An Asymptotic Analysis of Minibatch-Based Momentum Methods for Linear Regression Models

Momentum methods have been shown to accelerate the convergence of the standard gradient descent algorithm in practice and theory. In particular, the minibatch-based gradient descent methods with momentum (MGDM) are widely used to solve large-scale optimization problems with massive datasets. Despite the success of the MGDM methods in practice, their theoretical properties are still underexplored. To this end, we investigate the theoretical properties of MGDM methods based on the linear regression models. We first study the numerical convergence properties of the MGDM algorithm and further provide the theoretically optimal tuning parameters specification to achieve faster convergence rate. In addition, we explore the relationship between the statistical properties of the resulting MGDM estimator and the tuning parameters. Based on these theoretical findings, we give the conditions for the resulting estimator to achieve the optimal statistical efficiency. Finally, extensive numerical experiments are conducted to verify our theoretical results.Comment: 45 pages, 5 figure

Modeling Social Media User Content Generation Using Interpretable Point Process Models

In this article, we study the activity patterns of modern social media users on platforms such as Twitter and Facebook. To characterize the complex patterns we observe in users' interactions with social media, we describe a new class of point process models. The components in the model have straightforward interpretations and can thus provide meaningful insights into user activity patterns. A composite likelihood approach and a composite EM estimation procedure are developed to overcome the challenges that arise in parameter estimation. Using the proposed method, we analyze Donald Trump's Twitter data and study if and how his tweeting behavior evolved before, during and after the presidential campaign. Additionally, we analyze a large-scale social media data from Sina Weibo and identify interesting groups of users with distinct behaviors; in this analysis, we also discuss the effect of social ties on a user's online content generating behavior

Variations of deep soil moisture under different vegetation types and influencing factors in a watershed of the Loess Plateau, China

Soil moisture in deep soil layers is a relatively stable water resource for vegetation growth in the semi-arid Loess Plateau of China. Characterizing the variations in deep soil moisture and its influencing factors at a moderate watershed scale is important to ensure the sustainability of vegetation restoration efforts. In this study, we focus on analyzing the variations and factors that influence the deep soil moisture (DSM) in 80–500 cm soil layers based on a soil moisture survey of the Ansai watershed in Yan'an in Shanxi Province. Our results can be divided into four main findings. (1) At the watershed scale, higher variations in the DSM occurred at 120–140 and 480–500 cm in the vertical direction. At the comparable depths, the variation in the DSM under native vegetation was much lower than that in human-managed vegetation and introduced vegetation. (2) The DSM in native vegetation and human-managed vegetation was significantly higher than that in introduced vegetation, and different degrees of soil desiccation occurred under all the introduced vegetation types. Caragana korshinskii and black locust caused the most serious desiccation. (3) Taking the DSM conditions of native vegetation as a reference, the DSM in this watershed could be divided into three layers: (i) a rainfall transpiration layer (80–220 cm); (ii) a transition layer (220–400 cm); and (iii) a stable layer (400–500 cm). (4) The factors influencing DSM at the watershed scale varied with vegetation types. The main local controls of the DSM variations were the soil particle composition and mean annual rainfall; human agricultural management measures can alter the soil bulk density, which contributes to higher DSM in farmland and apple orchards. The plant growth conditions, planting density, and litter water holding capacity of introduced vegetation showed significant relationships with the DSM. The results of this study are of practical significance for vegetation restoration strategies, especially for the choice of vegetation types, planting zones, and proper human management measures

The Exploration and Evaluation of Generating Affective 360∘^\circ Panoramic VR Environments Through Neural Style Transfer

Affective virtual reality (VR) environments with varying visual style can impact users' valence and arousal responses. We applied Neural Style Transfer (NST) to generate 360$^\circ$ VR environments that elicited users' varied valence and arousal responses. From a user study with 30 participants, findings suggested that generative VR environments changed participants' arousal responses but not their valence levels. The generated visual features, e.g., textures and colors, also altered participants' affective perceptions. Our work contributes novel insights about how users respond to generative VR environments and provided a strategy for creating affective VR environments without altering content

The clinicopathological factors associated with disease progression in Luminal a breast cancer and characteristics of metastasis: A retrospective study from a single center in China

