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Data-driven Discovery: A New Era of Exploiting the Literature and Data

Ying Ding & Kyle Stirling, Ying Ding & Kyle Stirling
2016 Journal of Data and Information Science  
By combining PubMed literature and public datasets, Chen, Ding, and Wild (2012) can predict potential drug and target pairs based on publications and open datasets.  ... 
doi:10.20309/jdis.201622 fatcat:3ggjdqhx3vfvjalyhlomykax4i

Mining Knowledge Graph for Drug Discovery

Ying Ding
2020 Zenodo  
This talk showcases how to mine knowledge graph for drug discovery. It discusses the cutting-edge machine learning and deep learning algorithms to mine a knowledge graph for potential drug and target binding relationships. It highlights the pros and cons of the current mining algorithms and points out forward-looking views about knowledge graph factory and knowledge fingerprint.
doi:10.5281/zenodo.3836883 fatcat:l5cnup5o7jhqflt63mnwzf4r3y

Role of CT scan in differentiating the type of colorectal cancer

Zhen-Hui Li, Ding-Yun You, De-Pei Gao, Guang-Jun Yang, Xing-Xiang Dong, Da-Fu Zhang, Ying-Ying Ding
2017 OncoTargets and Therapy  
Most colorectal cancers are classical adenocarcinomas (AC), and less frequent subtypes include mucinous adenocarcinomas (MAC) and signet-ring cell carcinomas (SC). The purpose of this study was to evaluate the computed tomography (CT) findings that can help to differentiate MAC and SC from AC. Methods: CT scans of 168 patients with pathologically proven MAC and 67 patients with pathologically proven SC were analyzed, and 220 patients with classical AC were also included as a control group. CT
more » ... ndings of the three groups were compared and contrasted in terms of the bowel involvement patterns, contrast enhancement patterns, and presence or absence of bowel obstruction, intratumoral calcification, pericolic fat infiltration, and local tumor extension to adjacent organs. Statistical analyses were made by using the one-way analysis of variance, least significant difference test, and Pearson's chi-square test. Results: Compared with classical AC, the MAC showed more severe (6.29±2.69 cm vs 4.57±1.74 cm, P,0.001) and higher percentage of occurrence of eccentric bowel-wall thickening (37.2% vs 11.5%, P,0.001). Heterogeneous contrast enhancement was most common in MAC (P,0.01), and MAC showed more areas with hypoattenuation (P,0.001). The presence of intratumoral calcification was most frequent in MAC (17.9% vs 2% vs 6.8%) (P,0.001); the SC also were more severe (5.75±2.28 cm vs 4.57±1.74 cm. P=0.001) than AC, but SC tend to show more cases of concentric even bowel-wall thickening (67.2%); homogeneous contrast enhancement was most common in SC (P,0.01), and it showed a target appearance. The presence of peritoneal seeding was most frequent in SC (35.8% vs 8% vs 2.7%, P,0.001), while the presence of regional lymph node metastasis (P=0.190) and direct invasion of adjacent organs or metastasis (P=0.323) were not significantly different among them. Conclusion: Some radiological features by CT can be used to classify different colon tumor types.
doi:10.2147/ott.s131008 pmid:28490887 pmcid:PMC5414631 fatcat:tpty4bg5ifavba2qcksllhllgu

Online Pairwise Learning Algorithms with Kernels [article]

Yiming Ying, Ding-Xuan Zhou
2015 arXiv   pre-print
Pairwise learning usually refers to a learning task which involves a loss function depending on pairs of examples, among which most notable ones include ranking, metric learning and AUC maximization. In this paper, we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS), which we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works Kar,Wang which require
more » ... the iterates are restricted to a bounded domain or the loss function is strongly-convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem which guarantees the almost surely convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely-used kernels in the setting of pairwise learning and illustrate the above convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.
arXiv:1502.07229v1 fatcat:5ybfdkgudjh6fethgmkngzfalm

General Scaled Support Vector Machines [article]

Xin Liu, Ying Ding, Forrest Sheng Bao
2010 arXiv   pre-print
Support Vector Machines (SVMs) are popular tools for data mining tasks such as classification, regression, and density estimation. However, original SVM (C-SVM) only considers local information of data points on or over the margin. Therefore, C-SVM loses robustness. To solve this problem, one approach is to translate (i.e., to move without rotation or change of shape) the hyperplane according to the distribution of the entire data. But existing work can only be applied for 1-D case. In this
more » ... r, we propose a simple and efficient method called General Scaled SVM (GS-SVM) to extend the existing approach to multi-dimensional case. Our method translates the hyperplane according to the distribution of data projected on the normal vector of the hyperplane. Compared with C-SVM, GS-SVM has better performance on several data sets.
arXiv:1009.5268v1 fatcat:7cw4lhjq6fbuvmbzzvdf3amqg4

