Accurate Model Research Articles

MuToN Quantifies Binding Affinity Changes upon Protein Mutations by Geometric Deep Learning.

Assessing changes in protein-protein binding affinity due to mutations helps understanding a wide range of crucial biological processes within cells. Despite significant efforts to create accurate computational models, predicting how mutations affect affinity remains challenging due to the complexity of the biological mechanisms involved. In the present work, a geometric deep learning framework called MuToN is introduced for quantifying protein binding affinity change upon residue mutations. The method, designed with geometric attention networks, is mechanism-aware. It captures changes in the protein binding interfaces of mutated complexes and assesses the allosteric effects of amino acids. Experimental results highlight MuToN's superiority compared to existing methods. Additionally, MuToN's flexibility and effectiveness are illustrated by its precise predictions of binding affinity changes between SARS-CoV-2 variants and the ACE2 complex.

Possibilities of Predicting the Manifestation of HELLP Syndrome

Introduction. Despite the use of modern principles of treatment of severe preeclampsia, mortality rates for mother and newborn in the development of life-threatening complication of preeclampsia, such as HELLP syndrome, remains high. The introduction of accurate models of early diagnosis and prediction of the probability of manifestation and severity of the HELLP syndrome into everyday medical practice will improve the safety of delivery of pregnant women with severe preeclampsia.The aim of the study is to determine the current state of the issue and systematize current data on methods of predicting the probability of HELLP syndrome manifestation.Materials and methods. An analytical review of the literature. A qualitative analysis of clinical trials and reviews on prediction of HELLP syndrome was conducted using the following data sources: PubMed and Google Scholar. The search was carried out in Russian and English, using the keywords “predictors”, or “prediction”, and “HELLP syndrome”. The date of the last search query is 22 March 2024.Results. Anamnestic data and initial characteristics of patients with HELLP syndrome were analyzed.Discussion. The analytical review included publications devoted to the study of the influence of predictive capabilities of potential biochemical markers, clinical and anamnestic signs and instrumental examination data on the probability of HELLP syndrome development.Conclusion. Adequate prediction of the manifestation of HELLP syndrome is possible on the basis of a comprehensive analysis of all identified factors, allowing the identification of effective prognostic models to improve maternal and fetal outcomes in pregnant women with severe preeclampsia.

Modeling cardiac microcirculation for the simulation of coronary flow and 3D myocardial perfusion.

Accurate modeling of blood dynamics in the coronary microcirculation is a crucial step toward the clinical application of in silico methods for the diagnosis of coronary artery disease. In this work, we present a new mathematical model of microcirculatory hemodynamics accounting for microvasculature compliance and cardiac contraction; we also present its application to a full simulation of hyperemic coronary blood flow and 3D myocardial perfusion in real clinical cases. Microvasculature hemodynamics is modeled with a compliant multi-compartment Darcy formulation, with the new compliance terms depending on the local intramyocardial pressure generated by cardiac contraction. Nonlinear analytical relationships for vessels distensibility are included based on experimental data, and all the parameters of the model are reformulated based on histologically relevant quantities, allowing a deeper model personalization. Phasic flow patterns of high arterial inflow in diastole and venous outflow in systole are obtained, with flow waveforms morphology and pressure distribution along the microcirculation reproduced in accordance with experimental and in vivo measures. Phasic diameter change for arterioles and capillaries is also obtained with relevant differences depending on the depth location. Coronary blood dynamics exhibits a disturbed flow at the systolic onset, while the obtained 3D perfusion maps reproduce the systolic impediment effect and show relevant regional and transmural heterogeneities in myocardial blood flow (MBF). The proposed model successfully reproduces microvasculature hemodynamics over the whole heartbeat and along the entire intramural vessels. Quantification of phasic flow patterns, diameter changes, regional and transmural heterogeneities in MBF represent key steps ahead in the direction of the predictive simulation of cardiac perfusion.

