Independent Test Dataset Research Articles

DsRNAPredictor-II: An improved predictor of identifying dsRNA and its silencing efficiency for Tribolium castaneum based on sequence length distribution

RNA interference (RNAi) has been widely utilized to investigate gene functions and has significant potential for control of pest insects. However, recent studies have revealed that the target insect species, dsRNA molecule length, target genes, and other experimental factors can affect the efficiency of RNAi mediated control, restricting the further development and application of this technology. Therefore, the aim of this study was to establish a deep learning model using bioinformatics to help researchers identify dsRNA fragments with the highest RNAi efficiency. In this study, we optimized an existing model, namely, dsRNAPredictor, by designing sub-models based on different sequence lengths. Accordingly, the data were divided into two groups: 130–399 bp and 400–616 bp long sequences. Then, one-hot encoding was employed to extract sequence information. The convolutional neural network framework comprising three convolutional layers, three average pooling layers, a flattened layer, and three dense layers was employed as the classifier. By adjusting the parameters, we established two sub-models for different sequence distributions. Using multiple independent test datasets and conducting hypothesis testing, we demonstrated that our model exhibits superior performance and strong robustness to dsRNAPredictor, respectively. Therefore, our model may help design dsRNAs with pre-screening potential and facilitate further research and applications.

Exploratory study on the enhancement of O-RADS application effectiveness for novice ultrasonographers via deep learning.

The study aimed to create a deep convolutional neural network (DCNN) model based on ConvNeXt-Tiny to identify classic benign lesions (CBL) from other lesions (OL) within the Ovarian-Adnexal Reporting and Data System (O-RADS), enhancing the system's utility for novice ultrasonographers. Two sets of sonographic images of pathologically confirmed adnexal lesions were retrospectively collected [development dataset (DD) and independent test dataset (ITD)]. The ConvNeXt-Tiny model, optimized through transfer learning, was trained on the DD using the original images directly and after automatic lesion segmentation by a U-Net model. Models derived from both training paradigms were validated on the ITD for sensitivity, specificity, accuracy, and area under the curve (AUC). Two novice ultrasonographers were assessed in O-RADS with and without assistance from the model for Application Effectiveness. The ConvNeXt-Tiny model trained on original images scored AUCs of 0.978 for DD and 0.955 for ITD, while the U-Net segmented image model achieved 0.967 for DD and 0.923 for ITD; neither showed significant differences. When assessing the malignancy of lesions using O-RADS 4 and 5, the diagnostic performances of two novice ultrasonographers and senior ultrasonographer, as well as model-assisted classifications, showed no significant differences, except for one novice's low accuracy. This approach reduced classification time by 62 and 64 min. The kappa values with senior doctors' classifications rose from 0.776 and 0.761 to 0.914 and 0.903, respectively. The ConvNeXt-Tiny model demonstrated excellent and stable performance in distinguishing CBL from OL within O-RADS. The diagnostic performance of novice ultrasonographers using O-RADS is essentially equivalent to that of senior ultrasonographer, and the assistance of the model can enhance their classification efficiency and consistency with the results of senior ultrasonographer.

Using Machine Learning and Feature Importance to Identify Risk Factors for Mortality in Pediatric Heart Surgery.

Background: The objective of this IRB-approved retrospective monocentric study was to identify risk factors for mortality after surgery for congenital heart defects (CHDs) in pediatric patients using machine learning (ML). CHD belongs to the most common congenital malformations, and remains the leading mortality cause from birth defects. Methods: The most recent available hospital encounter for each patient with an age <18 years hospitalized for CHD-related cardiac surgery between the years 2011 and 2020 was included in this study. The cohort consisted of 1302 eligible patients (mean age [SD]: 402.92 [±562.31] days), who were categorized into four disease groups. A random survival forest (RSF) and the 'eXtreme Gradient Boosting' algorithm (XGB) were applied to model mortality (incidence: 5.6% [n = 73 events]). All models were then applied to predict the outcome in an independent holdout test dataset (40% of the cohort). Results: RSF and XGB achieved average C-indices of 0.85 (±0.01) and 0.79 (±0.03), respectively. Feature importance was assessed with 'SHapley Additive exPlanations' (SHAP) and 'Time-dependent explanations of machine learning survival models' (SurvSHAP(t)), both of which revealed high importance of the maximum values of serum creatinine observed within 72 h post-surgery for both ML methods. Conclusions: ML methods, along with model explainability tools, can reveal interesting insights into mortality risk after surgery for CHD. The proposed analytical workflow can serve as a blueprint for translating the analysis into a federated setting that builds upon the infrastructure of the German Medical Informatics Initiative.

DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features.

The CRISPR/Cas9 system developed from Streptococcus pyogenes (SpCas9) has high potential in gene editing. However, its successful application is hindered by the considerable variability in target efficiencies across different single guide RNAs (sgRNAs). Although several deep learning models have been created to predict sgRNA on-target activity, the intrinsic mechanisms of these models are difficult to explain, and there is still scope for improvement in prediction performance. To overcome these issues, we propose an ensemble interpretable model termed DeepMEns based on deep learning to predict sgRNA on-target activity. By using five different training and validation datasets, we constructed five sub-regressors, each comprising three parts. The first part uses one-hot encoding, wherein 0-1 representation of the secondary structure is used as the input to the convolutional neural network (CNN) with Transformer encoder. The second part uses the DNA shape feature matrix as the input to the CNN with Transformer encoder. The third part uses positional encoding feature matrices as the proposed input into a long short-term memory network with an attention mechanism. These three parts are concatenated through the flattened layer, and the final prediction result is the average of the five sub-regressors. Extensive benchmarking experiments indicated that DeepMEns achieved the highest Spearman correlation coefficient for 6 of 10 independent test datasets as compared to previous predictors, this finding confirmed that DeepMEns can accomplish state-of-the-art performance. Moreover, the ablation analysis also indicated that the ensemble strategy may improve the performance of the prediction model.

A nomogram model to predict recurrence of early-onset endometrial cancer after resection based on clinical parameters and immunohistochemical markers: a multi-institutional study.

This study aimed to investigate the prognosis value of the clinical parameters and immunohistochemical markers of patients with early-onset endometrial cancer (EC) and establish a nomogram to accurately predict recurrence-free survival (RFS) of early-onset EC after resection. A training dataset containing 458 patients and an independent testing dataset consisting of 170 patients were employed in this retrospective study. The independent risk factors related to RFS were confirmed using Cox regression models. A nomogram model was established to predict RFS at 3 and 5 years post-hysterectomy. The C-index, area under the curve (AUC) of the receiver operating characteristic (ROC) curve, and calibration curve were calculated to assess the predictive accuracy of the nomogram. In all early-onset EC patients, more than half (368/628, 58.6%) were diagnosed in the age range of 45-49 years. Meanwhile, the recurrence rate of early-onset EC is approximately 10.8%. Multivariate Cox regression analyses showed that histological subtype, FIGO stage, myometrial invasion, lymphovascular space invasion (LVSI), P53 expression, and MMR status were independent prognostic factors related to RFS (all P < 0.05) and established the nomogram predicting 3- and 5-year RFS. The C-index and calibration curves of the nomogram demonstrated a close correlation between predicted and actual RFS. Patients were divided into high- and low-risk groups according to the model of RFS. Combining clinical parameters and immunohistochemical markers, we developed a robust nomogram to predict RFS after surgery for early-onset EC patients. This nomogram can predict prognosis well and guide treatment decisions.

Cone-Beam CT to CT Image Translation Using a Transformer-Based Deep Learning Model for Prostate Cancer Adaptive Radiotherapy.

