Research articles

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  • Although technologies enable large-scale profiling of chromatin accessibility at the single-cell level, there are methodological challenges due to high dimensionality and high sparsity of data. Liu and colleagues describe a computational tool for the simultaneous determination of latent representation and clustering of cells from single-cell ATAC-seq data using a pair of generative adversarial networks.

    • Qiao Liu
    • Shengquan Chen
    • Wing Hung Wong
    Article
  • There is an urgent need to identify drugs that may be effective against SARS-CoV-2. A platform with a range of machine learning models is made available to predict anti-COVID-19 activity in candidate drugs and to help prioritize compounds for virtual screening.

    • Govinda B. KC
    • Giovanni Bocci
    • Tudor I. Oprea
    Article
  • Tackling scientific problems often requires computational models that bridge several spatial and temporal scales. A new simulation framework employing machine learning, which is scalable and can be used on standard laptops as well as supercomputers, promises exhaustive multiscale explorations.

    • Harsh Bhatia
    • Timothy S. Carpenter
    • Peer-Timo Bremer
    Article
  • Recurrent neural networks (RNNs) can learn to process temporal information, such as speech or movement. New work makes such approaches more powerful and flexible by describing theory and experiments demonstrating that RNNs can learn from a few examples to generalize and predict complex dynamics including chaotic behaviour.

    • Jason Z. Kim
    • Zhixin Lu
    • Danielle S. Bassett
    Article
  • Bats with sophisticated biosonar systems move their ears at a high speed to help localize sound sources. Yin and Müller present a system inspired by this strategy, which can localize sounds with high accuracy and with a single detector, using a flexible silicone model of a bat’s ear and a deep convolutional neural network to process the complex Doppler signatures.

    • Xiaoyan Yin
    • Rolf Müller
    Article
  • Predicting what comes next in a previously unseen time series of input data is a challenging task for machine learning. A novel unsupervised learning scheme termed predictive principal component analysis can extract the most informative components for predicting future inputs with low computational cost.

    • Takuya Isomura
    • Taro Toyoizumi
    Article
  • Identifying cancer driver genes from high-throughput genomic data is an important task to understand the molecular basis of cancer and to develop new treatments including precision medicine. To tackle this challenge, EMOGI, a new deep learning method based on graph convolutional networks is developed, which combines protein–protein interaction networks with multiomics datasets.

    • Roman Schulte-Sasse
    • Stefan Budach
    • Annalisa Marsico
    Article
  • Rechargeable lithium-ion batteries play a crucial role in many modern-day applications, including portable electronics and electric vehicles, but they degrade over time. To ensure safe operation, a battery’s ‘state of health’ should be monitored in real time, and this machine learning pipeline, tested on a variety of charging conditions, can provide such an online estimation of battery state of health.

    • Darius Roman
    • Saurabh Saxena
    • David Flynn
    Article
  • A generative approach called SliceGAN is demonstrated that can construct complex three-dimensional (3D) images from representative two-dimensional (2D) image examples. This is a promising approach in particular for studying microstructured materials where acquiring good-quality 3D data is challenging; 3D datasets can be created with SliceGAN, making use of high-quality 2D imaging techniques that are widely available.

    • Steve Kench
    • Samuel J. Cooper
    Article
  • Being able to precisely analyse behaviour is essential for the study of motor behaviour in health and disease, but is often time- and labour-intensive. Brattoli et al. develop an automatic approach based on deep learning for analysing motor behaviour and evaluate it on different species and diverse motor functions.

    • Biagio Brattoli
    • Uta Büchler
    • Björn Ommer
    Article
  • Identifying salient input features can be a challenge in neural networks. The authors developed a variable selection procedure with false discovery rate control that works on classification or regression problems, one or multiple output neurons, and deep or shallow neural networks.

    • Zixuan Song
    • Jun Li
    Article
  • The recent advances in computational chemistry rely on large data collections of chemical compounds and reactions. However, not all entries in these datasets are correct. Toniato and colleagues present here an automated approach to identify incorrect reactions, using the effect of catastrophic forgetting in neural networks.

    • Alessandra Toniato
    • Philippe Schwaller
    • Teodoro Laino
    Article
  • Neural networks are known as universal approximators of continuous functions, but they can also approximate any mathematical operator (mapping a function to another function), which is an important capability for complex systems such as robotics control. A new deep neural network called DeepONet can lean various mathematical operators with small generalization error.

    • Lu Lu
    • Pengzhan Jin
    • George Em Karniadakis
    Article
  • The morphology of a robot determines how efficiently it can traverse different terrain. Nygaard and colleagues present here a robot that can adapt it’s morphology when it is detecting different terrain and learn which configuration is most effective.

    • Tønnes F. Nygaard
    • Charles P. Martin
    • David Howard
    Article
  • At present, deep learning models in genomics are manually tuned through trial and error, which is time consuming and imposes a barrier for biomedical researchers not trained in machine learning. The authors develop an automated framework to design and apply convolutional neural networks for genomic sequences.

    • Zijun Zhang
    • Christopher Y. Park
    • Olga G. Troyanskaya
    Article
  • Many machine learning-based approaches have been developed for the prognosis and diagnosis of COVID-19 from medical images and this Analysis identifies over 2,200 relevant published papers and preprints in this area. After initial screening, 62 studies are analysed and the authors find they all have methodological flaws standing in the way of clinical utility. The authors have several recommendations to address these issues.

    • Michael Roberts
    • Derek Driggs
    • Carola-Bibiane Schönlieb
    Analysis Open Access
  • Cancers are complex diseases that are increasingly studied using a diverse set of omics data. At the same time, histological images show the interaction of cells, which is not visible with bulk omics methods. Binder and colleagues present a method to learn from both kinds of data, such that molecular markers can be associated with visible patterns in the tissue samples and be used for more accurate breast cancer diagnosis.

    • Alexander Binder
    • Michael Bockmayr
    • Frederick Klauschen
    Article