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OmniGraph: Rich Representation and Graph Kernel Learning [article]

Boyi Xie, Rebecca J. Passonneau
2015 arXiv   pre-print
As in Xie et al. (2013) , we refer to the company we make predictions about as the designated entity.  ...  Xie et al. (2013) point out that this is consistent with the direction component of the three-part ADS model (Rydberg and Shephard, 2003) .  ... 
arXiv:1510.02983v1 fatcat:lkb55ctmyvhlbp5bx6zejw2qpa

Kernelized Locality-Sensitive Hashing for Semi-Supervised Agglomerative Clustering [article]

Boyi Xie, Shuheng Zheng
2013 arXiv   pre-print
Large scale agglomerative clustering is hindered by computational burdens. We propose a novel scheme where exact inter-instance distance calculation is replaced by the Hamming distance between Kernelized Locality-Sensitive Hashing (KLSH) hashed values. This results in a method that drastically decreases computation time. Additionally, we take advantage of certain labeled data points via distance metric learning to achieve a competitive precision and recall comparing to K-Means but in much less computation time.
arXiv:1301.3575v1 fatcat:ifsaw5vg5nfgdnbarrzt2p3il4

Supervised HDP Using Prior Knowledge [chapter]

Boyi Xie, Rebecca J. Passonneau
2012 Lecture Notes in Computer Science  
End users can find topic model results difficult to interpret and evaluate. To address user needs, we present a semi-supervised hierarchical Dirichlet process for topic modeling that incorporates user-defined prior knowledge. Applied to a large electronic dataset, the generated topics are more fine-grained, more distinct, and align better with users' assignments of topics to documents.
doi:10.1007/978-3-642-31178-9_21 fatcat:reba5ivkobfyjiq2iehegimagm

Construction of Aseptic Culture System for Spores of Sphaeropteris lepifera

Yan Zhang, Xiuying Zhang, Yuxuan Xie, Zebin Lin, Boyi Chen, Bangping Cai
2021 Bioscience Methods  
2021, Construction of aseptic culture system for spores of Sphaeropteris lepifera, Bioscience Methods, 12(6): 1-8 (Abstract Through the aseptic culture test of Sphaeropteris lepifera (J Sm. ex Hook.) R. M. Tryon, try to screen out the best conditions for each process of aseptic culture for spores of Sphaeropteris lepifera, in order to establish a systematic, efficient and complete aseptic culture technology system for spores of Sphaeropteris lepifera, and try to achieve factory production of
more » ... aeropteris lepifera seedlings. The mature dark brown spores off leaf from Sphaeropteris lepifera were used as explants, disinfected with 75% alcohol for 10 s and 0.1% Hg for 6 min. The induced germination medium is 1/5 MS+6-BA 0.5 mg/L+IBA 0.5 mg/L. The proliferation medium is 1/2 MS + 6-BA 0.3 mg/L+ IBA 0.05 mg/L. The differentiation medium is MS+6-BA 0.05 mg/L+ IBA 0.05 mg/L. And the rooting medium is MS + 6-BA 0.2 mg/L + IBA 0.2 mg/L. The culture temperature is (25±2)℃, the light source is fluorescent, the illumination time is 12 h/d, and the illumination intensity is 2000 lx.
doi:10.5376/bm.2021.12.0006 fatcat:rcziddzw2vfcfchpbd2tsysow4

Off-Policy Evaluation and Learning from Logged Bandit Feedback: Error Reduction via Surrogate Policy [article]

