Test Set Research Articles

Uninvolved liver dose prediction in stereotactic body radiation therapy for liver cancer based on the neural network method

BACKGROUND The quality of a radiotherapy plan often depends on the knowledge and expertise of the plan designers. AIM To predict the uninvolved liver dose in stereotactic body radiotherapy (SBRT) for liver cancer using a neural network-based method. METHODS A total of 114 SBRT plans for liver cancer were used to test the neural network method. Sub-organs of the uninvolved liver were automatically generated. Correlations between the volume of each sub-organ, uninvolved liver dose, and neural network prediction model were established using MATLAB. Of the cases, 70% were selected as the training set, 15% as the validation set, and 15% as the test set. The regression R -value and mean square error (MSE) were used to evaluate the model. RESULTS The volume of the uninvolved liver was related to the volume of the corresponding sub-organs. For all sets of R -values of the prediction model, except for Dn0 which was 0.7513, all R -values of Dn10-Dn100 and Dnmean were > 0.8. The MSE of the prediction model was also low. CONCLUSION We developed a neural network-based method to predict the uninvolved liver dose in SBRT for liver cancer. It is simple and easy to use and warrants further promotion and application.

Deep learning of echocardiography distinguishes between presence and absence of late gadolinium enhancement on cardiac magnetic resonance in patients with hypertrophic cardiomyopathy

BackgroundHypertrophic cardiomyopathy (HCM) can cause myocardial fibrosis, which can be a substrate for fatal ventricular arrhythmias and subsequent sudden cardiac death. Although late gadolinium enhancement (LGE) on cardiac magnetic resonance (CMR) represents myocardial fibrosis and is associated with sudden cardiac death in patients with HCM, CMR is resource-intensive, can carry an economic burden, and is sometimes contraindicated. In this study for patients with HCM, we aimed to distinguish between patients with positive and negative LGE on CMR using deep learning of echocardiographic images.MethodsIn the cross-sectional study of patients with HCM, we enrolled patients who underwent both echocardiography and CMR. The outcome was positive LGE on CMR. Among the 323 samples, we randomly selected 273 samples (training set) and employed deep convolutional neural network (DCNN) of echocardiographic 5-chamber view to discriminate positive LGE on CMR. We also developed a reference model using clinical parameters with significant differences between patients with positive and negative LGE. In the remaining 50 samples (test set), we compared the area under the receiver-operating-characteristic curve (AUC) between a combined model using the reference model plus the DCNN-derived probability and the reference model.ResultsAmong the 323 CMR studies, positive LGE was detected in 160 (50%). The reference model was constructed using the following 7 clinical parameters: family history of HCM, maximum left ventricular (LV) wall thickness, LV end-diastolic diameter, LV end-systolic volume, LV ejection fraction < 50%, left atrial diameter, and LV outflow tract pressure gradient at rest. The discriminant model combining the reference model with DCNN-derived probability significantly outperformed the reference model in the test set (AUC 0.86 [95% confidence interval 0.76–0.96] vs. 0.72 [0.57–0.86], P = 0.04). The sensitivity, specificity, positive predictive value, and negative predictive value of the combined model were 0.84, 0.76, 0.78, and 0.83, respectively.ConclusionCompared to the reference model solely based on clinical parameters, our new model integrating the reference model and deep learning-based analysis of echocardiographic images demonstrated superiority in distinguishing LGE on CMR in patients with HCM. The novel deep learning-based method can be used as an assistive technology to facilitate the decision-making process of performing CMR with gadolinium enhancement.

