Mathematics and computing articles within Nature Communications

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  • Article
    | Open Access

    Deviations from Brownian motion leading to anomalous diffusion are ubiquitously found in transport dynamics but often difficult to characterize. Here the authors compare approaches for single trajectory analysis through an open competition, showing that machine learning methods outperform classical approaches.

    • Gorka Muñoz-Gil
    • , Giovanni Volpe
    •  & Carlo Manzo

  • Article
    | Open Access

    Recovery of underlying governing laws or equations describing the evolution of complex systems from data can be challenging if dataset is damaged or incomplete. The authors propose a learning approach which allows to discover governing partial differential equations from scarce and noisy data.

    • Zhao Chen
    • , Yang Liu
    •  & Hao Sun

  • Article
    | Open Access

    Establishing the time since death (TSD) is vital in many forensic investigations. By combining thermometry, photogrammetry and numerical thermodynamic modelling, the TSD can be determined non-invasively for bodies of arbitrary shape and posture with an unprecedented accuracy of 0.26 h ± 1.38 h.

    • Leah S. Wilk
    • , Gerda J. Edelman
    •  & Maurice C. G. Aalders

  • Article
    | Open Access

    The effectiveness of digital contact tracing for COVID-19 control remains uncertain. Here, the authors use data from the Smittestopp app, used in Norway in spring 2020, and estimate that 80% of nearby devices were detected by the app, and at least 11% of close contacts were not visible to manual contact tracing.

    • Ahmed Elmokashfi
    • , Joakim Sundnes
    •  & Olav Lysne

  • Article
    | Open Access

    The authors propose a new framework, deep evolutionary reinforcement learning, evolves agents with diverse morphologies to learn hard locomotion and manipulation tasks in complex environments, and reveals insights into relations between environmental physics, embodied intelligence, and the evolution of rapid learning.

    • Agrim Gupta
    • , Silvio Savarese
    •  & Li Fei-Fei

  • Article
    | Open Access

    Household air pollution derived from cooking fuels is a major source of health and environmental problems. Here, the authors provide detailed global, regional and country estimates of cooking fuel usage from 1990 to 2030 and project that 31% of people will still be mainly using polluting fuels in 2030.

    • Oliver Stoner
    • , Jessica Lewis
    •  & Heather Adair-Rohani

  • Article
    | Open Access

    Differential expression analysis of single-cell transcriptomics allows scientists to dissect cell-type-specific responses to biological perturbations. Here, the authors show that many commonly used methods are biased and can produce false discoveries.

    • Jordan W. Squair
    • , Matthieu Gautier
    •  & Grégoire Courtine

  • Article
    | Open Access

    Ultrasound is an important imaging modality for the detection and characterization of breast cancer, but it has been noted to have high false-positive rates. Here, the authors present an artificial intelligence system that achieves radiologist-level accuracy in identifying breast cancer in ultrasound imaging.

    • Yiqiu Shen
    • , Farah E. Shamout
    •  & Krzysztof J. Geras

  • Article
    | Open Access

    Some regions on the Moon are permanently covered in shadow and are therefore extremely difficult to see into. We develop a deep learning driven algorithm which enhances images of these regions, allowing us to see inside them with high resolution for the first time.

    • V. T. Bickel
    • , B. Moseley
    •  & M. Shirley

  • Article
    | Open Access

    Characterizing an unknown, complex system, like an accelerator, in multi-dimensional space is a challenging task. Here the authors report a Bayesian active learning method - Constrained Proximal Bayesian Exploration - for the characterization of a complex, constrained measurement as a function of multiple free parameters.

    • Ryan Roussel
    • , Juan Pablo Gonzalez-Aguilera
    •  & Auralee Edelen

  • Article
    | Open Access

    Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.

    • Warren S. D. Tennant
    • , Eric Cardinale
    •  & Raphaëlle Métras

  • Article
    | Open Access

    Social media platforms moderating misinformation have been accused of political bias. Here, the authors use neutral social bots to show that, while there is no strong evidence for such a bias, the content to which Twitter users are exposed depends strongly on the political leaning of early Twitter connections.

    • Wen Chen
    • , Diogo Pacheco
    •  & Filippo Menczer

  • Article
    | Open Access

    Reservoir computers are artificial neural networks that can be trained on small data sets, but require large random matrices and numerous metaparameters. The authors propose an improved reservoir computer that overcomes these limitations and shows advantageous performance for complex forecasting tasks

    • Daniel J. Gauthier
    • , Erik Bollt
    •  & Wendson A. S. Barbosa

  • Article
    | Open Access

    Image-based simulation for obtaining physical quantities is limited by the uncertainty in the underlying image segmentation. Here, the authors introduce a workflow for efficiently quantifying segmentation uncertainty and creating uncertainty distributions of the resulting physics quantities.

    • Michael C. Krygier
    • , Tyler LaBonte
    •  & Scott A. Roberts

  • Article
    | Open Access

    Finding a biologically-relevant inductive bias for training DNNs on large fitness landscapes is challenging. Here, the authors propose a method called Epistatic Net that improves DNN prediction accuracy and interpretation speed by integrating the knowledge that higher-order epistatic interactions are usually sparse.

