BACKGROUND: Postacute sequelae of COVID-19 (PASC), also known as long COVID, is a broad grouping of a range of long-term symptoms following acute COVID-19. These symptoms can occur across a range of biological systems, leading to challenges in determining risk factors for PASC and the causal etiology of this disorder. An understanding of characteristics that are predictive of future PASC is valuable, as this can inform the identification of high-risk individuals and future preventative efforts. However, current knowledge regarding PASC risk factors is limited.
OBJECTIVE: Using a sample of 55,257 patients (at a ratio of 1 patient with PASC to 4 matched controls) from the National COVID Cohort Collaborative, as part of the National Institutes of Health Long COVID Computational Challenge, we sought to predict individual risk of PASC diagnosis from a curated set of clinically informed covariates. The National COVID Cohort Collaborative includes electronic health records for more than 22 million patients from 84 sites across the United States.
METHODS: We predicted individual PASC status, given covariate information, using Super Learner (an ensemble machine learning algorithm also known as stacking) to learn the optimal combination of gradient boosting and random forest algorithms to maximize the area under the receiver operator curve. We evaluated variable importance (Shapley values) based on 3 levels: individual features, temporal windows, and clinical domains. We externally validated these findings using a holdout set of randomly selected study sites.
RESULTS: We were able to predict individual PASC diagnoses accurately (area under the curve 0.874). The individual features of the length of observation period, number of health care interactions during acute COVID-19, and viral lower respiratory infection were the most predictive of subsequent PASC diagnosis. Temporally, we found that baseline characteristics were the most predictive of future PASC diagnosis, compared with characteristics immediately before, during, or after acute COVID-19. We found that the clinical domains of health care use, demographics or anthropometry, and respiratory factors were the most predictive of PASC diagnosis.
CONCLUSIONS: The methods outlined here provide an open-source, applied example of using Super Learner to predict PASC status using electronic health record data, which can be replicated across a variety of settings. Across individual predictors and clinical domains, we consistently found that factors related to health care use were the strongest predictors of PASC diagnosis. This indicates that any observational studies using PASC diagnosis as a primary outcome must rigorously account for heterogeneous health care use. Our temporal findings support the hypothesis that clinicians may be able to accurately assess the risk of PASC in patients before acute COVID-19 diagnosis, which could improve early interventions and preventive care. Our findings also highlight the importance of respiratory characteristics in PASC risk assessment.
UNASSIGNED: RR2-10.1101/2023.07.27.23293272.

Synaptic connectivity defines groups of neurons that engage in correlated activity during specific functional tasks. These co-active groups of neurons form ensembles, the operational units involved in, for example, sensory perception, motor coordination and memory (then called an engram). Traditionally, ensemble formation has been thought to occur via strengthening of synaptic connections via long-term potentiation (LTP) as a plasticity mechanism. This synaptic theory of memory arises from the learning rules formulated by Hebb and is consistent with many experimental observations. Here, we propose, as an alternative, that the intrinsic excitability of neurons and its plasticity constitute a second, non-synaptic mechanism that could be important for the initial formation of ensembles. Indeed, enhanced neural excitability is widely observed in multiple brain areas subsequent to behavioral learning. In cortical structures and the amygdala, excitability changes are often reported as transient, even though they can last tens of minutes to a few days. Perhaps it is for this reason that they have been traditionally considered as modulatory, merely supporting ensemble formation by facilitating LTP induction, without further involvement in memory function (memory allocation hypothesis). We here suggest-based on two lines of evidence-that beyond modulating LTP allocation, enhanced excitability plays a more fundamental role in learning. First, enhanced excitability constitutes a signature of active ensembles and, due to it, subthreshold synaptic connections become suprathreshold in the absence of synaptic plasticity (iceberg model). Second, enhanced excitability promotes the propagation of dendritic potentials toward the soma and allows for enhanced coupling of EPSP amplitude (LTP) to the spike output (and thus ensemble participation). This permissive gate model describes a need for permanently increased excitability, which seems at odds with its traditional consideration as a short-lived mechanism. We propose that longer modifications in excitability are made possible by a low threshold for intrinsic plasticity induction, suggesting that excitability might be on/off-modulated at short intervals. Consistent with this, in cerebellar Purkinje cells, excitability lasts days to weeks, which shows that in some circuits the duration of the phenomenon is not a limiting factor in the first place. In our model, synaptic plasticity defines the information content received by neurons through the connectivity network that they are embedded in. However, the plasticity of cell-autonomous excitability could dynamically regulate the ensemble participation of individual neurons as well as the overall activity state of an ensemble.

