Test Dataset Research Articles

Estimating software reliability using size-biased modelling

Software testing is an important step in software development where inputs are administered repeatedly to detect bugs present in the software. In this paper, we have considered the estimation of total number of bugs and software reliability as a size-biased sampling problem by introducing the concept of eventual bug size as a latent variable. We have developed a Bayesian generalised linear mixed model (GLMM) using software testing detection data to estimate software reliability and stopping phase. The model uses size-biased approach where the probability of detecting a bug is an increasing function of eventual size of the bug which is as an index for the potential number of inputs that may eventually pass through the bug. We have tested the sensitivity of the reliability estimates by varying the number of inputs and detection probability via a simulation study and have found that the key parameters could be accurately estimated. Further, we have applied our model to two empirical data sets – one from a commercial software and the other from ISRO launch mission software testing data set. The hierarchical modelling approach provides a unified modelling framework that may find applications in other fields (e.g. hydrocarbon explorations) apart from software management.

Segmentation of mediastinal lymph nodes in CT with anatomical priors.

Lymph nodes (LNs) in the chest have a tendency to enlarge due to various pathologies, such as lung cancer or pneumonia. Clinicians routinely measure nodal size to monitor disease progression, confirm metastatic cancer, and assess treatment response. However, variations in their shapes and appearances make it cumbersome to identify LNs, which reside outside of most organs. We propose to segment LNs in the mediastinum by leveraging the anatomical priors of 28 different structures (e.g., lung, trachea etc.) generated by the public TotalSegmentator tool. The CT volumes from 89 patients available in the public NIH CT Lymph Node dataset were used to train three 3D off-the-shelf nnUNet models to segment LNs. The public St. Olavs dataset containing 15 patients (out-of-training-distribution) was used to evaluate the segmentation performance. For LNs with short axis diameter 8mm, the 3D cascade nnUNet model obtained the highest Dice score of 67.9 ± 23.4 and lowest Hausdorff distance error of 22.8 ± 20.2. For LNs of all sizes, the Dice score was 58.7 ± 21.3 and this represented a 10% improvement over a recently published approach evaluated on the same test dataset. To our knowledge, we are the first to harness 28 distinct anatomical priors to segment mediastinal LNs, and our work can be extended to other nodal zones in the body. The proposed method has the potential for improved patient outcomes through the identification of enlarged nodes in initial staging CT scans.

Rapid in-situ calibration of computational micro-spectrometer with few-shot meta-learning

Computational micro-spectrometers comprised of detector arrays and encoding structure arrays, such as on-chip Fabry-Perot (FP) cavity filters, have great potential in many in-situ applications owing to their compact size and snapshot imaging ability. Given manufacturing deviation and environmental influence are inevitable, easy and effective calibration for spectrometer is necessary, especially for in-situ applications. Currently calibration strategies based on iterative algorithms or neural networks require accurate measurements of pixel-level (spectral) encoding functions through monochromator or large amounts of standard samples. These procedures are time-consuming and expensive, thereby impeding in-situ applications. Meta-learning algorithms with few-shot learning ability can address this challenge by incorporating the prior knowledge in the simulated dataset. In this work, we propose a meta-learning algorithm free of measuring encoding function or large amounts of standard samples to calibrate a micro-spectrometer with manufacturing deviation effectively. Our micro-spectrometer comprises 16 types of FP filters covering a wavelength range of 550-720 nm. The center wavelength of each filter type deviates from the design up to 6 nm. After calibration with 15 different color data, the average reconstruction error on the test dataset decreased from 7.2 × 10 − 3 to 1.2 × 10 − 3, and further decreased to 9.4 × 10 − 4 when the calibration data increased to 24. The performance is comparable to algorithms trained with measured encoding function both in reconstruction error and generalization ability. We estimated that the cost of in-situ calibration through reflectance measurements of color chart decreased to one percent of the cost through monochromator measurements. By exploiting prior deviation information in simulation data with meta-learning, the efficiency and cost of calibration are significantly improved, thereby facilitating the large-scale production and in-situ application of micro-spectrometers.

