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Keywords = Bayesian evolutionary optimization

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17 pages, 474 KB  
Article
Planning and Decision-Making Method for Incomplete Information Game Among Multiple Energy Entities Considering Environmental Costs and Carbon Trading Mechanism
by Zhipeng Lu, Yuejiao Wang, Pu Zhao, Song Yang, Yu Zhang, Nan Yang and Lei Zhang
Processes 2026, 14(6), 899; https://doi.org/10.3390/pr14060899 - 11 Mar 2026
Viewed by 256
Abstract
With the rapid development of integrated energy systems (IES) towards integration and marketization, the collaborative planning of multi-energy entities has become a research hotspot. However, in real-world market environments, various energy entities often face information asymmetry and competitive interests, posing significant challenges to [...] Read more.
With the rapid development of integrated energy systems (IES) towards integration and marketization, the collaborative planning of multi-energy entities has become a research hotspot. However, in real-world market environments, various energy entities often face information asymmetry and competitive interests, posing significant challenges to the optimal scheduling of the system. To address the incomplete information and competitive constraints among multiple energy hubs (EH) within IES, this paper constructs a multi-entity game planning model that accounts for environmental costs and carbon trading mechanisms. The model employs Bayesian game methods to handle the incomplete information among EH and analyzes the dynamic interactive behaviors of market entities under different strategies through multilateral incomplete information evolutionary game theory. Meanwhile, this paper incorporates carbon trading mechanisms along with the coupling technologies of power-to-gas (P2G) and carbon capture systems (CCS) to balance the economic efficiency and environmental protection. Additionally, in response to investment uncertainty, the real options theory is utilized for evaluation, and then a multi-entity incomplete information planning model is constructed, which is solved by using a nested algorithm proposed in this paper. This approach balances the interests of various entities and enhances the comprehensive long-term investment returns considering options. Simulation results demonstrate that the model effectively reflects the game behaviors among multi-energy entities under incomplete information, yielding optimized scheduling solutions that closely align with real-world scenarios. It improves economic benefits while reducing environmental pollution, providing theoretical foundations and methodological support for the planning of integrated energy systems involving multiple entities in electricity market environments. Full article
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22 pages, 5399 KB  
Article
Bridge Deformation Prediction with BGCO-PIC-DA-LSTM Based on Prior-Informed Multi-Source Fusion and Dual-Stream Residual Attention
by Pengchen Qin and Feng Wang
Appl. Sci. 2026, 16(6), 2681; https://doi.org/10.3390/app16062681 - 11 Mar 2026
Viewed by 256
Abstract
Accurate deflection prediction is vital for structural health monitoring of large-span bridges yet remains challenging due to complex nonlinear environmental couplings. This paper proposes a hybrid deep learning framework, BGCO-PIC-DA-LSTM, for precise bridge deflection prediction. First, a Prior-Informed Correlation (PIC) strategy incorporating temperature [...] Read more.
Accurate deflection prediction is vital for structural health monitoring of large-span bridges yet remains challenging due to complex nonlinear environmental couplings. This paper proposes a hybrid deep learning framework, BGCO-PIC-DA-LSTM, for precise bridge deflection prediction. First, a Prior-Informed Correlation (PIC) strategy incorporating temperature lag terms is introduced to enhance the statistical consistency of input features. Second, a dual-stream residual Bi-LSTM network integrating adaptive temporal attention is developed to simultaneously capture long-term evolutionary trends and instantaneous dynamic fluctuations. Furthermore, a Bayesian-Gradient Cooperative Optimization (BGCO) strategy is employed to automatically configure optimal hyperparameters. Validation using in situ data from a large-span cable-stayed bridge demonstrates that the proposed method significantly outperforms baseline algorithms in prediction accuracy and robustness. Additionally, the prediction residuals exhibit characteristics approximating zero-mean Gaussian white noise, establishing a reference baseline for structural state evolution and providing a certain basis for identifying potential performance shifts. Full article
(This article belongs to the Section Civil Engineering)
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35 pages, 20162 KB  
Article
An Efficient and Sparse Kernelized Grey RVFL Network for Energy Forecasting
by Wenkang Gong and Gaofeng Zong
Systems 2026, 14(3), 257; https://doi.org/10.3390/systems14030257 - 28 Feb 2026
Viewed by 249
Abstract
Reliable energy forecasting is essential for the planning and dispatch of power and fuel systems; however, energy series are often short and exhibit pronounced nonlinearity. To tackle this small sample setting, we propose a gray random vector functional link (GRVFL) framework and further [...] Read more.