Cone-beam computed tomography (CBCT) is widely utilized in image-guided radiation therapy; however, its image quality is poor compared to planning CT (pCT), thus restricting its utility for adaptive radiotherapy (ART). Our objective was to enhance CBCT image quality utilizing a transformer-based deep learning model, SwinUNETR, which we compared with a conventional convolutional neural network (CNN) model, U-net. This retrospective study involved 260 patients undergoing prostate radiotherapy, with 245 patients used for training and 15 patients reserved as an independent hold-out test dataset. Employing a CycleGAN framework, we generated synthetic CT (sCT) images from CBCT images, employing SwinUNETR and U-net as generators. We evaluated sCT image quality and assessed its dosimetric impact for photon therapy through gamma analysis and dose-volume histogram (DVH) comparisons. The mean absolute error values for the CT numbers, calculated using all voxels within the patient's body contour and taking the pCT images as a reference, were 84.07, 73.49, and 64.69 Hounsfield units for CBCT, U-net, and SwinUNETR images, respectively. Gamma analysis revealed superior agreement between the dose on the pCT images and on the SwinUNETR-based sCT plans compared to those based on U-net. DVH parameters calculated on the SwinUNETR-based sCT deviated by < 1% from those in pCT plans. Our study showed that, compared to the U-net model, SwinUNETR could proficiently generate more precise sCT images from CBCT images, facilitating more accurate dose calculations. This study demonstrates the superiority of transformer-based models over conventional CNN-based approaches for CBCT-to-CT translation, contributing to the advancement of image synthesis techniques in ART.

Application of CT-based foundational artificial intelligence and radiomics models for prediction of survival for lung cancer patients treated on the NRG/RTOG 0617 clinical trial.

To apply CT-based foundational artificial intelligence (AI) and radiomics models for predicting overall survival (OS) for patients with locally advanced non-small cell lung cancer (NSCLC). Data for 449 patients retrospectively treated on the NRG Oncology/Radiation Therapy Oncology Group (RTOG) 0617 clinical trial were analyzed. Foundational AI, radiomics, and clinical features were evaluated using univariate cox regression and correlational analyses to determine independent predictors of survival. Several models were fit using these predictors and model performance was evaluated using nested cross-validation and unseen independent test datasets via area under receiver-operator-characteristic curves, AUCs. For all patients, the combined foundational AI and clinical models achieved AUCs of 0.67 for the Random Forest (RF) model. The combined radiomics and clinical models achieved RF AUCs of 0.66. In the low-dose arm, foundational AI alone achieved AUC of 0.67, while AUC for the ensemble radiomics and clinical models was 0.65 for the support vector machine (SVM). In the high-dose arm, AUC values were 0.67 for combined radiomics and clinical models and 0.66 for the foundational AI model. This study demonstrated encouraging results for application of foundational AI and radiomics models for prediction of outcomes. More research is warranted to understand the value of ensemble models toward improving performance via complementary information. Using foundational AI and radiomics-based models we were able to identify significant signatures of outcomes for NSCLC patients retrospectively treated on a national cooperative group clinical trial. Associated models will be important for application toward prospective patients.

Stack-AVP: A Stacked Ensemble Predictor Based on Multi-view Information for Fast and Accurate Discovery of Antiviral Peptides

AVPs, or antiviral peptides, are short chains of amino acids capable of inhibiting viral replication, preventing viral entry, or disrupting viral membranes. They represent a promising area of research for developing new antiviral therapies due to their potential to target a broad spectrum of viruses, incorporating those resistant to traditional antiviral drugs. However, traditional experimental methods for identifying AVPs are often costly and labour-intensive. Thus far, multiple computational methods have been introduced for the in silico identification of AVPs, but these methods still have certain shortcomings. In this study, we propose a novel stacked ensemble learning framework, termed Stack-AVP, for fast and accurate AVP identification. In Stack-AVP, we investigated heterogeneous prediction models, which were trained with 12 commonly used machine learning algorithms coupled with a wide range of multiple feature encoding schemes. Subsequently, these prediction models were adopted to generate multi-view features providing class information and probability information. Finally, we applied our feature selection method to determine the best feature subset for the construction of the final stacked model. Comparative assessments on the independent test dataset revealed that Stack-AVP surpassed the performance of current state-of-the-art methods, with an accuracy of 0.930, MCC of 0.860, and AUC of 0.975. Furthermore, it was found that our multi-view features exhibited a crucial mechanism to improve the prediction performance of AVPs. To facilitate experimental scientists in performing high-throughput identification of AVPs, the prediction sever Stack-AVP is publicly accessible at https://pmlabqsar.pythonanywhere.com/Stack-AVP.

