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Ji Chen
Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong, China

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Conference paper
Published: 06 May 2021 in Communications in Computer and Information Science
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Long-tail effect is common in recommender systems, meaning that a tiny number of users have lots of interaction with items, while the majority of users have extremely little interaction. Most of existing approaches to recommender systems, especially methods based on collaborative filtering, suffer severely from long-tail problems due to the low resource issue. In order to handle the problem of long-tail recommendation, we utilize knowledge graph to enrich the representation of users and items. As auxiliary prior information source, knowledge graph has been popular technology for recommender systems nowadays, while it is rarely exploited with respect to the low resource issue. In this paper, we propose a knowledge-enhanced collaborative meta learner, which combines the priors in knowledge graph and collaborative information between head users to promote long-tail recommendation performance. We conduct several experiments on two real world datasets for long-tail recommendation. The results show that our approach outperforms several commonly used recommendation methods in the long tail scenario.

ACS Style

Bo Wen; Shumin Deng; Huajun Chen. Knowledge-Enhanced Collaborative Meta Learner for Long-Tail Recommendation. Communications in Computer and Information Science 2021, 322 -333.

AMA Style

Bo Wen, Shumin Deng, Huajun Chen. Knowledge-Enhanced Collaborative Meta Learner for Long-Tail Recommendation. Communications in Computer and Information Science. 2021; ():322-333.

Chicago/Turabian Style

Bo Wen; Shumin Deng; Huajun Chen. 2021. "Knowledge-Enhanced Collaborative Meta Learner for Long-Tail Recommendation." Communications in Computer and Information Science , no. : 322-333.

Journal article
Published: 24 February 2021 in BMC Medical Informatics and Decision Making
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Background In this work, we aimed to demonstrate how to utilize the lab test results and other clinical information to support precision medicine research and clinical decisions on complex diseases, with the support of electronic medical record facilities. We defined “clinotypes” as clinical information that could be observed and measured objectively using biomedical instruments. From well-known ‘omic’ problem definitions, we defined problems using clinotype information, including stratifying patients—identifying interested sub cohorts for future studies, mining significant associations between clinotypes and specific phenotypes-diseases, and discovering potential linkages between clinotype and genomic information. We solved these problems by integrating public omic databases and applying advanced machine learning and visual analytic techniques on two-year health exam records from a large population of healthy southern Chinese individuals (size n = 91,354). When developing the solution, we carefully addressed the missing information, imbalance and non-uniformed data annotation issues. Results We organized the techniques and solutions to address the problems and issues above into CPA framework (Clinotype Prediction and Association-finding). At the data preprocessing step, we handled the missing value issue with predicted accuracy of 0.760. We curated 12,635 clinotype-gene associations. We found 147 Associations between 147 chronic diseases-phenotype and clinotypes, which improved the disease predictive performance to AUC (average) of 0.967. We mined 182 significant clinotype-clinotype associations among 69 clinotypes. Conclusions Our results showed strong potential connectivity between the omics information and the clinical lab test information. The results further emphasized the needs to utilize and integrate the clinical information, especially the lab test results, in future PheWas and omic studies. Furthermore, it showed that the clinotype information could initiate an alternative research direction and serve as an independent field of data to support the well-known ‘phenome’ and ‘genome’ researches.

ACS Style

Thanh Nguyen; Tongbin Zhang; Geoffrey Fox; Sisi Zeng; Ni Cao; Chuandi Pan; Jake Y. Chen. Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. BMC Medical Informatics and Decision Making 2021, 21, 1 -12.

AMA Style

Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen. Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. BMC Medical Informatics and Decision Making. 2021; 21 (3):1-12.

Chicago/Turabian Style

Thanh Nguyen; Tongbin Zhang; Geoffrey Fox; Sisi Zeng; Ni Cao; Chuandi Pan; Jake Y. Chen. 2021. "Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams." BMC Medical Informatics and Decision Making 21, no. 3: 1-12.

Journal article
Published: 09 January 2021 in Journal of Web Semantics
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Data stream learning has been largely studied for extracting knowledge structures from continuous and rapid data records. As data is evolving on a temporal basis, its underlying knowledge is subject to many challenges. Concept drift,1 as one of core challenge from the stream learning community, is described as changes of statistical properties of the data over time, causing most of machine learning models to be less accurate as changes over time are in unforeseen ways. This is particularly problematic as the evolution of data could derive to dramatic change in knowledge. We address this problem by studying the semantic representation of data streams in the Semantic Web, i.e., ontology streams. Such streams are ordered sequences of data annotated with ontological vocabulary. In particular we exploit three levels of knowledge encoded in ontology streams to deal with concept drifts: i) existence of novel knowledge gained from stream dynamics, ii) significance of knowledge change and evolution, and iii) (in)consistency of knowledge evolution. Such knowledge is encoded as knowledge graph embeddings through a combination of novel representations: entailment vectors, entailment weights, and a consistency vector. We illustrate our approach on classification tasks of supervised learning. Key contributions of the study include: (i) an effective knowledge graph embedding approach for stream ontologies, and (ii) a generic consistent prediction framework with integrated knowledge graph embeddings for dealing with concept drifts. The experiments have shown that our approach provides accurate predictions towards air quality in Beijing and bus delay in Dublin with real world ontology streams.