Reliable energy forecasting is essential for the planning and dispatch of power and fuel systems; however, energy series are often short and exhibit pronounced nonlinearity. To tackle this small sample setting, we propose a gray random vector functional link (GRVFL) framework and further derive a kernelized variant (KGRVFL). In GRVFL, an RVFL network is integrated into gray system modeling, and the parameters are learned via sparsity-regularized regression, enabling stable and reproducible training without backpropagation or evolutionary optimization. Hyperparameters are tuned using Bayesian optimization driven by a Top-k mean absolute percentage error (Top-k MAPE) criterion to improve robustness. To further promote compactness, we introduce a fractional ratio-type Fr-1 penalty and solve the resulting problem efficiently using a fractional coordinate descent (FCD) algorithm. The proposed methods are assessed on six real-world energy datasets using eight evaluation metrics. Comparisons with nine gray model baselines and six machine learning forecasters demonstrate that the sparse KGRVFL (SKGRVFL) achieves higher predictive accuracy and improved training stability under small sample conditions. Full article
(This article belongs to the Section Systems Engineering)
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21 pages, 1214 KB  
Article
Bayesian vs. Evolutionary Optimization for Cryptocurrency Perpetual Trading: The Role of Parameter Space Topology
by Petar Zhivkov and Juri Kandilarov
Mathematics 2026, 14(5), 761; https://doi.org/10.3390/math14050761 - 25 Feb 2026
Viewed by 1085
Abstract
Hyperparameter optimization for cryptocurrency trading strategies encounters distinct challenges owing to continuous operation, volatility rates 3–4 times higher than equity indices, and price dynamics influenced by market sentiment. Bayesian optimization (Tree-Structured Parzen Estimator, TPE) and evolutionary algorithms (Differential Evolution, DE) are great for [...] Read more.
Hyperparameter optimization for cryptocurrency trading strategies encounters distinct challenges owing to continuous operation, volatility rates 3–4 times higher than equity indices, and price dynamics influenced by market sentiment. Bayesian optimization (Tree-Structured Parzen Estimator, TPE) and evolutionary algorithms (Differential Evolution, DE) are great for machine learning, but there are not many systematic comparisons for trading cryptocurrencies. This research evaluates Random Sampling, TPE, and DE through 36 factorial experiments, comprising 3 trading strategies (3, 4, and 5 hyperparameters) × 3 optimizers × 4 cryptocurrency pairs (BTC/USDT, ETH/USDT, INJ/USDT, SOL/USDT), resulting in 14,400 backtesting trials with walk-forward validation. TPE won 75% of strategy–asset pairs (9 of 12), reaching 90% of optimal performance within 13–17% of trial budgets. We find strategy-specific optimizer compatibility: mean-reversion strategies show DE underperformance independent of topology (−1% to −8%), whereas trend-following strategies show consistent DE competitiveness across assets (+13% to +37%). Most notably, for the same strategy, parameter space topology differs significantly between assets (trend following: 4.6% viable on BTC to 82% on ETH = 17.8×; mean reversion: 10.8% on ETH to 92% on SOL = 8.5×), indicating that topology results from strategy–asset interaction rather than intrinsic properties. Complete testing failures and widespread severe overfitting point to regime non-stationarity as a fundamental problem. Among the contributions are: (1) evidence shows that topological effects are dominated by optimizer–strategy compatibility (DE fails on mean-reversion strategies even in 92% viable spaces, but succeeds on trend-following strategies regardless of topology, spanning 13.6–82% viable spaces); (2) this is the first systematic Bayesian versus evolutionary comparison across 4 cryptocurrency assets; (3) parameter space topology emerges from strategy–asset interaction, varying up to 17.8-fold; and (4) single-period backtests inadequately identify parameter instability. Full article
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23 pages, 2076 KB  
Article
SymXplorer: Symbolic Analog Topology Exploration of a Tunable Common-Gate Bandpass TIA for Radio-over-Fiber Applications
by Danial Noori Zadeh and Mohamed B. Elamien
Electronics 2026, 15(3), 515; https://doi.org/10.3390/electronics15030515 - 25 Jan 2026
Viewed by 446
Abstract
While circuit parameter optimization has matured significantly, the systematic discovery of novel circuit topologies remains a bottleneck in analog design automation. This work presents SymXplorer, an open-source Python framework designed for automated topology exploration through symbolic modeling of analog components. The framework enables [...] Read more.
