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This study delves into the crucial aspect of network topology in artificial neural networks (NNs) and its impact on model performance. Addressing the need to comprehend how network structures influence learning capabilities, the research contrasts traditional multilayer perceptrons (MLPs) with models built on various complex topologies using novel network generation techniques. Drawing insights from synthetic datasets, the study reveals the remarkable accuracy of complex NNs, particularly in high-difficulty scenarios, outperforming MLPs. Our exploration extends to real-world datasets, highlighting the task-specific nature of optimal network topologies and unveiling trade-offs, including increased computational demands and reduced robustness to graph damage in complex NNs compared to MLPs. This research underscores the pivotal role of complex topologies in addressing challenging learning tasks. However, it also signals the necessity for deeper insights into the complex interplay among topological attributes influencing NN performance. By shedding light on the advantages and limitations of complex topologies, this study provides valuable guidance for practitioners and paves the way for future endeavors to design more efficient and adaptable neural architectures across various applications.
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http://dx.doi.org/10.1016/j.neunet.2023.12.012 | DOI Listing |
Nat Microbiol
September 2025
Division of Computational Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Although dynamical systems models are a powerful tool for analysing microbial ecosystems, challenges in learning these models from complex microbiome datasets and interpreting their outputs limit use. We introduce the Microbial Dynamical Systems Inference Engine 2 (MDSINE2), a Bayesian method that learns compact and interpretable ecosystems-scale dynamical systems models from microbiome timeseries data. Microbial dynamics are modelled as stochastic processes driven by interaction modules, or groups of microbes with similar interaction structure and responses to perturbations, and additionally, noise characteristics of data are modelled.
View Article and Find Full Text PDFACS Omega
September 2025
Shandong Provincial Key Laboratory of Oil, Gas and New Energy Storage and Transportation Safety, China University of Petroleum, Qingdao, Shandong 266580, People's Republic of China.
The natural gas pipeline network has a complex topology with variable flow directions, and the supply demand relationships between nodes exhibit cyclical, fluctuating, and time-varying trends. Developing efficient, accurate, and fast intelligent control algorithms is crucial for optimizing the distribution of natural gas networks. Analyzing the operational data from a provincial network over three years revealed that abnormal flow data, such as supply interruptions due to incidents, early fulfillment of supply, and insufficient flow distribution, can cause deviations between the actual transmission volume and the planned transmission volume predicted by the uneven coefficient method.
View Article and Find Full Text PDFNAR Genom Bioinform
September 2025
Centre for Integrative Biology and Systems Medicine (IBSE), Wadhwani School of Data Science and AI, Indian Institute of Technology (IIT) Madras, Chennai 600036, India.
Genome graphs provide a powerful reference structure for representing genetic diversity. Their structure emphasizes the polymorphic regions in a collection of genomes, enabling network-based comparisons of population-level variation. However, current tools are limited in their ability to quantify and compare structural features across large genome graphs.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
September 2025
CFisUC, Department of Physics, University of Coimbra, 3004-516, Coimbra, Portugal.
With the goal of manipulating (bio)chemical processes, photoswitches emerge as important assets in molecular nanotechnology. To guide synthetic strategies toward increasingly more efficient systems, conformational dynamics studies performed with atomic rigor are in demand, particularly if this information can be extracted with control over the size of a perturbing solvation layer. Here, we use jet-cooled rotational spectroscopy and quantum chemistry calculations to unravel the structure and micro-hydration dynamics of a prototype photoswitch.
View Article and Find Full Text PDFMol Cell Proteomics
September 2025
Institute of Biotechnology, HiLIFE, Faculty of Medicine, University of Helsinki, Helsinki, Finland. Electronic address:
Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based approaches, including cross-linking MS (XL-MS), hydrogen-deuterium exchange MS (HDX-MS), and limited proteolysis MS (LiP-MS), now enable unprecedented insights into protein topology, conformational dynamics, and protein-protein interactions. These methods, complemented by affinity purification (AP), co-immunoprecipitation (co-IP), proximity labeling (PL), and spatial proteomics techniques, have expanded our ability to characterize the structural proteome at a systems-wide scale.
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