Rhythm classifier: artificial intelligence for rhythm classification in insertable cardiac monitor

Abstract Background Though detections improved significantly, separating atrial tachycardia/atrial flutter (AT/AFL) from atrial fibrillations (AF) in insertable cardiac monitors (ICM) remains a challenge. Objective Using artificial intelligence (AI) algorithms to classify AF and AT/AFL in ICM detected episodes, which may reduce episode review burden. Methods Both raw EGM signal and the QRS diminished version of the raw signal were used to extract 14 AF and AT/AFL features from each episode. Extracted features were then represented as an ensemble of features and used to train and test the AI model. Modified ResNet18 network was used as the AI model. All episodes from a random selection of 80% of patients were used as training dataset, another 10% were used as validation, and 10% were used as test dataset, to evaluate model performance. AI model probability threshold was chosen based on validation set results. Episode detection sensitivity, specificity, and area under the curve (AUC) of receiver operating characteristics (ROC) curve in the independent test dataset are reported. Results AF and AT/AFL episodes detected in 918 LINQ ICM patients (5,253 AF and 4,705 AT/AFL – 745 pts and 8,950 false detection episodes) were included. Training dataset consisted of 15,183 episodes (735 pts), validation set consisted of 1,901 episodes (91 pts), and test set consisted of 1,824 episodes (92 pts). At chosen threshold in validation set, AF and AT/AFL detection had sensitivity of 90% and 73.3%, respectively, and specificity of 93.2% and 95%, respectively, with AUC of 0.966. In test data, AF and AT/AFL obtained relative sensitivity of 84.7% and 85.7%, respectively, with specificity of 88% and 86.5%, respectively (Fig. A). With ROC-AUC of 0.956 (Fig. B), the relative diagnostic yield of AF and AT/AFL on test data was 95.6%. Conclusion The trained AI model provides a relative sensitivity of about 85% for AF vs. AT/AFL classification and reduces inappropriate ICM detections by 79%. Adding more episodes may improve the performance.

Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model.

O-linked glycosylation, an essential post-translational modification process in Homo sapiens, involves attaching sugar moieties to the oxygen atoms of serine and/or threonine residues. It influences various biological and cellular functions. While threonine or serine residues within protein sequences are potential sites for O-linked glycosylation, not all serine and/or threonine residues undergo this modification, underscoring the importance of characterizing its occurrence. This study presents a novel approach for predicting intracellular and extracellular O-linked glycosylation events on proteins, which are crucial for comprehending cellular processes. Two base multi-layer perceptron models were trained by leveraging a stacked generalization framework. These base models respectively use ProtT5 and Ankh O-linked glycosylation site-specific embeddings whose combined predictions are used to train the meta-multi-layer perceptron model. Trained on extensive O-linked glycosylation datasets, the stacked-generalization model demonstrated high predictive performance on independent test datasets. Furthermore, the study emphasizes the distinction between nucleocytoplasmic and extracellular O-linked glycosylation, offering insights into their functional implications that were overlooked in previous studies. By integrating the protein language model's embedding with stacked generalization techniques, this approach enhances predictive accuracy of O-linked glycosylation events and illuminates the intricate roles of O-linked glycosylation in proteomics, potentially accelerating the discovery of novel glycosylation sites. Stack-OglyPred-PLM produces Sensitivity, Specificity, Matthews Correlation Coefficient, and Accuracy of 90.50%, 89.60%, 0.464, and 89.70%, respectively on a benchmark NetOGlyc-4.0 independent test dataset. These results demonstrate that Stack-OglyPred-PLM is a robust computational tool to predict O-linked glycosylation sites in proteins. The developed tool, programs, training, and test dataset are available at https://github.com/PakhrinLab/Stack-OglyPred-PLM.