ACS Style

Jiaoyan Chen; Freddy Lécué; Jeff Z. Pan; Shumin Deng; Huajun Chen. Knowledge graph embeddings for dealing with concept drift in machine learning. Journal of Web Semantics 2021, 67, 100625 .

AMA Style

Jiaoyan Chen, Freddy Lécué, Jeff Z. Pan, Shumin Deng, Huajun Chen. Knowledge graph embeddings for dealing with concept drift in machine learning. Journal of Web Semantics. 2021; 67 ():100625.

Chicago/Turabian Style

Jiaoyan Chen; Freddy Lécué; Jeff Z. Pan; Shumin Deng; Huajun Chen. 2021. "Knowledge graph embeddings for dealing with concept drift in machine learning." Journal of Web Semantics 67, no. : 100625.

Journal article
Published: 27 November 2020 in Nucleic Acids Research
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PAGER-CoV (http://discovery.informatics.uab.edu/PAGER-CoV/) is a new web-based database that can help biomedical researchers interpret coronavirus-related functional genomic study results in the context of curated knowledge of host viral infection, inflammatory response, organ damage, and tissue repair. The new database consists of 11 835 PAGs (Pathways, Annotated gene-lists, or Gene signatures) from 33 public data sources. Through the web user interface, users can search by a query gene or a query term and retrieve significantly matched PAGs with all the curated information. Users can navigate from a PAG of interest to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships, totaling 19 996 993. Users can also retrieve enriched PAGs from an input list of COVID-19 functional study result genes, customize the search data sources, and export all results for subsequent offline data analysis. In a case study, we performed a gene set enrichment analysis (GSEA) of a COVID-19 RNA-seq data set from the Gene Expression Omnibus database. Compared with the results using the standard PAGER database, PAGER-CoV allows for more sensitive matching of known immune-related gene signatures. We expect PAGER-CoV to be invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients.

ACS Style

Zongliang Yue; Eric Zhang; Clark Xu; Sunny Khurana; Nishant Batra; Son Do Hai Dang; James J Cimino; Jake Y Chen. PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. Nucleic Acids Research 2020, 49, D589 -D599.

AMA Style

Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J Cimino, Jake Y Chen. PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. Nucleic Acids Research. 2020; 49 (D1):D589-D599.

Chicago/Turabian Style

Zongliang Yue; Eric Zhang; Clark Xu; Sunny Khurana; Nishant Batra; Son Do Hai Dang; James J Cimino; Jake Y Chen. 2020. "PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies." Nucleic Acids Research 49, no. D1: D589-D599.

Journal article
Published: 05 November 2020 in Ecological Indicators
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Exploring the impact of climate change on drought under changing environmental conditions is crucial for agriculture, ecology, and human society. To evaluate the role of climate change on drought, this study selected the Songnen Plain (SNP) in Northeast China as a study area in which to quantify the relative contributions of climatic variables to the drought trend in accordance with the Standardized Precipitation and Evapotranspiration Index (SPEI). A series of SPEI-based numerical experiments, using combinations of observational and nonlinear detrended climatic variable data series, was used as a synthetic approach with which to analyze the relative impact of the individual climatic variables. Results indicated that drought on the SNP has been mitigated marginally during 1961–2016, mainly during spring, winter, the growing season, and on the annual timescale. Significant trends were detected in relation to temperature, sunshine duration, and wind speed, and these variables had differing roles in drought evolution. An increasing trend in temperature was found to aggravate drought tendency at all investigated timescales; however, decreasing trends in net radiation and wind speed offset the drought tendency caused by rising temperature. The positive contribution of wind speed was larger than the negative contribution of temperature, especially in areas around 46°N. Although the change of precipitation was not significant, it promoted drought mitigation on the SNP in spring, winter, the growing season, and on the annual timescale. The analysis framework used in this study was shown useful for improving understanding of the relationship between climate change and drought evolution, and it could prove helpful in providing rational and regulatory policy strategies regarding drought relief.

ACS Style

Ruxin Zhao; Huixiao Wang; Ji Chen; Guobin Fu; Chesheng Zhan; Huicai Yang. Quantitative analysis of nonlinear climate change impact on drought based on the standardized precipitation and evapotranspiration index. Ecological Indicators 2020, 121, 107107 .

AMA Style

Ruxin Zhao, Huixiao Wang, Ji Chen, Guobin Fu, Chesheng Zhan, Huicai Yang. Quantitative analysis of nonlinear climate change impact on drought based on the standardized precipitation and evapotranspiration index. Ecological Indicators. 2020; 121 ():107107.

Chicago/Turabian Style

Ruxin Zhao; Huixiao Wang; Ji Chen; Guobin Fu; Chesheng Zhan; Huicai Yang. 2020. "Quantitative analysis of nonlinear climate change impact on drought based on the standardized precipitation and evapotranspiration index." Ecological Indicators 121, no. : 107107.

