A study of "left against medical advice" emergency department patients: an optimized explainable artificial intelligence framework.

The issue of left against medical advice (LAMA) patients is common in today's emergency departments (EDs). This issue represents a medico-legal risk and may result in potential readmission, mortality, or revenue loss. Thus, understanding the factors that cause patients to "leave against medical advice" is vital to mitigate and potentially eliminate these adverse outcomes. This paper proposes a framework for studying the factors that affect LAMA in EDs. The framework integrates machine learning, metaheuristic optimization, and model interpretation techniques. Metaheuristic optimization is used for hyperparameter optimization-one of the main challenges of machine learning model development. Adaptive tabu simulated annealing (ATSA) metaheuristic algorithm is utilized for optimizing the parameters of extreme gradient boosting (XGB). The optimized XGB models are used to predict the LAMA outcomes for patients under treatment in ED. The designed algorithms are trained and tested using four data groups which are created using feature selection. The model with the best predictive performance is then interpreted using the SHaply Additive exPlanations (SHAP) method. The results show that best model has an area under the curve (AUC) and sensitivity of 76% and 82%, respectively. The best model was explained using SHAP method.

Integration of simulated annealing into pigeon inspired optimizer algorithm for feature selection in network intrusion detection systems.

In the context of the 5G network, the proliferation of access devices results in heightened network traffic and shifts in traffic patterns, and network intrusion detection faces greater challenges. A feature selection algorithm is proposed for network intrusion detection systems that uses an improved binary pigeon-inspired optimizer (SABPIO) algorithm to tackle the challenges posed by the high dimensionality and complexity of network traffic, resulting in complex models, reduced accuracy, and longer detection times. First, the raw dataset is pre-processed by uniquely one-hot encoded and standardized. Next, feature selection is performed using SABPIO, which employs simulated annealing and the population decay factor to identify the most relevant subset of features for subsequent review and evaluation. Finally, the selected subset of features is fed into decision trees and random forest classifiers to evaluate the effectiveness of SABPIO. The proposed algorithm has been validated through experimentation on three publicly available datasets: UNSW-NB15, NLS-KDD, and CIC-IDS-2017. The experimental findings demonstrate that SABPIO identifies the most indicative subset of features through rational computation. This method significantly abbreviates the system's training duration, enhances detection rates, and compared to the use of all features, minimally reduces the training and testing times by factors of 3.2 and 0.3, respectively. Furthermore, it enhances the F1-score of the feature subset selected by CPIO and Boost algorithms when compared to CPIO and XGBoost, resulting in improvements ranging from 1.21% to 2.19%, and 1.79% to 4.52%.

Opportunity Analysis of Phosphorus Recovery from Municipal Wastewater for Cropland Based on the Simulated Vehicle Transport Distance in the Yangtze River Delta, China.

With the rapid depletion of phosphate rocks and increasing agricultural demand, establishing a phosphorus (P) flow "loop" rather than a one-way trajectory between cropland and urban areas was imperative. Recovering P from municipal wastewater stood as a viable strategy to mitigate reliance on traditional P-containing chemical fertilizer. This study analyzed the intricate relationships between the potentials of P recovery from municipal wastewater and the P demand of croplands in the populated Yangtze River Delta (YRD), China. An indicator of the P vehicle transport distance was constructed and calculated to estimate the potential to recover and reuse P in agriculture, applying the simulated annealing (SA) algorithm and road networks obtained from OpenStreetMap (OSM). The results indicated that, on a regional scale, recovered P from municipal wastewater could fulfill 14.0% of the cropland P demands in the YRD, with a median P vehicle transport distance of 3.1 km/Mg of P. Notably, the P vehicle transport distance varied largely depending upon the cropland distributions, road density, and P recovery potential from municipal wastewater. The novel methodology developed here determined the optimal transportation routes for P recovery from wastewater treatment plants (WWTPs) to cropland, which played a crucial role in refining the wastewater management strategies aligned with the United Nations Sustainable Development Goals.

Deep simulated annealing for the discovery of novel dental anesthetics with local anesthesia and anti-inflammatory properties.