Precipitation Retrieval from FY-3G/MWRI-RM Based on SMOTE-LGBM

Using the FY-3G/MWRI-RM observations, this paper proposes a precipitation retrieval method that combines the Synthetic Minority Over-sampling Technique with Light Gradient Boosting Machine (SMOTE-LGBM) and analyzes the impact of MWRI-RM channel settings on precipitation retrieval. The SMOTE-LGBM-based model consists of two LGBM models for precipitation identification and estimation, respectively. The SMOTE method is used to address the imbalance between precipitation and non-precipitation samples. Using the Integrated Multi-Satellite Retrievals for the Global Precipitation Measurement (IMERG) product as a reference, we validate the retrieved precipitation by the SMOTE-LGBM-based model with an independent testing dataset. The critical success indexes are 0.483 and 0.526, and the Pearson correlation coefficients are 0.611 and 0.645 for the ocean and land regions, respectively. The spatial distributions of the retrieved and IMERG accumulated precipitation in the testing dataset are similar. In addition, we visualize and analyze the cases of Meiyu and two typhoons. The results indicate that the SMOTE-LGBM-based model effectively represents the spatial distribution characteristics of precipitation and achieves high agreement with IMERG precipitation products. Overall, the SMOTE-LGBM-based model successfully retrieves precipitation from MWRI-RM and provides accurate precipitation products for FY-3G/MWRI-RM for the first time.

MetaCGRP is a high-precision meta-model for large-scale identification of CGRP inhibitors using multi-view information

Migraine is considered one of the debilitating primary headache conditions with an estimated worldwide occurrence of approximately 14–15%, contributing highly to factors responsible for global disability. Calcitonin gene-related peptide (CGRP) is a neuropeptide that plays a crucial role in the pathophysiology of migraines and thus, its inhibition can help relieve migraine symptoms. However, conventional process of CGRP drug development has been laborious and time-consuming with incurred costs exceeding one billion dollars. On the other hand, machine learning (ML)-based approaches that are capable of accurately identifying CGRP inhibitors could greatly facilitate in expediting the discovery of novel CGRP drugs. Therefore, this study proposes a novel and high-accuracy meta-model, namely MetaCGRP, that can precisely identify CGRP inhibitors. To the best of our knowledge, MetaCGRP is the first SMILES-based approach that has been developed to identify CGRP inhibitors without the use of 3D structural information. In brief, we initially employed different molecular representation methods coupled with popular ML algorithms to construct a pool of baseline models. Then, all baseline models were optimized and used to generate multi-view features. Finally, we employed the feature selection method to optimize the multi-view features and determine the best feature subset to enable the construction of the meta-model. Both cross-validation and independent tests indicated that MetaCGRP clearly outperforms several conventional ML classifiers, with accuracies of 0.898 and 0.799 on the training and independent test datasets, respectively. In addition, MetaCGRP in conjunction with molecular docking was utilized to identify five potential natural product candidates from Thai herbal pharmacopoeia and analyze their binding affinity and interactions to CGRP. To facilitate community-wide efforts in expediting the discovery of novel CGRP inhibitors, a user-friendly web server for MetaCGRP is freely available at https://pmlabqsar.pythonanywhere.com/MetaCGRP.

MMG4: Recognition of G4-Forming Sequences Based on Markov Model.

G-quadruplexes (G4s) are special nucleic acid structures with various important biological functions. Existing tools and technologies for G4-forming sequences recognition are limited to time-consuming and costly methods such as circular dichroism and nuclear magnetic resonance. Developing a fast and accurate model for G4-forming sequences recognition has far-reaching significance. In this study, MMG4, a novel model to recognize G4-forming sequences based on Markov model (MM), was developed and the phenomenon of high recognition accuracy in the central region of the sequence and low accuracy in the two end regions was discovered. It was further found that the differences in base transfer probabilities, ratio distribution, and G4-motif structural content in different regions may be the causes of this phenomenon. The study also explored the impact of sequence length on recognition accuracy and found the optimal recognition interval to be [910-1049], with the highest recognition accuracy reaching 85.95%. By extracting sequence features, the study constructed three types of machine learning models: random forest (RF), support vector machine, and back-propagation neural network. It was found that recognition performance of MM was significantly better than that of the other three machine learning models, proving that the recognition method based on MM can effectively capture the correlation information between adjacent nucleotides of G4. By combining MM with the three machine learning models, the predictive performance of MMG4 improved. Among them, the RF model combined with MM has the best performance, achieving an area under the receiver operating characteristic curve value of 0.93 and an area under the precision-recall curve value of 0.9. Finally, the study validated the model robustness and generalization ability through independent testing dataset.