Journal article
Published: 23 October 2020 in Nature Communications
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The world has experienced dramatic urbanization in recent decades. However, we still lack information about the characteristics of urbanization in large cities throughout the world. After analyzing 841 large cities with built-up areas (BUAs) of over 100 km2 from 2001 to 2018, here we found an uneven distribution of urbanization at different economic levels. On average, large cities in the low-income and lower-middle-income countries had the highest urban population growth, and BUA expansion in the upper-middle-income countries was more than three times that of the high-income countries. Globally, more than 10% of BUAs in 325 large cities showed significant greening (P < 0.05) from 2001 to 2018. In particular, China accounted for 32% of greening BUAs in the 841 large cities, where about 108 million people lived. Our quantitative results provide information for future urban sustainable development, especially for rational urbanization of the developing world.

ACS Style

Liqun Sun; Ji Chen; Qinglan Li; Dian Huang. Dramatic uneven urbanization of large cities throughout the world in recent decades. Nature Communications 2020, 11, 1 -9.

AMA Style

Liqun Sun, Ji Chen, Qinglan Li, Dian Huang. Dramatic uneven urbanization of large cities throughout the world in recent decades. Nature Communications. 2020; 11 (1):1-9.

Chicago/Turabian Style

Liqun Sun; Ji Chen; Qinglan Li; Dian Huang. 2020. "Dramatic uneven urbanization of large cities throughout the world in recent decades." Nature Communications 11, no. 1: 1-9.

Journal article
Published: 16 August 2020 in Journal of Power Sources
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Symmetrical solid oxide cells (SSOCs) have been extensively recognized due to their simple cell configuration, low cost and reliability. High performance electrode is the key determinant of SSOCs. Herein, a multifunctional perovskite oxide La0.6Ca0.4Fe0.8Ni0.2O3-δ (LCaFN) is investigated as electrode for SSOCs. The results confirm that LCaFN shows excellent oxygen reduction reaction (ORR), oxygen evolution reaction (OER), carbon dioxide reduction reaction (CO2-RR) and hydrogen oxidation reaction (HOR) catalytic activity. In SOFC mode, the SSOCs with LCaFN achieve good electrochemical performance with maximum power density of 300 mW cm−2 at 800 °C. For pure CO2 electrolysis in SOEC mode, polarization resistance of 0.055 Ω cm2 and current density of 1.5 A cm−2 are achieved at 2.0 V at 800 °C. Besides, the cell shows excellent stability both in SOFC mode and SOEC mode. Most importantly, SSOCs with symmetrical LCaFN electrodes show robust and regenerative performance under anodic or cathodic process during the switching gas, showing the great reliability of the SSOCs. The results show that this novel electrode offers a promising strategy for operation of SSOCs.

ACS Style

Yunfeng Tian; Yun Liu; Lichao Jia; Aaron Naden; Jing Chen; Bo Chi; Jian Pu; John Irvine; Jian Li. A novel electrode with multifunction and regeneration for highly efficient and stable symmetrical solid oxide cell. Journal of Power Sources 2020, 475, 228620 .

AMA Style

Yunfeng Tian, Yun Liu, Lichao Jia, Aaron Naden, Jing Chen, Bo Chi, Jian Pu, John Irvine, Jian Li. A novel electrode with multifunction and regeneration for highly efficient and stable symmetrical solid oxide cell. Journal of Power Sources. 2020; 475 ():228620.

Chicago/Turabian Style

Yunfeng Tian; Yun Liu; Lichao Jia; Aaron Naden; Jing Chen; Bo Chi; Jian Pu; John Irvine; Jian Li. 2020. "A novel electrode with multifunction and regeneration for highly efficient and stable symmetrical solid oxide cell." Journal of Power Sources 475, no. : 228620.

Journal article
Published: 16 August 2020 in Water
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This study analyzed the microphysical characteristics of stratiform and convective precipitation over an inland arid region of Qinghai–Tibet Plateau in summer for the first time. The observed precipitation data were from the OTT Parsivel2 laser raindrop spectrometer and the raindrop size distribution can be described by a gamma distribution and a general exponential distribution. The results indicate that: (1) compared to the exponential distribution, the gamma distribution is the better function with which to describe the raindrop size distribution in this region; (2) the raindrop sizes are mainly below 1 mm, and the raindrop sizes which contribute most to the rainfall intensity are below 2 mm for stratiform precipitation and convective precipitation; (3) the mean values of microphysical parameters, e.g., rainfall intensity, radar reflectivity factor, and liquid water content, are higher for convective precipitation than stratiform precipitation; and (4) the standard Z–R relationship underestimates the radar reflectivity factor in this region. Overall, the obtained results will enhance our understanding and facilitate future studies regarding the microphysical characteristics of precipitation in such regions. For example, the obtained Z–R relationship can be a reference for estimating the radar reflectivity factor in this region with higher accuracy.

ACS Style

Hongwei Xie; Peichong Pan; Haiyun Shi; Ji Chen; Jinzhao Wang. Observed Microphysical Characteristics of Stratiform and Convective Precipitation over an Inland Arid Region of the Qinghai–Tibet Plateau. Water 2020, 12, 2300 .

