Many studies have demonstrated the importance of accurately identifying miRNA-disease associations (MDAs) for understanding disease mechanisms. However, the number of known MDAs is significantly fewer than the unknown pairs. Here, we propose RSANMDA, a subview attention network for predicting MDAs. We first extract miRNA and disease features from multiple similarity matrices. Next, using resampling techniques, we generate different subviews from known MDAs. Each subview undergoes multi-head graph attention to capture its features, followed by semantic attention to integrate features across subviews. Finally, combining raw and training features, we use a multilayer scoring perceptron for prediction. In the experimental section, we conducted comparative experiments with other advanced models on both HMDD v2.0 and HMDD v3.2 datasets. We also performed a series of ablation studies and parameter tuning exercises. Comprehensive experiments conclusively demonstrate the superiority of our model. Case studies on lung, breast, and esophageal cancers further validate our method\'s predictive capability for identifying disease-related miRNAs.

OBJECTIVE: The minimum sample size for multistakeholder Delphi surveys remains understudied. Drawing from three large international multistakeholder Delphi surveys, this study aimed to: 1) investigate the effect of increasing sample size on replicability of results; 2) assess whether the level of replicability of results differed with participant characteristics: for example, gender, age, and profession.
METHODS: We used data from Delphi surveys to develop guidance for improved reporting of health-care intervention trials: SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) and CONSORT (Consolidated Standards of Reporting Trials) extension for surrogate end points (n = 175, 22 items rated); CONSORT-SPI [CONSORT extension for Social and Psychological Interventions] (n = 333, 77 items rated); and core outcome set for burn care (n = 553, 88 items rated). Resampling with replacement was used to draw random subsamples from the participant data set in each of the three surveys. For each subsample, the median value of all rated survey items was calculated and compared to the medians from the full participant data set. The median number (and interquartile range) of medians replicated was used to calculate the percentage replicability (and variability). High replicability was defined as ≥80% and moderate as 60% and <80% RESULTS: The average median replicability (variability) as a percentage of total number of items rated from the three datasets was 81% (10%) at a sample size of 60. In one of the datasets (CONSORT-SPI), a ≥80% replicability was reached at a sample size of 80. On average, increasing the sample size from 80 to 160 increased the replicability of results by a further 3% and reduced variability by 1%. For subgroup analysis based on participant characteristics (eg, gender, age, professional role), using resampled samples of 20 to 100 showed that a sample size of 20 to 30 resulted to moderate replicability levels of 64% to 77%.
CONCLUSIONS: We found that a minimum sample size of 60-80 participants in multistakeholder Delphi surveys provides a high level of replicability (≥80%) in the results. For Delphi studies limited to individual stakeholder groups (such as researchers, clinicians, patients), a sample size of 20 to 30 per group may be sufficient.

This chapter shows applying the Asymmetric Within-Sample Transformation to single-cell RNA-Seq data matched with a previous dropout imputation. The asymmetric transformation is a special winsorization that flattens low-expressed intensities and preserves highly expressed gene levels. Before a standard hierarchical clustering algorithm, an intermediate step removes noninformative genes according to a threshold applied to a per-gene entropy estimate. Following the clustering, a time-intensive algorithm is shown to uncover the molecular features associated with each cluster. This step implements a resampling algorithm to generate a random baseline to measure up/downregulated significant genes. To this aim, we adopt a GLM model as implemented in DESeq2 package. We render the results in graphical mode. While the tools are standard heat maps, we introduce some data scaling to clarify the results\' reliability.

UNASSIGNED: Missing data are common when analyzing real data. One popular solution is to impute missing data so that one complete dataset can be obtained for subsequent data analysis. In the present study, we focus on missing data imputation using classification and regression trees (CART).
UNASSIGNED: We consider a new perspective on missing data in a CART imputation problem and realize the perspective through some resampling algorithms. Several existing missing data imputation methods using CART are compared through simulation studies, and we aim to investigate the methods with better imputation accuracy under various conditions. Some systematic findings are demonstrated and presented. These imputation methods are further applied to two real datasets: Hepatitis data and Credit approval data for illustration.
UNASSIGNED: The method that performs the best strongly depends on the correlation between variables. For imputing missing ordinal categorical variables, the rpart package with surrogate variables is recommended under correlations larger than 0 with missing completely at random (MCAR) and missing at random (MAR) conditions. Under missing not at random (MNAR), chi-squared test methods and the rpart package with surrogate variables are suggested. For imputing missing quantitative variables, the iterative imputation method is most recommended under moderate correlation conditions.

