Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.

Cryo-electron tomography (cryo-ET) provides 3D visualization of subcellular components in the near-native state and at sub-molecular resolutions in single cells, demonstrating an increasingly important role in structural biology in situ. However, systematic recognition and recovery of macromolecular structures in cryo-ET data remain challenging as a result of low signal-to-noise ratio (SNR), small sizes of macromolecules, and high complexity of the cellular environment. Subtomogram structural classification is an essential step for such task. Although acquisition of large amounts of subtomograms is no longer an obstacle due to advances in automation of data collection, obtaining the same number of structural labels is both computation and labor intensive. On the other hand, existing deep learning based supervised classification approaches are highly demanding on labeled data and have limited ability to learn about new structures rapidly from data containing very few labels of such new structures. In this work, we propose a novel approach for subtomogram classification based on few-shot learning. With our approach, classification of unseen structures in the training data can be conducted given few labeled samples in test data through instance embedding. Experiments were performed on both simulated and real datasets. Our experimental results show that we can make inference on new structures given only five labeled samples for each class with a competitive accuracy (> 0.86 on the simulated dataset with SNR = 0.1), or even one sample with an accuracy of 0.7644. The results on real datasets are also promising with accuracy > 0.9 on both conditions and even up to 1 on one of the real datasets. Our approach achieves significant improvement compared with the baseline method and has strong capabilities of generalizing to other cellular components

Sedimentary evolution during the last ~1.9 Ma near the western margin of the modern Bohai Sea

© 2016. Because the Bohai Sea is a semi-enclosed sea connected to the North Yellow Sea only via the Bohai Strait, its sedimentary evolution during the Quaternary has been complex. In particular, the timing of Quaternary transgressions, especially Pleistocene transgressions, in the region, has long been a matter of controversy. Thus, the sedimentary history of the Bohai Sea in the Quaternary is still poorly understood. Borehole core YRD-1101 (200.30 m long), drilled in 2011 on the northern coast of the modern Yellow River delta, covers the last ~1.90 Ma, as indicated by paleomagnetic measurements. Here we report the results of integrated analyses of the core, including its sedimentary characteristics, downcore changes in environmental proxies (benthic foraminifers and ostracods), and accelerator mass spectrometry (AMS) 14C and optically stimulated luminescence (OSL) dates. From ~1.9 to ~0.83 Ma, the environment was fluvial. The first Quaternary transgression occurred at ~0.83 Ma (the latest Early Pleistocene), presumably caused by minor subsidence of the Miaodao Islands Uplift. Several relatively weak transgressions occurred from ~0.83 Ma to the end of the Middle Pleistocene, and three major marine sedimentary beds, here called T-3, T-2, and T-1 in ascending order, recorded in the early to middle MIS 5, the early MIS 3, and the middle to late Holocene, respectively, were presumably caused by major subsidence of the Miaodao Islands Uplift. In transgression strength, T-3 was weaker than T-2, which was basically the same as T-1. We interpret the change in transgression strength to reflect the interplay of sea-level changes, neotectonic subsidence, and sediment supply changes. Comparisons with other cores from around the Bohai Sea showed that the thickness of the Quaternary sedimentary sequence differs significantly among them, and both the T-2 and T-3 clearly display differences in thickness, facies sequence, and completeness among the cores, highlighting the important role of tectonic activity in the evolution of the Quaternary stratigraphy in the Bohai Bay Basin