Efficient maximum power point extraction using hybrid optimisation based parameter estimation model of solar double diode model

ABSTRACT PV systems operate most efficiently when they are operated at their Maximum Power Point (MPP). Despite the wide range of MPPT approaches available, there is potential to improve the efficiency of MPP Tracking (MPPT). One method to achieve this improvement is to use model-based MPPT techniques, which can speed up the MPP search process by estimating the MPP with a high degree of accuracy. The main objective of the research, which is to create an efficient double-diode model-based MPPT technique with a focus on hybrid Optimisation, is informed by this justification. The suggested method for predicting the MPP voltage makes use of an accurate double-diode model for PV modules that is dependent on temperature and irradiance. This research employs a parameter estimation system based on the proposed Optimisation algorithm known as Memory Integrated Sand Cat Swarm Optimisation Algorithm (MI-SCS) to overcome the limitations of standard parameter estimate methods, which are related to the availability of experimental p-V curves or datasheets with precise temperature and irradiance values. The method that is being given is based on the integration of the Crow Search Optimisation (CSO) Algorithm with the Sand Cat Swarm Optimisation (SCSO) algorithm.

Myelodysplastic syndrome risk assessment using priority linked correlated feature set using ResNet50

Myelodysplastic syndrome (MDS) is more common as people get older, and the best way to treat these conditions is to catch them early. Acute myeloid leukemia (AML) is a more aggressive form of MDS; about 30 % of cases advance to this disease. The key to intervening before MDS develops into AML is early identification. If doctors can diagnose MDS early, they can start treatment sooner, which could slow the disease’s progression and enhance patients’ quality of life. But because it is so similar to other conditions, MDS is frequently misdiagnosed. Early detection of MDS can let medical experts to provide better treatment, which may slow the disease’s progression and boost survival rates. Assessment of Bone Marrow (BM) histopathology is used to diagnose MDS and myeloproliferative neoplasm (MPN) by identifying dysplastic cellular shape, cellularity, and blast excess. Deep Learning (DL) algorithms can account for the genome’s numerous complicated interconnections, allowing for the creation of more accurate prognostication models. The ResNet50 network consists of 50 layers: 48 convolutional layers, 1 MaxPool layer, and 1 average pool layer. This research presents a Priority Linked Correlated Feature Set using ResNet50 (PLCFS-ResNet50) for risk assessment of MDS. The proposed model uses the feature subset for training the Resnet50 model and for risk assessment so that proper diagnosis can be done in advance. The proposed model achieves 98.6 % accuracy in feature set generation and 98.7 % accuracy in risk assessment of MDS. The proposed model when contrasted with the traditional model exhibits better prediction levels.

Efficient maximum power point extraction using hybrid optimisation based parameter estimation model of solar double diode model

ABSTRACT PV systems operate most efficiently when they are operated at their Maximum Power Point (MPP). Despite the wide range of MPPT approaches available, there is potential to improve the efficiency of MPP Tracking (MPPT). One method to achieve this improvement is to use model-based MPPT techniques, which can speed up the MPP search process by estimating the MPP with a high degree of accuracy. The main objective of the research, which is to create an efficient double-diode model-based MPPT technique with a focus on hybrid Optimisation, is informed by this justification. The suggested method for predicting the MPP voltage makes use of an accurate double-diode model for PV modules that is dependent on temperature and irradiance. This research employs a parameter estimation system based on the proposed Optimisation algorithm known as Memory Integrated Sand Cat Swarm Optimisation Algorithm (MI-SCS) to overcome the limitations of standard parameter estimate methods, which are related to the availability of experimental p-V curves or datasheets with precise temperature and irradiance values. The method that is being given is based on the integration of the Crow Search Optimisation (CSO) Algorithm with the Sand Cat Swarm Optimisation (SCSO) algorithm.