Yuan Xie, Boyi Liu, Qiang Liu, Zhaoran Wang, Yuan Zhou, Jian Peng
2018 arXiv   pre-print
When learning from a batch of logged bandit feedback, the discrepancy between the policy to be learned and the off-policy training data imposes statistical and computational challenges. Unlike classical supervised learning and online learning settings, in batch contextual bandit learning, one only has access to a collection of logged feedback from the actions taken by a historical policy, and expect to learn a policy that takes good actions in possibly unseen contexts. Such a batch learning
more » ... ing is ubiquitous in online and interactive systems, such as ad platforms and recommendation systems. Existing approaches based on inverse propensity weights, such as Inverse Propensity Scoring (IPS) and Policy Optimizer for Exponential Models (POEM), enjoy unbiasedness but often suffer from large mean squared error. In this work, we introduce a new approach named Maximum Likelihood Inverse Propensity Scoring (MLIPS) for batch learning from logged bandit feedback. Instead of using the given historical policy as the proposal in inverse propensity weights, we estimate a maximum likelihood surrogate policy based on the logged action-context pairs, and then use this surrogate policy as the proposal. We prove that MLIPS is asymptotically unbiased, and moreover, has a smaller nonasymptotic mean squared error than IPS. Such an error reduction phenomenon is somewhat surprising as the estimated surrogate policy is less accurate than the given historical policy. Results on multi-label classification problems and a large- scale ad placement dataset demonstrate the empirical effectiveness of MLIPS. Furthermore, the proposed surrogate policy technique is complementary to existing error reduction techniques, and when combined, is able to consistently boost the performance of several widely used approaches.
arXiv:1808.00232v1 fatcat:4pm7vkdnlvaw3l65gjx6qinvla

Leveraging Subjective Human Annotation for Clustering Historic Newspaper Articles [article]

Haimonti Dutta, William Chan, Deepak Shankargouda, Manoj Pooleery, Axinia Radeva, Kyle Rego, Boyi Xie, Rebecca Passonneau, Austin Lee and Barbara Taranto
2012 arXiv   pre-print
The New York Public Library is participating in the Chronicling America initiative to develop an online searchable database of historically significant newspaper articles. Microfilm copies of the newspapers are scanned and high resolution Optical Character Recognition (OCR) software is run on them. The text from the OCR provides a wealth of data and opinion for researchers and historians. However, categorization of articles provided by the OCR engine is rudimentary and a large number of the
more » ... cles are labeled editorial without further grouping. Manually sorting articles into fine-grained categories is time consuming if not impossible given the size of the corpus. This paper studies techniques for automatic categorization of newspaper articles so as to enhance search and retrieval on the archive. We explore unsupervised (e.g. KMeans) and semi-supervised (e.g. constrained clustering) learning algorithms to develop article categorization schemes geared towards the needs of end-users. A pilot study was designed to understand whether there was unanimous agreement amongst patrons regarding how articles can be categorized. It was found that the task was very subjective and consequently automated algorithms that could deal with subjective labels were used. While the small scale pilot study was extremely helpful in designing machine learning algorithms, a much larger system needs to be developed to collect annotations from users of the archive. The "BODHI" system currently being developed is a step in that direction, allowing users to correct wrongly scanned OCR and providing keywords and tags for newspaper articles used frequently. On successful implementation of the beta version of this system, we hope that it can be integrated with existing software being developed for the Chronicling America project.
arXiv:1208.3530v1 fatcat:zyrcsngcgngrlnwzehzdiqdj24

Semantic Frames to Predict Stock Price Movement

Boyi Xie, Rebecca J. Passonneau, Leon Wu, Germán Creamer
2013 Annual Meeting of the Association for Computational Linguistics  
Semantic frames are a rich linguistic resource. There has been much work on semantic frame parsers, but less that applies them to general NLP problems. We address a task to predict change in stock price from financial news. Semantic frames help to generalize from specific sentences to scenarios, and to detect the (positive or negative) roles of specific companies. We introduce a novel tree representation, and use it to train predictive models with tree kernels using support vector machines. Our
more » ... experiments test multiple text representations on two binary classification tasks, change of price and polarity. Experiments show that features derived from semantic frame parsing have significantly better performance across years on the polarity task.
dblp:conf/acl/XiePWC13 fatcat:qc2n7ng2oraylcnlmkzfktqmnm

Robust Fused Lasso Penalized Huber Regression with Nonasymptotic Property and Implementation Studies [article]

