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GO Hessian for Expectation-Based Objectives [article]

Yulai Cong, Miaoyun Zhao, Jianqiao Li, Junya Chen, Lawrence Carin
2020 arXiv   pre-print
An unbiased low-variance gradient estimator, termed GO gradient, was proposed recently for expectation-based objectives E_q_γ(y) [f(y)], where the random variable (RV) y may be drawn from a stochastic computation graph with continuous (non-reparameterizable) internal nodes and continuous/discrete leaves. Upgrading the GO gradient, we present for E_q_γ(y) [f(y)] an unbiased low-variance Hessian estimator, named GO Hessian. Considering practical implementation, we reveal that GO Hessian is
more » ... -use with auto-differentiation and Hessian-vector products, enabling efficient cheap exploitation of curvature information over stochastic computation graphs. As representative examples, we present the GO Hessian for non-reparameterizable gamma and negative binomial RVs/nodes. Based on the GO Hessian, we design a new second-order method for E_q_γ(y) [f(y)], with rigorous experiments conducted to verify its effectiveness and efficiency.
arXiv:2006.08873v1 fatcat:hrvztiwjynbzbmuztvzu7fcq3q

MS2 RNA aptamer enhances prime editing in rice [article]

Yiping Chai, Yuanyuan Jiang, Junya Wang, Dexin Qiao, Yu Zhang, Cuiping Xin, Yun Zhou, Xue-Chen Wang, Qi-Jun Chen
2021 bioRxiv   pre-print
Prime editing is a universal and very promising precise genome editing technology. However, optimization of prime editor (PE) from different aspects remains vital for its use as a routine tool in plant basic research and crop molecular breeding. In this report, we tested MS2-based prime editor (MS2PE). We fused the M-MLV reverse transcriptase (RT) gene variant to the MS2 RNA binding protein gene, MCP, and allowed the MCP-RT fusion gene to co-express with the SpCas9 nickase gene, SpCas9H840A,
more » ... various engineered pegRNAs harboring MS2 RNA (MS2pegR). Compared with control PEs, MS2PEs significantly enhanced editing efficiency at four of six targets in rice protoplasts, and achieved 1.2~10.1-fold increase in editing efficiency at five of six targets in transgenic rice lines. Furthermore, we tested total 22 different MS2pegR scaffolds, 3 RT variants or genes, 2 MCP variants, and various combinations of the Cas9 nickase, RT, and MCP modules. Our results demonstrated an alternative strategy for enhancing prime editing.
doi:10.1101/2021.10.20.465209 fatcat:bltdd4jpkbektdycbmokxedisq

Variational Inference with Holder Bounds [article]

Junya Chen, Danni Lu, Zidi Xiu, Ke Bai, Lawrence Carin, Chenyang Tao
2021 arXiv   pre-print
Correspond to: Junya Chen: junya.chen@duke.edu, Chenyang Tao: chenyang.tao@duke.edu et al., 2014) , variational inference (VI) has become a popular approach for general latent variable models (Blei et  ...  For Cifar10 dataset, we use three-layer Conv2d (filters: 64 × 4 × 4 − 128 × 4 × 4 − 512 × 4 × 4) with ReLU activation as encoder (Chen et al., 2021b) .  ...  The following facts are handy for our derivations F Additional Results and Analyses for Real-World Datasets In Figure S11 we compare the effective sample-size (ESS) (Chen et al., 2021a) of different  ... 
arXiv:2111.02947v2 fatcat:cms2wta3z5fxja3mpubwgnioeq

On Fenchel Mini-Max Learning

Chenyang Tao, Liqun Chen, Shuyang Dai, Junya Chen, Ke Bai, Dong Wang, Jianfeng Feng, Wenlian Lu, Georgiy V. Bobashev, Lawrence Carin
2019 Neural Information Processing Systems  
J Chen was partially supported by China Scholarship Council (CSC). W Lu and J Feng were supported by the Shanghai Municipal Science and Technology Major Project and ZJ Lab (No. 2018SHZDZX01).  ...  Note these bounds are tight as the proposal q β (z|x) approaches the true posterior p θ (z|x) (Lemma 5.1, Chen et al. [13] ).  ... 
dblp:conf/nips/TaoCDCBWFLBC19 fatcat:xdy3ksngobbbzbwxfriiabnqle