AMA Style

Hongwei Xie, Peichong Pan, Haiyun Shi, Ji Chen, Jinzhao Wang. Observed Microphysical Characteristics of Stratiform and Convective Precipitation over an Inland Arid Region of the Qinghai–Tibet Plateau. Water. 2020; 12 (8):2300.

Chicago/Turabian Style

Hongwei Xie; Peichong Pan; Haiyun Shi; Ji Chen; Jinzhao Wang. 2020. "Observed Microphysical Characteristics of Stratiform and Convective Precipitation over an Inland Arid Region of the Qinghai–Tibet Plateau." Water 12, no. 8: 2300.

Journal article
Published: 17 June 2020 in The Journal of Immunology
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IL-23 promotes autoimmune disease, including Th17 CD4 T cell development and autoantibody production. In this study, we show that a deficiency of the p19 component of IL-23 in the autoimmune BXD2 (BXD2-p19−/−) mouse leads to a shift of the follicular T helper cell program from follicular T helper (Tfh)–IL-17 to Tfh–IFN-γ. Although the germinal center (GC) size and the number of GC B cells remained the same, BXD2-p19−/− mice exhibited a lower class-switch recombination (CSR) in the GC B cells, leading to lower serum levels of IgG2b. Single-cell transcriptomics analysis of GC B cells revealed that whereas Ifngr1, Il21r, and Il4r genes exhibited a synchronized expression pattern with Cxcr5 and plasma cell program genes, Il17ra exhibited a synchronized expression pattern with Cxcr4 and GC program genes. Downregulation of Ighg2b in BXD2-p19−/− GC B cells was associated with decreased expression of CSR-related novel base excision repair genes that were otherwise predominantly expressed by Il17ra+ GC B cells in BXD2 mice. Together, these results suggest that although IL-23 is dispensable for GC formation, it is essential to promote a population of Tfh–IL-17 cells. IL-23 acts indirectly on Il17ra+ GC B cells to facilitate CSR-related base excision repair genes during the dark zone phase of GC B cell development.

ACS Style

Huixian Hong; Min Gao; Qi Wu; PingAr Yang; Shanrun Liu; Hao Li; Peter D. Burrows; Daniel Cua; Jake Y. Chen; Hui-Chen Hsu; John D. Mountz. IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice. The Journal of Immunology 2020, 205, 346 -358.

AMA Style

Huixian Hong, Min Gao, Qi Wu, PingAr Yang, Shanrun Liu, Hao Li, Peter D. Burrows, Daniel Cua, Jake Y. Chen, Hui-Chen Hsu, John D. Mountz. IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice. The Journal of Immunology. 2020; 205 (2):346-358.

Chicago/Turabian Style

Huixian Hong; Min Gao; Qi Wu; PingAr Yang; Shanrun Liu; Hao Li; Peter D. Burrows; Daniel Cua; Jake Y. Chen; Hui-Chen Hsu; John D. Mountz. 2020. "IL-23 Promotes a Coordinated B Cell Germinal Center Program for Class-Switch Recombination to IgG2b in BXD2 Mice." The Journal of Immunology 205, no. 2: 346-358.

Preprint content
Published: 14 May 2020
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Advances in single-cell RNA sequencing (scRNA-seq) have furthered the simultaneous classification of thousands of cells in a single assay based on transcriptome profiling. In most analysis protocols, single-cell type annotation relies on marker genes or RNA-seq profiles, resulting in poor extrapolation. Here, we introduce scDeepSort (https://github.com/ZJUFanLab/scDeepSort), a reference-free cell-type annotation tool for single-cell transcriptomics that uses a deep learning model with a weighted graph neural network. Using human and mouse scRNA-seq data resources, we demonstrate the feasibility of scDeepSort and its high accuracy in labeling 764,741 cells involving 56 human and 32 mouse tissues. Significantly, scDeepSort outperformed reference-dependent methods in annotating 76 external testing scRNA-seq datasets, including 126,384 cells (85.79%) from ten human tissues and 134,604 cells from 12 mouse tissues (81.30%). scDeepSort accurately revealed cell identities without prior reference knowledge, thus potentially providing new insights into mechanisms underlying biological processes, disease pathogenesis, and disease progression at a single-cell resolution.

ACS Style

Xin Shao; Haihong Yang; Xiang Zhuang; Jie Liao; Yueren Yang; Penghui Yang; Junyun Cheng; Xiaoyan Lu; Huajun Chen; Xiaohui Fan. Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network. 2020, 1 .

AMA Style

Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Yueren Yang, Penghui Yang, Junyun Cheng, Xiaoyan Lu, Huajun Chen, Xiaohui Fan. Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network. . 2020; ():1.

Chicago/Turabian Style

Xin Shao; Haihong Yang; Xiang Zhuang; Jie Liao; Yueren Yang; Penghui Yang; Junyun Cheng; Xiaoyan Lu; Huajun Chen; Xiaohui Fan. 2020. "Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network." , no. : 1.