Diagnostic Identification of Acute Brain Dysfunction in Pediatric Sepsis and Septic Shock in the Electronic Health Record: A Comparison of Four Definitions in a Reference Dataset.

Acute brain dysfunction (ABD) in pediatric sepsis has a prevalence of 20%, but can be difficult to identify. Our previously validated ABD computational phenotype (CPABD) used variables obtained from the electronic health record indicative of clinician concern for acute neurologic or behavioral change. We tested whether the CPABD has better diagnostic performance to identify confirmed ABD than other definitions using the Glasgow Coma Scale or delirium scores. Diagnostic testing in a curated cohort of pediatric sepsis/septic shock patients. Quaternary freestanding children's hospital. The test dataset comprised 527 children with sepsis/septic shock managed between 2011 and 2021 with a prevalence (pretest probability) of confirmed ABD of 30% (159/527). CPABD was based on use of neuroimaging, electroencephalogram, and/or administration of new antipsychotic medication. We compared the performance of the CPABD with three GCS/delirium-based definitions of ABD-Proulx et al, International Pediatric Sepsis Consensus Conference, and Pediatric Organ Dysfunction Information Update Mandate. The posttest probability of identifying ABD was highest in CPABD (0.84) compared with other definitions. CPABD also had the highest sensitivity (83%; 95% CI, 76-89%) and specificity (93%; 95% CI, 90-96%). The false discovery rate was lowest in CPABD (1-in-6) as was the false omission rate (1-in-14). Finally, the prevalence threshold for the definitions varied, with the CPABD being the definition closest to 20%. In our curated dataset of pediatric sepsis/septic shock, CPABD had favorable characteristics to identify confirmed ABD compared with GCS/delirium-based definitions. The CPABD can be used to further study the impact of ABD in studies using large electronic health datasets.

Hybrid feature selection in a machine learning predictive model for perioperative myocardial injury in noncoronary cardiac surgery with cardiopulmonary bypass.

Perioperative myocardial injury (PMI) is associated with increased mobility and mortality after noncoronary cardiac surgery. However, limited studies have developed a predictive model for PMI. Therefore, we used hybrid feature selection (FS) methods to establish a predictive model for PMI in noncoronary cardiac surgery with cardiopulmonary bypass (CPB). This was a single-center retrospective study conducted at the Fuwai Hospital in China. Patients aged 18-70years who underwent elective noncoronary surgery with CPB at our institution from December 2018 to April 2021 were enrolled. The primary outcome was PMI, defined as the postoperative cardiac troponin I (cTnI) levels exceeding 220 times of upper reference limit (URL). Statistical analyses were conducted by Python (Python Software Foundation, version 3.9.7 and integrated development environment Jupyter Notebook 1.1.0) and SPSS software version 26.0 (IBM Corp., Armonk, New York, USA). A total of 1130 patients were eventually eligible for this study. The incidence of PMI was 20.3% (229/1130) in the overall patients, 20.6% (163/791) in the training dataset, and 19.5% (66/339) in the testing dataset. The logistic regression model performed the best AUC of 0.6893 (95 CI%: 0.6371-0.7382) by the traditional selection method, and the random forest model performed the best AUC of 0.6937 (95 CI%: 0.6416-0.7423) by the union of Wrapper and Embedded method, and the CatBoost model performed the best AUC of 0.6828 (95 CI%: 0.6304-0.7320) by the union of Embedded and forward logistic regression technique, and the Naïve Bayes model achieved the best AUC with 0.7254 (95 CI%: 0.6746-0.7723) by forwarding logistic regression method. Moreover, the decision tree, KNeighborsClassifier, and support vector machine models performed the worse AUC in all selection forms. Furthermore, the SHapley Additive exPlanations plot showed that prolonged CPB, aortic clamp time, and preoperative low platelets count were strongly related to the PMI risk. In total, four category feature selection methods were utilized, comprising five individual selection techniques and 15 combined methods. Notably, the combination of logistic regression and embedded methods demonstrated outstanding performance in predicting PMI risk. We also concluded that the machine learning model, including random forest, catboost, and Naive Bayes, were suitable candidates for establishing PMI predictive model. Nevertheless, additional investigation and validation are imperative for substantiating these finding.