While circuit parameter optimization has matured significantly, the systematic discovery of novel circuit topologies remains a bottleneck in analog design automation. This work presents SymXplorer, an open-source Python framework designed for automated topology exploration through symbolic modeling of analog components. The framework enables a component-agnostic approach to architecture-level synthesis, integrating stability analysis and higher-order filter exploration within a streamlined API. By modeling non-idealities as lumped parameters, the framework accounts for physical constraints directly within the symbolic analysis. To facilitate circuit sizing, SymXplorer incorporates a multi-objective optimization toolbox featuring Bayesian optimization and evolutionary algorithms for simulation-in-the-loop evaluation. Using this framework, we conduct a systematic search for differential Common-Gate (CG) Bandpass Transimpedance Amplifier (TIA) topologies tailored for 5G New Radio (NR) Radio-over-Fiber applications. We propose a novel, orthogonally tunable Bandpass TIA architecture identified by the tool. Implementation in 65 nm CMOS technology demonstrates the efficacy of the framework. Post-layout results exhibit a tunable gain of 30–50 dBΩ, a center frequency of 3.5 GHz, and a tuning range of 500 MHz. The design maintains a power consumption of less than 400 μW and an input-referred noise density of less than 50 pA/Hz across the passband. Finally, we discuss how this symbolic framework can be integrated into future agentic EDA workflows to further automate the analog design cycle. SymXplorer is open-sourced to encourage innovation in symbolic-driven analog design automation. Full article
(This article belongs to the Section Circuit and Signal Processing)
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37 pages, 3749 KB  
Article
Quantum-Enhanced Residual Convolutional Attention Architecture for Renewable Forecasting in Off-Grid Cloud Microgrids
by Ibrahim Alzamil
Mathematics 2026, 14(1), 181; https://doi.org/10.3390/math14010181 - 3 Jan 2026
Cited by 1 | Viewed by 562
Abstract
Multimodal forecasting is increasingly needed to maintain energy levels, storage capacity, and compute efficiency in off-grid, renewable-powered cloud environments. Variable sensor quality, uncertain interactions with renewable energy, and rapidly changing weather patterns make real-time forecasting difficult. Current transformer, GNN, and CNN systems suffer [...] Read more.
