PAGE: A Simple and Optimal Probabilistic Gradient Estimator for Nonconvex Optimization

In this paper, we propose a novel stochastic gradient estimator -- ProbAbilistic Gradient Estimator (PAGE) -- for nonconvex optimization. PAGE is easy to implement as it is designed via a small adjustment to vanilla SGD: in each iteration, PAGE uses the vanilla minibatch SGD update with probability $p_t$ or reuses the previous gradient with a small adjustment, at a much lower computational cost, with probability $1-p_t$. We give a simple formula for the optimal choice of $p_t$. Moreover, we prove the first tight lower bound $\Omega(n+\frac{\sqrt{n}}{\epsilon^2})$ for nonconvex finite-sum problems, which also leads to a tight lower bound $\Omega(b+\frac{\sqrt{b}}{\epsilon^2})$ for nonconvex online problems, where $b:= \min\{\frac{\sigma^2}{\epsilon^2}, n\}$. Then, we show that PAGE obtains the optimal convergence results $O(n+\frac{\sqrt{n}}{\epsilon^2})$ (finite-sum) and $O(b+\frac{\sqrt{b}}{\epsilon^2})$ (online) matching our lower bounds for both nonconvex finite-sum and online problems. Besides, we also show that for nonconvex functions satisfying the Polyak-\L{}ojasiewicz (PL) condition, PAGE can automatically switch to a faster linear convergence rate $O(\cdot\log \frac{1}{\epsilon})$. Finally, we conduct several deep learning experiments (e.g., LeNet, VGG, ResNet) on real datasets in PyTorch showing that PAGE not only converges much faster than SGD in training but also achieves the higher test accuracy, validating the optimal theoretical results and confirming the practical superiority of PAGE.Comment: 25 pages; accepted by ICML 2021 (long talk

Variable Nanoparticle-Cell Adhesion Strength Regulates Cellular Uptake

In receptor-mediated endocytosis, cells exercise biochemical control over the mechanics of adhesion to engulf foreign particles, featuring a variable adhesion strength. Here we present a thermodynamic model with which we elucidate that the variable adhesion strength critically governs the cellular uptake, yielding an uptake phase diagram in the space of ligand density and particle size. We identify from the diagram an endocytosed phase with markedly high uptake, encompassed by a lower and an upper phase boundary that are set, respectively, by the enthalpic and entropic limits of the adhesion strength. The phase diagram may provide useful guidance to the rational design of nanoparticle-based therapeutic and diagnostic agents

Effects of tree trunks on estimation of clumping index and LAI from HemiView and terrestrial LiDAR

Estimating clumping indices is important for determining the leaf area index (LAI) of forest canopies. The spatial distribution of the clumping index is vital for LAI estimation. However, the neglect of woody tissue can result in biased clumping index estimates when indirectly deriving them from the gap probability and LAI observations. It is difficult to effectively and automatically extract woody tissue from digital hemispherical photos. In this study, a method for the automatic detection of trunks from Terrestrial Laser Scanning (TLS) data was used. Between-crown and within-crown gaps from TLS data were separated to calculate the clumping index. Subsequently, we analyzed the gap probability, clumping index, and LAI estimates based on TLS and HemiView data in consideration of woody tissue (trunks). Although the clumping index estimated from TLS had better agreement (R-2 = 0.761) than that from HemiView, the change of angular distribution of the clumping index affected by the trunks from TLS data was more obvious than with the HemiView data. Finally, the exclusion of the trunks led to a reduction in the average LAI by similar to 19.6% and 8.9%, respectively, for the two methods. These results also showed that the detection of woody tissue was more helpful for the estimation of clumping index distribution. Moreover, the angular distribution of the clumping index is more important for the LAI estimate than the average clumping index value. We concluded that woody tissue should be detected for the clumping index estimate from TLS data, and 3D information could be used for estimating the angular distribution of the clumping index, which is essential for highly accurate LAI field measurements

Ionic Liquids as Bifunctional Cosolvents Enhanced CO₂ Conversion Catalysed by NADH-Dependent Formate Dehydrogenase

Efficient CO2 conversion by formate dehydrogenase is limited by the low CO2 concentrations that can be reached in traditional buffers. The use of ionic liquids was proposed as a manner to increase CO2 concentration in the reaction system. It has been found, however, that the required cofactor (NADH) heavily degraded during the enzymatic reaction and that acidity was the main reason. Acidity, indeed, resulted in reduction of the conversion of CO2 into formic acid and contributed to overestimate the amount of formic acid produced when the progression of the reaction was followed by a decrease in NADH absorbance (method N). Stability of NADH and the mechanism of NADH degradation was investigated by UV, NMR and by DFT calculations. It was found that by selecting neutral-basic ionic liquids and by adjusting the concentration of the ionic liquid in the buffer, the concentration of NADH can be maintained in the reaction system with little loss. Conversion of CO2 to methanol in BmimBF(4) (67.1%) was more than twice as compared with the conversion attained by the enzymatic reaction in phosphate buffer (24.3%)