Variational Annealing of GANs: A Langevin Perspective

Chenyang Tao, Shuyang Dai, Liqun Chen, Ke Bai, Junya Chen, Chang Liu, Ruiyi Zhang, Georgiy V. Bobashev, Lawrence Carin
2019 International Conference on Machine Learning  
J Chen was partially supported by China Scholarship Council (CSC) and Shanghai Municipal Science and Technology Major Project (No.2018SHZDZX01). C Liu was also supported by CSC.  ...  ., SVGD, MMD-GAN, OT-GAN, π-SGLD, (Chen et al., 2018) ) and hybrid schemes (e.g., SPOS, (Zhang et al., 2018) ).  ... 
dblp:conf/icml/TaoDCBCLZBC19 fatcat:ovi3g2at5bhdtebjsmu3p5dedy

Reconsidering Generative Objectives For Counterfactual Reasoning

Danni Lu, Chenyang Tao, Junya Chen, Fan Li, Feng Guo, Lawrence Carin
2020 Neural Information Processing Systems  
J Chen was partially supported by China Scholarship Council (CSC) and Shanghai Municipal Science and Technology Major Project under Grant 2018SHZDZX01 and ZJLab.  ... 
dblp:conf/nips/LuTCLGC20 fatcat:6tr7m7datnfxvgvsaml3ql3zfy

Identifying Emerging Phenomenon in Plant Long Temporal Phenotyping Experiments [article]

Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S Dina, Xuequn Shang, David M Kramer, Jin Chen
2018 bioRxiv   pre-print
Identifying Emerging Phenomenon in Plant Long Temporal Phenotyping Experiments Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S Dina, Xuequn Shang, David M Kramer, Jin Chen Abstract-The rapid improvement of  ... 
doi:10.1101/454686 fatcat:lgccu5fyw5f5fccjbuxozcfmna

Identification of markers for migrasome detection

Xiaoxin Zhao, Yaxin Lei, Jiajia Zheng, Junya Peng, Ying Li, Li Yu, Yang Chen
2019 Cell Discovery  
This research was supported by the Ministry of Science and Technology of the People's Republic of China (2018YFA0507102 to Yang Chen, 2016YFA0500202 and 2017YFA0503404 to Li Yu), and the National Natural  ...  C O R R E S P O N D E N C E O p e n A c c e s s Identification of markers for migrasome detection Xiaoxin Zhao 1 , Yaxin Lei 1 , Jiajia Zheng 2 , Junya Peng 3 , Ying Li 4 , Li Yu 1 and Yang Chen 5 Dear  ... 
doi:10.1038/s41421-019-0093-y pmid:31123599 pmcid:PMC6527679 fatcat:fhqhr7knvbdlba36gxmb2sc4my

Genome-Wide Association Studies Using Haplotypes and Individual SNPs in Simmental Cattle

Yang Wu, Huizhong Fan, Yanhui Wang, Lupei Zhang, Xue Gao, Yan Chen, Junya Li, HongYan Ren, Huijiang Gao, Zhongxue Chen
2014 PLoS ONE  
Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was
more » ... nducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.
doi:10.1371/journal.pone.0109330 pmid:25330174 pmcid:PMC4203724 fatcat:prdd2irjofgg7itpba6fuya67y

A case of ring chromosome 3, 46,XX,-3,+r(3)(p26q29)

Mashio Kitatani, Hiroaki Takahashi, Junya Yasuda, Chen Cheng Chen, Fukumi Ida, Shoichiro Shike
1984 The Japanese Journal of Human Genetics  
We will discuss a girl with the karyotype 46,XX,-3,+r(3) (p26q29). She had growth and borderline mental retardation, craniofacial anomalies and microcephalus.
doi:10.1007/bf01873537 pmid:6513151 fatcat:wpp4heqpzrc27jk3ou3vqdq4ay

Ultrahigh-channel-count fiber Bragg grating based on the triple sampling method

Xuxing Chen, Junya Hayashi, Hongpu Li
2011 Optics Communications  
A triple sampling method enabling to have excellent channel uniformity and high in-band energy efficiency is firstly proposed for the design of an ultrahigh-channel-count fiber Bragg grating (FBG), which is based on the simultaneous utilization of two amplitude-assisted phase sampling (AAPS) functions and a phase-only sampling (POS) function. As an example, one linearly chirped FBG with consecutive 1215 channels enabling to cover all fiber telecom bands (O+E+S+C+L+U) is numerically
more » ... which has a length of 9 cm, a dispersion of -1360 ps/nm, and a channel spacing of 50 GHz. The maximum index-change required for 10 dB strength of the FBG is less than 6 ×10 -3 .
doi:10.1016/j.optcom.2010.12.029 fatcat:rc55ckeffveufipy5ujrsfif6m