Multimodal forecasting is increasingly needed to maintain energy levels, storage capacity, and compute efficiency in off-grid, renewable-powered cloud environments. Variable sensor quality, uncertain interactions with renewable energy, and rapidly changing weather patterns make real-time forecasting difficult. Current transformer, GNN, and CNN systems suffer from sensor noise instability, multimodal temporal–spectral correlation issues, and challenges in the interpretability of operational decision-making. In this research, Q-RCANeX, a quantum-guided residual convolutional attention network for off-grid cloud infrastructures, estimates battery state of charge, renewable energy sources, and microgrid efficiency to overcome these restrictions. The system uses a Hybrid Quantum–Bayesian Evolutionary Optimizer, quantum feature embedding, temporal–spectral attention, residual convolutional encoding, and signal decomposition preprocessing. These parameters reinforce features, reduce noise, and align forecasting behavior with microgrid dynamics. Q-RCANeX obtains 98.6% accuracy, 0.992 AUC, and 0.986 R3 values for REAF, WGF, SOC-F, and EEIF forecasting tasks, according to a statistical study. Additionally, it determines inference latency to 4.9 ms and model size to 18.5 MB. Even with 20% of sensor data missing or noisy, the model outperforms 12 state-of-the-art baselines and maintains 96.8% accuracy using ANOVA, Wilcoxon, Nemenyi, and Holm tests. The findings indicate that the forecasting framework has high accuracy, clarity, and resilience to failures. This makes it useful for real-time, off-grid management of renewable cloud microgrids. Full article
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29 pages, 3214 KB  
Article
Robust Voltage Control in Distribution Networks via CVaR-Based Bayesian Optimization
by Ye-Ning Tian
Electronics 2026, 15(1), 154; https://doi.org/10.3390/electronics15010154 - 29 Dec 2025
Viewed by 331
Abstract
The rapid proliferation of distributed solar photovoltaic systems has intensified voltage fluctuations and uncertainty in distribution networks. Traditional Volt/VAR control strategies often struggle with robustness against extreme scenarios and impose high communication overheads. To address these challenges, this paper proposes a Bayesian Evolutionary [...] Read more.
The rapid proliferation of distributed solar photovoltaic systems has intensified voltage fluctuations and uncertainty in distribution networks. Traditional Volt/VAR control strategies often struggle with robustness against extreme scenarios and impose high communication overheads. To address these challenges, this paper proposes a Bayesian Evolutionary Optimization with Conditional Value at Risk (BEO-CVaR) framework for optimizing Volt/VAR control rules. This novel approach integrates Conditional Value at Risk (CVaR) into the objective function to explicitly mitigate tail risks arising from grid uncertainties. Furthermore, it employs Bayesian Evolutionary Optimization (BEO) utilizing Gaussian process surrogate modeling to efficiently solve the computationally expensive, black-box optimization problem. Validation on a standard IEEE test feeder demonstrates that BEO-CVaR achieves superior voltage regulation, strict adherence to safety standards, and significantly reduced communication requirements compared to conventional decentralized strategies. Additionally, the framework’s scalability and robustness are verified through extensive experiments across varying dimensions of decision spaces, confirming its effectiveness in complex multi-inverter coordination scenarios. Full article
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14 pages, 1191 KB  
Article
Superior RdRp Function Drives the Dominance of Prevalent GI.3 Norovirus Lineages
by Qianxin Lu, Huisha Du, Xin Jiang, Bingwen Zeng, Tianhui Li and Ying-Chun Dai
Microorganisms 2026, 14(1), 11; https://doi.org/10.3390/microorganisms14010011 - 19 Dec 2025
Viewed by 450
Abstract
The GI.3 norovirus is the most detected and recombinant-rich genotype within genogroup I, yet the mechanistic basis for its epidemiological success remains poorly understood. This study integrates Bayesian evolutionary analysis with in vitro enzymology to investigate the link between RdRp function and the [...] Read more.