Background/Aim: This study investigated the clinicopathological factors associated with outcomes in patients with Luminal A breast cancer. Patients and Methods: Retrospective analysis of the association of clinicopathological factors and breast cancer outcome in 421 patients with newly diagnosed Luminal-A breast cancer that were enrolled from January 2008 to December 2014. Clinicopathological data were analyzed to validate the relationship with disease free survival (DFS) and overall survival (OS). Kaplan-Meier curves and log-rank tests were used to analyze the value of clinicopathological factors (tumor size, node status and lymphovascular invasion), and subsequent Cox regression analysis revealed significant prognostic factors. Results: With a median of 61 months follow up, the 5-year DFS and 5-year OS rate were 98.3% and 99.3%. Cox multivariate regression analysis showed that clinical anatomic stage, tumor size, status of lymph nodes, lymphovascular invasion and systemic treatment are strong prognostic factors for clinical outcome in patients with Luminal-A breast cancer. Of all 413 patients with stage I-III breast cancer, 14 presented with metastasis (3.4%) during the follow up. Bone (6/14, 42.9%) was the most common site of metastasis followed by liver (5/14, 35.7%) and lung (4/14, 28.6%). The median survival time after metastasis was 20.4 months. Of all the sites of distant metastasis, liver metastasis was the only factor that affected survival time after metastasis (χ2=6.263, p=0.012). Conclusion: Patients with Luminal A breast cancer have excellent outcomes. Liver metastasis is an important factor compressing the survival time after distant metastasis presents

Scaffold Structural Microenvironmental Cues to Guide Tissue Regeneration in Bone Tissue Applications

In the process of bone regeneration, new bone formation is largely affected by physico-chemical cues in the surrounding microenvironment. Tissue cells reside in a complex scaffold physiological microenvironment. The scaffold should provide certain circumstance full of structural cues to enhance multipotent mesenchymal stem cell (MSC) differentiation, osteoblast growth, extracellular matrix (ECM) deposition, and subsequent new bone formation. This article reviewed advances in fabrication technology that enable the creation of biomaterials with well-defined pore structure and surface topography, which can be sensed by host tissue cells (esp., stem cells) and subsequently determine cell fates during differentiation. Three important cues, including scaffold pore structure (i.e., porosity and pore size), grain size, and surface topography were studied. These findings improve our understanding of how the mechanism scaffold microenvironmental cues guide bone tissue regeneration

Differentiable Logic Machines

The integration of reasoning, learning, and decision-making is key to build more general AI systems. As a step in this direction, we propose a novel neural-logic architecture that can solve both inductive logic programming (ILP) and deep reinforcement learning (RL) problems. Our architecture defines a restricted but expressive continuous space of first-order logic programs by assigning weights to predicates instead of rules. Therefore, it is fully differentiable and can be efficiently trained with gradient descent. Besides, in the deep RL setting with actor-critic algorithms, we propose a novel efficient critic architecture. Compared to state-of-the-art methods on both ILP and RL problems, our proposition achieves excellent performance, while being able to provide a fully interpretable solution and scaling much better, especially during the testing phase

Fusion of EML4 and ALK is associated with development of lung adenocarcinomas lacking EGFR and KRAS mutations and is correlated with ALK expression

<p>Abstract</p> <p>Background</p> <p>The anaplastic lymphoma kinase (<it>ALK</it>) gene is frequently involved in translocations that lead to gene fusions in a variety of human malignancies, including lymphoma and lung cancer. Fusion partners of <it>ALK </it>include <it>NPM</it>, <it>EML4</it>, <it>TPM3</it>, <it>ATIC</it>, <it>TFG</it>, <it>CARS</it>, and <it>CLTC</it>. Characterization of ALK fusion patterns and their resulting clinicopathological profiles could be of great benefit in better understanding the biology of lung cancer.</p> <p>Results</p> <p>RACE-coupled PCR sequencing was used to assess <it>ALK </it>fusions in a cohort of 103 non-small cell lung carcinoma (NSCLC) patients. Within this cohort, the <it>EML4</it>-<it>ALK </it>fusion gene was identified in 12 tumors (11.6%). Further analysis revealed that <it>EML4</it>-<it>ALK </it>was present at a frequency of 16.13% (10/62) in patients with adenocarcinomas, 19.23% (10/52) in never-smokers, and 42.80% (9/21) in patients with adenocarcinomas lacking <it>EGFR </it>and <it>KRAS </it>mutations. The <it>EML4</it>-<it>ALK </it>fusion was associated with non-smokers (<it>P </it>= 0.03), younger age of onset (<it>P </it>= 0.03), and adenocarcinomas without <it>EGFR</it>/<it>KRAS </it>mutations (<it>P </it>= 0.04). A trend towards improved survival was observed for patients with the <it>EML4</it>-<it>ALK </it>fusion, although it was not statistically significant (<it>P </it>= 0.20). Concurrent deletion in <it>EGFR </it>exon 19 and fusion of <it>EML4</it>-<it>ALK </it>was identified for the first time in a Chinese female patient with an adenocarcinoma. Analysis of ALK expression revealed that ALK mRNA levels were higher in tumors positive for the <it>EML</it>-<it>ALK </it>fusion than in negative tumors (normalized intensity of 21.99 vs. 0.45, respectively; <it>P </it>= 0.0018). However, expression of EML4 did not differ between the groups.</p> <p>Conclusions</p> <p>The <it>EML4</it>-<it>ALK </it>fusion gene was present at a high frequency in Chinese NSCLC patients, particularly in those with adenocarcinomas lacking <it>EGFR</it>/<it>KRAS </it>mutations. The <it>EML4</it>-<it>ALK </it>fusion appears to be tightly associated with ALK mRNA expression levels. RACE-coupled PCR sequencing is a highly sensitive method that could be used clinically for the identification of <it>EML4</it>-<it>ALK</it>-positive patients.</p