Coupled natural-social water system in a subwatershed of the Tennessee River Basin

Regional water cycle systems are increasingly characterized by the dual effect of natural and social processes, which have profound impacts on global water security. However, accurately interpreting the changes in the coupled natural-social water system and identifying the driving factors pose significant challenges. Here, we attempted to model a coupled natural-social water system in the East Fork Poplar Creek (EFPC) watershed of the Tennessee River, United States. The study area features two social water cycle components: a local water transfer project and the Oak Ridge Wastewater Treatment Facility (ORWTF). We conducted the Soil and Water Assessment Tool (SWAT) modeling in the open-source light-weight QGIS software, with the synthesis of various climate and land use change scenarios in both historical periods (1980–2016) and future periods (2017–2050). We achieved more accurate and realistic model simulations when considering the social water cycle components, indicating that the social water cycle accounted for 13–18 % of the observed streamflow. Climate variation/change dominates natural runoff changes. Though land use and cover change (LUCC) had minimal effect on natural runoff, it already had a profound impact on the process of runoff generation: LUCC has a notable impact on its components, i.e., surface runoff (RS) and subsurface runoff (RSS). Specifically, LUCC would be responsible for 152 % and 45 % of the changes in RS and RSS, respectively, in future periods. This study highlights the significance of artificial water discharge and withdrawal impacts on the water cycle and emphasizes the need for water resources management measures that fully consider natural-social hydrological processes.

In Hot Water: Current Thermal Threshold Methods Unlikely to Predict Invasive Species Shifts in NW Atlantic.

As global temperatures continue to rise, accurate predicted species distribution models will be important for forecasting the movement of range-shifting species. These predictions rely on measurements of organismal thermal tolerance, which can be measured using classical threshold concepts such as Arrhenius Break Temperatures and Critical Thermal Temperatures, or through ecologically relevant measurements-such as the temperature at which reproduction and growth occur. Many species, including invasive species, exhibit thermal plasticity, so these thresholds may change based on ambient temperature, life stage, and measurement techniques. Here, we review thermal thresholds for 15 invertebrate species invasive to the Gulf of Maine. The high degree of variability within a species and between applied conceptual frameworks suggests that modeling the future distribution of these species in all ecosystems, but especially in the rapidly warming Northwest Atlantic and Gulf of Maine, will be challenging. While each of these measurement techniques are valid, we suggest contextualization and integration of threshold measurements for accurate modeling.

Jointly efficient encoding and decoding in neural populations.

The efficient coding approach proposes that neural systems represent as much sensory information as biological constraints allow. It aims at formalizing encoding as a constrained optimal process. A different approach, that aims at formalizing decoding, proposes that neural systems instantiate a generative model of the sensory world. Here, we put forth a normative framework that characterizes neural systems as jointly optimizing encoding and decoding. It takes the form of a variational autoencoder: sensory stimuli are encoded in the noisy activity of neurons to be interpreted by a flexible decoder; encoding must allow for an accurate stimulus reconstruction from neural activity. Jointly, neural activity is required to represent the statistics of latent features which are mapped by the decoder into distributions over sensory stimuli; decoding correspondingly optimizes the accuracy of the generative model. This framework yields in a family of encoding-decoding models, which result in equally accurate generative models, indexed by a measure of the stimulus-induced deviation of neural activity from the marginal distribution over neural activity. Each member of this family predicts a specific relation between properties of the sensory neurons-such as the arrangement of the tuning curve means (preferred stimuli) and widths (degrees of selectivity) in the population-as a function of the statistics of the sensory world. Our approach thus generalizes the efficient coding approach. Notably, here, the form of the constraint on the optimization derives from the requirement of an accurate generative model, while it is arbitrary in efficient coding models. Moreover, solutions do not require the knowledge of the stimulus distribution, but are learned on the basis of data samples; the constraint further acts as regularizer, allowing the model to generalize beyond the training data. Finally, we characterize the family of models we obtain through alternate measures of performance, such as the error in stimulus reconstruction. We find that a range of models admits comparable performance; in particular, a population of sensory neurons with broad tuning curves as observed experimentally yields both low reconstruction stimulus error and an accurate generative model that generalizes robustly to unseen data.

Jointly efficient encoding and decoding in neural populations.