Development and Validation of an Explainable Deep Learning Model to Predict In-Hospital Mortality for Patients With Acute Myocardial Infarction: Algorithm Development and Validation Study.

Acute myocardial infarction (AMI) is one of the most severe cardiovascular diseases and is associated with a high risk of in-hospital mortality. However, the current deep learning models for in-hospital mortality prediction lack interpretability. This study aims to establish an explainable deep learning model to provide individualized in-hospital mortality prediction and risk factor assessment for patients with AMI. In this retrospective multicenter study, we used data for consecutive patients hospitalized with AMI from the Chongqing University Central Hospital between July 2016 and December 2022 and the Electronic Intensive Care Unit Collaborative Research Database. These patients were randomly divided into training (7668/10,955, 70%) and internal test (3287/10,955, 30%) data sets. In addition, data of patients with AMI from the Medical Information Mart for Intensive Care database were used for external validation. Deep learning models were used to predict in-hospital mortality in patients with AMI, and they were compared with linear and tree-based models. The Shapley Additive Explanations method was used to explain the model with the highest area under the receiver operating characteristic curve in both the internal test and external validation data sets to quantify and visualize the features that drive predictions. A total of 10,955 patients with AMI who were admitted to Chongqing University Central Hospital or included in the Electronic Intensive Care Unit Collaborative Research Database were randomly divided into a training data set of 7668 (70%) patients and an internal test data set of 3287 (30%) patients. A total of 9355 patients from the Medical Information Mart for Intensive Care database were included for independent external validation. In-hospital mortality occurred in 8.74% (670/7668), 8.73% (287/3287), and 9.12% (853/9355) of the patients in the training, internal test, and external validation cohorts, respectively. The Self-Attention and Intersample Attention Transformer model performed best in both the internal test data set and the external validation data set among the 9 prediction models, with the highest area under the receiver operating characteristic curve of 0.86 (95% CI 0.84-0.88) and 0.85 (95% CI 0.84-0.87), respectively. Older age, high heart rate, and low body temperature were the 3 most important predictors of increased mortality, according to the explanations of the Self-Attention and Intersample Attention Transformer model. The explainable deep learning model that we developed could provide estimates of mortality and visual contribution of the features to the prediction for a patient with AMI. The explanations suggested that older age, unstable vital signs, and metabolic disorders may increase the risk of mortality in patients with AMI.

Artificial intelligence-based tools with automated segmentation and measurement on CT images to assist accurate and fast diagnosis in acute pancreatitis.

To develop an artificial intelligence (AI) tool with automated pancreas segmentation and measurement of pancreatic morphological information on CT images to assist improved and faster diagnosis in acute pancreatitis. This study retrospectively contained 1124 patients suspected for AP and received non-contrast and enhanced abdominal CT examination between September 2013 to September 2022. Patients were divided into training (N = 688), validation (N = 145), testing dataset (N = 291, N = 104 for normal pancreas, N = 98 for AP, N = 89 for AP complicated with PDAC (AP&PDAC)). A model based on convolutional neural network (MSAnet) was developed. The pancreas segmentation and measurement were performed via eight open-source models and MSAnet based tools, and the efficacy was evaluated using Dice similarity coefficient (DSC) and Intersection over union (IoU). The DSC and IoU for patients with different ages were also compared. The outline of tumor and edema in the AP and were segmented by clustering. The diagnostic efficacy for radiologists with or without the assistance of MSAnet tool in AP and AP&PDAC was evaluated using receiver operation curve and confusion matrix. Among all models, MSAnet based tool showed best performance on the training and validation dataset, and had high efficacy on testing dataset. The performance was age-affected. With assistance of the AI tool, the diagnosis time was significantly shortened by 26.8% and 32.7% for junior and senior radiologists, respectively. The area under curve in diagnosis of AP was improved from 0.91 to 0.96 for junior radiologist and 0.98 to 0.99 for senior radiologist. In AP&PDAC diagnosis, AUC was increased from 0.85 to 0.92 for junior and 0.97 to 0.99 for senior. MSAnet based tools showed good pancreas segmentation and measurement performance, which help radiologists improve diagnosis efficacy and workflow in both AP and AP with PDAC conditions. This study developed an AI tool with automated pancreas segmentation and measurement and provided evidence for AI tool assistance in improving the workflow and accuracy of AP diagnosis.

