Research articles

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  • This work unifies an interdisciplinary literature of over 230 computational methods for measuring interactions from complex systems, revealing previously unreported theoretical connections and demonstrating practical benefits of broad methodological comparison.

    • Oliver M. Cliff
    • Annie G. Bryant
    • Ben D. Fulcher
    Article
  • Real-world social networks are often ephemeral and subject to exogenous restructuring. Q. Su et al. show that dynamic networks can foster cooperative behavior.

    • Qi Su
    • Alex McAvoy
    • Joshua B. Plotkin
    Article
  • A system called ORFanage can analyze RNA-seq data to find novel protein variants and improve gene annotations. In addition, the method is fast and scalable, being able to filter out noise and thus greatly improving the quality of transcriptome assemblies.

    • Ales Varabyou
    • Beril Erdogdu
    • Mihaela Pertea
    Article
  • The study presents a mobility centrality index to delineate urban dynamics in quasi-real time with mobile-phone data. The results indicate that urban structures were becoming more monocentric during the COVID-19 lockdown periods in major cities in Spain.

    • Yanyan Xu
    • Luis E. Olmos
    • Marta C. González
    Article
  • Neural ADMIXTURE is a neural-network-based, interpretable autoencoder that performs rapid genomic clustering in biobank-scale databases.

    • Albert Dominguez Mantes
    • Daniel Mas Montserrat
    • Alexander G. Ioannidis
    ArticleOpen Access
  • A theoretical framework for quantum neural network (QNN) overparametrization, a phase transition in loss landscape complexity, is established. The precise characterization of the critical number of parameters offered is expected to impact QNN design.

    • Martín Larocca
    • Nathan Ju
    • Marco Cerezo
    Article
  • A platform for single-cell meta-analysis of inflammatory bowel disease, named scIBD, enables identification of rare or less-characterized cell types and the dissection of the commonalities and differences between ulcerative colitis and Crohn’s disease.

    • Hu Nie
    • Peilu Lin
    • Lei Zhang
    Brief Communication
  • This study presents an ab initio approach for the real-time charge carrier quantum dynamics in the momentum space, which is computationally more efficient than conventional real-space non-adiabatic molecular dynamics method. The method is applied to study hot carrier dynamics in graphene, which provides insights about the phonon-specific relaxation mechanism.

    • Zhenfa Zheng
    • Yongliang Shi
    • Jin Zhao
    Article
  • Kirigami is an ancient art form that is now increasingly studied and applied in science and technology. This work presents an additive approach for the computational design of kirigami and two fabrication strategies for its physical instantiation.

    • Levi H. Dudte
    • Gary P. T. Choi
    • L. Mahadevan
    Article