The GI.3 norovirus is the most detected and recombinant-rich genotype within genogroup I, yet the mechanistic basis for its epidemiological success remains poorly understood. This study integrates Bayesian evolutionary analysis with in vitro enzymology to investigate the link between RdRp function and the evolutionary dynamics of GI.3 NoV. We analyzed 831 GI.3 sequences, finding that prevalent strains (GI.3[P3] and GI.3[P13]) exhibited significantly higher evolutionary rates in both the RdRp and VP1 genes than non-prevalent strains (GI.3[P10] and GI.3[P14]). While the RdRp gene displayed a strong molecular clock signal, the VP1 gene’s evolution was more complex, showing cluster-specific trends. Functionally, the RdRps from prevalent strains demonstrated superior enzymatic activity and substrate affinity (Km: GI.3[P13] = 0.092 mM; GI.3[P3] = 0.176 mM) compared to non-prevalent strains (Km: GI.3[P14] = 0.273 mM). Notably, GI.3 RdRp required higher manganese ion concentrations for optimal activity than previously reported for GII strains, suggesting a potential biochemical constraint. Our findings demonstrate a clear correlation between RdRp enzymatic efficiency, evolutionary rate, and strain prevalence. We propose that a highly active RdRp may potentially accelerate VP1 evolution and confer a replicative advantage, underpinning the dominance of specific GI.3 lineages. This work provides crucial experimental evidence linking viral polymerase function to evolutionary and epidemiological outcomes. Full article
(This article belongs to the Section Virology)
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46 pages, 7479 KB  
Review
Performance-Driven Generative Design in Buildings: A Systematic Review
by Yiyang Huang, Zhenhui Zhang, Ping Su, Tingting Li, Yucan Zhang, Xiaoxu He and Huawei Li
Buildings 2025, 15(24), 4556; https://doi.org/10.3390/buildings15244556 - 17 Dec 2025
Cited by 1 | Viewed by 1642
Abstract
Buildings are under increasing pressure to address decarbonization and climate adaptation, which is pushing design practice from post hoc performance checks to performance-driven generative design (PDGD). This review maps the current state of PDGD in buildings and proposes an engineering-oriented framework that links [...] Read more.
Buildings are under increasing pressure to address decarbonization and climate adaptation, which is pushing design practice from post hoc performance checks to performance-driven generative design (PDGD). This review maps the current state of PDGD in buildings and proposes an engineering-oriented framework that links research methods to deployable workflows. Using a PRISMA-based systematic search, we identify 153 core studies and code them along five dimensions: design objects and scales, objectives and metrics, algorithms and tools, workflows, and data and validation. The corpus shows a strong focus on facades, envelopes, and single-building massing, dominated by energy, daylight and thermal comfort objectives, and a widespread reliance on parametric platforms connected to performance simulation software with multi-objective optimization. From this evidence we extract three typical workflow routes: parametric evolutionary multi-objective optimization, surrogate or Bayesian optimization, and data- or model-driven generation. Persistent weaknesses include fragmented metric conventions, limited cross-case or field validation, and risks to reproducibility. In response, we propose a harmonized objective–metric system, an evidence pyramid for PDGD, and a reproducibility checklist with practical guidance, which together aim to make PDGD workflows more comparable, auditable, and transferable for design practice. Full article
(This article belongs to the Section Construction Management, and Computers & Digitization)
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22 pages, 649 KB  
Article
CoEGAN-BO: Synergistic Co-Evolution of GANs and Bayesian Optimization for High-Dimensional Expensive Many-Objective Problems
by Jie Tian, Hongli Bian, Yuyao Zhang, Xiaoxu Zhang and Hui Liu
Mathematics 2025, 13(21), 3444; https://doi.org/10.3390/math13213444 - 29 Oct 2025
Viewed by 768
Abstract
Bayesian optimization (BO) struggles with data scarcity and poor scalability in high-dimensional many-objective optimization problems. To address this, we propose Co-Evolutionary GAN–Bayesian Optimization (CoEGAN-BO), a novel framework that synergizes generative adversarial networks (GANs) with Bayesian co-evolutionary search for data-driven optimization. The GAN module [...] Read more.