MedKnee: A New Deep Learning-Based Software for Automated Prediction of Radiographic Knee Osteoarthritis

In computer-aided medical diagnosis, deep learning techniques have shown that it is possible to offer performance similar to that of experienced medical specialists in the diagnosis of knee osteoarthritis. In this study, a new deep learning (DL) software, called “MedKnee” is developed to assist physicians in the diagnosis process of knee osteoarthritis according to the Kellgren and Lawrence (KL) score. To accomplish this task, 5000 knee X-ray images obtained from the Osteoarthritis Initiative public dataset (OAI) were divided into train, valid, and test datasets in a ratio of 7:1:2 with a balanced distribution across each KL grade. The pre-trained Xception model is used for transfer learning and then deployed in a Graphical User Interface (GUI) developed with Tkinter and Python. The suggested software was validated on an external public database, Medical Expert, and compared with a rheumatologist’s diagnosis on a local database, with the involvement of a radiologist for arbitration. The MedKnee achieved an accuracy of 95.36% when tested on Medical Expert-I and 94.94% on Medical Expert-II. In the local dataset, the developed tool and the rheumatologist agreed on 23 images out of 30 images (74%). The MedKnee’s satisfactory performance makes it an effective assistant for doctors in the assessment of knee osteoarthritis.

Operational Forecasting of Global Ionospheric TEC Maps 1-, 2-, and 3-Day in Advance by ConvLSTM Model

In this paper, we propose a global ionospheric total electron content (TEC) maps (GIM) prediction model based on deep learning methods that is both straightforward and practical, meeting the requirements of various applications. The proposed model utilizes an encoder-decoder structure with a Convolution Long Short-Term Memory (ConvLSTM) network and has a spatial resolution of 5° longitude and 2.5° latitude, with a time resolution of 1 h. We utilized the Center for Orbit Determination in Europe (CODE) GIM dataset for 18 years from 2002 to 2019, without requiring any other external input parameters, to train the ConvLSTM models for forecasting GIM 1, 2, and 3 days in advance. Using the CODE GIM data from 1 January 2020 to 31 December 2023 as the test dataset, the performance evaluation results show that the average root mean square errors (RMSE) for 1, 2 and 3 days of forecasts are 2.81 TECU, 3.16 TECU, and 3.41 TECU, respectively. These results show improved performance compared to the IRI-Plas model and CODE’s 1-day forecast product c1pg, and comparable to CODE’s 2-day forecast c2pg. The model’s predictions get worse as the intensity of the storm increases, and the prediction error of the model increases with the lead time.

Automatic segmentation of dura for quantitative analysis of lumbar stenosis: A deep learning study with 518 CT myelograms.

The diagnosis of lumbar spinal stenosis (LSS) can be challenging because radicular pain is not often present in the culprit-level localization. Accurate segmentation and quantitative analysis of the lumbar dura on radiographic images are key to the accurate differential diagnosis of LSS. The aim of this study is to develop an automatic dura-contouring tool for radiographic quantification on computed tomography myelogram (CTM) for patients with LSS. A total of 518 CTM cases with or without lumbar stenosis were included in this study. A deep learning (DL) segmentation algorithm 3-dimensional (3D) U-Net was deployed. A total of 210 labeled cases were used to develop the dura-contouring tool, with the ratio of the training, independent testing, and external validation datasets being 150:30:30. The Dice score (DCS) was the primary measure to evaluate the segmentation performance of the 3D U-Net, which was subsequently developed as the dura-contouring tool to segment another unlabeled 308 CTM cases with LSS. Automatic masks of 446 slices on the stenotic levels were then meticulously reviewed and revised by human experts, and the cross-sectional area (CSA) of the dura was compared. The mean DCS of the 3D U-Net were 0.905±0.080, 0.933±0.018, and 0.928±0.034 in the five-fold cross-validation, the independent testing, and the external validation datasets, respectively. The segmentation performance of the dura-contouring tool was also comparable to that of the second observer (the human expert). With the dura-contouring tool, only 59.0% (263/446) of the automatic masks of the stenotic slices needed to be revised. In the revised cases, there were no significant differences in the dura CSA between automatic masks and corresponding revised masks (p=0.652). Additionally, a strong correlation of dura CSA was found between the automatic masks and corresponding revised masks (r=0.805). A dura-contouring tool was developed that could automatically segment the dural sac on CTM, and it demonstrated high accuracy and generalization ability. Additionally, the dura-contouring tool has the potential to be applied in patients with LSS because it facilitates the quantification of the dural CSA on stenotic slices.