Preprint content
Published: 05 March 2020
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In this work, we design the Polar Gini Curve (PGC) technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data. Theoretically, a Polar Gini Curve characterizes the shape and ‘evenness’ of cell-point distribution of cell-point set. To quantify whether a gene could be a marker in a cell cluster, we can combine two Polar Gini Curves: one drawn upon the cell-points expressing the gene, and the other drawn upon all cell-points in the cluster. We hypothesize that the closers these two curves are, the more likely the gene would be cluster markers. We demonstrate the framework in several simulation case-studies. Applying our framework in analyzing neonatal mouse heart single-cell data, the detected biomarkers may characterize novel subtypes of cardiac muscle cells. The source code and data for PGC could be found athttps://figshare.com/projects/Polar_Gini_Curve/76749.

ACS Style

Thanh Minh Nguyen; Jacob John Jeevan; Nuo Xu; Jake Y. Chen. Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information. 2020, 1 .

AMA Style

Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen. Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information. . 2020; ():1.

Chicago/Turabian Style

Thanh Minh Nguyen; Jacob John Jeevan; Nuo Xu; Jake Y. Chen. 2020. "Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information." , no. : 1.

Journal article
Published: 01 March 2020 in Journal of Applied Meteorology and Climatology
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This study investigated heavy frontal rainfall that occurred on 13–14 October 2011 over the Pearl River Delta (PRD) in China. The frontal rainstorm was simulated using the WRF-ARW Model (version 3.3), which included its urban canopy model. Although the model-simulated convection occurred 2 h early and the second precipitation peak was underestimated, the model represented the formation, development, and extinction of the frontal rainfall and captured the distribution of the peak value. In addition, the averaged value of 49.7 W m−2 was taken as the anthropogenic heat flux (AHF) of the PRD, and two land-use datasets were adopted: one for 1992 and the other for 2011. The simulation revealed that AHF and urban land-use change (ULUC) increased the total rainfall over the PRD by 6.3% and 7.4% and increased the maximum hourly rainfall intensity by 24.6% and 21.2%, respectively. Furthermore, to elucidate the mechanism of AHF and ULUC influence, the rainstorm structure, low-level jet (LLJ), and CAPE of the rainfall event were analyzed. It was found that AHF and ULUC enhanced two strong southward LLJs located over the urban areas, which carried abundant water vapor to the PRD and generated additional upper-level CAPE. This not only sustained steady ascent of the air, but it also created conditions favorable for downward motion, resulting in large persistent convective clouds and heavy frontal rainfall.

ACS Style

Junpeng Wen; Ji Chen; Wenshi Lin; Baolin Jiang; Suishan Xu; Jing Lan. Impacts of Anthropogenic Heat Flux and Urban Land-Use Change on Frontal Rainfall near Coastal Regions: A Case Study of a Rainstorm over the Pearl River Delta, South China. Journal of Applied Meteorology and Climatology 2020, 59, 363 -379.

AMA Style

Junpeng Wen, Ji Chen, Wenshi Lin, Baolin Jiang, Suishan Xu, Jing Lan. Impacts of Anthropogenic Heat Flux and Urban Land-Use Change on Frontal Rainfall near Coastal Regions: A Case Study of a Rainstorm over the Pearl River Delta, South China. Journal of Applied Meteorology and Climatology. 2020; 59 (3):363-379.

Chicago/Turabian Style

Junpeng Wen; Ji Chen; Wenshi Lin; Baolin Jiang; Suishan Xu; Jing Lan. 2020. "Impacts of Anthropogenic Heat Flux and Urban Land-Use Change on Frontal Rainfall near Coastal Regions: A Case Study of a Rainstorm over the Pearl River Delta, South China." Journal of Applied Meteorology and Climatology 59, no. 3: 363-379.

Conference paper
Published: 19 February 2020 in Communications in Computer and Information Science
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In e-Commerce, we are interested in deals by lifestyle which will improve the diversity of items shown to users. A lifestyle, an important motivation for consumption, is a person’s pattern of living in the world as expressed in activities, interests, and opinions. In this paper, we focus on the key task for deals by lifestyle, establishing linkage between items and lifestyles. We build an item-lifestyle knowledge graph to fully utilize the information about them and formulate it as a knowledge graph link prediction task. A lot of knowledge graph embedding methods are proposed to accomplish relational learning in academia. Although these methods got impressive results on benchmark datasets, they can’t provide insights and explanations for their prediction which limit their usage in industry. In this scenario, we concern about not only linking prediction results, but also explanations for predicted results and human-understandable rules, because explanations help us deal with uncertainty from algorithms and rules can be easily transferred to other platforms. Our proposal includes an explainable knowledge graph embedding method (XTransE), an explanation generator and a rule collector, which outperforms traditional classifier models and original embedding method during prediction, and successfully generates explanations and collects meaningful rules.

ACS Style

Wen Zhang; Shumin Deng; Han Wang; Qiang Chen; Wei Zhang; Huajun Chen. XTransE: Explainable Knowledge Graph Embedding for Link Prediction with Lifestyles in e-Commerce. Communications in Computer and Information Science 2020, 78 -87.