The efficient coding approach proposes that neural systems represent as much sensory information as biological constraints allow. It aims at formalizing encoding as a constrained optimal process. A different approach, that aims at formalizing decoding, proposes that neural systems instantiate a generative model of the sensory world. Here, we put forth a normative framework that characterizes neural systems as jointly optimizing encoding and decoding. It takes the form of a variational autoencoder: sensory stimuli are encoded in the noisy activity of neurons to be interpreted by a flexible decoder; encoding must allow for an accurate stimulus reconstruction from neural activity. Jointly, neural activity is required to represent the statistics of latent features which are mapped by the decoder into distributions over sensory stimuli; decoding correspondingly optimizes the accuracy of the generative model. This framework yields in a family of encoding-decoding models, which result in equally accurate generative models, indexed by a measure of the stimulus-induced deviation of neural activity from the marginal distribution over neural activity. Each member of this family predicts a specific relation between properties of the sensory neurons-such as the arrangement of the tuning curve means (preferred stimuli) and widths (degrees of selectivity) in the population-as a function of the statistics of the sensory world. Our approach thus generalizes the efficient coding approach. Notably, here, the form of the constraint on the optimization derives from the requirement of an accurate generative model, while it is arbitrary in efficient coding models. Moreover, solutions do not require the knowledge of the stimulus distribution, but are learned on the basis of data samples; the constraint further acts as regularizer, allowing the model to generalize beyond the training data. Finally, we characterize the family of models we obtain through alternate measures of performance, such as the error in stimulus reconstruction. We find that a range of models admits comparable performance; in particular, a population of sensory neurons with broad tuning curves as observed experimentally yields both low reconstruction stimulus error and an accurate generative model that generalizes robustly to unseen data.

Prediction of Anthracnose Risk in Large-Leaf Tea Trees Based on the Atmospheric Environmental Changes in Yunnan Tea Gardens—Cox Regression Model and Machine Learning Model

Crop diseases pose a major threat to agricultural production, quality, and sustainable development, highlighting the importance of early disease risk prediction for effective disease control. Tea anthracnose can easily occur in Yunnan under high-temperature and high-humidity environments, which seriously affects the ecosystem of tea gardens. Therefore, the establishment of accurate, non-destructive, and rapid prediction models has a positive impact on the conservation of biodiversity in tea plantations. Because of the linear relationship between disease occurrence and environmental conditions, the growing environmental conditions can be effectively used to predict crop diseases. Based on the climate data collected by Internet of Things devices, this study uses LASSO-COX-NOMOGRAM to analyze the expression of tea anthracrum to different degrees through Limma difference analysis, and it combines Cox single-factor analysis to study the influence mechanism of climate and environmental change on tea anthracrum. Modeling factors were screened by LASSO regression, 10-fold cross-validation and Cox multi-factor analysis were used to establish the basis of the model, the nomogram prediction model was constructed, and a Shiny- and DynNOM-visualized prediction system was built. The experimental results showed that the AUC values of the model were 0.745 and 0.731 in the training set and 0.75 and 0.747 in the verification set, respectively, when the predicted change in tea anthracnose disease risk was greater than 30% and 60%, and the calibration curve was in good agreement with the ideal curve. The accuracy of external verification was 83.3% for predicting tea anthracnose of different degrees. At the same time, compared with the traditional prediction method, the method is not affected by the difference in leaf background, which provides research potential for early prevention and phenotypic analysis, and also provides an effective means for tea disease identification and harm analysis.

Feature Selection and Performance Evaluation of Buzzer Classification Model

In the rapidly evolving digital age, social media platforms have transformed into battleground for shaping public opinion. Among these platforms, X has been particularly susceptible to the phenomenon of 'buzzers', paid or coordinated actors who manipulate online discussions and influence public sentiment. This manipulation poses significant challenges for users, researchers, and policymakers alike, necessitating robust detection measures and strategic feature selection for accurate classification models. This research explores the utilization of various feature selection techniques to identify the most influential features among the 24 features employed in the classification modeling using Support Vector Machine. This study found that selecting 11 key features yields a remarkably effective classification model, achieving an impressive F1-score of 87.54 in distinguishing between buzzer and non-buzzer accounts. These results suggest that focusing on the relevant features can improve the accuracy and efficiency of buzzer detection models. By providing a more robust and adaptable solution to buzzer detection, our research has the potential to advance social media research and policy. This enabling researchers and policymakers to devise strategies aimed at mitigating misinformation dissemination and cultivating an environment of trust and integrity within social media platforms, thus fostering healthier online interactions and discourse.