Multifunctional therapeutics have emerged as a solution to the constraints imposed by drugs with singular or insufficient therapeutic effects. The primary challenge is to integrate diverse pharmacophores within a single-molecule framework. To address this, we introduced DeepSA, a novel edit-based generative framework that utilizes deep simulated annealing for the modification of articaine, a well-known local anesthetic. DeepSA integrates deep neural networks into metaheuristics, effectively constraining molecular space during compound generation. This framework employs a sophisticated objective function that accounts for scaffold preservation, anti-inflammatory properties, and covalent constraints. Through a sequence of local editing to navigate the molecular space, DeepSA successfully identified AT-17, a derivative exhibiting potent analgesic properties and significant anti-inflammatory activity in various animal models. Mechanistic insights into AT-17 revealed its dual mode of action: selective inhibition of NaV1.7 and 1.8 channels, contributing to its prolonged local anesthetic effects, and suppression of inflammatory mediators via modulation of the NLRP3 inflammasome pathway. These findings not only highlight the efficacy of AT-17 as a multifunctional drug candidate but also highlight the potential of DeepSA in facilitating AI-enhanced drug discovery, particularly within stringent chemical constraints.

Design of a sustainable supply chain network of biomass renewable energy in the case of disruption.

Non-renewable energy sources, including fossil fuels, are a type of energy whose consumption rate far exceeds its natural production rate. Therefore, non-renewable resources will be exhausted if alternative energy is not fully developed, leading to an energy crisis in the near future. In this paper, a mathematical model has been proposed for the design of the biomass supply chain of field residues that includes several fields where residue is transferred to hubs after collecting the residue in the hub, the residue is transferred to reactors. In reactors, the residue is converted into gas, which is transferred to condenser and transformers, converted into electricity and sent to demand points through the network. In this paper, the criteria of stability and disturbance were considered, which have been less discussed in related research, and the purpose of the proposed model was to maximize the profit from the sale of energy, including the selling price minus the costs. Genetic algorithm (GA) and simulated annealing (SA) algorithm have been used to solve the model. Then, to prove the complexity of the problem, different and random examples have been presented in different dimensions of the problem. Also, the efficiency of the algorithm in small and large dimensions was proved by comparing GA and SA due to the low deviation of the solutions and the methods used have provided acceptable results suitable for all decision-makers. Also, the effectiveness of the algorithm in small and large dimensions is proven by comparing the genetic algorithm and simulated annealing, and the genetic algorithm's values are better, considering the deviation of 2.9%.and have provided solution methods suitable for all decision makers.

A three-phase algorithm for the pollution traveling Salesman problem.

This paper studies a variant of the Pollution Traveling Salesman Problem (PTSP) focused on fuel consumption and pollution emissions (PTSPC). The PTSPC generalizes the well-known Traveling Salesman Problem (TSP), classified as NP-Hard. In the PTSPC, a vehicle must deliver a load to each customer through a Hamiltonian cycle, minimizing an objective function that considers the speed of each edge, the mass of the truck, the mass of the load pending delivery, and the distance traveled. We have proposed a three-phase algorithm for the PTSPC. The first phase solves the Traveling Salesman Problem (TSP) exactly with a time limit and heuristically using a Nearest Neighborhood Search approach. This phase considers the constraints associated with the PTSPC by using commercial software. In the second phase, both the obtained solutions and their inverse sequences from the initial phase undergo enhancement utilizing metaheuristic algorithms tailored for the PTSPC. These algorithms include Variable Neighborhood Search (VNS), Tabu Search (TS), and Simulated Annealing (SA). Subsequently, for the third phase, the best solution identified in the second phase-determined by having the minimum value by the PTSPC objective function-is subjected to resolution by a mathematical model designed for the PTSPC, considering the heuristic emphasis of commercial software. The efficiency of the former algorithm has been validated through experimentation involving the adaptation of instances from the Pollution Routing Problem (PRP) to the PTSPC. This approach demonstrates the capacity to yield high-quality solutions within acceptable computing times.

Hybrid genetic algorithm-simulated annealing based electric vehicle charging station placement for optimizing distribution network resilience.

Rapid placement of electric vehicle charging stations (EVCSs) is essential for the transportation industry in response to the growing electric vehicle (EV) fleet. The widespread usage of EVs is an essential strategy for reducing greenhouse gas emissions from traditional vehicles. The focus of this study is the challenge of smoothly integrating Plug-in EV Charging Stations (PEVCS) into distribution networks, especially when distributed photovoltaic (PV) systems are involved. A hybrid Genetic Algorithm and Simulated Annealing method (GA-SAA) are used in the research to strategically find the optimal locations for PEVCS in order to overcome this integration difficulty. This paper investigates PV system situations, presenting the problem as a multicriteria task with two primary objectives: reducing power losses and maintaining acceptable voltage levels. By optimizing the placement of EVCS and balancing their integration with distributed generation, this approach enhances the sustainability and reliability of distribution networks.

Sensitivity Analyses of Clinical Trial Designs: Selecting Scenarios and Summarizing Operating Characteristics.