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia

<p>Abstract</p> <p>Background</p> <p>It is widely recognized that interspecific hybridization may induce "genome shock", and lead to genetic and epigenetic instabilities in the resultant hybrids and/or backcrossed introgressants. A prominent component involved in the genome shock is reactivation of cryptic transposable elements (TEs) in the hybrid genome, which is often associated with alteration in the elements' epigenetic modifications like cytosine DNA methylation. We have previously reported that introgressants derived from hybridization between <it>Oryza sativa </it>(rice) and <it>Zizania latifolia </it>manifested substantial methylation re-patterning and rampant mobilization of two TEs, a <it>copia </it>retrotransposon <it>Tos17 </it>and a MITE <it>mPing</it>. It was not known however whether other types of TEs had also been transpositionally reactivated in these introgressants, their relevance to alteration in cytosine methylation, and their impact on expression of adjacent cellular genes.</p> <p>Results</p> <p>We document in this study that the <it>Dart </it>TE family was transpositionally reactivated followed by stabilization in all three studied introgressants (RZ1, RZ2 and RZ35) derived from introgressive hybridization between rice (cv. Matsumae) and <it>Z. latifolia</it>, while the TEs remained quiescent in the recipient rice genome. Transposon-display (TD) and sequencing verified the element's mobility and mapped the excisions and re-insertions to the rice chromosomes. Methylation-sensitive Southern blotting showed that the <it>Dart </it>TEs were heavily methylated along their entire length, and moderate alteration in cytosine methylation patterns occurred in the introgressants relative to their rice parental line. Real-time qRT-PCR quantification on the relative transcript abundance of six single-copy genes flanking the newly excised or inserted <it>Dart</it>-related TE copies indicated that whereas marked difference in the expression of all four genes in both tissues (leaf and root) were detected between the introgressants and their rice parental line under both normal and various stress conditions, the difference showed little association with the presence or absence of the newly mobilized <it>Dart-</it>related TEs.</p> <p>Conclusion</p> <p>Introgressive hybridization has induced transpositional reactivation of the otherwise immobile <it>Dart</it>-related TEs in the parental rice line (cv. Matsumae), which was accompanied with a moderate alteration in the element's cytosine methylation. Significant difference in expression of the <it>Dart</it>-adjacent genes occurred between the introgressants and their rice parental line under both normal and various abiotic stress conditions, but the alteration in gene expression was not coupled with the TEs.</p

Towards understanding the robustness against evasion attack on categorical inputs

International audienceCharacterizing and assessing the adversarial risk of a classifier with categorical inputs has been a practically important yet rarely explored research problem. Conventional wisdom attributes the difficulty of solving the problem to its combinatorial nature. Previous research efforts tackling this problem are specific to use cases and heavily depend on domain knowledge. Such limitations prevent their general applicability in real-world applications with categorical data. Our study novelly shows that provably optimal adversarial robustness assessment is computationally feasible for any classifier with a mild smoothness constraint. We theoretically analyze the impact factors of adversarial vulnerability of a classifier with categorical inputs via an information-theoretic adversarial risk analysis. Corroborating these theoretical findings with a substantial experimental study over various real-world categorical datasets, we can empirically assess the impact of the key adversarial risk factors over a targeted learning system with categorical inputs

AdvCat: Domain-Agnostic Robustness Assessment for Cybersecurity-Critical Applications with Categorical Inputs

Machine Learning-as-a-Service systems (MLaaS) have been largely developed for cybersecurity-critical applications, such as detecting network intrusions and fake news campaigns. Despite effectiveness, their robustness against adversarial attacks is one of the key trust concerns for MLaaS deployment. We are thus motivated to assess the adversarial robustness of the Machine Learning models residing at the core of these security-critical applications with categorical inputs. Previous research efforts on accessing model robustness against manipulation of categorical inputs are specific to use cases and heavily depend on domain knowledge, or require white-box access to the target ML model. Such limitations prevent the robustness assessment from being as a domain-agnostic service provided to various real-world applications. We propose a provably optimal yet computationally highly efficient adversarial robustness assessment protocol for a wide band of ML-driven cybersecurity-critical applications. We demonstrate the use of the domain-agnostic robustness assessment method with substantial experimental study on fake news detection and intrusion detection problems.Comment: IEEE BigData 202

Molecular Composition of Dissolved Organic Matter in the Changjiang (Yangtze River) – Imprints of Anthropogenic Impact