Tree-based classification model for Long-COVID infection prediction with age stratification using data from the National COVID Cohort Collaborative.

We propose and validate a domain knowledge-driven classification model for diagnosing post-acute sequelae of SARS-CoV-2 infection (PASC), also known as Long COVID, using Electronic Health Records (EHRs) data. We developed a robust model that incorporates features strongly indicative of PASC or associated with the severity of COVID-19 symptoms as identified in our literature review. The XGBoost tree-based architecture was chosen for its ability to handle class-imbalanced data and its potential for high interpretability. Using the training data provided by the Long COVID Computation Challenge (L3C), which was a sample of the National COVID Cohort Collaborative (N3C), our models were fine-tuned and calibrated to optimize Area Under the Receiver Operating characteristic curve (AUROC) and the F1 score, following best practices for the class-imbalanced N3C data. Our age-stratified classification model demonstrated strong performance with an average 5-fold cross-validated AUROC of 0.844 and F1 score of 0.539 across the young adult, mid-aged, and older-aged populations in the training data. In an independent testing dataset, which was made available after the challenge was over, we achieved an overall AUROC score of 0.814 and F1 score of 0.545. The results demonstrated the utility of knowledge-driven feature engineering in a sparse EHR data and demographic stratification in model development to diagnose a complex and heterogeneously presenting condition like PASC. The model's architecture, mirroring natural clinician decision-making processes, contributed to its robustness and interpretability, which are crucial for clinical translatability. Further, the model's generalizability was evaluated over a new cross-sectional data as provided in the later stages of the L3C challenge. The study proposed and validated the effectiveness of age-stratified, tree-based classification models to diagnose PASC. Our approach highlights the potential of machine learning in addressing the diagnostic challenges posed by the heterogeneity of Long-COVID symptoms.

CoNglyPred: Accurate Prediction of N-Linked Glycosylation Sites Using ESM-2 and Structural Features With Graph Network and Co-Attention.

N-Linked glycosylation is crucial for various biological processes such as protein folding, immune response, and cellular transport. Traditional experimental methods for determining N-linked glycosylation sites entail substantial time and labor investment, which has led to the development of computational approaches as a more efficient alternative. However, due to the limited availability of 3D structural data, existing prediction methods often struggle to fully utilize structural information and fall short in integrating sequence and structural information effectively. Motivated by the progress of protein pretrained language models (pLMs) and the breakthrough in protein structure prediction, we introduced a high-accuracy model called CoNglyPred. Having compared various pLMs, we opt for the large-scale pLM ESM-2 to extract sequence embeddings, thus mitigating certain limitations associated with manual feature extraction. Meanwhile, our approach employs a graph transformer network to process the 3D protein structures predicted by AlphaFold2. The final graph output and ESM-2 embedding are intricately integrated through a co-attention mechanism. Among a series of comprehensive experiments on the independent test dataset, CoNglyPred outperforms state-of-the-art models and demonstrates exceptional performance in case study. In addition, we are the first to report the uncertainty of N-linked glycosylation predictors using expected calibration error and expected uncertainty calibration error.

IACP-DFSRA: Identification of Anticancer Peptides Based on a Dual-channel Fusion Strategy of ResCNN and Attention