Weibull parametric model for survival analysis in women with endometrial cancer using clinical and T2-weighted MRI radiomic features

BackgroundSemiparametric survival analysis such as the Cox proportional hazards (CPH) regression model is commonly employed in endometrial cancer (EC) study. Although this method does not need to know the baseline hazard function, it cannot estimate event time ratio (ETR) which measures relative increase or decrease in survival time. To estimate ETR, the Weibull parametric model needs to be applied. The objective of this study is to develop and evaluate the Weibull parametric model for EC patients’ survival analysis.MethodsTraining (n = 411) and testing (n = 80) datasets from EC patients were retrospectively collected to investigate this problem. To determine the optimal CPH model from the training dataset, a bi-level model selection with minimax concave penalty was applied to select clinical and radiomic features which were obtained from T2-weighted MRI images. After the CPH model was built, model diagnostic was carried out to evaluate the proportional hazard assumption with Schoenfeld test. Survival data were fitted into a Weibull model and hazard ratio (HR) and ETR were calculated from the model. Brier score and time-dependent area under the receiver operating characteristic curve (AUC) were compared between CPH and Weibull models. Goodness of the fit was measured with Kolmogorov-Smirnov (KS) statistic.ResultsAlthough the proportional hazard assumption holds for fitting EC survival data, the linearity of the model assumption is suspicious as there are trends in the age and cancer grade predictors. The result also showed that there was a significant relation between the EC survival data and the Weibull distribution. Finally, it showed that Weibull model has a larger AUC value than CPH model in general, and it also has smaller Brier score value for EC survival prediction using both training and testing datasets, suggesting that it is more accurate to use the Weibull model for EC survival analysis.ConclusionsThe Weibull parametric model for EC survival analysis allows simultaneous characterization of the treatment effect in terms of the hazard ratio and the event time ratio (ETR), which is likely to be better understood. This method can be extended to study progression free survival and disease specific survival.Trial registrationClinicalTrials.gov NCT03543215, https://clinicaltrials.gov/, date of registration: 30th June 2017.

Natural language processing augments comorbidity documentation in neurosurgical inpatient admissions.

To establish whether or not a natural language processing technique could identify two common inpatient neurosurgical comorbidities using only text reports of inpatient head imaging. A training and testing dataset of reports of 979 CT or MRI scans of the brain for patients admitted to the neurosurgery service of a single hospital in June 2021 or to the Emergency Department between July 1-8, 2021, was identified. A variety of machine learning and deep learning algorithms utilizing natural language processing were trained on the training set (84% of the total cohort) and tested on the remaining images. A subset comparison cohort (n = 76) was then assessed to compare output of the best algorithm against real-life inpatient documentation. For "brain compression", a random forest classifier outperformed other candidate algorithms with an accuracy of 0.81 and area under the curve of 0.90 in the testing dataset. For "brain edema", a random forest classifier again outperformed other candidate algorithms with an accuracy of 0.92 and AUC of 0.94 in the testing dataset. In the provider comparison dataset, for "brain compression," the random forest algorithm demonstrated better accuracy (0.76 vs 0.70) and sensitivity (0.73 vs 0.43) than provider documentation. For "brain edema," the algorithm again demonstrated better accuracy (0.92 vs 0.84) and AUC (0.45 vs 0.09) than provider documentation. A natural language processing-based machine learning algorithm can reliably and reproducibly identify selected common neurosurgical comorbidities from radiology reports. This result may justify the use of machine learning-based decision support to augment provider documentation.