A natural language processing approach to detect inconsistencies in death investigation notes attributing suicide circumstances

BackgroundData accuracy is essential for scientific research and policy development. The National Violent Death Reporting System (NVDRS) data is widely used for discovering the patterns and causing factors of death. Recent studies suggested the annotation inconsistencies within the NVDRS and the potential impact on erroneous suicide-circumstance attributions.MethodsWe present an empirical Natural Language Processing (NLP) approach to detect annotation inconsistencies and adopt a cross-validation-like paradigm to identify possible label errors. We analyzed 267,804 suicide death incidents between 2003 and 2020 from the NVDRS. We measured annotation inconsistency by the degree of changes in the F-1 score.ResultsOur results show that incorporating the target state’s data into training the suicide-circumstance classifier brings an increase of 5.4% to the F-1 score on the target state’s test set and a decrease of 1.1% on other states’ test set.ConclusionsTo conclude, we present an NLP framework to detect the annotation inconsistencies, show the effectiveness of identifying and rectifying possible label errors, and eventually propose an improvement solution to improve the coding consistency of human annotators.

Building a pelvic organ prolapse diagnostic model using vision transformer on multi-sequence MRI.

Although the uterus, bladder, and rectum are distinct organs, their muscular fasciae are often interconnected. Clinical experience suggests that they may share common risk factors and associations. When one organ experiences prolapse, it can potentially affect the neighboring organs. However, the current assessment of disease severity still relies on manual measurements, which can yield varying results depending on the physician, thereby leading to diagnostic inaccuracies. This study aims to develop a multilabel grading model based on deep learning to classify the degree of prolapse of three organs in the female pelvis using stress magnetic resonance imaging (MRI) and provide interpretable result analysis. We utilized sagittal MRI sequences taken at rest and during maximum Valsalva maneuver from 662 subjects. The training set included 464 subjects, the validation set included 98 subjects, and the test set included 100 subjects (training set n=464, validation set n=98, test set n=100). We designed a feature extraction module specifically for pelvic floor MRI using the vision transformer architecture and employed label masking training strategy and pre-training methods to enhance model convergence. The grading results were evaluated using Precision, Kappa, Recall, and Area Under the Curve (AUC). To validate the effectiveness of the model, the designed model was compared with classic grading methods. Finally, we provided interpretability charts illustrating the model's operational principles on the grading task. In terms of POP grading detection, the model achieved an average Precision, Kappa coefficient, Recall, and AUC of 0.86, 0.77, 0.76, and 0.86, respectively. Compared to existing studies, our model achieved the highest performance metrics. The average time taken to diagnose a patient was 0.38s. The proposed model achieved detection accuracy that is comparable to or even exceeds that of physicians, demonstrating the effectiveness of the vision transformer architecture and label masking training strategy for assisting in the grading of POP under static and maximum Valsalva conditions. This offers a promising option for computer-aided diagnosis and treatment planning of POP.

ERTH scheduler: enhanced red-tailed hawk algorithm for multi-cost optimization in cloud task scheduling

Effective task scheduling has become the key to optimizing resource allocation, reducing operation costs, and enhancing the user experience. The complexity and dynamics of cloud computing environments require task scheduling algorithms that can flexibly respond to multiple computing demands and changing resource states. Therefore, we propose an enhanced Red-tailed Hawk algorithm (named ERTH) based on multiple elite policies and chaotic mapping, while applying this approach in conjunction with the proposed scheduling model to optimize the efficiency of task scheduling in cloud computing environments. We apply the ERTH algorithm to a real cloud computing environment and conduct a comparison with the original RTH and other conventional algorithms. The proposed ERTH algorithm has better convergence speed and stability in most cases of small and large-scale tasks and performs better in minimizing the task completion time and system load cost. Specifically, our experiments show that the ERTH algorithm reduces the total system cost by 34.8% and 36.4% relative to the traditional algorithm for tasks of different sizes. Further, evaluations in the IEEE Congress on Evolutionary Computation (CEC) benchmark test sets show that the ERTH algorithm outperforms the traditional or emerging algorithms in several performance metrics such as mean, standard deviation, etc. The proposal and validation of the ERTH algorithm are of great significance in promoting the application of intelligent optimization algorithms in cloud computing.