The use of simulation-based sensitivity analyses is fundamental for evaluating and comparing candidate designs of future clinical trials. In this context, sensitivity analyses are especially useful to assess the dependence of important design operating characteristics with respect to various unknown parameters. Typical examples of operating characteristics include the likelihood of detecting treatment effects and the average study duration, which depend on parameters that are unknown until after the onset of the clinical study, such as the distributions of the primary outcomes and patient profiles. Two crucial components of sensitivity analyses are (i) the choice of a set of plausible simulation scenarios and (ii) the list of operating characteristics of interest. We propose a new approach for choosing the set of scenarios to be included in a sensitivity analysis. We maximize a utility criterion that formalizes whether a specific set of sensitivity scenarios is adequate to summarize how the operating characteristics of the trial design vary across plausible values of the unknown parameters. Then, we use optimization techniques to select the best set of simulation scenarios (according to the criteria specified by the investigator) to exemplify the operating characteristics of the trial design. We illustrate our proposal in three trial designs.

Mathematical Modeling of Photo- and Thermomorphogenesis in Plants.

Increased day lengths and warm conditions inversely affect plant growth by directly modulating nuclear phyB, ELF3, and COP1 levels. Quantitative measures of the hypocotyl length have been key to gaining a deeper understanding of this complex regulatory network, while similar quantitative data are the foundation for many studies in plant biology. Here, we explore the application of mathematical modeling, specifically ordinary differential equations (ODEs), to understand plant responses to these environmental cues. We provide a comprehensive guide to constructing, simulating, and fitting these models to data, using the law of mass action to study the evolution of molecular species. The fundamental principles of these models are introduced, highlighting their utility in deciphering complex plant physiological interactions and testing hypotheses. This brief introduction will not allow experimentalists without a mathematical background to run their own simulations overnight, but it will help them grasp modeling principles and communicate with more theory-inclined colleagues.

CheekAge: a next-generation buccal epigenetic aging clock associated with lifestyle and health.

Epigenetic aging clocks are computational models that predict age using DNA methylation information. Initially, first-generation clocks were developed to make predictions using CpGs that change with age. Over time, next-generation clocks were created using CpGs that relate to both age and health. Since existing next-generation clocks were constructed in blood, we sought to develop a next-generation clock optimized for prediction in cheek swabs, which are non-invasive and easy to collect. To do this, we collected MethylationEPIC data as well as lifestyle and health information from 8045 diverse adults. Using a novel simulated annealing approach that allowed us to incorporate lifestyle and health factors into training as well as a combination of CpG filtering, CpG clustering, and clock ensembling, we constructed CheekAge, an epigenetic aging clock that has a strong correlation with age, displays high test-retest reproducibility across replicates, and significantly associates with a plethora of lifestyle and health factors, such as BMI, smoking status, and alcohol intake. We validated CheekAge in an internal dataset and multiple publicly available datasets, including samples from patients with progeria or meningioma. In addition to exploring the underlying biology of the data and clock, we provide a free online tool that allows users to mine our methylomic data and predict epigenetic age.

Optimal Design of Sparse Matrix Phased Array Using Simulated Annealing for Volumetric Ultrasonic Imaging with Total Focusing Method.

The total focusing method (TFM) is often considered to be the 'gold standard' for ultrasonic imaging in the field of nondestructive testing. The use of matrix phased arrays as probes allows for high-resolution volumetric TFM imaging. Conventional TFM imaging involves the use of full matrix capture (FMC) for ultrasonic signals acquisition, but in the case of a matrix phased array, this approach is associated with a huge volume of data to be acquired and processed. This severely limits the frame rate of volumetric imaging with 2D probes and necessitates the use of high-end equipment. Thus, the aim of this research was to develop a novel design method for determining the optimal sparse 2D probe configuration for specific conditions of ultrasonic imaging. The developed approach is based on simulated annealing and involves implementing the solution of the sparse matrix phased array layout optimization problem. In order to implement simulated annealing for the aforementioned task, its parameters were set, the acceptance function was introduced, and the approaches were proposed to compute beam directivity diagrams of sparse matrix phased arrays in TFM imaging. Experimental studies have shown that the proposed approach provides high-quality volumetric imaging with a decrease in data volume of up to 84% compared to that obtained using the FMC data acquisition method.

Improved adaptive regularization for simulated annealing inversion of transient electromagnetic.