Hybrid deep learning and optimal graph search method for optical coherence tomography layer segmentation in diseases affecting the optic nerve

Accurate segmentation of retinal layers in optical coherence tomography (OCT) images is critical for assessing diseases that affect the optic nerve, but existing automated algorithms often fail when pathology causes irregular layer topology, such as extreme thinning of the ganglion cell-inner plexiform layer (GCIPL). Deep LOGISMOS, a hybrid approach that combines the strengths of deep learning and 3D graph search to overcome their limitations, was developed to improve the accuracy, robustness and generalizability of retinal layer segmentation. The method was trained on 124 OCT volumes from both eyes of 31 non-arteritic anterior ischemic optic neuropathy (NAION) patients and tested on three cross-sectional datasets with available reference tracings: Test-NAION (40 volumes from both eyes of 20 NAION subjects), Test-G (29 volumes from 29 glaucoma subjects/eyes), and Test-JHU (35 volumes from 21 multiple sclerosis and 14 control subjects/eyes) and one longitudinal dataset without reference tracings: Test-G-L (155 volumes from 15 glaucoma patients/eyes). In the three test datasets with reference tracings (Test-NAION, Test-G, and Test-JHU), Deep LOGISMOS achieved very high Dice similarity coefficients (%) on GCIPL: 89.97±3.59, 90.63±2.56, and 94.06±1.76, respectively. In the same context, Deep LOGISMOS outperformed the Iowa reference algorithms by improving the Dice score by 17.5, 5.4, and 7.5, and also surpassed the deep learning framework nnU-Net with improvements of 4.4, 3.7, and 1.0. For the 15 severe glaucoma eyes with marked GCIPL thinning (Test-G-L), it demonstrated reliable regional GCIPL thickness measurement over five years. The proposed Deep LOGISMOS approach has potential to enhance precise quantification of retinal structures, aiding diagnosis and treatment management of optic nerve diseases.

Improving prediction of tacrolimus concentration using a combination of population pharmacokinetic modeling and machine learning in chinese renal transplant recipients

AimsThe population pharmacokinetic (PPK) model-based machine learning (ML) approach offers a novel perspective on individual concentration prediction. This study aimed to establish a PPK-based ML model for predicting tacrolimus (TAC) concentrations in Chinese renal transplant recipients.MethodsConventional TAC monitoring data from 127 Chinese renal transplant patients were divided into training (80%) and testing (20%) datasets. A PPK model was developed using the training group data. ML models were then established based on individual pharmacokinetic data derived from the PPK basic model. The prediction performances of the PPK-based ML model and Bayesian forecasting approach were compared using data from the test group.ResultsThe final PPK model, incorporating hematocrit and CYP3A5 genotypes as covariates, was successfully established. Individual predictions of TAC using the PPK basic model, postoperative date, CYP3A5 genotype, and hematocrit showed improved rankings in ML model construction. XGBoost, based on the TAC PPK, exhibited the best prediction performance.ConclusionThe PPK-based machine learning approach emerges as a superior option for predicting TAC concentrations in Chinese renal transplant recipients.

ProBAN: Neural network algorithm for predicting binding affinity in protein-protein complexes.

Determining binding affinities in protein-protein and protein-peptide complexes is a challenging task that directly impacts the development of peptide and protein pharmaceuticals. Although several models have been proposed to predict the value of the dissociation constant and the Gibbs free energy, they are currently not capable of making stable predictions with high accuracy, in particular for complexes consisting of more than two molecules. In this work, we present ProBAN, a new method for predicting binding affinity in protein-protein complexes based on a deep convolutional neural network. Prediction is carried out for the spatial structures of complexes, presented in the format of a 4D tensor, which includes information about the location of atoms and their abilities to participate in various types of interactions realized in protein-protein and protein-peptide complexes. The effectiveness of the model was assessed both on an internal test data set containing complexes consisting of three or more molecules, as well as on an external test for the PPI-Affinity service. As a result, we managed to achieve the best prediction quality on these data sets among all the analyzed models: on the internal test, Pearson correlation R = 0.6, MAE = 1.60, on the external test, R = 0.55, MAE = 1.75. The open-source code, the trained ProBAN model, and the collected dataset are freely available at the following link https://github.com/EABogdanova/ProBAN.