Machine learning model base on metabolomics and proteomics to predict cognitive impairment in Parkinson’s disease

There is an urgent need to identify predictive biomarkers of Parkinson’s disease (PD) with cognitive impairment (PDCI) in order to individualize patient management, ensure timely intervention, and improve prognosis. The aim of this study was to screen for these biomarkers by comparing the plasma proteome and metabolome of PD patients with or without cognitive impairment. Proteomics and metabolomics analyses were performed on a discover cohort. A machine learning model was used to identify candidate protein and metabolite biomarkers of PDCI, which were validated in an independent cohort. The predictive ability of these biomarkers for PDCI was evaluated by plotting receiver operating characteristic curves and calculating the area under the curve (AUC). Moreover, we assessed the predictive ability of these proteins in combination with neuroimaging. In the discover cohort (n = 100), we identified 25 protein features with best results in the machine learning model, including top-ranked PSAP and H3C15. The two-proteins were used for model construction, achieving an Area under the curve (AUC) of 0.951 in the train set and AUC of 0.981 in the test set. Similarly, the model gives a rank list of endogenous metabolite features, Glycocholic Acid and 6-Methylnicotinamide were two top features. Combining these two markers further got the AUC of 0.969 in train set and 0.867 in the test set. To validate the performance of the protein biomarkers, we performed targeted analysis of selected proteins (H3C15 and PSAP) and proteins likely associated with PDCI (NCAM2 and LAMB2) using parallel reaction monitoring in validation cohort (n = 116). The AUC of the classifier built with H3C15 and PSAP is 0.813. Moreover, when combining H3C15, PSAP, NCAM2, and LAMB2, the model achieved AUC of 0.983 in the train set, AUC of 0.981 in the test set, and AUC of 0.839 in the validation set. Furthermore, we verified that these protein markers we discovered can improve the predictive effect of neuroimaging on PDCI: the classifier built with neuroimaging features had AUC of 0.833, which improved to 0.905 when combined with H3C15. Taken together, our integrated proteomics and metabolomics analysis successfully identified potential biomarkers for PDCI. Additionally, H3C15 showed promise in enhancing the predictive performance of neuroimaging for cognitive impairment.

Habitat-based CT radiomics enhances the ability to predict spread through air spaces in stage T1 invasive lung adenocarcinoma

IntroductionSpread through air spaces (STAS) represents a novel invasive pattern in lung adenocarcinoma (LUAD) and is a risk factor for poor prognosis in stage T1 LUAD. This study aims to develop and validate a CT habitat imaging analysis model for predicting STAS in stage T1 invasive LUAD.MethodsWe retrospectively analyzed 217 patients with preoperative stage T1 invasive LUAD (115 STAS-positive and 102 STAS-negative cases, including 151 in the train set and 66 in the test set). Semi-automatic segmentation was performed on the regions of interest (ROIs) in all CT images, with an automatic 3mm expansion around the tumor, considering the intratumoral and peritumoral 3mm area. This area was divided into three sub-regions via K-means clustering, and 1197 radiomic features were extracted from each sub-region and the overall combined region. After dimension reduction through the Mann-Whitney U test, Pearson correlation analysis, and least absolute shrinkage and selection operator(LASSO), the best features for each sub-region and overall were selected. Models were then built using the selected radiomic features through the Adaptive Boosting (AdaBoost) and Multilayer Perceptron (MLP) classifiers. Four different models were established based on different sub-regions and the overall features. The performance of these models was evaluated through receiver operating characteristic curves (AUC) under the DeLong test, calibration curves via the Hosmer-Lemeshow test, and decision curve analysis to assess the performance of these features.ResultsIn this study, we evaluated the predictive performance of AdaBoost and MLP classifiers on rad feature models across various subregions and the overall dataset. In the test set, the AdaBoost classifier achieved a maximum AUC of 0.871 in Habitat 3, whereas the MLP classifier demonstrated slightly superior performance with an AUC of 0.879. Both classifiers exhibited high efficiency in habitat 3, with the MLP algorithm showing enhanced model performance.ConclusionsCT habitat imaging analysis for the preoperative prediction of STAS in stage T1 invasive LUAD shows satisfactory diagnostic performance, with the habitat3 model exhibiting the highest efficacy, reflecting tumor heterogeneity.