Bayesian optimization (BO) struggles with data scarcity and poor scalability in high-dimensional many-objective optimization problems. To address this, we propose Co-Evolutionary GAN–Bayesian Optimization (CoEGAN-BO), a novel framework that synergizes generative adversarial networks (GANs) with Bayesian co-evolutionary search for data-driven optimization. The GAN module generates synthetic samples conditioned on promising regions identified by BO, while a co-evolutionary mechanism maintains two interacting populations: one explores the GAN’s latent space for diversity, and the other exploits BO’s probabilistic model for convergence. A bi-stage infilling strategy further enhances efficiency: early iterations prioritize exploration via Lp-norm-based candidate selection, later switching to a max–min distance criterion for Pareto refinement. Experiments on expensive multi/many-objective benchmarks show that CoEGAN-BO outperforms four state-of-the-art surrogate-assisted algorithms, achieving superior convergence and diversity under limited evaluation budgets. Full article
(This article belongs to the Special Issue Multi-Objective Optimizations and Their Applications)
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28 pages, 1816 KB  
Article
A Social Network Group Decision-Making Method for Flood Disaster Chains Considering Evolutionary Trends and Decision-Makers’ Risk Preferences
by Ruohan Ma, Zhiying Wang, Lemei Zhu, Anbang Zhang and Yiwen Wang
Mathematics 2025, 13(18), 2943; https://doi.org/10.3390/math13182943 - 11 Sep 2025
Viewed by 673
Abstract
To address the impact of the dynamic evolution of flood disaster chains and decision-makers’ (DMs’) risk preference heterogeneity on group decision-making, this study proposes a social network group decision-making method that integrates the evolutionary trend of the flood disaster chain with DMs’ risk [...] Read more.
To address the impact of the dynamic evolution of flood disaster chains and decision-makers’ (DMs’) risk preference heterogeneity on group decision-making, this study proposes a social network group decision-making method that integrates the evolutionary trend of the flood disaster chain with DMs’ risk preferences. First, a Bayesian network is constructed to quantify the disaster chain’s evolution, dynamically adjusting DMs’ evaluation values. Second, DMs’ risk preference types are identified based on the evaluation values, and a bounded confidence (BC) model, incorporating risk preferences, self-confidence and trust networks, is developed to promote consensus formation. Then, the optimal alternative is selected through weighted aggregation and used to update the Bayesian network dynamically during implementation. Finally, the effectiveness and superiority of the proposed method are verified using the flood disaster chain from the “7∙20” extreme rainfall disaster in Zhengzhou, Henan Province, China. The results show that risk-seeking DMs reduce BC values and resist consensus, whereas risk-averse DMs enlarge BC values and accelerate convergence. Moreover, worsening flood disaster chain trends drive DMs to update the optimal alternative. These findings show that the method captures both dynamic disaster evolution and behavioral heterogeneity, providing realistic and adaptive decision support in flood emergency scenarios. Full article
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32 pages, 9674 KB  
Article
A Spatiotemporal Multimodal Framework for Air Pollution Prediction Based on Bayesian Optimization—Evidence from Sichuan, China
by Fengfan Zhang, Jiabei Hu and Ming Zeng
Atmosphere 2025, 16(8), 958; https://doi.org/10.3390/atmos16080958 - 11 Aug 2025
Cited by 1 | Viewed by 1803
Abstract
In regions characterized by complex terrain and diverse pollution sources, high-precision air pollution prediction remains challenging due to nonlinear spatiotemporal coupling and the difficulty of modeling local pollutant agglomeration. To address these issues, this study proposes a CNN–LSTM–Transformer multimodal prediction framework integrated with [...] Read more.