Combining deep learning with physical parameters in POC and PIC inversion from spaceborne lidar CALIOP

POC and PIC are indispensable components in the global ocean carbon cycle, their transport and space distribution being driven by the biological carbon pump and the carbonate pump. However, passive ocean color remote sensing, usually employed for POC and PIC research, experiences serious shortcomings in polar winter conditions due to its reliance on sunlight, leading to scarce data coverage in the polar regions. In contrast, CALIOP has shown considerable promise in high-latitude ocean observing. Past approaches to estimate POC from CALIOP data relied on bbp measurements obtained through the application of algorithms that presume an empirical linear correlation between bbp and the backscatter coefficient measured at 180°. This method does not account for any spatiotemporal variability in the conversion coefficient. Furthermore, the potential of CALIOP to provide estimates of PIC has not been explored yet. Here, we developed an innovative Two-Branch-Two-Step (TBTS) model to estimate POC and PIC from CALIOP data, which effectively expands the spatial coverage of the MODIS products. This method exploits the strength of deep learning while encapsulating the generalizability of physical parameters. This method consists of two branches: (1) a deep learning branch based on lidar attenuated backscatter waveform and (2) a branch focusing on physical parameters, including the total column-integrated depolarization ratio and the subsurface cross-polarized component of column-integrated backscatter. The model’s generalizability and accuracy are confirmed through the evaluation of a test dataset and validation using in-situ measurements. Our model outperforms several other prevalent machine learning models. We also dissected the importance of different parts of the input data using SHAP tools, thereby providing insights into the black-box nature of deep learning models. Using CALIOP products, we put forth the inaugural estimation of interannually resolved PIC and POC standing stocks in polar regions. The implementation of CALIOP in polar regions bridges the gap inherent in passive ocean color measurements. Lidar-derived total global PIC standing stock is estimated to be 8% higher than that from MODIS, while the POC standing stock is boosted by 17.2%. The carbon standing stock in polar regions exhibits significant inter-annual variability and apparent seasonal periodicity. Hence, results from this research effort clearly reveal that the exploitation of the CALIOP-derived POC and PIC measurements, in combination with the application of new approaches and algorithms to future space lidar data, will undeniably enhance our comprehension of the polar ocean carbon cycle. However, it is important to acknowledge that the CALIOP products may inherit biases from the MODIS data used for training. Hence, where MODIS data is available, it’s still the “better” product to use, but where there isn’t MODIS data, the CALIOP product is extremely useful, especially in the polar regions.

Optimizing compressive strength of quaternary-blended cement concrete through ensemble-instance-based machine learning

Optimizing the composition of concrete, particularly when incorporating ordinary Portland cement (OPC) along with supplementary materials such as ground granulated blast furnace slag (BF), fly ash (FA), and silica fume (SF), poses challenges due to the intricate nonlinearity inherent in concrete properties. Addressing this challenge has urged growing interest in employing Machine Learning (ML) techniques for precise property assessment. In this investigation, various predictive models, encompassing eXtra Gradient Boosting (XGB), random forests (RF), and K-Nearest Neighbor (KNN) algorithms were formulated to predict the compressive strength (CS) of ternary-blended concrete incorporating OPC, BF, FA, and SF. Through comprehensive analysis of an extensive dataset comprising 810 distinct records, the study identifies optimal concrete blends, providing invaluable insights for practical applications. Evaluation of ML models underscores the superior performance of XGB, with a coefficient of multiple determination (R2) values of 0.923 and 0.997 for training and testing datasets, respectively, indicative of exceptional predictive accuracy. Additionally, SHAP values underscore the importance of input age, water–binder ratio, and OPC content. This research enhances understanding of ternary-blended concrete characteristics, offering practical implications for construction practices and laying a foundation for future research endeavors to refine ML models, explore attribute interactions, and optimize concrete constituent proportions for broader civil engineering applications.