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences

Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation without sequence guidance often suffers from errors caused by cross-chain interaction or noise densities, which would accumulate and mislead the subsequent steps. Here, we present EModelX, a fully automated cryo-EM protein complex structure modeling method, which achieves sequence-guiding modeling through cross-modal alignments between cryo-EM maps and protein sequences. EModelX first employs multi-task deep learning to predict Cα atoms, backbone atoms, and amino acid types from cryo-EM maps, which is subsequently used to sample Cα traces with amino acid profiles. The profiles are then aligned with protein sequences to obtain initial structural models, which yielded an average RMSD of 1.17 Å in our test set, approaching atomic-level precision in recovering PDB-deposited structures. After filling unmodeled gaps through sequence-guiding Cα threading, the final models achieved an average TM-score of 0.808, outperforming the state-of-the-art method. The further combination with AlphaFold can improve the average TM-score to 0.911. Analyzes conducted by comparing some EModelX-built models and PDB structures highlight its potential to improve PDB structures. EModelX is accessible at https://bio-web1.nscc-gz.cn/app/EModelX.

Deciphering Cathepsin K inhibitors: a combined QSAR, docking and MD simulation based machine learning approaches for drug design

ABSTRACT Cathepsin K (CatK), a lysosomal cysteine protease, contributes to skeletal abnormalities, heart diseases, lung inflammation, and central nervous system and immune disorders. Currently, CatK inhibitors are associated with severe adverse effects, therefore limiting their clinical utility. This study focuses on exploring quantitative structure–activity relationships (QSAR) on a dataset of CatK inhibitors (1804) compiled from the ChEMBL database to predict the inhibitory activities. After data cleaning and pre-processing, a total of 1568 structures were selected for exploratory data analysis which revealed physicochemical properties, distributions and statistical significance between the two groups of inhibitors. PubChem fingerprinting with 11 different machine-learning classification models was computed. The comparative analysis showed the ET model performed well with accuracy values for the training set (0.999), cross-validation (0.970) and test set (0.977) in line with OECD guidelines. Moreover, to gain structural insights on the origin of CatK inhibition, 15 diverse molecules were selected for molecular docking. The CatK inhibitors (1 and 2) exhibited strong binding energies of −8.3 and −7.2 kcal/mol, respectively. MD simulation (300 ns) showed strong structural stability, flexibility and interactions in selected complexes. This synergy between QSAR, docking, MD simulation and machine learning models strengthen our evidence for developing novel and resilient CatK inhibitors.

An archive-assisted multi-modal multi-objective evolutionary algorithm

The multi-modal multi-objective optimization problems (MMOPs) pertain to characteristic of the decision space that exhibit multiple sets of Pareto optimal solutions that are either identical or similar. The resolution of these problems necessitates the utilization of optimization algorithms to locate multiple Pareto sets (PSs). However, existing multi-modal multi-objective evolutionary algorithms (MMOEAs) encounter difficulties in concurrently enhancing solution quality in both decision space and objective space. In order to deal with this predicament, this paper presents an Archive-assisted Multi-modal Multi-objective Evolutionary Algorithm, called A-MMOEA. This algorithm maintains a main population and an external archive, which is leveraged to improve the fault tolerance of individual screening. To augment the quality of solutions in the archive, an archive evolution mechanism (AEM) is formulated for updating the archive and an archive output mechanism (AOM) is used to output the final solutions. Both mechanisms incorporate a comprehensive crowding distance metric that employs objective space crowding distance to facilitate the calculation of decision space crowding distance. Besides, a data screening method is employed in the AOM to alleviate the negative impact on the final results arising from undesirable individuals resulting from diversity search. Finally, in order to enable individuals to effectively escape the limitation of niches and further enhance diversity of population, a diversity search method with level-based evolution mechanism (DSMLBEM) is proposed. The proposed algorithm’s performance is evaluated through extensive experiments conducted on two distinct test sets. Final results indicate that, in comparison to other commonly used algorithms, this approach exhibits favorable performance.

Modeling Many-Body Interactions in Water with Gaussian Process Regression.