Bug numbers matter: An empirical study of effort‐aware defect prediction using class labels versus bug numbers

AbstractPrevious research have utilized public software defect datasets such as NASA, RELINK, and SOFTLAB, which only contain class label information. Most effort‐aware defect prediction (EADP) studies are carried out around these datasets. However, EADP studies typically relying on predicted bug number (i.e., considering modules as effort) or density (i.e., considering lines of code as effort) for ranking software modules. To explore the impact of bug number information in constructing EADP models, we access the performance degradation of the best‐performing learning‐to‐rank methods when using class labels instead of bug numbers for training. The experimental results show that using class labels instead of bug numbers in building EADP models results in an decrease in the detected bugs when module is considering as effort. When effort is LOC, using class labels to construct EADP models can lead to a significant increase in the initial false alarms and a significant increase in the modules that need to be inspected. Therefore, we recommend not only the class labels but also the bug number information should be disclosed when publishing software defect datasets, in order to construct more accurate EADP models.

ASO Author Reflections: Accurate and User-Friendly Models for Predicting Oncologic Outcomes Following Partial Nephrectomy in Patients with cT1-ccRCC.

ASO Author Reflections: Accurate and User-Friendly Models for Predicting Oncologic Outcomes Following Partial Nephrectomy in Patients with cT1-ccRCC.

Machine learning for gap‐filling in greenhouse gas emissions databases

AbstractGreenhouse gas (GHG) emissions datasets are often incomplete due to inconsistent reporting and poor transparency. Filling the gaps in these datasets allows for more accurate targeting of strategies aiming to accelerate the reduction of GHG emissions. This study evaluates the potential of machine learning methods to automate the completion of GHG datasets. We use three datasets of increasing complexity with 18 different gap‐filling methods and provide a guide to which methods are useful in which circumstances. If few dataset features are available, or the gap consists only of a missing time step in a record, then simple interpolation is often the most accurate method and complex models should be avoided. However, if more features are available and the gap involves non‐reporting emitters, then machine learning methods can be more accurate than simple extrapolation. Furthermore, the secondary output of feature importance from complex models allows for data collection prioritization to accelerate the improvement of datasets. Graph‐based methods are particularly scalable due to the ease of updating predictions given new data and incorporating multimodal data sources. This study can serve as a guide to the community upon which to base ever more integrated frameworks for automated detailed GHG emissions estimations, and implementation guidance is available at https://hackmd.io/@luke‐scot/ML‐for‐GHG‐database‐completion and https://doi.org/10.5281/zenodo.10463104. This article met the requirements for a gold‐gold JIE data openness badge described at http://jie.click/badges.

Recent Progress in the Electroweak Structure of Light Nuclei Using Quantum Monte Carlo Methods

Nuclei will play a prominent role in searches for physics beyond the Standard Model as the active material in experiments. In order to reliably interpret new physics signals, one needs an accurate model of the underlying nuclear dynamics. In this review, we discuss recent progress made with quantum Monte Carlo approaches for calculating the electroweak structure of light nuclei. We place particular emphasis on recent β decay, muon capture, neutrinoless double β decay, and electron scattering results.