Deep learning based digital pathology for predicting treatment response to first-line PD-1 blockade in advanced gastric cancer

BackgroundAdvanced unresectable gastric cancer (GC) patients were previously treated with chemotherapy alone as the first-line therapy. However, with the Food and Drug Administration’s (FDA) 2022 approval of programmed cell death protein 1 (PD-1) inhibitor combined with chemotherapy as the first-li ne treatment for advanced unresectable GC, patients have significantly benefited. However, the significant costs and potential adverse effects necessitate precise patient selection. In recent years, the advent of deep learning (DL) has revolutionized the medical field, particularly in predicting tumor treatment responses. Our study utilizes DL to analyze pathological images, aiming to predict first-line PD-1 combined chemotherapy response for advanced-stage GC.MethodsIn this multicenter retrospective analysis, Hematoxylin and Eosin (H&E)-stained slides were collected from advanced GC patients across four medical centers. Treatment response was evaluated according to iRECIST 1.1 criteria after a comprehensive first-line PD-1 immunotherapy combined with chemotherapy. Three DL models were employed in an ensemble approach to create the immune checkpoint inhibitors Response Score (ICIsRS) as a novel histopathological biomarker derived from Whole Slide Images (WSIs).ResultsAnalyzing 148,181 patches from 313 WSIs of 264 advanced GC patients, the ensemble model exhibited superior predictive accuracy, leading to the creation of ICIsNet. The model demonstrated robust performance across four testing datasets, achieving AUC values of 0.92, 0.95, 0.96, and 1 respectively. The boxplot, constructed from the ICIsRS, reveals statistically significant disparities between the well response and poor response (all p-values < = 0.001).ConclusionICIsRS, a DL-derived biomarker from WSIs, effectively predicts advanced GC patients’ responses to PD-1 combined chemotherapy, offering a novel approach for personalized treatment planning and allowing for more individualized and potentially effective treatment strategies based on a patient’s unique response situations.

Image ciphertexts classification method based on ghost imaging and intraclass-interclass difference

In this paper, based on ghost imaging encryption, the preservation of Manhattan distance feature in ciphertext compared with plaintext is analyzed by utilizing the intraclass-interclass difference of image classification, and a classification method for image ciphertexts is proposed. After calculating Manhattan distance for both plaintexts and ciphertexts, respectively, the intraclass-interclass difference can be determined. The image that minimizes the intraclass-interclass difference is taken as the centroid to verify the consistency of the classification for various plaintext-ciphertext pairs under the same operation. The feasibility of proposed method is verified by numerical simulations, that the values of ACC and Weighted-F2 can be up to 90% when the MNIST is adopted as the test dataset. The whole process can be regarded as a kind of classification process by homomorphic encryption, however, different from the traditional homomorphic encryption methods based on mathematical model, the proposed method is accomplished based on the optical theory, and it does not require a lot of pre-training through models such as deep learning and neural networks, that means, reducing the computational expenses.

GreenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets.

To study gene regulation through transcription factors and chromatin modifiers, a variety of genome-wide techniques are used. Recently, CUT&RUN-based technologies have become popular, but a pipeline for the comprehensive analysis of CUT&RUN datasets is currently lacking. Here, we present the "greenPipes" package, which includes fine-tuned parameters specifically for bioinformatic analyses of greenCUT&RUN and CUT&RUN datasets. greenPipes provides additional functionalities for data analysis and data integration with other -omics technologies, which are either not available in other pipelines developed for CUT&RUN datasets or scattered in the literature as individual packages. Source code and a manual of the greenPipes are freely available on GitHub website (https://github.com/snizam001/greenPipes). The test datasets, comprehensive annotation files and other datasets are available at https://osf.io/ruhj9/. The handbook of greenPipes is available online at Bioinformatics as Supplementary text.