Xin Xin, Boyi Xie, Yunhai Xiao
2022 arXiv   pre-print
For some special data in reality, such as the genetic data, adjacent genes may have the similar function. Thus ensuring the smoothness between adjacent genes is highly necessary. But, in this case, the standard lasso penalty just doesn't seem appropriate anymore. On the other hand, in high-dimensional statistics, some datasets are easily contaminated by outliers or contain variables with heavy-tailed distributions, which makes many conventional methods inadequate. To address both issues, in
more » ... paper, we propose an adaptive Huber regression for robust estimation and inference, in which, the fused lasso penalty is used to encourage the sparsity of the coefficients as well as the sparsity of their differences, i.e., local constancy of the coefficient profile. Theoretically, we establish its nonasymptotic estimation error bounds under ℓ_2-norm in high-dimensional setting. The proposed estimation method is formulated as a convex, nonsmooth and separable optimization problem, hence, the alternating direction method of multipliers can be employed. In the end, we perform on simulation studies and real cancer data studies, which illustrate that the proposed estimation method is more robust and predictive.
arXiv:2209.13281v2 fatcat:alhg73kzcrhllp3occvdq7gcxi

Analytics for Power Grid Distribution Reliability in New York City

Cynthia Rudin, Şeyda Ertekin, Rebecca Passonneau, Axinia Radeva, Ashish Tomar, Boyi Xie, Stanley Lewis, Mark Riddle, Debbie Pangsrivinij, Tyler McCormick
2014 Interfaces  
We summarize the first major effort to use analytics for preemptive maintenance and repair of an electrical distribution network. This is a large-scale multi-year effort between scientists and students at Columbia and MIT and engineers from Con Edison, which operates the world's oldest and largest underground electrical system. Con Edison's preemptive maintenance programs are less than a decade old, and are made more effective with the use of analytics developing alongside the maintenance
more » ... ms themselves. Some of the data used for our projects are historical records dating as far back as the 1880's, and some of the data are free text documents typed by dispatchers. The operational goals of this work are to assist with Con Edison's preemptive inspection and repair program, and its vented cover replacement program. This has a continuing impact on public safety, operating costs, and reliability of electrical service in New York City.
doi:10.1287/inte.2014.0748 fatcat:levz3n5i7fe3lnb2m74c6ye4a4

Degradation characterization and pathway analysis of chlortetracycline and oxytetracycline in a microbial fuel cell

Ji Wang, Boyi Zhou, Ruijia Ge, Tian-shun Song, Jinping Yu, Jingjing Xie
2018 RSC Advances  
The wide presence of antibiotics in the environment has raised concerns about their potential impact on ecological and human health.
doi:10.1039/c8ra04904a pmid:35542450 pmcid:PMC9084353 fatcat:5jphpg552rgkhnb6qqcewgcyvq

Company Mention Detection for Large Scale Text Mining

Rebecca J. Passonneau, Tifara Ramelson, Boyi Xie
2014 Proceedings of the International Conference on Knowledge Discovery and Information Retrieval  
The remaining framework relies on the implementation described in (Xie et al., 2013) .  ...  Clearly, the initial NER method from (Xie et al., 2013) far outperforms this baseline, yet leaves much room for improvement in recall.  ... 
doi:10.5220/0005174405120520 dblp:conf/ic3k/PassonneauRX14 fatcat:aks2su6mtrdg5gs7nnfoimbi5m

Histone deacetylase inhibitor sodium butyrate suppresses proliferation and promotes apoptosis in osteosarcoma cells by regulation of the MDM2–p53 signaling