In regions characterized by complex terrain and diverse pollution sources, high-precision air pollution prediction remains challenging due to nonlinear spatiotemporal coupling and the difficulty of modeling local pollutant agglomeration. To address these issues, this study proposes a CNN–LSTM–Transformer multimodal prediction framework integrated with Bayesian Optimization. First, the Local Moran’s Index (LMI) is introduced as a spatial perception feature and concatenated with pollutant concentration sequences before being input into the CNN module. This design enhances the model’s ability to identify local pollutant clustering and spatial heterogeneity. Second, the LSTM architecture adopts a dual-channel structure: the main channel employs bidirectional LSTM to extract temporal dependencies, while the auxiliary channel uses unidirectional LSTM to capture evolutionary trends. A Transformer with a multi-head attention mechanism is then introduced to perform global modeling. Bayesian Optimization is employed to automatically adjust key hyperparameters, thereby improving the model’s stability and convergence efficiency. Empirical results based on atmospheric pollution monitoring data from Sichuan Province during 2021–2024 demonstrate that the proposed model outperforms various mainstream methods in predicting six pollutants in Chengdu. For instance, the MAE for PM2.5 decreased by 14.9–22.1%, while the coefficient of determination (R2) remained stable between 87% and 89%. The accuracy decay rate across four-day forecasts was controlled within 12.4%. Furthermore, in PM2.5 generalization prediction tasks across four other cities—Yibin, Zigong, Nanchong, and Mianyang—the model exhibited superior stability and robustness, achieving an average R2 of 87.4%. These findings highlight the model’s long-term stability and regional generalization capability, offering reliable technical support for air pollution prediction and control strategies in Sichuan Province and potentially beyond. Full article
(This article belongs to the Special Issue Applications of Artificial Intelligence in Atmospheric Sciences)
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16 pages, 2207 KB  
Article
Mitogenomic Insights into Adaptive Evolution of African Ground Squirrels in Arid Environments
by Yamin Xing, Xibao Wang, Yao Chen, Yongquan Shang, Haotian Cai, Liangkai Wang and Xiaoyang Wu
Diversity 2025, 17(8), 538; https://doi.org/10.3390/d17080538 - 31 Jul 2025
Viewed by 982
Abstract
African ground squirrels (Xerus spp.), the inhabitants of African arid zones, face extreme heat and water scarcity driving selection for metabolic optimization. We assembled and annotated the first mitogenomes of Xerus inauris and Xerus rutilus (16,525–16,517 bp), revealing conserved vertebrate architecture with [...] Read more.
African ground squirrels (Xerus spp.), the inhabitants of African arid zones, face extreme heat and water scarcity driving selection for metabolic optimization. We assembled and annotated the first mitogenomes of Xerus inauris and Xerus rutilus (16,525–16,517 bp), revealing conserved vertebrate architecture with genus-specific traits. Key features include Xerus rutilus’s elongated ATP6 (680 vs. 605 bp), truncated ATP8ATP6 spacers (4 vs. 43 bp), and tRNA-Pro control regions with 78.1–78.3% AT content. Their nucleotide composition diverged from that of related sciurids, marked by reduced T (25.78–26.9%) and extreme GC skew (−0.361 to −0.376). Codon usage showed strong Arg-CGA bias (RSCU = 3.78–3.88) and species-specific elevations in Xerus rutilus’s UGC-Cys (RSCU = 1.83 vs. 1.17). Phylogenetics positioned Xerus as sister to Ratufa bicolor (Bayesian PP = 0.928; ML = 1.0), aligning with African biogeographic isolation. Critically, we identified significant signatures of positive selection in key mitochondrial genes linked to arid adaptation. Positive selection signals in ND4 (ω = 1.8 × background), ND1, and ATP6 (p < 0.0033) correspond to enhanced proton gradient efficiency and ATP synthesis–molecular adaptations likely crucial for optimizing energy metabolism under chronic water scarcity and thermoregulatory stress in desert environments. Distinct evolutionary rates were observed across mitochondrial genes and complexes: Genes encoding Complex I subunits (ND2, ND6) and Complex III (Cytb) exhibited accelerated evolution in arid-adapted lineages, while genes encoding Complex IV subunits (COXI) and Complex V (ATP8) remained highly conserved. These findings resolve the Xerus mitogenomic diversity, demonstrating adaptive plasticity balancing arid-energy optimization and historical diversification while filling critical genomic gaps for this xeric-adapted lineage. Full article
(This article belongs to the Section Animal Diversity)
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24 pages, 5785 KB  
Article
Phylogenetic Reassessment of Murinae Inferred from the Mitogenome of the Monotypic Genus Dacnomys Endemic to Southeast Asia: New Insights into Genetic Diversity Erosion
by Zhongsong Wang, Di Zhao, Wenyu Song and Wenge Dong
Biology 2025, 14(8), 948; https://doi.org/10.3390/biology14080948 - 28 Jul 2025
Viewed by 1594
Abstract
The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits [...] Read more.