AMA Style

Wen Zhang, Shumin Deng, Han Wang, Qiang Chen, Wei Zhang, Huajun Chen. XTransE: Explainable Knowledge Graph Embedding for Link Prediction with Lifestyles in e-Commerce. Communications in Computer and Information Science. 2020; ():78-87.

Chicago/Turabian Style

Wen Zhang; Shumin Deng; Han Wang; Qiang Chen; Wei Zhang; Huajun Chen. 2020. "XTransE: Explainable Knowledge Graph Embedding for Link Prediction with Lifestyles in e-Commerce." Communications in Computer and Information Science , no. : 78-87.

Journal article
Published: 01 January 2020 in International Journal of Biological Sciences
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Neoadjuvant chemotherapy has been used increasingly in patients with early-stage or locally advanced breast carcinoma, and has been recommended as a general approach in locally advanced-stage diseases. Assessing therapy response could offer prognostic information to help determine subsequent nursing plan; particularly it is essential to identify responders and non-responders for the sake of helping develop follow-up treatment strategies. However, at present, diagnostic accuracy of preoperative clinical examination are still not satisfactory. Here we presented an alternate approach to monitor tumor and stroma changes associated with neoadjuvant therapy responses in breast carcinoma, with a great potential for becoming a new diagnostic tool-multiphoton microscopy. Imaging results showed that multiphoton imaging techniques have the ability to label-freely visualize tumor response such as tumor necrosis, and stromal response including fibrosis, mucinous response, inflammatory response as well as vascular hyperplasia in situ at cellular and subcellular levels. Moreover, using automated image analysis and a set of scoring methods, we found significant differences in the area of cell nucleus and in the content of collagen fibers between the pre-treatment and post-treatment breast carcinoma tissues. In summary, this study was conducted to pathologically evaluate the response of breast carcinoma to preoperative chemotherapy as well as to assess the efficacy of multiphoton microscopy in detecting these pathological changes, and experimental results demonstrated that this microscope may be a promising tool for label-free, real-time assessment of treatment response without the use of any exogenous contrast agents.

ACS Style

LianHuang Li; Zhonghua Han; Lida Qiu; Deyong Kang; Zhenlin Zhan; Haohua Tu; Jianxin Chen. Label-free multiphoton imaging to assess neoadjuvant therapy responses in breast carcinoma. International Journal of Biological Sciences 2020, 16, 1376 -1387.

AMA Style

LianHuang Li, Zhonghua Han, Lida Qiu, Deyong Kang, Zhenlin Zhan, Haohua Tu, Jianxin Chen. Label-free multiphoton imaging to assess neoadjuvant therapy responses in breast carcinoma. International Journal of Biological Sciences. 2020; 16 (8):1376-1387.

Chicago/Turabian Style

LianHuang Li; Zhonghua Han; Lida Qiu; Deyong Kang; Zhenlin Zhan; Haohua Tu; Jianxin Chen. 2020. "Label-free multiphoton imaging to assess neoadjuvant therapy responses in breast carcinoma." International Journal of Biological Sciences 16, no. 8: 1376-1387.

Articles
Published: 12 December 2019 in Environmental Education Research
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The New Ecological Paradigm (NEP) scale is used worldwide to predict people’s environmental worldviews. However, some researchers criticize its unidimensional structure and limited ability to predict pro-environmental behavior (PEB). The Two Major Environmental Values (2-MEV) scale, which considers environmental attitudes in two dimensions—preservation and utilization—may overcome these deficiencies. To examine if the 2-MEV exceeds the NEP scale in predictability of people’s environmental attitudes in China and its applicability to Chinese children, we modified the 2-MEV scale in Chinese and used it to question 490 students (aged 9–12) in China. The results show that the modified version demonstrated good reliability and internal consistency. Furthermore, the 2-MEV demonstrated significantly a higher predictive power of PEB than the NEP. We thus contend the 2-MEV is a promising measurement for gauging Chinese children’s environmental attitudes. The application of the 2-MEV in different contexts and the improvement of NEP was discussed.

ACS Style

Wanlu Liu; Jin Chen. Modified Two Major Environmental Values scale for measuring Chinese children’s environmental attitudes. Environmental Education Research 2019, 26, 130 -147.

AMA Style

Wanlu Liu, Jin Chen. Modified Two Major Environmental Values scale for measuring Chinese children’s environmental attitudes. Environmental Education Research. 2019; 26 (1):130-147.

Chicago/Turabian Style

Wanlu Liu; Jin Chen. 2019. "Modified Two Major Environmental Values scale for measuring Chinese children’s environmental attitudes." Environmental Education Research 26, no. 1: 130-147.

Book chapter
Published: 22 November 2019 in Food Contaminants and Residue Analysis
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Halogenated flame retardants (HFRs) are a group of chemicals, mainly based on bromine and chlorine, which are added to the consumer products. Due to the characteristics of trace amounts in the environment, the analysis of emerging HFRs was of great concern. Environmental pollution levels and sources, migration and transformation of these emerging HFRs depends on the development of analytical techniques. This has led to a wide variety of analytical approaches for sample extraction, cleanup, qualitative and quantitative analysis and other steps of emerging HFRs. However, the interferences of a plenty of co-effluent materials and individual congeners make the analysis of trace emerging HFRs challenging. The current sample pretreatment techniques and analytical methodologies for the detection and quantification of emerging BFRs (HBCD, TBBPA, etc.) and CFRs (DP, SCCPs) in environment samples were discussed in this chapter. In addition, we hope to make some recommendations regarding the need for further method development.