Chuhai Xie, Boyi Wu, Binwei Chen, Qunwei Shi, Jianhong Guo, Ziwen Fan, Yan Huang
2016 OncoTargets and Therapy  
Histone deacetylase inhibitors have been reported to induce tumor cell growth arrest, differentiation, and apoptosis. This study aimed to investigate the effects of one histone deacetylase inhibitor -sodium butyrate (SB) -on osteosarcoma (OS) cell proliferation and apoptosis and also the molecular mechanisms by which SB exerts regulatory effects on OS cells. U2OS and MG63 cells were treated with SB at various concentrations. Then, cell proliferation and apoptosis were determined by 3-(4,
more » ... hylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide and flow cytometry assays, respectively; the expression of Ki67, Bax, Bcl-2, MDM2, and p53 proteins was determined by using Western blot assay. The results showed that SB suppressed proliferation in a concentration-dependent manner and promoted apoptosis of OS cells. In addition, SB enhanced p53 expression and decreased MDM2 expression, indicating that SB can regulate MDM2-p53 feedback loop. p53 inhibited proliferation and promoted apoptosis, whereas MDM2 promoted proliferation and suppressed apoptosis, which indicated that functional effect of SB on OS cell lines at least in part depended on the MDM2-p53 signaling. We also explored the effect of SB on OS cells in vivo and found that SB suppressed the growth of OS cells with no noticeable effect on activity and body weight of mice in vivo. These findings will offer new clues for OS development and progression and offer SB as a potent targeted agent for OS treatment.
doi:10.2147/ott.s105418 pmid:27445491 pmcid:PMC4938147 fatcat:ncpqflylc5hubnq2qtcdiduseu

CircSAMD4A regulates cell progression and epithelial‑mesenchymal transition by sponging miR‑342‑3p via the regulation of FZD7 expression in osteosarcoma

Chuhai Xie, Binwei Chen, Boyi Wu, Jianhong Guo, Yulong Shi, Yanming Cao
2020 International Journal of Molecular Medicine  
Osteosarcoma (OS) is a primary malignant tumor with a complex etiology. Therefore, research into the pathogenesis of osteosarcoma is considered a priority. Circular RNAs play important roles in cell metabolism and in the immune response and are closely associated with cancer treatment. However, research into the association of circular RNAs with osteosarcoma is limited. In the present study, CircSAMD4A was validated by RT‑qPCR and agarose gel electrophoresis. CircSAMD4A and miR‑342‑3p
more » ... was detected by RT‑qPCR. The relative protein expression levels were measured by western blot analysis. MTT assay and flow cytometry were used to detect cell cytotoxicity and apoptosis, respectively. Transwell assay was applied to assess cell migration and invasion. Dual‑luciferase reporter assay was used to determine the association among CircSAMD4A, Frizzled‑7 (FZD7) and miR‑342‑3p. In vivo, subcutaneous tumor formation assay was performed in an experiment with nude mice. The results revealed that the expression levels of CircSAMD4A and FZD7 were upregulated, while those of miR‑342‑3p were downregulated in OS tissues and cells. The inhibition of CircSAMD4A suppressed cell progression and epithelial‑mesenchymal transition (EMT), and promoted cell apoptosis in OS. The reduction of miR‑342‑3p reversed the effects of CircSAMD4A downregulation on cell cytotoxicity, migration, invasion, apoptosis and EMT in OS, while FZD7 overexpression blocked the effect of miR‑342‑3p upregulation on OS progression. The suppressive effect of sh‑CircSAMD4A on tumor growth was thus verified in OS. Overall, the present study demonstrated that CircSAMD4A affected cell cytotoxicity, invasion, apoptosis, migration and EMT by regulating the miR‑342‑3p/FDZ7 axis in OS, thereby providing a novel regulatory mechanism and a potential therapeutic target for OS.
doi:10.3892/ijmm.2020.4585 pmid:32319545 pmcid:PMC7255482 fatcat:i3sz563ekjeypjj2uqkpzlacgy

Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

Chunhua Zhu, Boyi Sun, Taigang Liu, Huajun Zheng, Wenyi Gu, Wei He, Fengjiao Sun, Yaping Wang, Meicheng Yang, Weicheng Bei, Xu Peng, Qunxin She (+2 others)
2017 BMC Genomics  
Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival. Abstract Background: Vibrio parahaemolyticus causes serious seafood-borne gastroenteritis and death in humans. Raw seafood is often subjected to post-harvest processing and low-temperature storage. To date, very little information is available regarding the biological functions of cold shock proteins (CSPs) in
more » ... low-temperature survival of the bacterium. In this study, we determined the complete genome sequence of V. parahaemolyticus CHN25 (serotype: O5:KUT). The two main CSP-encoding genes (VpacspA and VpacspD) were deleted from the bacterial genome, and comparative transcriptomic analysis between the mutant and wild-type strains was performed to dissect the possible molecular mechanisms that underlie low-temperature adaptation by V. parahaemolyticus. Results: The 5,443,401-bp V. parahaemolyticus CHN25 genome (45.2% G + C) consisted of two circular chromosomes and three plasmids with 4,724 predicted protein-encoding genes. One dual-gene and two single-gene deletion mutants were generated for VpacspA and VpacspD by homologous recombination. The growth of the ΔVpacspA mutant was strongly inhibited at 10°C, whereas the VpacspD gene deletion strongly stimulated bacterial growth at this low temperature compared with the wild-type strain. The complementary phenotypes were observed in the reverse mutants (ΔVpacspAcom, and ΔVpacspD-com). The transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 were significantly altered in the ΔVpacspA mutant when it was grown at 10°C. These included genes that were involved in amino acid degradation, secretion systems, sulphur metabolism and glycerophospholipid metabolism along with ATP-binding cassette transporters. However, a low temperature elicited significant expression changes for 10.0% of the genes in the ΔVpacspD mutant, including those involved in the phosphotransferase system and in the metabolism of nitrogen and amino acids. The major metabolic pathways that were altered by the dual-gene deletion mutant (ΔVpacspAD) radically differed from those that were altered by single-gene mutants. Comparison of the transcriptome profiles further revealed numerous differentially expressed genes that were shared among the three mutants and regulators that were specifically, coordinately or antagonistically modulated by VpaCspA and VpaCspD. Our data also revealed several possible molecular coping strategies for low-temperature adaptation by the bacterium. (Continued on next page)
doi:10.1186/s12864-017-3784-5 pmid:28583064 pmcid:PMC5460551 fatcat:devb546slff45l5n4ewibe6oki

Gene Expression Profiling of Contralateral Dorsal Root Ganglia Associated with Mirror-Image Pain in a Rat Model of Complex Regional Pain Syndrome Type-I

Huimin Nie, Boyu Liu, Chengyu Yin, Ruixiang Chen, Jie Wang, Danyi Zeng, Yan Tai, Jingdun Xie, Dongwei He, Boyi Liu
2021 Journal of Pain Research  
Mirror-image pain (MIP), which develops from the healthy body region contralateral to the actual injured site, is a mysterious pain phenomenon accompanying many chronic pain conditions, such as complex regional pain syndrome (CRPS). However, the pathogenesis of MIP still remains largely unknown. The purpose of this study is to perform an expression profiling to identify genes related to MIP in an animal model of CRPS-I. We established a rat chronic post-ischemic pain (CPIP) model to mimic human
more » ... CRPS-I. RNA-sequencing (RNA-Seq), bioinformatics, qPCR, immunostaining, and animal behavioral assays were used to screen potential genes in the contralateral dorsal root ganglia (DRG) that may be involved in MIP. The CPIP model rats developed robust and persistent MIP in contralateral hind paws. Bilateral DRG neurons did not exhibit obvious neuronal damage. RNA-Seq of contralateral DRG from CPIP model rats identified a total 527 differentially expressed genes (DEGs) vs sham rats. The expression changes of several representative DEGs were further verified by qPCR. Bioinformatics analysis indicated that the immune system process, innate immune response, and cell adhesion were among the mostly enriched biological processes, which are important processes involved in pain sensitization, neuroinflammation, and chronic pain. We further identified DEGs potentially involved in pain mechanisms or enriched in small- to medium-sized sensory neurons or TRPV1-lineage nociceptors. By comparing with published datasets summarizing genes enriched in pain mechanisms, we sorted out a core set of genes which might contribute to nociception and the pain mechanism in MIP. We provided by far the first study to profile gene expression changes and pathway analysis of contralateral DRG for the studying of MIP mechanisms. This work may provide novel insights into understanding the mysterious mechanisms underlying MIP.
doi:10.2147/jpr.s322372 pmid:34512013 pmcid:PMC8426644 fatcat:2tuak57q6nfuzjldgk6rit47ba
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