Understanding the biogeochemical transformation of dissolved organic matter (DOM) across fluvial networks will ultimately help to predict anthropogenic influences. To date, few studies have evaluated the anthropogenic impact on the spatial and temporal changes of DOM composition in large river systems. Here, FT-ICR-MS combined with excitation-emission matrix spectroscopy (EEMs) and biomarkers were applied to resolve chemical differences of DOM collected from the Changjiang basin at different hydrological and environmental conditions. PCA and cluster analysis illustrated that samples collected from lake systems and northern and southern tributaries differed from the two batches of main stream samples, particularly due to higher contribution of nitrogen and sulfur containing compounds. Correlation of land-use information along the tributaries with different PCA loadings indicated that agricultural, forest and wetland areas and wastewater discharge control the composition of DOM within these subregions. Higher heteroatom content (especially CHONx) in the low discharge period (2009) may be contributed by paddy soil leaching into groundwater. The relative peak magnitude of sulfur containing formulas was elevated during flood season (2010), which may be related to pollutions in areas of high population density. In addition, lignin phenol concentrations were higher in the flood season because of elevated soil erosion. Consequently, land use and human activities can strongly alter the quality and composition of DOM in watersheds flowing through densely populated regions, which may also impact or influence the riverine carbon flux in anthropogenically disturbed river systems

Aerosols as a source of dissolved black carbon to the ocean

溶解黑碳（dissolved black carbon, DBC）在开阔大洋的年龄可达上万年，是海洋中到目前为止已知的年龄最老、最大的惰性溶解有机碳。因此海洋溶解黑碳的源汇问题是全球碳循环研究的重要部分。该研究团队通过测定2015年春季东、黄海以及西北太平洋的气溶胶中水溶性有机碳(water soluble organic carbon, WSOC)、水溶性黑碳 (water soluble black carbon, WSBC)的含量，并结合超高分辨质谱---傅里叶变换离子回旋共振质谱 (FT-ICR-MS)，解析了海洋气溶胶中溶解黑碳的浓度以及分子组成。进一步分析发现气溶胶中溶解黑碳的浓度与水溶性有机碳浓度显著高度相关。预测的未来生物质燃烧以及沙尘输送的变化可能增加大气沉降溶解黑碳的通量，影响区域甚至全球碳库。该研究结果将有助于把溶解黑碳纳入到海洋碳循环研究模型中。 近海海洋环境科学国家重点实验室助理教授鲍红艳为论文第一作者，高树基教授为共同通讯作者。【Abstract】Dissolved black carbon (DBC) is the largest known slow-cycling organic carbon pool in the world’s oceans. Atmospheric deposition could significantly contribute to the oceanic DBC pool, but respective information is lacking. Here we estimate that, during the dust outbreak season, the atmospheric dry deposition of water-soluble black carbon (WSBC) is～ 40% of the riverine input to the China coastal seas. The molecular composition of atmospheric WSBC determined by ultrahigh-resolution mass spectrometry, reveals similar soil-derived sources as for riverine discharge. WSBC is significantly positively correlated with water-soluble organic carbon (WSOC) in marine aerosols, and water-soluble black carbon contributes on average 2.8 ± 0.65% to the total WSOC. Based on this relationship, the global atmospheric deposition of DBC to the ocean is estimated to be 1.8 ± 0.83 Tg yr−1. Anticipated future changes in biomass burning and dust mobilization might increase these numbers, with consequences for regional ecosystems and global carbon reservoirs.This study was funded by the Major State Basic Research Development Program of China (973 program) (No. 2014CB953702) and the China Postdoctoral Science Foundation (No. 2013M540529). Hanse-Wissenschaftskolleg (the Institute for Advanced Study in Germany) is acknowledged for its support of Dr. H. Bao. 本研究受到973项目“不同营养水平下海洋氮循环关键过程及其对大气物质沉降的响应”（No.2014CB953702）以及中国博士后科学基金（No.2013M540529）的资助； 鲍红艳博士在德国的工作受到德国Hanse-Wissenschaftskolleg奖学金的资助

The physical constraints on a new LoBAL QSO at z=4.82

Very few low-ionization broad absorption line (LoBAL) QSOs have been found at high redshifts to date. One high-redshift LoBAL QSO, J0122+1216, was recently discovered at the Lijiang 2.4-m Telescope with an initial redshift determination of 4.76. Aiming to investigate its physical properties, we carried out follow-up observations in the optical and near-IR spectroscopy. Near-IR spectra from UKIRT and P200 confirms that it is a LoBAL, with a new redshift determination of $4.82\pm0.01$ based on the \mgii~ emission-line. The new \mgii~ redshift determination reveals strong blueshifts and asymmetry of the high-ionization emission lines. We estimated a black hole mass of $\sim 2.3\times 10^9 M_\odot$ and Eddington ratio of $\sim 1.0$ according to the empirical \mgii-based single-epoch relation and bolometric correction factor. It is possible that strong outflows are the result of an extreme quasar environment driven by the high Eddington ratio. A lower limit on the outflowing kinetic power ($>0.9\% L_{Edd}$) was derived from both emission and absorption lines, indicating these outflows play a significant role in the feedback process to regulate the growth of its black hole as well as host galaxy evolution.Comment: 12 pages, 10 figures. Accepted for publication in The Astrophysical Journa