Corn (Zea mays L.) is the most abundant food/feed crop, making accurate yield estimation a critical data point for monitoring global food production. Sensors with varying spatial/spectral configurations have been used to develop corn yield models from intra-field (0.1 m ground sample distance (GSD)) to regional scales (>250 m GSD). Understanding the spatial and spectral dependencies of these models is imperative to result interpretation, scaling, and deploying models. We leveraged high spatial resolution hyperspectral data collected with an unmanned aerial system mounted sensor (272 spectral bands from 0.4-1 μm at 0.063 m GSD) to estimate silage yield. We subjected our imagery to three band selection algorithms to quantitatively assess spectral reflectance features applicability to yield estimation. We then derived 11 spectral configurations, which were spatially resampled to multiple GSDs, and applied to a support vector regression (SVR) yield estimation model. Results indicate that accuracy degrades above 4 m GSD across all configurations, and a seven-band multispectral sensor which samples the red edge and multiple near-infrared bands resulted in higher accuracy in 90% of regression trials. These results bode well for our quest toward a definitive sensor definition for global corn yield modeling, with only temporal dependencies requiring additional investigation.

The temporal aspect of groundwater vulnerability to contaminants such as nitrate is often overlooked, assuming vulnerability has a static nature. This study bridges this gap by employing machine learning with Detecting Breakpoints and Estimating Segments in Trend (DBEST) algorithm to reveal the underlying relationship between nitrate, water table, vegetation cover, and precipitation time series, that are related to agricultural activities and groundwater demand in a semi-arid region. The contamination probability of Lenjanat Plain has been mapped by comparing random forest (RF), support vector machine (SVM), and K-nearest-neighbors (KNN) models, fed with 32 input variables (dem-derived factors, physiography, distance and density maps, time series data). Also, imbalanced learning and feature selection techniques were investigated as supplementary methods, adding up to four scenarios. Results showed that the RF model, integrated with forward sequential feature selection (SFS) and SMOTE-Tomek resampling method, outperformed the other models (F1-score: 0.94, MCC: 0.83). The SFS techniques outperformed other feature selection methods in enhancing the accuracy of the models with the cost of computational expenses, and the cost-sensitive function proved more efficient in tackling imbalanced data issues than the other investigated methods. The DBEST method identified significant breakpoints within each time series dataset, revealing a clear association between agricultural practices along the Zayandehrood River and substantial nitrate contamination within the Lenjanat region. Additionally, the groundwater vulnerability maps created using the candid RF model and an ensemble of the best RF, SVM, and KNN models predicted mid to high levels of vulnerability in the central parts and the downhills in the southwest.

Breast cancer is the most prevalent type of cancer in women. Risk factor assessment can aid in directing counseling regarding risk reduction and breast cancer surveillance. This research aims to (1) investigate the relationship between various risk factors and breast cancer incidence using the BCSC (Breast Cancer Surveillance Consortium) Risk Factor Dataset and create a prediction model for assessing the risk of developing breast cancer; (2) diagnose breast cancer using the Breast Cancer Wisconsin diagnostic dataset; and (3) analyze breast cancer survivability using the SEER (Surveillance, Epidemiology, and End Results) Breast Cancer Dataset. Applying resampling techniques on the training dataset before using various machine learning techniques can affect the performance of the classifiers. The three breast cancer datasets were examined using a variety of pre-processing approaches and classification models to assess their performance in terms of accuracy, precision, F-1 scores, etc. The PCA (principal component analysis) and resampling strategies produced remarkable results. For the BCSC Dataset, the Random Forest algorithm exhibited the best performance out of the applied classifiers, with an accuracy of 87.53%. Out of the different resampling techniques applied to the training dataset for training the Random Forest classifier, the Tomek Link exhibited the best test accuracy, at 87.47%. We compared all the models used with previously used techniques. After applying the resampling techniques, the accuracy scores of the test data decreased even if the training data accuracy increased. For the Breast Cancer Wisconsin diagnostic dataset, the K-Nearest Neighbor algorithm had the best accuracy with the original dataset test set, at 94.71%, and the PCA dataset test set exhibited 95.29% accuracy for detecting breast cancer. Using the SEER Dataset, this study also explores survival analysis, employing supervised and unsupervised learning approaches to offer insights into the variables affecting breast cancer survivability. This study emphasizes the significance of individualized approaches in the management and treatment of breast cancer by incorporating phenotypic variations and recognizing the heterogeneity of the disease. Through data-driven insights and advanced machine learning, this study contributes significantly to the ongoing efforts in breast cancer research, diagnostics, and personalized medicine.