    • Amirali Aghazadeh
    • , Hunter Nisonoff
    •  & Kannan Ramchandran

  • Article
    | Open Access

    Network dismantling allows to find minimum set of units attacking which leads to system’s break down. Grassia et al. propose a deep-learning framework for dismantling of large networks which can be used to quantify the vulnerability of networks and detect early-warning signals of their collapse.

    • Marco Grassia
    • , Manlio De Domenico
    •  & Giuseppe Mangioni

  • Article
    | Open Access

    Forecasting models have been used extensively to inform decision making during the COVID-19 pandemic. In this preregistered and prospective study, the authors evaluated 14 short-term models for Germany and Poland, finding considerable heterogeneity in predictions and highlighting the benefits of combined forecasts.

    • J. Bracher
    • , D. Wolffram
    •  & Frost Tianjian Xu

  • Article
    | Open Access

    Accurate seasonal forecasts of sea ice are highly valuable, particularly in the context of sea ice loss due to global warming. A new machine learning tool for sea ice forecasting offers a substantial increase in accuracy over current physics-based dynamical model predictions.

    • Tom R. Andersson
    • , J. Scott Hosking
    •  & Emily Shuckburgh

  • Article
    | Open Access

    Neural Networks are known to perform poorly outside of their training domain. Here the authors propose an inverse sampling strategy to train neural network potentials enabling to drive atomistic systems towards high-likelihood and high-uncertainty configurations without the need for molecular dynamics simulations.

    • Daniel Schwalbe-Koda
    • , Aik Rui Tan
    •  & Rafael Gómez-Bombarelli

  • Article
    | Open Access

    Lineage tracing and snapshots of transcriptional state at the single-cell level are powerful, complementary tools for studying development. Here, the authors propose a mathematical method combining lineage tracing with trajectory inference to improve our understanding of development.

    • Aden Forrow
    •  & Geoffrey Schiebinger

  • Review Article
    | Open Access

    Seed banks are generated when individuals enter a dormant state, a phenomenon that has evolved among diverse taxa, but that is also found in stem cells, brains, and tumors. Here, Lennon et al. synthesize the fundamentals of seed-bank theory and the emergence of complex patterns and dynamics in mathematics and the life sciences.

    • Jay T. Lennon
    • , Frank den Hollander
    •  & Jochen Blath

  • Article
    | Open Access

    Storage technology based on DNA is emerging as an information dense and durable medium. Here the authors use machine learning-based encoding and hybridization probes to execute similarity searches in a DNA database.

    • Callista Bee
    • , Yuan-Jyue Chen
    •  & Luis Ceze

  • Article
    | Open Access

    Prediction of contagion dynamics is of relevance for epidemic and social complex networks. Murphy et al. propose a data-driven approach based on deep learning which allows to learn mechanisms governing network dynamics and make predictions beyond the training data for arbitrary network structures.

    • Charles Murphy
    • , Edward Laurence
    •  & Antoine Allard

  • Article
    | Open Access

    The analysis of networks and network processes can require low-dimensional representations, possible for specific structures only. The authors propose a geometric formalism which allows to unfold the mechanisms of dynamical processes propagation in various networks, relevant for control and community detection.

    • Adam Gosztolai
    •  & Alexis Arnaudon

  • Article
    | Open Access

    Quantitative methods to assess the quality of hPSC-derived organoids have not been developed. Here they present a prediction algorithm to assess the transcriptomic similarity between hPSC-derived organoids and the corresponding human target organs and perform validation on lung bud organoids, antral gastric organoids, and cardiomyocytes.

    • Mi-Ok Lee
    • , Su-gi Lee
    •  & Hyun-Soo Cho

  • Article
    | Open Access

    Wavefront shaping is used to overcome scattering in biological tissues during imaging, but determining the compensation is slow. Here, the authors use holographic phase stepping interferometry, where new phase information is updated after each measurement, enabling fast improvement of the wavefront correction.

    • Molly A. May
    • , Nicolas Barré
    •  & Alexander Jesacher

  • Article
    | Open Access

    In many machine learning applications, one uses pre-trained neural networks, having limited access to training and test data. Martin et al. show how to predict trends in the quality of such neural networks without access to this information, relevant for reproducibility, diagnostics, and validation.

    • Charles H. Martin
    • , Tongsu (Serena) Peng
    •  & Michael W. Mahoney

  • Article
    | Open Access

    Mechanisms of cluster formation in networks with directed links differ from those in undirected networks. Lodi et al. propose a method to compute interdependencies among clusters of nodes in directed networks. They show that clusters can be one-way dependent, as found in social and neural networks.

    • Matteo Lodi
    • , Francesco Sorrentino
    •  & Marco Storace

  • Article
    | Open Access

    Population structure can influence the probability of and time to fixation of new mutants. Here, Tkadlec et al. demonstrate mathematically that structures that increase fixation probability necessarily slow fixation, but also identify amplifying structures with minimal reductions in fixation time.

