature selection method (in eight studies). Eleven studies confirmed the stability of selected features using cross-validation or bootstrap. Nine classifiers were used to build models that achieved area under the curves (AUCs) of 0.74 to 1.00 for characterizing benign and malignant SGTs and 0.80 to 0.96 for characterizing pleomorphic adenomas and Warthin's tumors. Performances were validated using cross-validation, internal, and external datasets in four, six, and two studies, respectively. No single feature consistently appeared in the final models across the studies. No standardized procedure was used for radiomics analysis in characterizing SGTs on MRIs, and various models were proposed. The need for a standard procedure for radiomics analysis is emphasized.