Avoiding Deceptive Annotations in the Semantic Web

Yihong Ding, David W. Embley, Ying Ding, M. Omair Shafiq
2006 International Semantic Web Conference  
Deceptive annotations are becoming an important problem as more and more people start to tag documents, and the problem has become an argument to against the Semantic Web. Skeptics believe that developers make mistakes when annotating documents, and developers may even abuse annotations from time to time. Due to the difficulty of detecting and resolving deceptive tags, these skeptics openly wonder whether semantic annotations may bring more trouble than benefit. In this paper we present a
more » ... ion avoidance resolution method. By adding personal specifications about ontology concepts through instance recognition semantics, Semantic Web users can avoid being deceived by improperly annotated data. At the same time, our deception avoidance strategy also passively discourages annotators from falsely tagging documents by decreasing the profit they can gain from deceptive annotations. Finally, our deception avoidance mechanism still preserves the right to annotate text without restriction.
dblp:conf/semweb/DingEDS06 fatcat:7g5mgjk7b5h55mm2wo47a5mqg4

A CUDA-Based Real Parameter Optimization Benchmark [article]

Ke Ding, Ying Tan
2014 arXiv   pre-print
Benchmarking is key for developing and comparing optimization algorithms. In this paper, a CUDA-based real parameter optimization benchmark (cuROB) is introduced. Test functions of diverse properties are included within cuROB and implemented efficiently with CUDA. Speedup of one order of magnitude can be achieved in comparison with CPU-based benchmark of CEC'14.
arXiv:1407.7737v1 fatcat:uef6aclzazee3mdd6yojxffonu

Strain modulation of photocurrent in Weyl semimetal TaIrTe4 [article]

Ying Ding, XinRu Wang, LieHong Liao, XinYu Chen, JiaYan Zhang, YueYue Wang, Hao Ying, Yuan Li
2022 arXiv   pre-print
We study the effect of the strain on the energy bands of TaIrTe4 sheet and the photocurrent in the Cu-TaIrTe4-Cu heterojunction by using the quantum transport simulations. It is found that the Weyl points can be completely broken with increasing of the strain along z dirction. One can obtain a large photocurrent in the Cu-TaIrTe4-Cu heterojunction in the absence of the strain. While the photocurrent can be sharply enhanced by the strain and reach a large value. Accordingly, the maximum values
more » ... the photocurrent can be explained in terms of the transitions between peaks of density of states and band structures. The strain-induced energy bands and photocurrent exhibit anisotropic behaviors. Our results provide a novel route to effectively modulate the energy bands and the photocurrent by utilizing mechanical methods for TaIrTe4-based devices.
arXiv:2206.08281v1 fatcat:wbwdhwcxunes5d6e4wpcimli3u

Cyclodextrin-Based Nanoplatforms for Tumor Phototherapy: An Update

Xingjie Wu, Ying Chen, Qianqian Guo, Ling Tao, Yang Ding, Xianguang Ding, Xiangchun Shen
2022 Pharmaceutics  
Tumor phototherapies are light-mediated tumor treatment modalities, which usually refer to tumor photothermal therapy (PTT) and photodynamic therapy (PDT). Due to the outstanding spatial-temporal control over treatment through light irradiation, tumor phototherapies display extremely low side effects during treatment and are believed to be a tumor treatment method with a clinical translation potential. However, current tumor phototherapy nanoplatforms face obstacles, including light
more » ... induced skin burning, tumor hypoxia microenvironments, limited light penetration depth, et al. Therefore, one important research direction is developing a tumor phototherapy nanoplatform with multifunctionality and enhanced pharmacological effects to overcome the complexity of tumor treatment. On the other hand, cyclodextrins (CDs) are starch-originated circular oligosaccharides with negligible toxicity and have been used to form supermolecular nanostructures through a host–guest interaction between the inner cavity of CDs and functional biomolecules. In the past few years, numerous studies have focused on CD-based multifunctional tumor phototherapy nanoplatforms with an enhanced photoeffect, responsive morphological transformation, and elevated drug bioavailability. This review focuses on the preparation methods of CD-based tumor phototherapy nanoplatforms and their unique physiochemical properties for improving anti-tumor pharmacological efficacy.
doi:10.3390/pharmaceutics14071375 pmid:35890271 pmcid:PMC9323899 fatcat:cz7hloggu5g6jojq34tg6borfi