Geophysical inversion usually involves ill-posed problem. Regularization is the most commonly used method to mitigate this problem. There are many regularization parameter selection methods, among which the adaptive regularization method can automatically update parameters during iteration, reducing the difficulty of parameter selection. Therefore, it is widely used in linear inversion. However, there are very few studies on the use of adaptive regularization methods in stochastic optimization algorithms. The biggest difficulty is that in stochastic optimization algorithms, the search direction of any iteration is completely random. Data fitting term and stabilizing term vary in a wide range, making it difficult for traditional methods to work. In this paper, we consider the contributions of the data fitting term and the stabilizing term in the objective function and give an improved adaptive regularization method for very fast simulated annealing (VFSA) inversion for transient electromagnetic (TEM) data. The optimized method adjusts the two terms dynamically to make them in balance. We have designed several numerical experiments, and the experimental results demonstrate that the method in this paper not only accelerates the convergence, but also the inversion results are very little affected by the initial regularization parameter. Finally, we apply this method to field data, and the inversion results show very good agreements with nearby borehole data.

Multi-target field control for matrix gradient coils.

OBJECTIVE: Conventional single-target field control for matrix gradient coils will add control complexity in MRI spatial encoding, such as designing specialized fields and sequences. This complexity can be reduced by multi-target field control, which is realized by optimizing the coil structure according to target fields. METHODS: Based on the principle of multi-target field control, the X, Y and Z gradient fields can be set as target fields, and all coil elements can then be divided into three groups to generate these fields. An improved simulated annealing algorithm is proposed to optimize the coil element distribution of each group to generate the corresponding target field. In the improved simulated annealing process, two swapping modes are presented, and randomly selected with certain probabilities that are set to 0.25, 0.5 and 0.75, respectively. The flexibility of the final designed structure is demonstrated by a spherical harmonic basis up to the full second order with single-target field control. An experimental platform is built to measure the gradient fields generated by the designed structure with multi-target target control. RESULTS: With three probabilities of swapping modes, three similar coil element distributions are optimized, and their maximum magnetic field errors for generating X, Y and Z gradients are all below 5%. The structure selected for the final design is the one with a probability of 0.75, considering the coil performance and structural symmetry. The maximum error for all target fields generated by single-target field control is also below 5%. The experimental results show that the measured gradient fields along the axes have enough strength and high linearity. CONCLUSIONS: With the proposed improved simulated annealing algorithm and swapping modes, multi-target field control for matrix gradient coils is verified and achieved in this study by optimizing the coil element distribution. Moreover, this study provides a solution to simplify the complexity of controlling the matrix gradient coil in spatial encoding.

Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.

Understanding phylogenetic relationships among species is essential for many biological studies, which call for an accurate phylogenetic tree to understand major evolutionary transitions. The phylogenetic analyses present a major challenge in estimation accuracy and computational efficiency, especially recently facing a wave of severe emerging infectious disease outbreaks. Here, we introduced a novel, efficient framework called Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) for new sample placement for viruses. In this study, a brand-new recoding method called Frequency Vector Recoding was implemented to approximate the phylogenetic distance, and the Phylogenetic Simulated Annealing Search algorithm was developed to match the recoded distance matrix with the phylogenetic tree. Meanwhile, the indel (insertion/deletion) was heuristically introduced to foreign sequence recognition for the first time. Here, we compared the Bd-RPC with the recent placement software (PAGAN2, EPA-ng, TreeBeST) and evaluated it in Alphacoronavirus, Alphaherpesvirinae, and Betacoronavirus by using Split and Robinson-Foulds distances. The comparisons showed that Bd-RPC maintained the highest precision with great efficiency, demonstrating good performance in new sample placement on all three virus genera. Finally, a user-friendly website (http://www.bd-rpc.xyz) is available for users to classify new samples instantly and facilitate exploration of the phylogenetic research in viruses, and the Bd-RPC is available on GitHub (http://github.com/Bin-Ma/bd-rpc).

LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin.

The connection between the patterns observed in 3C-type experiments and the modeling of polymers remains unresolved. This paper presents a simulation pipeline that generates thermodynamic ensembles of 3D structures for topologically associated domain (TAD) regions by loop extrusion model (LEM). The simulations consist of two main components: a stochastic simulation phase, employing a Monte Carlo approach to simulate the binding positions of cohesins, and a dynamical simulation phase, utilizing these cohesins' positions to create 3D structures. In this approach, the system's total energy is the combined result of the Monte Carlo energy and the molecular simulation energy, which are iteratively updated. The structural maintenance of chromosomes (SMC) protein complexes are represented as loop extruders, while the CCCTC-binding factor (CTCF) locations on DNA sequence are modeled as energy minima on the Monte Carlo energy landscape. Finally, the spatial distances between DNA segments from ChIA-PET experiments are compared with the computer simulations, and we observe significant Pearson correlations between predictions and the real data. LoopSage model offers a fresh perspective on chromatin loop dynamics, allowing us to observe phase transition between sparse and condensed states in chromatin.