Finite-Time Consensus Learning for Decentralized Optimization with Nonlinear Gossiping [article]

Junya Chen, Sijia Wang, Lawrence Carin, Chenyang Tao
2021 arXiv   pre-print
TINYIMAGENET data partition among workers (Chen et al., 2020) .  ...  ., 2007; Chen et al., 2017) . λ 2 (L) is known as the algebraic connectivity of W. Synchronization and convergence Now let us compare centralized optimized and decentralized linear gossiping.  ... 
arXiv:2111.02949v2 fatcat:b6vi643dzna77hz45rqm6z723i

WRN participates in translesion synthesis pathway through interaction with NBS1

Junya Kobayashi, Michiyo Okui, Aroumougame Asaithamby, Sandeep Burma, Benjamin P.C. Chen, Keiji Tanimoto, Shinya Matsuura, Kenshi Komatsu, David J. Chen
2010 Mechanisms of Ageing and Development  
formation after etoposide treatment was detected only in the S phase, but this was not observed in G1 phase cells, although phophorylated DNA-PKcs foci were observed in G1 phase cells only ( Fig. 3B ; Chen  ...  reported to play a possible role in HR pathway, the combination of mismatched base pair accumulation through un-regulated TLS and abnormal HR regulation may lead to reported genomic deletions in WS cells (Chen  ... 
doi:10.1016/j.mad.2010.06.005 pmid:20600238 pmcid:PMC2911442 fatcat:6lv5qcobufgczekona6atxtkwq

Genomic and TCR Repertoire Intratumor Heterogeneity of Small-cell Lung Cancer and its Impact on Survival [article]

Ming Chen, Runzhe Chen, Ying Jin, Jun Li, Jiexin Zhang, Junya Fujimoto, Won-Chul Lee, xin hu, Shawna Maria Hubert, Julie George, Xiao Hu, Yamei Chen (+25 others)
2020 bioRxiv   pre-print
Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, we revealed a rather homogeneous mutational landscape but extremely suppressed and heterogeneous T cell receptor (TCR) repertoire in SCLCs. Higher mutational burden, lower chromosomal copy number aberration (CNA) burden, less CNA ITH and less TCR ITH were associated with longer overall survival of SCLC patients.
more » ... Compared to non-small cell lung cancers (NSCLCs), SCLCs had similar predicted neoantigen burden and mutational ITH, but significantly more suppressed and heterogeneous TCR repertoire that may be associated with higher CNA burden and CNA ITH in SCLC. Novel therapeutic strategies targeting CNA could potentially improve the tumor immune microenvironment and response to immunotherapy in SCLC.
doi:10.1101/2020.06.30.180844 fatcat:xeyumsikqrcwrlt36lyzblkgs4

Improving the Efficiency of Genomic Selection in Chinese Simmental beef cattle [article]

Jiangwei Xia, Yang Wu, Huizhong Fang, Wengang Zhang, Yuxin Song, Lupei Zhang, Xue Gao, Yan Chen, Junya Li, Huijiang Gao
2015 bioRxiv   pre-print
Genomic selection is an accurate and efficient method of estimating genetic merits by using high-density genome-wide single nucleotide polymorphisms (SNPs).In this study, we investigate an approach to increase the efficiency of genomic prediction by using genome-wide markers. The approach is a feature selection based on genomic best linear unbiased prediction (GBLUP),which is a statistical method used to predict breeding values using SNPs for selection in animal and plant breeding. The
more » ... of this study is the choice of kinship matrix for genomic best linear unbiased prediction (GBLUP).The G-matrix is using the information of genome-wide dense markers. We compare three kinds of kinships based on different combinations of centring and scaling of marker genotypes.And find a suitable kinship approach that adjusts for the resource population of Chinese Simmental beef cattle.Single nucleotide polymorphism (SNPs) can be used to estimate kinship matrix and individual inbreeding coefficients more accurately. So in our research a genomic relationship matrix was developed for 1059 Chinese Simmental beef cattle using 640000 single nucleotide polymorphisms and breeding values were estimated using phenotypes about Carcass weight and Sirloin weight. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Another aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship in the Chinese Simmental beef cattle. We find that the feature selection of GBLUP using Xu's and the Astle and Balding's kinships model performed similarly well, and were the best-performing methods in our study. Inbreeding and kinship matrix can be estimated with high accuracy using ≥12,000s in Chinese Simmental beef cattle.
doi:10.1101/022673 fatcat:frmql7tf7jdcpmpajs3apvtkwa
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