ACS Style

Yuan Gao; Rong Cao; Haijun Zhang; Jiping Chen. Analysis of emerging halogenated flame retardants in environment. Food Contaminants and Residue Analysis 2019, 41 -70.

AMA Style

Yuan Gao, Rong Cao, Haijun Zhang, Jiping Chen. Analysis of emerging halogenated flame retardants in environment. Food Contaminants and Residue Analysis. 2019; ():41-70.

Chicago/Turabian Style

Yuan Gao; Rong Cao; Haijun Zhang; Jiping Chen. 2019. "Analysis of emerging halogenated flame retardants in environment." Food Contaminants and Residue Analysis , no. : 41-70.

Journal article
Published: 21 November 2019 in Scientific Reports
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Soil moisture plays an important role in land-atmosphere interactions, agricultural drought monitoring, and water resource management, particularly across arid regions. However, it is challenging to simulate soil moisture of high spatial resolution and to evaluate soil moisture at fine spatial resolution in arid regions in Northwest China due to considerable uncertainties in forcing data and limited in situ measurements. Then, the data set was used to produce the 1 km high-resolution atmospheric forcing datasets and to drive the Community Land Model version 3.5 (CLM3.5) for simulating spatiotemporally continuous surface soil moisture. The capabilities of soil moisture simulation using CLM3.5 forced by the XJLDAS-driven field were validated against data obtained at three soil layers (0–10, 0–20, and 0–50 cm) from 54 soil moisture stations in Xinjiang. Results show that the simulated soil moisture agreed well with the observations [CORR > 0.952], and the intra-annual soil moisture in Xinjiang gradually increased during May through August. The main factors that affect changes in soil moisture across the study region were precipitation and snowmelt. The overall finding of this study is that an XJLDAS, high-resolution forcing data driven CLM3.5 can be used to generate accurate and continuous soil moisture of high resolution (1km) in Xinjiang. This study can help understand the spatiotemporal features of the soil moisture, and provide important input for hydrological studies and agricultural water resources management over the arid region.

ACS Style

Xianyong Meng; Hao Wang; Ji Chen; Mingxiang Yang; Zhihua Pan. High-resolution simulation and validation of soil moisture in the arid region of Northwest China. Scientific Reports 2019, 9, 1 -17.

AMA Style

Xianyong Meng, Hao Wang, Ji Chen, Mingxiang Yang, Zhihua Pan. High-resolution simulation and validation of soil moisture in the arid region of Northwest China. Scientific Reports. 2019; 9 (1):1-17.

Chicago/Turabian Style

Xianyong Meng; Hao Wang; Ji Chen; Mingxiang Yang; Zhihua Pan. 2019. "High-resolution simulation and validation of soil moisture in the arid region of Northwest China." Scientific Reports 9, no. 1: 1-17.

Journal article
Published: 12 November 2019 in Neurophotonics
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β -Amyloid ( A β ) plaque, representing the progressive accumulation of the protein that mainly consists of A β , is one of the prominent pathological hallmarks of Alzheimer's disease (AD). Label-free imaging of A β plaques holds the potential to be a histological examination tool for diagnosing AD. We applied label-free multiphoton microscopy to identify extracellular A β plaque as well as intracellular A β accumulation for the first time from AD mouse models. We showed that a two-photon-excited fluorescence signal is a sensitive optical marker for revealing the spatial-temporal progression and the surrounding morphological changes of A β deposition, which demonstrated that both extracellular and intracellular A β accumulations play an important role in the progression of AD. Moreover, combined with a custom-developed image-processing program, we established a rapid method to visualize different degrees of A β deposition by color coding. These results provide an approach for investigating pathophysiology of AD that can complement traditional biomedical procedures.

ACS Style

Shu Wang; Bingbing Lin; Guimin Lin; Caihong Sun; Ruolan Lin; Jia Huang; Jing Tao; Xingfu Wang; Yunkun Wu; Lidian Chen; Jianxin Chen. Label-free multiphoton imaging of β-amyloid plaques in Alzheimer’s disease mouse models. Neurophotonics 2019, 6, 045008 .

AMA Style

Shu Wang, Bingbing Lin, Guimin Lin, Caihong Sun, Ruolan Lin, Jia Huang, Jing Tao, Xingfu Wang, Yunkun Wu, Lidian Chen, Jianxin Chen. Label-free multiphoton imaging of β-amyloid plaques in Alzheimer’s disease mouse models. Neurophotonics. 2019; 6 (4):045008.

Chicago/Turabian Style

Shu Wang; Bingbing Lin; Guimin Lin; Caihong Sun; Ruolan Lin; Jia Huang; Jing Tao; Xingfu Wang; Yunkun Wu; Lidian Chen; Jianxin Chen. 2019. "Label-free multiphoton imaging of β-amyloid plaques in Alzheimer’s disease mouse models." Neurophotonics 6, no. 4: 045008.