We report a first-principles water dimer potential that captures many-body interactions through Gaussian process regression (GPR). Modeling is upgraded from previous work by using a custom kernel function implemented through the KeOps library, allowing for much larger GPR models to be constructed and interfaced with the next-generation machine learning force field FFLUX. A new synthetic water dimer data set, called WD24, is used for model training. The resulting models can predict 90% of dimer geometries within chemical accuracy for a test set and in a simulation. The curvature of the potential energy surface is captured by the models, and a successful geometry optimization is completed with a total energy error of just 2.6 kJ mol-1, from a starting structure where water molecules are separated by nearly 4.3 Å. Dimeric modeling of a flexible, noncrystalline system with FFLUX is shown for the first time.

Impact of the Minimization of Standard Deviation Before Zeroization of the Mean Bias on the Performance of IOL Power Formulas.

In cataract surgery, accurate intraocular lens (IOL) power calculations are crucial for optimal postoperative refractive outcomes. This study explores the impact of prioritizing the reduction of the standard deviation (SD) of prediction errors before mean prediction error (PE) adjustment on IOL calculation formula precision and accuracy. We conducted a retrospective analysis of 4885 eyes from 2611 patients, all implanted with the same IOL model, comparing four traditional IOL power calculation formulas: SRK/T, Holladay 1, Haigis, and Hoffer Q. We introduced new constants aiming to minimize the SD of PE (new_const) against traditionally optimized constants (classic_const), using a heteroscedastic statistical method for comparison. Validation of precision improvements used a secondary dataset of 262 eyes from 132 patients. We observed significant reductions in mean absolute error (MAE) across training and test sets for Hoffer Q, Holladay, and Haigis formulas, indicating accuracy enhancements. Optimized constants significantly reduced SDs for Haigis from 0.3255 to 0.3153 and for Hoffer Q from 0.3521 to 0.3387. These optimizations also increased the proportion of eyes achieving PE within ±0.25D. SRK/T showed improved SD from 0.3596 to 0.3585. However, Holladay 1 showed minimal change with no significant improvement. In the test dataset, significant reductions in SD were observed for Haigis and Hoffer Q. Prioritizing SD minimization before adjusting mean PE significantly improves the precision of selected IOL power formulas, enhancing postoperative refractive outcomes. The effectiveness varies among formulas, underscoring the need for formula-specific adjustments. The study presents a novel two-step approach for optimizing IOL power calculations.

Revamping Image-Recipe Cross-Modal Retrieval with Dual Cross Attention Encoders

The image-recipe cross-modal retrieval task, which retrieves the relevant recipes according to food images and vice versa, is now attracting widespread attention. There are two main challenges for image-recipe cross-modal retrieval task. Firstly, a recipe’s different components (words in a sentence, sentences in an entity, and entities in a recipe) have different weight values. If a recipe’s different components own the same weight, the recipe embeddings cannot pay more attention to the important components. As a result, the important components make less contribution to the retrieval task. Secondly, the food images have obvious properties of locality and only the local food regions matter. There are still difficulties in enhancing the discriminative local region features in the food images. To address these two problems, we propose a novel framework named Dual Cross Attention Encoders for Cross-modal Food Retrieval (DCA-Food). The proposed framework consists of a hierarchical cross attention recipe encoder (HCARE) and a cross attention image encoder (CAIE). HCARE consists of three types of cross attention modules to capture the important words in a sentence, the important sentences in an entity and the important entities in a recipe, respectively. CAIE extracts global and local region features. Then, it calculates cross attention between them to enhance the discriminative local features in the food images. We conduct the ablation studies to validate our design choices. Our proposed approach outperforms the existing approaches by a large margin on the Recipe1M dataset. Specifically, we improve the R@1 performance by +2.7 and +1.9 on the 1k and 10k testing sets, respectively.

Using Machine Learning on MRI Radiomics to Diagnose Parotid Tumours Before Comparing Performance with Radiologists: A Pilot Study.