The knowledge of the causal mechanisms underlying one single system may not be sufficient to answer certain questions. One can gain additional insights from comparing and contrasting the causal mechanisms underlying multiple systems and uncovering consistent and distinct causal relationships. For example, discovering common molecular mechanisms among different diseases can lead to drug repurposing. The problem of comparing causal mechanisms among multiple systems is non-trivial, since the causal mechanisms are usually unknown and need to be estimated from data. If we estimate the causal mechanisms from data generated from different systems and directly compare them (the naive method), the result can be sub-optimal. This is especially true if the data generated by the different systems differ substantially with respect to their sample sizes. In this case, the quality of the estimated causal mechanisms for the different systems will differ, which can in turn affect the accuracy of the estimated similarities and differences among the systems via the naive method. To mitigate this problem, we introduced the bootstrap estimation and the equal sample size resampling estimation method for estimating the difference between causal networks. Both of these methods use resampling to assess the confidence of the estimation. We compared these methods with the naive method in a set of systematically simulated experimental conditions with a variety of network structures and sample sizes, and using different performance metrics. We also evaluated these methods on various real-world biomedical datasets covering a wide range of data designs.

The fast rate of replacement of natural areas by expanding cities is a key threat to wildlife worldwide. Many wild species occur in cities, yet little is known on the dynamics of urban wildlife assemblages due to species\' extinction and colonization that may occur in response to the rapidly evolving conditions within urban areas. Namely, species\' ability to spread within urban areas, besides habitat preferences, is likely to shape the fate of species once they occur in a city. Here we use a long-term dataset on mammals occurring in one of the largest and most ancient cities in Europe to assess whether and how spatial spread and association with specific habitats drive the probability of local extinction within cities. Our analysis included mammalian records dating between years 1832 and 2023, and revealed that local extinctions in urban areas are biased towards species associated with wetlands and that were naturally rare within the city. Besides highlighting the role of wetlands within urban areas for conserving wildlife, our work also highlights the importance of long-term biodiversity monitoring in highly dynamic habitats such as cities, as a key asset to better understand wildlife trends and thus foster more sustainable and biodiversity-friendly cities.

Several methods in survival analysis are based on the proportional hazards assumption. However, this assumption is very restrictive and often not justifiable in practice. Therefore, effect estimands that do not rely on the proportional hazards assumption are highly desirable in practical applications. One popular example for this is the restricted mean survival time (RMST). It is defined as the area under the survival curve up to a prespecified time point and, thus, summarizes the survival curve into a meaningful estimand. For two-sample comparisons based on the RMST, previous research found the inflation of the type I error of the asymptotic test for small samples and, therefore, a two-sample permutation test has already been developed. The first goal of the present paper is to further extend the permutation test for general factorial designs and general contrast hypotheses by considering a Wald-type test statistic and its asymptotic behavior. Additionally, a groupwise bootstrap approach is considered. Moreover, when a global test detects a significant difference by comparing the RMSTs of more than two groups, it is of interest which specific RMST differences cause the result. However, global tests do not provide this information. Therefore, multiple tests for the RMST are developed in a second step to infer several null hypotheses simultaneously. Hereby, the asymptotically exact dependence structure between the local test statistics is incorporated to gain more power. Finally, the small sample performance of the proposed global and multiple testing procedures is analyzed in simulations and illustrated in a real data example.