Research article
Published: 11 November 2019 in Quantitative Biology
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In network biology researchers generate biomolecular networks with candidate genes or proteins experimentally-derived from high-throughput data and known biomolecular associations. Current bioinformatics research focuses on characterizing candidate genes/proteins, or nodes, with network characteristics, e.g., betweenness centrality. However, there have been few research reports to characterize and prioritize biomolecular associations (“edges”), which can represent gene regulatory events essential to biological processes. We developed Weighted In-Path Edge Ranking (WIPER), a new computational algorithm which can help evaluate all biomolecular interactions/associations (“edges”) in a network model and generate a rank order of every edge based on their in-path traversal scores and statistical significance test result. To validate whether WIPER worked as we designed, we tested the algorithm on synthetic network models. Our results showed WIPER can reliably discover both critical “well traversed in-path edges”, which are statistically more traversed than normal edges, and “peripheral in-path edges”, which are less traversed than normal edges. Compared with other simple measures such as betweenness centrality, WIPER provides better biological interpretations. In the case study of analyzing postanal pig hearts gene expression, WIPER highlighted new signaling pathways suggestive of cardiomyocyte regeneration and proliferation. In the case study of Alzheimer’s disease genetic disorder association, WIPER reports SRC:APP, AR:APP, APP:FYN, and APP:NES edges (gene-gene associations) both statistically and biologically important from PubMed co-citation. We believe that WIPER will become an essential software tool to help biologists discover and validate essential signaling/regulatory events from high-throughput biology data in the context of biological networks. The free WIPER API is described at https://discovery.informatics.uab.edu/wiper/

ACS Style

Zongliang Yue; Thanh Nguyen; Eric Zhang; Jianyi Zhang; Jake Y. Chen. WIPER: Weighted in-Path Edge Ranking for biomolecular association networks. Quantitative Biology 2019, 7, 313 -326.

AMA Style

Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen. WIPER: Weighted in-Path Edge Ranking for biomolecular association networks. Quantitative Biology. 2019; 7 (4):313-326.

Chicago/Turabian Style

Zongliang Yue; Thanh Nguyen; Eric Zhang; Jianyi Zhang; Jake Y. Chen. 2019. "WIPER: Weighted in-Path Edge Ranking for biomolecular association networks." Quantitative Biology 7, no. 4: 313-326.

Journal article
Published: 18 October 2019 in Water
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The temporal and spatial differentiation of the underlying surface in East Asia is complex. Due to a lack of meteorological observation data, human cognition and understanding of the surface processes (runoff, snowmelt, soil moisture, water production, etc.) in the area have been greatly limited. With the Heihe River Basin, a poorly gauged region in the cold region of Western China, selected as the study area, three meteorological datasets are evaluated for their suitability to drive the Soil and Water Assessment Tool (SWAT): China Meteorological Assimilation Driving Datasets for the SWAT model (CMADS), Climate Forecast System Reanalysis (CFSR), and Traditional Weather Station (TWS). Resultingly, (1) the runoff output of CMADS + SWAT mode is generally better than that of the other two modes (CFSR + SWAT and TWS + SWAT) and the monthly and daily Nash–Sutcliffe efficiency ranges of the CMADS + SWAT mode are 0.75–0.95 and 0.58–0.77, respectively; (2) the CMADS + SWAT and TWS + SWAT results were fairly similar to the actual data (especially for precipitation and evaporation), with the results produced by CMADS + SWAT lower than those produced by TWS + SWAT; (3) the CMADS + SWAT mode has a greater ability to reproduce water balance than the other two modes. Overestimation of CFSR precipitation results in greater error impact on the uncertainty output of the model, whereas the performances of CMADS and TWS are more similar. This study addresses the gap in the study of surface processes by CMADS users in Western China and provides an important scientific basis for analyzing poorly gauged regions in East Asia.

ACS Style

Xianyong Meng; Xuesong Zhang; Mingxiang Yang; Hao Wang; Ji Chen; Zhihua Pan; Yiping Wu. Application and Evaluation of the China Meteorological Assimilation Driving Datasets for the SWAT Model (CMADS) in Poorly Gauged Regions in Western China. Water 2019, 11, 2171 .

AMA Style

Xianyong Meng, Xuesong Zhang, Mingxiang Yang, Hao Wang, Ji Chen, Zhihua Pan, Yiping Wu. Application and Evaluation of the China Meteorological Assimilation Driving Datasets for the SWAT Model (CMADS) in Poorly Gauged Regions in Western China. Water. 2019; 11 (10):2171.

Chicago/Turabian Style

Xianyong Meng; Xuesong Zhang; Mingxiang Yang; Hao Wang; Ji Chen; Zhihua Pan; Yiping Wu. 2019. "Application and Evaluation of the China Meteorological Assimilation Driving Datasets for the SWAT Model (CMADS) in Poorly Gauged Regions in Western China." Water 11, no. 10: 2171.