The parotid glands are the largest of the major salivary glands. They can harbour both benign and malignant tumours. Preoperative work-up relies on MR images and fine needle aspiration biopsy, but these diagnostic tools have low sensitivity and specificity, often leading to surgery for diagnostic purposes. The aim of this paper is (1) to develop a machine learning algorithm based on MR images characteristics to automatically classify parotid gland tumours and (2) compare its results with the diagnoses of junior and senior radiologists in order to evaluate its utility in routine practice. While automatic algorithms applied to parotid tumours classification have been developed in the past, we believe that our study is one of the first to leverage four different MRI sequences and propose a comparison with clinicians. In this study, we leverage data coming from a cohort of 134 patients treated for benign or malignant parotid tumours. Using radiomics extracted from the MR images of the gland, we train a random forest and a logistic regression to predict the corresponding histopathological subtypes. On the test set, the best results are given by the random forest: we obtain a 0.720 accuracy, a 0.860 specificity, and a 0.720 sensitivity over all histopathological subtypes, with an average AUC of 0.838. When considering the discrimination between benign and malignant tumours, the algorithm results in a 0.760 accuracy and a 0.769 AUC, both on test set. Moreover, the clinical experiment shows that our model helps to improve diagnostic abilities of junior radiologists as their sensitivity and accuracy raised by 6 % when using our proposed method. This algorithm may be useful for training of physicians. Radiomics with a machine learning algorithm may help improve discrimination between benign and malignant parotid tumours, decreasing the need for diagnostic surgery. Further studies are warranted to validate our algorithm for routine use.

A deep learning model to enhance the classification of primary bone tumors based on incomplete multimodal images in X-ray, CT, and MRI

BackgroundAccurately classifying primary bone tumors is crucial for guiding therapeutic decisions. The National Comprehensive Cancer Network guidelines recommend multimodal images to provide different perspectives for the comprehensive evaluation of primary bone tumors. However, in clinical practice, most patients’ medical multimodal images are often incomplete. This study aimed to build a deep learning model using patients’ incomplete multimodal images from X-ray, CT, and MRI alongside clinical characteristics to classify primary bone tumors as benign, intermediate, or malignant.MethodsIn this retrospective study, a total of 1305 patients with histopathologically confirmed primary bone tumors (internal dataset, n = 1043; external dataset, n = 262) were included from two centers between January 2010 and December 2022. We proposed a Primary Bone Tumor Classification Transformer Network (PBTC-TransNet) fusion model to classify primary bone tumors. Areas under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity were calculated to evaluate the model’s classification performance.ResultsThe PBTC-TransNet fusion model achieved satisfactory micro-average AUCs of 0.847 (95% CI: 0.832, 0.862) and 0.782 (95% CI: 0.749, 0.817) on the internal and external test sets. For the classification of benign, intermediate, and malignant primary bone tumors, the model respectively achieved AUCs of 0.827/0.727, 0.740/0.662, and 0.815/0.745 on the internal/external test sets. Furthermore, across all patient subgroups stratified by the distribution of imaging modalities, the PBTC-TransNet fusion model gained micro-average AUCs ranging from 0.700 to 0.909 and 0.640 to 0.847 on the internal and external test sets, respectively. The model showed the highest micro-average AUC of 0.909, accuracy of 84.3%, micro-average sensitivity of 84.3%, and micro-average specificity of 92.1% in those with only X-rays on the internal test set. On the external test set, the PBTC-TransNet fusion model gained the highest micro-average AUC of 0.847 for patients with X-ray + CT.ConclusionsWe successfully developed and externally validated the transformer-based PBTC-Transnet fusion model for the effective classification of primary bone tumors. This model, rooted in incomplete multimodal images and clinical characteristics, effectively mirrors real-life clinical scenarios, thus enhancing its strong clinical practicability.

