Active Learning to Classify Macromolecular Structures in situ for Less Supervision in Cryo-Electron Tomography

Motivation: Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning based subtomogram classification have played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. Results: To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labelling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources.Comment: Statement on authorship changes: Dr. Eric Xing was an academic advisor of Mr. Haohan Wang. Dr. Xing was not directly involved in this work and has no direct interaction or collaboration with any other authors on this work. Therefore, Dr. Xing is removed from the author list according to his request. Mr. Zhenxi Zhu's affiliation is updated to his current affiliatio

Photometry of Variable Stars from Dome A, Antarctica

Dome A on the Antarctic plateau is likely one of the best observing sites on Earth thanks to the excellent atmospheric conditions present at the site during the long polar winter night. We present high-cadence time-series aperture photometry of 10,000 stars with i<14.5 mag located in a 23 square-degree region centered on the south celestial pole. The photometry was obtained with one of the CSTAR telescopes during 128 days of the 2008 Antarctic winter. We used this photometric data set to derive site statistics for Dome A and to search for variable stars. Thanks to the nearly-uninterrupted synoptic coverage, we find 6 times as many variables as previous surveys with similar magnitude limits. We detected 157 variable stars, of which 55% are unclassified, 27% are likely binaries and 17% are likely pulsating stars. The latter category includes delta Scuti, gamma Doradus and RR Lyrae variables. One variable may be a transiting exoplanet.Comment: Accepted for publication in the Astronomical Journal. PDF version with high-resolution figures available at http://faculty.physics.tamu.edu/lmacri/papers/wang11.pd

Photometric Variability in the CSTAR Field: Results From the 2008 Data Set

The Chinese Small Telescope ARray (CSTAR) is the first telescope facility built at Dome A, Antarctica. During the 2008 observing season, the installation provided long-baseline and high-cadence photometric observations in the i-band for 18,145 targets within 20 deg2 CSTAR field around the South Celestial Pole for the purpose of monitoring the astronomical observing quality of Dome A and detecting various types of photometric variability. Using sensitive and robust detection methods, we discover 274 potential variables from this data set, 83 of which are new discoveries. We characterize most of them, providing the periods, amplitudes and classes of variability. The catalog of all these variables is presented along with the discussion of their statistical properties.Comment: 38 pages, 11 figures, 4 tables; Accepted for publication in ApJ

Herbivore exclusion stabilizes alpine grassland biomass production across spatial scales

There is growing evidence that land-use management practices such as livestock grazing can strongly impact the local diversity, functioning, and stability of grassland communities. However, whether these impacts depend on environmental condition and propagate to larger spatial scales remains unclear. Using an 8-year grassland exclosure experiment conducted at nine sites in the Tibetan Plateau covering a large precipitation gradient, we found that herbivore exclusion increased the temporal stability of alpine grassland biomass production at both the local and larger (site) spatial scales. Higher local community stability was attributed to greater stability of dominant species, whereas higher stability at the larger scale was linked to higher spatial asynchrony of productivity among local communities. Additionally, sites with higher mean annual precipitation had lower dominant species stability and lower grassland stability at both the spatial scales considered. Our study provides novel evidence that livestock grazing can impair grassland stability across spatial scales and climatic gradients

The First Release of the CSTAR Point Source Catalog from Dome A, Antarctica

In 2008 January the 24th Chinese expedition team successfully deployed the Chinese Small Telescope ARray (CSTAR) to DomeA, the highest point on the Antarctic plateau. CSTAR consists of four 14.5cm optical telescopes, each with a different filter (g, r, i and open) and has a 4.5degree x 4.5degree field of view (FOV). It operates robotically as part of the Plateau Observatory, PLATO, with each telescope taking an image every 30 seconds throughout the year whenever it is dark. During 2008, CSTAR #1 performed almost flawlessly, acquiring more than 0.3 million i-band images for a total integration time of 1728 hours during 158 days of observations. For each image taken under good sky conditions, more than 10,000 sources down to 16 mag could be detected. We performed aperture photometry on all the sources in the field to create the catalog described herein. Since CSTAR has a fixed pointing centered on the South Celestial Pole (Dec =-90 degree), all the sources within the FOV of CSTAR were monitored continuously for several months. The photometric catalog can be used for studying any variability in these sources, and for the discovery of transient sources such as supernovae, gamma-ray bursts and minor planets.Comment: 1 latex file and 9 figures The paper is accepted by PAS

Eclipsing Binaries From the CSTAR Project at Dome A, Antarctica

The Chinese Small Telescope ARray (CSTAR) has observed an area around the Celestial South Pole at Dome A since 2008. About $20,000$ light curves in the i band were obtained lasting from March to July, 2008. The photometric precision achieves about 4 mmag at i = 7.5 and 20 mmag at i = 12 within a 30 s exposure time. These light curves are analyzed using Lomb--Scargle, Phase Dispersion Minimization, and Box Least Squares methods to search for periodic signals. False positives may appear as a variable signature caused by contaminating stars and the observation mode of CSTAR. Therefore the period and position of each variable candidate are checked to eliminate false positives. Eclipsing binaries are removed by visual inspection, frequency spectrum analysis and locally linear embedding technique. We identify 53 eclipsing binaries in the field of view of CSTAR, containing 24 detached binaries, 8 semi-detached binaries, 18 contact binaries, and 3 ellipsoidal variables. To derive the parameters of these binaries, we use the Eclipsing Binaries via Artificial Intelligence (EBAI) method. The primary and the secondary eclipse timing variations (ETVs) for semi-detached and contact systems are analyzed. Correlated primary and secondary ETVs confirmed by false alarm tests may indicate an unseen perturbing companion. Through ETV analysis, we identify two triple systems (CSTAR J084612.64-883342.9 and CSTAR J220502.55-895206.7). The orbital parameters of the third body in CSTAR J220502.55-895206.7 are derived using a simple dynamical model.Comment: 41 pages, 12 figures; published online in ApJ

The sky brightness and transparency in i-band at Dome A, Antarctica

The i-band observing conditions at Dome A on the Antarctic plateau have been investigated using data acquired during 2008 with the Chinese Small Telescope ARray. The sky brightness, variations in atmospheric transparency, cloud cover, and the presence of aurorae are obtained from these images. The median sky brightness of moonless clear nights is 20.5 mag arcsec^{-2} in the SDSS $i$ band at the South Celestial Pole (which includes a contribution of about 0.06 mag from diffuse Galactic light). The median over all Moon phases in the Antarctic winter is about 19.8 mag arcsec^{-2}. There were no thick clouds in 2008. We model contributions of the Sun and the Moon to the sky background to obtain the relationship between the sky brightness and transparency. Aurorae are identified by comparing the observed sky brightness to the sky brightness expected from this model. About 2% of the images are affected by relatively strong aurorae.Comment: There are 1 Latex file and 14 figures accepted by A