Anticancer peptides (ACPs) have been widely applied in the treatment of cancer owing to good safety, rational side effects, and high selectivity. However, the number of ACPs that have been experimentally validated is limited as identification of ACPs is extremely expensive. Hence, accurate and cost-effective identification methods for ACPs are urgently needed. In this work, we proposed a deep learning-based model, named iACP-DFSRA, for ACPs identification. Specifically, we adopted two kinds of sequence embedding technologies, ProtBert_BFD pre-training language model and handcrafted features to encode protein sequences. Then, the LightGBM was used for feature selection, and the selected features were input into ResCNN and Attention mechanism, respectively, to extract local and global features. Finally, the concatenate features were deeply fused by using the Attention mechanism to allow key features to be paid more attention to by the model and make predictions by fully connected layer. The results of 10-fold cross-validation demonstrated that the iACP-DFSRA model delivered improved results in most metrics with Sp of 94.15%, Sn of 95.32%, Acc of 94.74% and MCC of 89.48% compared to the latest AACFlow model. Indeed, the iACP-DFSRA model is the only model with Acc > 90% and MCC > 80% on this independent test dataset. Furthermore, we have further demonstrated the superiority of our model on additional datasets. In addition, t-SNE and SHAP interpretation analysis demonstrated that it is crucial to use two channels for feature extraction and use the Attention mechanism for deep fusion, which helps the iACP-DFSRA to predict ACPs more effectively.

Muscle Fat and Volume Differences in People With Hip-Related Pain Compared With Controls: A Machine Learning Approach.

Hip-related pain (HRP) affects young to middle-aged active adults and impacts physical activity, finances and quality of life. HRP includes conditions like femoroacetabular impingement syndrome and labral tears. Lateral hip muscle dysfunction and atrophy in HRP are more pronounced in advanced hip pathology, with limited evidence in younger populations. While MRI use for assessing hip muscle morphology is increasing, with automated deep-learning techniques showing promise, studies assessing their accuracy are limited. Therefore, we aimed to compare hip intramuscular fat infiltrate (MFI) and muscle volume, in individuals with and without HRP as well as assess the reliability and accuracy of automated machine-learning segmentations compared with human-generated segmentation. This cross-sectional study included sub-elite/amateur football players (Australian football and soccer) with a greater than 6-month history of HRP [n = 180, average age 28.32, (standard deviation 5.88) years, 19% female] and a control group of sub-elite/amateur football players without pain [n = 48, 28.89 (6.22) years, 29% female]. Muscle volume and MFI of gluteus maximus, medius, minimis and tensor fascia latae were assessed using MRI. Associations between muscle volume and group were explored using linear regression models, controlling for body mass index, age, sport and sex. A convolutional neural network (CNN) machine-learning approach was compared with human-performed muscle segmentations in a subset of participants (n = 52) using intraclass correlation coefficients and Sorensen-Dice index. When considering adjusted estimates of muscle volume, there were significant differences observed between groups for gluteus medius (adjusted mean difference 23 858 mm3 [95% confidence interval 7563, 40 137]; p = 0.004) and tensor fascia latae (6660 mm3 [2440, 13 075]; p = 0.042). No differences were observed between groups for gluteus maximus (18 265 mm3 [-21 209, 50 782]; p = 0.419) or minimus (3893 mm3 [-2209, 9996]; p = 0.21). The CNN was trained for 30 000 iterations and assessed its accuracy and reliability on an independent testing dataset, achieving high segmentation accuracy (mean Sorenson-Dice index >0.900) and excellent muscle volume and MFI reliability (ICC2,1 > 0.900). The CNN outperformed manual raters, who had slightly lower interrater accuracy (Sorensen-Dice index >0.800) and reliability (ICC2,1 > 0.800). The increased muscle volumes in the symptomatic group compared with controls could be associated with increased myofibrillar size, sarcoplasmic hypertrophy or both. These changes may facilitate greater muscular efficiency for a given load, enabling the athlete to maintain their normal level of function. In addition, the CNNs for muscle segmentation was more efficient and demonstrated excellent reliability in comparison to manual segmentations.