Analysis of Differentially Expressed Proteins in Self-Paired Sera of Advanced Non-small Cell Lung Cancer Patients Responsive to Gefin

Background and objective All the advanced NSCLC patients that received EGFR-TKI therapy will eventually relapse after a period of efficacy. The aim of this study is to investigate the serum biomarkers as potential predictive factors for the efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) targeted therapy in advanced non-small cell lung cancer. Methods Twenty self-paired serum samples were collected from 9 advanced NSCLC patients that evaluated as disease control (SD or PR) after gefinitib therapy, at the time points of before and after gefinitib treatment but 2 weeks before being evaluated as disease progress. All samples were pre-separated by WCX microbeads, and then detected on the MALDI-TOF-MS platform of Bruker AutoflexTM. ClinProTools (Version: 2.1) was used to analyze the differentially expressed proteins. Results There were 7 protein peaks (m/z), 3242.09, 8 690.36, 2 952.64, 3 224.04, 1 450.51, 1 887.8 and 3 935.73 found statistically differentially expressed between the self-paired samples. Three proteins (3 242.09, 2 952.64 and 3 224.04) were down-regulated and four proteins (8 690.36, 1 450.51, 1 887.8 and 3 935.73) up-regulated in gefinitib treated sera. Conclusion The data here suggest that several specific protein peaks might indicate gefinitib resistance, yet the identities of these proteins and the mechanisms underlying the responsiveness to gefinitib treatment need further investigation

A Wheat Cinnamyl Alcohol Dehydrogenase TaCAD12 Contributes to Host Resistance to the Sharp Eyespot Disease

peer reviewedSharp eyespot, caused mainly by the necrotrophic fungus Rhizoctonia cerealis, is a destructive disease in hexaploid wheat (Triticum aestivum L.). In Arabidopsis, certain cinnamyl alcohol dehydrogenases (CADs) have been implicated in monolignol biosynthesis and in defense response to bacterial pathogen infection. However, little is known about CADs in wheat defense responses to necrotrophic or soil-borne pathogens. In this study, we isolate a wheat CAD gene TaCAD12 in response to R. cerealis infection through microarray-based comparative transcriptomics, and study the enzyme activity and defense role of TaCAD12 in wheat. The transcriptional levels of TaCAD12 in sharp eyespot-resistant wheat lines were significantly higher compared with those in susceptible wheat lines. The sequence and phylogenetic analyses revealed that TaCAD12 belongs to IV group in CAD family. The biochemical assay proved that TaCAD12 protein is an authentic CAD enzyme and possesses catalytic efficiencies toward both coniferyl aldehyde and sinapyl aldehyde. Knock-down of TaCAD12 transcript significantly repressed resistance of the gene-silenced wheat plants to sharp eyespot caused by R. cerealis, whereas TaCAD12 overexpression markedly enhanced resistance of the transgenic wheat lines to sharp eyespot. Furthermore, certain defense genes (Defensin, PR10, PR17c, and Chitinase1) and monolignol biosynthesis-related genes (TaCAD1, TaCCR, and TaCOMT1) were up-regulated in the TaCAD12-overexpressing wheat plants but down-regulated in TaCAD12-silencing plants. These results suggest that TaCAD12 positively contributes to resistance against sharp eyespot through regulation of the expression of certain defense genes and monolignol biosynthesis-related genes in wheat.Nationa l“KeySci-Tech” Projec