Estimating mean survival time: when is it possible? [article]

Ying Ding, Bin Nan
2013 arXiv   pre-print
Ritov (1990) ; Tsiatis (1990) ; Wei et al. (1990) ; Ying (1993) ; Jin et al. (2003) ; Ding & Nan (2011) , among many others.  ...  by Lai & Ying (1991) and Ying (1993) to show the desirable result.  ... 
arXiv:1307.8369v1 fatcat:xxbl7dlvorg2ziumfkionqxa5y

Automatic data placement and replication in grids

Ying Ding, Ying Lu
2009 2009 International Conference on High Performance Computing (HiPC)  
Data grids provide geographically distributed storage and computing resources for large data-intensive applications. To support fast data access and processing, effective data management is essential. In this paper, we propose two novel algorithms on data placement and data replication. We evaluate the algorithms through intensive simulations. Results show that the new algorithms achieve significant improvement in facilitating load balancing, reducing job response time, and saving network bandwidth.
doi:10.1109/hipc.2009.5433229 dblp:conf/hipc/DingL09 fatcat:4whizui5bvgr5mxwovkyulhori

New progress in femtosecond laser-assisted cataract surgery

Yong-Mou Zhou, Ying-Hui Ding, Ying-Li Lu
2021 Guoji Yanke Zazhi  
. • KEYWORDS: cataract surgeryꎻ femtosecond laserꎻ phacoemulsificationꎻ femtosecond laserassisted cataractꎻ refractive surgery Citation: Zhou YMꎬ Ding YHꎬ Lu YL.  ... 
doi:10.3980/j.issn.1672-5123.2021.12.15 doaj:c861e9ccd05b4d7b988586cf5aa1d9c8 fatcat:qyarwwe3frglxfttfdgigtyar4

Globally stabilized bent carbon–carbon triple bond by hydrogen-free inorganic–metallic scaffolding Al4F6

Ying-ying Xue, Ying Zhang, Zhong-hua Cui, Yi-hong Ding
2020 RSC Advances  
We report a novel C2Al4F6-01 with metal–inorganic Al4F6-scaffolding, which differs from hitherto known bent-CC types, which all involve carbon-based scaffoldings.
doi:10.1039/d0ra02280b pmid:35517486 pmcid:PMC9055247 fatcat:snxz65banbhsbl65bjm72a3kfm

Coronavirus Knowledge Graph: A Case Study [article]

Chongyan Chen, Islam Akef Ebeid, Yi Bu, Ying Ding
2020 arXiv   pre-print
The emergence of the novel COVID-19 pandemic has had a significant impact on global healthcare and the economy over the past few months. The virus's rapid widespread has led to a proliferation in biomedical research addressing the pandemic and its related topics. One of the essential Knowledge Discovery tools that could help the biomedical research community understand and eventually find a cure for COVID-19 are Knowledge Graphs. The CORD-19 dataset is a collection of publicly available
more » ... t research articles that have been recently published on COVID-19 and coronavirus topics. Here, we use several Machine Learning, Deep Learning, and Knowledge Graph construction and mining techniques to formalize and extract insights from the PubMed dataset and the CORD-19 dataset to identify COVID-19 related experts and bio-entities. Besides, we suggest possible techniques to predict related diseases, drug candidates, gene, gene mutations, and related compounds as part of a systematic effort to apply Knowledge Discovery methods to help biomedical researchers tackle the pandemic.
arXiv:2007.10287v1 fatcat:rzgsevv3jrhvrh74s34qyjof4q

Normative Beliefs and Sexual Risk in China

Li Li, Ying Ying Ding, Zunyou Wu, Mary Jane Rotheram-Borus, Sam Guo
2010 Aids and Behavior  
We examined normative beliefs about multiple sexual partners and social status in China and their association with risky sexual behaviors and sexually transmitted infections (STIs). Self-reported and biological markers of sexual risk were examined among 3,716 market vendors from a city in eastern China. Men who were older or with less education believed having multiple sexual partners was linked to higher social status. Adjusting for demographic characteristics, normative beliefs were
more » ... tly associated with having multiple sexual partners, while having multiple sexual partners was significantly associated with STIs. Normative beliefs regarding sexual behaviors may play an important role in individual risk behaviors. Future HIV/STI interventions must address community beliefs about the positive meaning of sexual risks, particularly among men with traditional beliefs about gender roles.
doi:10.1007/s10461-010-9835-4 pmid:20960047 pmcid:PMC3127001 fatcat:qbsuzbjflzf57ccfsbskflkwtu
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