Prediction of NOx Emissions in Thermal Power Plants Using a Dynamic Soft Sensor Based on Random Forest and Just-in-Time Learning Methods

Combustion optimization is an effective way to improve the efficiency of thermal power generation and reduce carbon and NOx emissions. Real-time and precise NOx emission prediction is the basis for combustion optimization control of thermal power plants. To construct an accurate NOx concentration prediction model, a novel just-in-time learning (JITL) method based on random forest (RF) is proposed in the present work. With this method, first, an improved permutation importance algorithm is proposed to extract important variables. In addition, a similarity index that incorporates temporal and spatial measures is defined to select a local training set representative of the process data. Moreover, considering the influence of model parameters on prediction performance under different working conditions, a process monitoring method based on a moving window (MW) is used to monitor the change in working conditions and guide online updating. The experimental results show that the proposed method has excellent prediction accuracy, with a coefficient of determination of 0.9319, a root-mean-square error of 3.6960 mg/m3, and an average absolute error of 2.7718 mg/m3 on the test set, making it superior to other traditional methods.

A new method for surge arrester placement in high‐voltage substations considering environmental effects

AbstractConventional approaches for determining the optimal locations of surge arresters (SAs) can result in an unnecessary increase in the number of these devices in high‐voltage substations. This study presents an effective technique for determining the optimal locations of SAs. The lightning back flashover (BF) and switching over‐voltages are predicted with the accurate modeling of the transient behavior of all elements of high‐voltage substations and transmission lines, considering the effect of environmental conditions. Also, the proposed limiting parameter Monte Carlo (MC‐LP) method is utilized to correctly select the probability distribution of the possible strokes for predicting the insulation risk (IR) of a transformer based on transient over‐voltage on the transformer end. Therefore, the most appropriate location to install an SA can be determined with a minimum number of calculations using the structural data of the substation, lines connected to it, and the transformer. Simulations are based on experimental results, and the number of calculations significantly decreases using the proposed algorithm. Simulations of the sample network and implementation of the proposed algorithm with MATLAB and EMTP‐RV prove the efficiency of the proposed method for optimum SA placement.

Towards Model-Driven Explainable Artificial Intelligence: Function Identification with Grammatical Evolution

Machine learning is a well-matured discipline, and exploration of datasets can be performed in an efficient way, leading to accurate and operational prediction and decision models. On the other hand, most methods tend to produce black-box-type models, which can be considered a serious drawback. This is so, since in case of numerous practical applications, it is also required to justify, explain, and uncover the inner decision mechanism so that an in-depth understanding of the causal and functional dependencies becomes possible and some responsibility for the decision can be considered. This paper addresses the critical need for model-driven eXplainable Artificial Intelligence (XAI) by exploring the limitations inherent in existing explanatory mechanisms, such as LIME or SHAP, which rely solely on input data. This seems to be an intrinsic limitation and a conceptual error, as no expert domain knowledge can come into play, and no analytical models of the phenomena under investigation are created. In order to deal with this issue, this paper puts forward the idea of building open, white-box explanatory models. To do that, we propose employing grammatical evolution tools combined with expert domain knowledge. The results demonstrate that the developed models can effectively explain the structure and behavior of decision models in terms of components, connections, causality, and simple functional dependencies.

Towards Model-Driven Explainable Artificial Intelligence: Function Identification with Grammatical Evolution

Machine learning is a well-matured discipline, and exploration of datasets can be performed in an efficient way, leading to accurate and operational prediction and decision models. On the other hand, most methods tend to produce black-box-type models, which can be considered a serious drawback. This is so, since in case of numerous practical applications, it is also required to justify, explain, and uncover the inner decision mechanism so that an in-depth understanding of the causal and functional dependencies becomes possible and some responsibility for the decision can be considered. This paper addresses the critical need for model-driven eXplainable Artificial Intelligence (XAI) by exploring the limitations inherent in existing explanatory mechanisms, such as LIME or SHAP, which rely solely on input data. This seems to be an intrinsic limitation and a conceptual error, as no expert domain knowledge can come into play, and no analytical models of the phenomena under investigation are created. In order to deal with this issue, this paper puts forward the idea of building open, white-box explanatory models. To do that, we propose employing grammatical evolution tools combined with expert domain knowledge. The results demonstrate that the developed models can effectively explain the structure and behavior of decision models in terms of components, connections, causality, and simple functional dependencies.