Extreme weather events, such as those associated with winds and precipitation, result in billions of euros in damages annually. While changes in extreme precipitation due to global warming have already been detected at sub-continental scales, their complex characteristics make them a challenges to asses at more regional scales. Extreme winds present an even greater challenge as the varying dynamical response to global warming exhibits high levels of uncertainty. This situation is complicated by local scale interactions with orography, cities, land-sea contrasts, etc. The dataset presented here attempts to address these challenges and provide information that will allow robust assessment of extreme winds and precipitation (maximum five day precipitation). We achieve this by leveraging a large ensemble (52 members) of high resolution (12 km) EURO-CORDEX simulations. The dataset will be of value, not only to the scientific community, but also practitioners in the public (e.g., municipal planners, government agencies) and private sectors (e.g., insurers and reinsurers).

UNASSIGNED: Analyzing genomic sequences plays a crucial role in understanding biological diversity and classifying Bamboo species. Existing methods for genomic sequence analysis suffer from limitations such as complexity, low accuracy, and the need for constant reconfiguration in response to evolving genomic datasets.
UNASSIGNED: This study addresses these limitations by introducing a novel Dual Heuristic Feature Selection-based Ensemble Classification Model (DHFS-ECM) for the precise identification of Bamboo species from genomic sequences.
UNASSIGNED: The proposed DHFS-ECM method employs a Genetic Algorithm to perform dual heuristic feature selection. This process maximizes inter-class variance, leading to the selection of informative N-gram feature sets. Subsequently, intra-class variance levels are used to create optimal training and validation sets, ensuring comprehensive coverage of class-specific features. The selected features are then processed through an ensemble classification layer, combining multiple stratification models for species-specific categorization.
UNASSIGNED: Comparative analysis with state-of-the-art methods demonstrate that DHFS-ECM achieves remarkable improvements in accuracy (9.5%), precision (5.9%), recall (8.5%), and AUC performance (4.5%). Importantly, the model maintains its performance even with an increased number of species classes due to the continuous learning facilitated by the Dual Heuristic Genetic Algorithm Model.
UNASSIGNED: DHFS-ECM offers several key advantages, including efficient feature extraction, reduced model complexity, enhanced interpretability, and increased robustness and accuracy through the ensemble classification layer. These attributes make DHFS-ECM a promising tool for real-time clinical applications and a valuable contribution to the field of genomic sequence analysis.

During the 2022-2023 unprecedented mpox epidemic, near real-time short-term forecasts of the epidemic\'s trajectory were essential in intervention implementation and guiding policy. However, as case levels have significantly decreased, evaluating model performance is vital to advancing the field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention and Our World in Data teams, we generated retrospective sequential weekly forecasts for Brazil, Canada, France, Germany, Spain, the United Kingdom, the United States and at the global scale using an auto-regressive integrated moving average (ARIMA) model, generalized additive model, simple linear regression, Facebook\'s Prophet model, as well as the sub-epidemic wave and n-sub-epidemic modelling frameworks. We assessed forecast performance using average mean squared error, mean absolute error, weighted interval scores, 95% prediction interval coverage, skill scores and Winkler scores. Overall, the n-sub-epidemic modelling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best most frequently. The n-sub-epidemic and spatial-wave frameworks considerably improved in average forecasting performance relative to the ARIMA model (greater than 10%) for all performance metrics. Findings further support sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases.

Despite achieving numerous successes with surface defect inspection based on deep learning, the industry still faces challenges in conducting packaging defect inspections that include critical information such as ingredient lists. In particular, while previous achievements primarily focus on defect inspection in high-quality images, they do not consider defect inspection in low-quality images such as those containing image blur. To address this issue, we proposed a noble inference technique named temporal-quality ensemble (TQE), which combines temporal and quality weights. Temporal weighting assigns weights to input images by considering the timing in relation to the observed image. Quality weight prioritizes high-quality images to ensure the inference process emphasizes clear and reliable input images. These two weights improve both the accuracy and reliability of the inference process of low-quality images. In addition, to experimentally evaluate the general applicability of TQE, we adopt widely used convolutional neural networks (CNNs) such as ResNet-34, EfficientNet, ECAEfficientNet, GoogLeNet, and ShuffleNetV2 as the backbone network. In conclusion, considering cases where at least one low-quality image is included, TQE has an F1-score approximately 17.64% to 22.41% higher than using single CNN models and about 1.86% to 2.06% higher than an average voting ensemble.

Subseasonal rainfall forecast skill is critical to support preparedness for hydrometeorological extremes. We assess how a process-informed evaluation, which subsamples forecasting model members based on their ability to represent potential predictors of rainfall, can improve monthly rainfall forecasts within Central America in the following month, using Costa Rica and Guatemala as test cases. We generate a constrained ensemble mean by subsampling 130 members from five dynamic forecasting models in the C3S multimodel ensemble based on their representation of both (a) zonal wind direction and (b) Pacific and Atlantic sea surface temperatures (SSTs), at the time of initialization. Our results show in multiple months and locations increased mean squared error skill by 0.4 and improved detection rates of rainfall extremes. This method is transferrable to other regions driven by slowly-changing processes. Process-informed subsampling is successful because it identifies members that fail to represent the entire rainfall distribution when wind/SST error increases.