Estimation of kinetic parameters in dynamic FDG PET imaging based on shortened protocols: a virtual clinical study.

This study investigated the estimation of kinetic parameters and production of related parametric Ki images in FDG PET imaging using the proposed shortened protocol (three 3-min/bed routine static images) by means of the simulated annealing (SA) algorithm. Six realistic heterogeneous tumors and various levels of [18F] FDG uptake were simulated by the XCAT phantom. An irreversible two-tissue compartment model (2TCM) using population-based input function was employed. By keeping two routine clinical scans fixed (60-min and 90-min post injection), the effect of the early scan time on optimizing the estimation of the pharmacokinetic parameters was investigated. The SA optimization algorithm was applied to estimate micro- and macro-parameters (K1, k2, k3, Ki). The minimum bias for most parameters was observed at a scan time of 20-min, which was < 10%. A highly significant correlation (> 0.9) as well as limited bias (< 10%) were observed between kinetic parameters generated from two methods [two-tissue compartment full dynamic scan (2TCM-full) and two-tissue compartment by SA algorithm (2TCM-SA)]. The analysis showed a strong correlation (> 0.8) between (2TCM-SA) Ki and SUV images. In addition, the tumor-to-background ratio (TBR) metric in the parametric (2TCM-SA) Ki images was significantly higher than SUV, although the SUV images provide better Contrast-to-noise ratio relative to parametric (2TCM-SA) Ki images. The proposed shortened protocol by the SA algorithm can estimate the kinetic parameters in FDG PET scan with high accuracy and robustness. It was also concluded that the parametric Ki images obtained from the 2TCM-SA as a complementary image of the SUV possess more quantification information than SUV images and can be used by the nuclear medicine specialist. This method has the potential to be an alternative to a full dynamic PET scan.

Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics.

Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.

Proactive dynamic vehicle routing problems considering cooperation services for the store-depot-integrated retailer.

Distribution costs remain consistently high in crowded city road networks, posing challenges for traditional distribution methods in efficiently handling dynamic online customer orders. To address this issue, this paper introduces the Proactive Dynamic Vehicle Routing Problem considering Cooperation Service (PDVRPCS) model. Based on proactive prediction and order-matching strategies, the model aims to develop a cost-effective and responsive distribution system. A novel solution framework is proposed, incorporating a proactive prediction method, a matching algorithm and a hybrid Genetic Algorithm-Simulated Annealing (GA-SA) algorithm. To validate the effectiveness of the proposed model and algorithm, a case study is conducted. The experimental results demonstrate that the dynamic scheme can significantly reduce the number of vehicles required for distribution, leading to cost reduction and increased efficiency.

SAMNA: accurate alignment of multiple biological networks based on simulated annealing.

Proteins are important parts of the biological structures and encode a lot of biological information. Protein-protein interaction network alignment is a model for analyzing proteins that helps discover conserved functions between organisms and predict unknown functions. In particular, multi-network alignment aims at finding the mapping relationship among multiple network nodes, so as to transfer the knowledge across species. However, with the increasing complexity of PPI networks, how to perform network alignment more accurately and efficiently is a new challenge. This paper proposes a new global network alignment algorithm called Simulated Annealing Multiple Network Alignment (SAMNA), using both network topology and sequence homology information. To generate the alignment, SAMNA first generates cross-network candidate clusters by a clustering algorithm on a k-partite similarity graph constructed with sequence similarity information, and then selects candidate cluster nodes as alignment results and optimizes them using an improved simulated annealing algorithm. Finally, the SAMNA algorithm was experimented on synthetic and real-world network datasets, and the results showed that SAMNA outperformed the state-of-the-art algorithm in biological performance.

Low distortion reversible database watermarking based on hybrid intelligent algorithm.

In many fields, such as medicine and the computer industry, databases are vital in the process of information sharing. However, databases face the risk of being stolen or misused, leading to security threats such as copyright disputes and privacy breaches. Reversible watermarking techniques ensure the ownership of shared relational databases, protect the rights of data owners and enable the recovery of original data. However, most of the methods modify the original data to a large extent and cannot achieve a good balance between protection against malicious attacks and data recovery. In this paper, we proposed a robust and reversible database watermarking technique using a hash function to group digital relational databases, setting the data distortion and watermarking capacity of the band weight function, adjusting the weight of the function to determine the watermarking capacity and the level of data distortion, using firefly algorithms (FA) and simulated annealing algorithms (SA) to improve the efficiency of the search for the location of the watermark embedded and, finally, using the differential expansion of the way to embed the watermark. The experimental results prove that the method maintains the data quality and has good robustness against malicious attacks.