Radiomics-based machine learning role in differential diagnosis between small renal oncocytoma and clear cells carcinoma on contrast-enhanced CT: A pilot study

PurposeTo investigate the potential role of radiomics-based machine learning in differentiating small renal oncocytoma (RO) from clear cells carcinoma (ccRCC) on contrast-enhanced CT (CECT). Material and methodsFifty-two patients with small renal masses who underwent CECT before surgery between January 2016 and December 2020 were retrospectively included in the study. At pathology examination 39 ccRCC and 13 RO were identified. All lesions were manually delineated unenhanced (B), arterial (A) and venous (V) phases. Radiomics features were extracted using three different fixed bin widths (bw) of 25 HU, 10 HU, and 5 HU from each phase (B, A, V), and with different combinations (B+A, B+V, B+A+V, A+V), leading to 21 different datasets. Montecarlo Cross Validation technique was used to quantify the estimator performance. The final model built using the hyperparameter selected with Optuna was trained again on the training set and the final performance evaluation was made on the test set. ResultsThe A+V bw 10 achieved the greater median (IQR) balanced accuracy considering all the models of 0.70 (0.64–0.75), while A bw 10 considering only the monophasic ones. The A bw 10 model achieved a median (IQR) sensitivity of 0.60 (0.40–0.60), specificity of 0.80 (0.73–0.87), AUC-ROC of 0.77 (0.66–0.84), accuracy of 0.75 (0.70–0.80), and a Phi Coefficient of 0.38 (0.20–0.47). None of the nine models with the lowest mean balanced accuracy values implemented features from A. ConclusionThe A bw 10 model was identified as the most efficient mono-phasic model in differentiating small RO from ccRCC.

High-dimensional analysis of NK cells in kidney transplantation uncovers subsets associated with antibody-independent graft dysfunction.

Natural Killer (NK) cells respond to diseased and allogeneic cells through NKG2A/HLA-E or Killer-cell Immunoglobulin-like receptor (KIR)/HLA-ABC interactions. Correlations between HLA/KIR disparities and kidney transplant pathology suggest an antibody-independent pathogenic role for NK cells in transplantation, but mechanisms remain unclear. Using CyTOF to characterize recipient peripheral NK cell phenotypes and function, we observed diverse NK cell subsets amongst participants that responded heterogeneously to allo-stimulators. NKG2A+/KIR+ NK cells responded more vigorously than other subsets, and this heightened response persisted post-kidney-transplant despite immunosuppression. In test and validation sets from two clinical trials, pre-transplant donor-induced release of cytotoxicity mediator, Ksp37, by NKG2A+ NK cells correlated with reduced long-term allograft function. Separate analyses showed Ksp37 gene expression in allograft biopsies lacking histological rejection correlated with death censored graft loss. Our findings support an antibody-independent role for NK cells in transplant injury and support further testing of pre-transplant, donor-reactive, NK cell-produced Ksp37 as a risk-assessing, transplantation biomarker.

J-PLUS: Bayesian object classification with a strum of BANNJOS

With its 12 optical filters, the Javalambre-Photometric Local Universe Survey (J-PLUS) provides an unprecedented multicolor view of the local Universe. The third data release (DR3) covers 3,192 deg$^2$ and contains 47.4 million objects. However, the classification algorithms currently implemented in the J-PLUS pipeline are deterministic and based solely on the morphology of the sources. Our goal is to classify the sources identified in the J-PLUS DR3 images as stars, quasi-stellar objects (QSOs), or galaxies. For this task, we present a machine learning pipeline that utilizes Bayesian neural networks to provide the full probability distribution function (PDF) of the classification. has been trained on photometric, astrometric, and morphological data from J-PLUS DR3 DR3, and using over 1.2 million objects with spectroscopic classification from DR18 DR9, the Early Data Release, and DR3. Results were validated on a test set of about $1.4 10^5$ objects and cross-checked against theoretical model predictions. outperforms all previous classifiers in terms of accuracy, precision, and completeness across the entire magnitude range. It delivers over $95&lt;!PCT!&gt;$ accuracy for objects brighter than $r = 21.5$ mag and $ 90&lt;!PCT!&gt;$ accuracy for those up to $r = 22$ mag, where J-PLUS completeness is $ 25&lt;!PCT!&gt;$. is also the first object classifier to provide the full PDF of the classification, enabling precise object selection for high purity or completeness, and for identifying objects with complex features, such as active galactic nuclei with resolved host galaxies. effectively classified J-PLUS sources into around 20 million galaxies, one million QSOs, and 26 million stars, with full PDFs for each, which allow for later refinement of the sample. The upcoming J-PAS survey, with its 56 color bands, will further enhance 's ability to detail the nature of each source.

