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1. Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization

   https://doi.org/10.1093/bioinformatics/btab794  

   Bandyopadhyay, Hmrishav ; Deng, Zihao ; Ding, Leiting ; Liu, Sinuo ; Uddin, Mostofa Rafid ; Zeng, Xiangrui ; Behpour, Sima ; Xu, Min ; Xu, ed., Jinbo ( November 2021 , Bioinformatics)

   Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms.

   In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with ‘warp’ modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data.

   https://github.com/xulabs/aitom.

   Supplementary data are available at Bioinformatics online.

    

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2. Improving Solar Energetic Particle Event Prediction through Multivariate Time Series Data Augmentation

   https://doi.org/10.3847/1538-4365/ad1de0  

   Hosseinzadeh, Pouya ; Filali Boubrahimi, Soukaina ; Hamdi, Shah Muhammad ( February 2024 , The Astrophysical Journal Supplement Series)

   Solar energetic particles (SEPs) are associated with extreme solar events that can cause major damage to space- and ground-based life and infrastructure. High-intensity SEP events, particularly ∼100 MeV SEP events, can pose severe health risks for astronauts owing to radiation exposure and affect Earth’s orbiting satellites (e.g., Landsat and the International Space Station). A major challenge in the SEP event prediction task is the lack of adequate SEP data because of the rarity of these events. In this work, we aim to improve the prediction of ∼30, ∼60, and ∼100 MeV SEP events by synthetically increasing the number of SEP samples. We explore the use of a univariate and multivariate time series of proton flux data as input to machine-learning-based prediction methods, such as time series forest (TSF). Our study covers solar cycles 22, 23, and 24. Our findings show that using data augmentation methods, such as the synthetic minority oversampling technique, remarkably increases the accuracy and F1-score of the classifiers used in this research, especially for TSF, where the average accuracy increased by 20%, reaching around 90% accuracy in the ∼100 MeV SEP prediction task. We also achieved higher prediction accuracy when using the multivariate time series data of the proton flux. Finally, we build a pipeline framework for our best-performing model, TSF, and provide a comprehensive hierarchical classification of the ∼100, ∼60, and ∼30 MeV and non-SEP prediction scenarios.

    

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3. AMR-meta: a k -mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

   https://doi.org/10.1093/gigascience/giac029  

   Marini, Simone ; Oliva, Marco ; Slizovskiy, Ilya B. ; Das, Rishabh A. ; Noyes, Noelle Robertson ; Kahveci, Tamer ; Boucher, Christina ; Prosperi, Mattia ( May 2022 , GigaScience)

   Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.

   We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2–0.9). On semi-synthetic metagenomic data—external test—on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.

   AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.

    

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4. Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms

   https://doi.org/10.1093/bioinformatics/btx230  

   Xu, Min ; Chai, Xiaoqi ; Muthakana, Hariank ; Liang, Xiaodan ; Yang, Ge ; Zeev-Ben-Mordehai, Tzviya ; Xing, Eric P. ( July 2017 , Bioinformatics)

   Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data.

   To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data.

   Source code freely available at http://www.cs.cmu.edu/∼mxu1/software.

   Supplementary data are available at Bioinformatics online.

    

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5. eCAMI: simultaneous classification and motif identification for enzyme annotation

   https://doi.org/10.1093/bioinformatics/btz908  

   Xu, Jing ; Zhang, Han ; Zheng, Jinfang ; Dovoedo, Philippe ; Yin, Yanbin ; Xu, ed., Jinbo ( December 2019 , Bioinformatics)

   Carbohydrate-active enzymes (CAZymes) are extremely important to bioenergy, human gut microbiome, and plant pathogen researches and industries. Here we developed a new amino acid k-mer-based CAZyme classification, motif identification and genome annotation tool using a bipartite network algorithm. Using this tool, we classified 390 CAZyme families into thousands of subfamilies each with distinguishing k-mer peptides. These k-mers represented the characteristic motifs (in the form of a collection of conserved short peptides) of each subfamily, and thus were further used to annotate new genomes for CAZymes. This idea was also generalized to extract characteristic k-mer peptides for all the Swiss-Prot enzymes classified by the EC (enzyme commission) numbers and applied to enzyme EC prediction.

   This new tool was implemented as a Python package named eCAMI. Benchmark analysis of eCAMI against the state-of-the-art tools on CAZyme and enzyme EC datasets found that: (i) eCAMI has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction. Lastly, we confirmed that the k-mer-based tools have the unique ability to identify the characteristic k-mer peptides in the predicted enzymes.

   https://github.com/yinlabniu/eCAMI and https://github.com/zhanglabNKU/eCAMI.

   Supplementary data are available at Bioinformatics online.

    

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