The convergence of smart technologies and predictive modelling in prisons presents an exciting opportunity to revolutionize the monitoring of inmate behaviour, allowing for the early detection of signs of distress and the effective mitigation of suicide risks. While machine learning algorithms have been extensively employed in predicting suicidal behaviour, a critical aspect that has often been overlooked is the interoperability of these models. Most of the work done on model interpretations for suicide predictions often limits itself to feature reduction and highlighting important contributing features only. To address this research gap, we used Anchor explanations for creating human-readable statements based on simple rules, which, to our knowledge, have never been used before for suicide prediction models. We also overcome the limitation of anchor explanations, which create weak rules on high-dimensionality datasets, by first reducing data features with the help of SHapley Additive exPlanations (SHAP). We further reduce data features through anchor interpretations for the final ensemble model of XGBoost and random forest. Our results indicate significant improvement when compared with state-of-the-art models, having an accuracy and precision of 98.6% and 98.9%, respectively. The F1-score for the best suicide ideation model appeared to be 96.7%.

Anterior cingulate cortex (ACC) activity is important for operations that require the ability to integrate multiple experiences over time, such as rule learning, cognitive flexibility, working memory, and long-term memory recall. To shed light on this, we analyzed neuronal activity while rats repeated the same behaviors during hour-long sessions to investigate how activity changed over time. We recorded neuronal ensembles as rats performed a decision-free operant task with varying reward likelihoods at three different response ports (n = 5). Neuronal state space analysis revealed that each repetition of a behavior was distinct, with more recent behaviors more similar than those further apart in time. ACC activity was dominated by a slow, gradual change in low-dimensional representations of neural state space aligning with the pace of behavior. Temporal progression, or drift, was apparent on the top principal component for every session and was driven by the accumulation of experiences and not an internal clock. Notably, these signals were consistent across subjects, allowing us to accurately predict trial numbers based on a model trained on data from a different animal. We observed that non-continuous ramping firing rates over extended durations (tens of minutes) drove the low-dimensional ensemble representations. 40% of ACC neurons\' firing ramped over a range of trial lengths and combinations of shorter duration ramping neurons created ensembles that tracked longer durations. These findings provide valuable insights into how the ACC, at an ensemble level, conveys temporal information by reflecting the accumulation of experiences over extended periods.

UNASSIGNED: Breast cancer remains a pressing global health concern, necessitating accurate diagnostics for effective interventions. Deep learning models (AlexNet, ResNet-50, VGG16, GoogLeNet) show remarkable microcalcification identification (>90%). However, distinct architectures and methodologies pose challenges. We propose an ensemble model, merging unique perspectives, enhancing precision, and understanding critical factors for breast cancer intervention. Evaluation favors GoogleNet and ResNet-50, driving their selection for combined functionalities, ensuring improved precision, and dependability in microcalcification detection in clinical settings.
UNASSIGNED: This study presents a comprehensive mammogram preprocessing framework using an optimized deep learning ensemble approach. The proposed framework begins with artifact removal using Otsu Segmentation and morphological operation. Subsequent steps include image resizing, adaptive median filtering, and deep convolutional neural network (D-CNN) development via transfer learning with ResNet-50 model. Hyperparameters are optimized, and ensemble optimization (AlexNet, GoogLeNet, VGG16, ResNet-50) are constructed to identify the localized area of microcalcification. Rigorous evaluation protocol validates the efficacy of individual models, culminating in the ensemble model demonstrating superior predictive accuracy.
UNASSIGNED: Based on our analysis, the proposed ensemble model exhibited exceptional performance in the classification of microcalcifications. This was evidenced by the model\'s average confidence score, which indicated a high degree of dependability and certainty in differentiating these critical characteristics. The proposed model demonstrated a noteworthy average confidence level of 0.9305 in the classification of microcalcification, outperforming alternative models and providing substantial insights into the dependability of the model. The average confidence of the ensemble model in classifying normal cases was 0.8859, which strengthened the model\'s consistent and dependable predictions. In addition, the ensemble models attained remarkably high performances in terms of accuracy, precision, recall, F1-score, and area under the curve (AUC).
UNASSIGNED: The proposed model\'s thorough dataset integration and focus on average confidence ratings within classes improve clinical diagnosis accuracy and effectiveness for breast cancer. This study introduces a novel methodology that takes advantage of an ensemble model and rigorous evaluation standards to substantially improve the accuracy and dependability of breast cancer diagnostics, specifically in the detection of microcalcifications.