YOLO-RWY: A Novel Runway Detection Model for Vision-Based Autonomous Landing of Fixed-Wing Unmanned Aerial Vehicles

In scenarios where global navigation satellite systems (GNSSs) and radio navigation systems are denied, vision-based autonomous landing (VAL) for fixed-wing unmanned aerial vehicles (UAVs) becomes essential. Accurate and real-time runway detection in VAL is vital for providing precise positional and orientational guidance. However, existing research faces significant challenges, including insufficient accuracy, inadequate real-time performance, poor robustness, and high susceptibility to disturbances. To address these challenges, this paper introduces a novel single-stage, anchor-free, and decoupled vision-based runway detection framework, referred to as YOLO-RWY. First, an enhanced data augmentation (EDA) module is incorporated to perform various augmentations, enriching image diversity, and introducing perturbations that improve generalization and safety. Second, a large separable kernel attention (LSKA) module is integrated into the backbone structure to provide a lightweight attention mechanism with a broad receptive field, enhancing feature representation. Third, the neck structure is reorganized as a bidirectional feature pyramid network (BiFPN) module with skip connections and attention allocation, enabling efficient multi-scale and across-stage feature fusion. Finally, the regression loss and task-aligned learning (TAL) assigner are optimized using efficient intersection over union (EIoU) to improve localization evaluation, resulting in faster and more accurate convergence. Comprehensive experiments demonstrate that YOLO-RWY achieves AP50:95 scores of 0.760, 0.611, and 0.413 on synthetic, real nominal, and real edge test sets of the landing approach runway detection (LARD) dataset, respectively. Deployment experiments on an edge device show that YOLO-RWY achieves an inference speed of 154.4 FPS under FP32 quantization with an image size of 640. The results indicate that the proposed YOLO-RWY model possesses strong generalization and real-time capabilities, enabling accurate runway detection in complex and challenging visual environments, and providing support for the onboard VAL systems of fixed-wing UAVs.

Predicting future hospital antimicrobial resistance prevalence using machine learning

BackgroundPredicting antimicrobial resistance (AMR), a top global health threat, nationwide at an aggregate hospital level could help target interventions. Using machine learning, we exploit historical AMR and antimicrobial usage to predict future AMR.MethodsAntimicrobial use and AMR prevalence in bloodstream infections in hospitals in England were obtained per hospital group (Trust) and financial year (FY, April–March) for 22 pathogen–antibiotic combinations (FY2016-2017 to FY2021-2022). Extreme Gradient Boosting (XGBoost) model predictions were compared to the previous value taken forwards, the difference between the previous two years taken forwards and linear trend forecasting (LTF). XGBoost feature importances were calculated to aid interpretability.ResultsHere we show that XGBoost models achieve the best predictive performance. Relatively limited year-to-year variability in AMR prevalence within Trust–pathogen–antibiotic combinations means previous value taken forwards also achieves a low mean absolute error (MAE), similar to or slightly higher than XGBoost. Using the difference between the previous two years taken forward or LTF performs consistently worse. XGBoost considerably outperforms all other methods in Trusts with a larger change in AMR prevalence from FY2020-2021 (last training year) to FY2021-2022 (held-out test set). Feature importance values indicate that besides historical resistance to the same pathogen–antibiotic combination as the outcome, complex relationships between resistance in different pathogens to the same antibiotic/antibiotic class and usage are exploited for predictions. These are generally among the top ten features ranked according to their mean absolute SHAP values.ConclusionsYear-to-year resistance has generally changed little within Trust–pathogen–antibiotic combinations. In those with larger changes, XGBoost models can improve predictions, enabling informed decisions, efficient resource allocation, and targeted interventions.