Using AI explainable models and handwriting/drawing tasks for psychological well-being

This study addresses the increasing threat to Psychological Well-Being (PWB) posed by Depression, Anxiety, and Stress conditions. Machine learning methods have shown promising results for several psychological conditions. However, the lack of transparency in existing models impedes practical application. The study aims to develop explainable machine learning models for depression, anxiety and stress prediction, focusing on features extracted from tasks involving handwriting and drawing.Two hundred patients completed the Depression, Anxiety, and Stress Scale (DASS-21) and performed seven tasks related to handwriting and drawing. Extracted features, encompassing pressure, stroke pattern, time, space, and pen inclination, were used to train the explainable-by-design Entropy-based Logic Explained Network (e-LEN) model, employing first-order logic rules for explanation. Performance comparison was performed with XGBoost, enhanced by the SHAP explanation method.The trained models achieved notable accuracy in predicting depression (0.749 ±0.089), anxiety (0.721 ±0.088), and stress (0.761 ±0.086) through 10-fold cross-validation (repeated 20 times). The e-LEN model’s logic rules facilitated clinical validation, uncovering correlations with existing clinical literature. While performance remained consistent for depression and anxiety on an independent test dataset, a slight degradation was observed for stress prediction in the test task.

Enhanced prognostic signature for lung adenocarcinoma through integration of adjacent normal and tumor gene expressions

BackgroundCancer prognosis-related signatures have traditionally been constructed based on gene expression profiles derived from tumor or normal tissues. However, the potential benefits of incorporating gene expression profiles from both tumor and normal tissues to improve signature performance have not been explored. MethodsIn this study, we developed three prognostic models for lung adenocarcinoma (LUAD) using gene expression profiles from tumor tissues, normal tissues, and a combination (COM) of both, sourced from The Cancer Genome Atlas (TCGA). To ensure comparability, the same workflow was followed for all three models. ResultsWhen applied to the TCGA LUAD dataset, the tumor-derived model exhibited the best overall performance, except in calibration analysis, where the normal-derived model performed better. The COM-derived model demonstrated intermediate performance. Validation on three independent test datasets revealed that the COM-derived model showed the best performance, while the normal-derived model showed the worst. In overall survival (OS) analysis, the low-risk group defined by the COM-derived model consistently exhibited longer mean survival times. The tumor-derived model did not consistently show this trend, and the normal-derived model produced opposite results. In discrimination analysis, no significant differences were observed. The COM-derived model demonstrated good discrimination ability for short periods, while the tumor-derived model performed better for longer periods. In calibration analysis, both the COM and tumor-derived models had similar absolute prediction errors, which were better than those of the normal-derived model. However, the tumor-derived model tended to underestimate survival rates. The clinical feature analysis and validation in GSE229705 indicate that the risk score (RS) from the COM model is the most clinically significant. These results demonstrate that the COM model's RS aligns more closely with clinical data, maintaining stable performance and the strongest generalizability. ConclusionsOverall, the COM-derived model demonstrated the best generalization ability. The superior performance of the tumor-derived model in the TCGA LUAD dataset might be due to overfitting. Our results suggest that appropriate combinations of gene expression data from tumor and normal tissues can enhance the predictive power of prognostic signatures.

Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial Peptides.

In recent years, the prediction of antimicrobial peptides (AMPs) has gained prominence due to their high antibacterial activity and reduced susceptibility to drug resistance, making them potential antibiotic substitutes. To advance the field of AMP recognition, an increasing number of natural language processing methods are being applied. These methods exhibit diversity in terms of pretraining models, pretraining data sets, word vector embeddings, feature encoding methods, and downstream classification models. Here, we provide a comprehensive survey of current BERT-based methods for AMP prediction. An independent benchmark test data set is constructed to evaluate the predictive capabilities of the surveyed tools. Furthermore, we compared the predictive performance of these computational methods based on six different AMP public databases. LM_pred (BFD) outperformed all other surveyed tools due to abundant pretraining data set and the unique vector embedding approach. To avoid the impact of varying training data sets used by different methods on prediction performance, we performed the 5-fold cross-validation experiments using the same data set, involving retraining. Additionally, to explore the applicability and generalization ability of the models, we constructed a short peptide data set and an external data set to test the retrained models. Although these prediction methods based on BERT can achieve good prediction performance, there is still room for improvement in recognition accuracy. With the continuous enhancement of protein language model, we proposed an AMP prediction method based on the ESM-2 pretrained model called iAMP-bert. Experimental results demonstrate that iAMP-bert outperforms other approaches. iAMP-bert is freely accessible to the public at http://iamp.aielab.cc/.