    • Josef Tkadlec
    • , Andreas Pavlogiannis
    •  & Martin A. Nowak

  • Article
    | Open Access

    The authors present a microwave imaging system that can operate in continuous transmit-receive mode. Using an array of transmitters, a single receiver and a reconstruction matrix that correlate random time patterns with the captured signal, they demonstrate real-time imaging and tracking through a wall.

    • Fabio C. S. da Silva
    • , Anthony B. Kos
    •  & Archita Hati

  • Article
    | Open Access

    Physical principles underlying machine learning analysis of quantum gas microscopy data are not well understood. Here the authors develop a neural network based approach to classify image data in terms of multi-site correlation functions and reveal the role of fourth-order correlations in the Fermi-Hubbard model.

    • Cole Miles
    • , Annabelle Bohrdt
    •  & Eun-Ah Kim

  • Article
    | Open Access

    Networks describe the intricate patterns of interaction occurring within ecological systems, but they are unfortunately difficult to construct from data. Here, the authors show how Bayesian statistical techniques can separate structure from noise in networks gathered in observational studies of plant-pollinator systems.

    • Jean-Gabriel Young
    • , Fernanda S. Valdovinos
    •  & M. E. J. Newman

  • Article
    | Open Access

    In-silico trials rely on virtual populations and interventions simulated using patient-specific models and may offer a solution to lower costs. Here, the authors present the flow diverter performance assessment in-silico trial, which models the treatment of intracranial aneurysms with a flow-diverting stent.

    • Ali Sarrami-Foroushani
    • , Toni Lassila
    •  & Alejandro F. Frangi

  • Article
    | Open Access

    Network embedding is a machine learning technique for construction of low-dimensional representations of large networks. Gu et al. propose a method for the identification of an optimal embedding dimension for the encoding of network structural information inspired by natural language processing.

    • Weiwei Gu
    • , Aditya Tandon
    •  & Filippo Radicchi

  • Article
    | Open Access

    Rapid, accurate and specific point-of-care diagnostics can help manage and contain fast-spreading infections. Here, the authors present a nanopore-based system that uses artificial intelligence to discriminate between four coronaviruses in saliva, with little need for sample pre-processing.

    • Masateru Taniguchi
    • , Shohei Minami
    •  & Kazunori Tomono

  • Article
    | Open Access

    Gravity waves are observed in Venus atmosphere, but their characteristics are not well-known. Here, the authors show spontaneous generation of gravity waves from the thermal tides in the Venus atmosphere as small-scale gravity waves are resolved in high-resolution general circulation model.

    • Norihiko Sugimoto
    • , Yukiko Fujisawa
    •  & Yoshi-Yuki Hayashi

  • Article
    | Open Access

    Osimertinib and dacomitinib are approved as first-line treatment of EGFR-mutant NSCLC but resistance can arise. Here, the authors use a computational model to identify an optimal dosing schedule for osimertinib and dacomitinib combination therapy that was confirmed tolerable and effective in an ongoing phase I clinical trial.

    • Kamrine E. Poels
    • , Adam J. Schoenfeld
    •  & Franziska Michor

  • Article
    | Open Access

    Mobility restrictions implemented to reduce the spread of COVID-19 have significantly impacted walking behavior. In this study, the authors integrated mobility data from mobile devices and area-level data to study the walking patterns of 1.62 million anonymous users in 10 US metropolitan areas.

    • Ruth F. Hunter
    • , Leandro Garcia
    •  & Esteban Moro

  • Article
    | Open Access

    Despite the consensus that mass vaccination against SARS-CoV-2 will ultimately end the pandemic, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. Here, the authors investigate relaxation scenarios using an age-structured transmission model that has been fitted to data for Portugal.

    • João Viana
    • , Christiaan H. van Dorp
    •  & Ganna Rozhnova

  • Article
    | Open Access

    Fluctuations in ecosystems and other large dynamical systems are driven by intrinsic and extrinsic noise and contain hidden information which is difficult to extract. Here, the authors derive analytical characterizations of fluctuations in random interacting systems, allowing inference of network properties from time series data.

    • Yvonne Krumbeck
    • , Qian Yang
    •  & Tim Rogers

  • Article
    | Open Access

    Social interaction outcomes can depend on the type of information individuals possess and how it is used in decision-making. Here, Zhou et al. find that self-evaluation based decision-making rules lead to evolutionary outcomes that are robust to different population structures and ways of self-evaluation.

    • Lei Zhou
    • , Bin Wu
    •  & Long Wang

  • Article
    | Open Access

    Reinbold et al. propose a physics-informed data-driven approach that successfully discovers a dynamical model using high-dimensional, noisy and incomplete experimental data describing a weakly turbulent fluid flow. This approach is relevant to other non-equilibrium spatially-extended systems.

    • Patrick A. K. Reinbold
    • , Logan M. Kageorge
    •  & Roman O. Grigoriev

  • Article
    | Open Access

    Generating new sensible molecular structures is a key problem in computer aided drug discovery. Here the authors propose a graph-based molecular generative model that outperforms previously proposed graph-based generative models of molecules and performs comparably to several SMILES-based models.

    • Omar Mahmood
    • , Elman Mansimov
    •  & Kyunghyun Cho

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