The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits diagnostic morphological adaptations—hypertrophied upper molars and cryptic pelage—that underpin niche differentiation in undisturbed tropical/subtropical forests. Despite its evolutionary distinctiveness, the conservation prioritization given to Dacnomys is hindered due to a deficiency of data and unresolved phylogenetic relationships. Here, we integrated morphological analyses with the first complete mitogenome (16,289 bp in size; no structural rearrangements) of D. millardi to validate its phylogenetic placement within the subfamily Murinae and provide novel insights into genetic diversity erosion. Bayesian and maximum likelihood phylogenies robustly supported Dacnomys as sister to Leopoldamys (PP = 1.0; BS = 100%), with an early Pliocene divergence (~4.8 Mya, 95% HPD: 3.65–5.47 Mya). Additionally, based on its basal phylogenetic position within Murinae, we propose reclassifying Micromys from Rattini to the tribe Micromyini. Codon usage bias analyses revealed pervasive purifying selection (Ka/Ks < 1), constraining mitogenome evolution. Genetic diversity analyses showed low genetic variation (CYTB: π = 0.0135 ± 0.0023; COX1: π = 0.0101 ± 0.0025) in fragmented populations. We propose three new insights into this genetic diversity erosion. (1) Evolutionary constraints: genome-wide evolutionary conservation and shallow evolutionary history (~4.8 Mya) limited mutation accumulation. (2) Anthropogenic pressures: deforestation-driven fragmentation of habitats (>20,000 km2/year loss since 2000) has reduced effective population size, exacerbating genetic drift. (3) Ecological specialization: long-term adaptation to stable niches favored genomic optimization over adaptive flexibility. These findings necessitate suitable conservation action by enforcing protection of core habitats to prevent deforestation-driven population collapses and advocating IUCN reclassification of D. millardi from Data Deficient to Near Threatened. Full article
(This article belongs to the Section Genetics and Genomics)
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17 pages, 382 KB  
Review
Physics-Informed Neural Networks: A Review of Methodological Evolution, Theoretical Foundations, and Interdisciplinary Frontiers Toward Next-Generation Scientific Computing
by Zhiyuan Ren, Shijie Zhou, Dong Liu and Qihe Liu
Appl. Sci. 2025, 15(14), 8092; https://doi.org/10.3390/app15148092 - 21 Jul 2025
Cited by 34 | Viewed by 22368
Abstract
Physics-informed neural networks (PINNs) have emerged as a transformative methodology integrating deep learning with scientific computing. This review establishes a three-dimensional analytical framework to systematically decode PINNs’ development through methodological innovation, theoretical breakthroughs, and cross-disciplinary convergence. The contributions include threefold: First, identifying the [...] Read more.
Physics-informed neural networks (PINNs) have emerged as a transformative methodology integrating deep learning with scientific computing. This review establishes a three-dimensional analytical framework to systematically decode PINNs’ development through methodological innovation, theoretical breakthroughs, and cross-disciplinary convergence. The contributions include threefold: First, identifying the co-evolutionary path of algorithmic architectures from adaptive optimization (neural tangent kernel-guided weighting achieving 230% convergence acceleration in Navier-Stokes solutions) to hybrid numerical-deep learning integration (5× speedup via domain decomposition) and second, constructing bidirectional theory-application mappings where convergence analysis (operator approximation theory) and generalization guarantees (Bayesian-physical hybrid frameworks) directly inform engineering implementations, as validated by 72% cost reduction compared to FEM in high-dimensional spaces (p<0.01,n=15 benchmarks). Third, pioneering cross-domain knowledge transfer through application-specific architectures: TFE-PINN for turbulent flows (5.12±0.87% error in NASA hypersonic tests), ReconPINN for medical imaging (SSIM=+0.18±0.04 on multi-institutional MRI), and SeisPINN for seismic systems (0.52±0.18 km localization accuracy). We further present a technological roadmap highlighting three critical directions for PINN 2.0: neuro-symbolic, federated physics learning, and quantum-accelerated optimization. This work provides methodological guidelines and theoretical foundations for next-generation scientific machine learning systems. Full article
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