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Conformally variational Riemannian invariants [article]

Jeffrey S. Case, Yueh-Ju Lin, Wei Yuan
2017 arXiv   pre-print
Indeed, Schoen and Yau [62, 63] and Gromov and Lawson [40, 41] proved global rigidity of the scalar curvature, and Lin and Yuan [51] have given partial results towards global rigidity for the Q-curvature  ... 
arXiv:1711.05579v1 fatcat:c6abfxwb3nfgjmfno2e7htezum

Multiphase interpolating digital power amplifiers for TX beamforming [article]

Zhidong Bai, Wen Yuan, Ali Azam, Jeffrey S. Walling
2020 arXiv   pre-print
Yuan. is with ASML, Inc., San Jose, CA 95131 (e-mail: wen.yuan@utah.edu). main methods: LO phase-shifting [1] , [2] , IF phase-shifting [3] and RF phase-shifting [4] , [5] architectures.  ... 
arXiv:2002.04152v1 fatcat:nn5kv7crg5b5zapwdikkx5tzya

Assembly of Long Error-Prone Reads Using Repeat Graphs [article]

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
2018 bioRxiv   pre-print
The problem of genome assembly is ultimately linked to the problem of the characterization of all repeat families in a genome as a repeat graph. The key reason the de Bruijn graph emerged as a popular short read assembly approach is because it offered an elegant representation of all repeats in a genome that reveals their mosaic structure. However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat
more » ... cterization. We present the Flye algorithm for constructing the A-Bruijn (assembly) graph from long error-prone reads, that, in contrast to the k-mer-based de Bruijn graph, assembles genomes using an alignment-based A-Bruijn graph. In difference from existing assemblers, Flye does not attempt to construct accurate contigs (at least at the initial assembly stage) but instead simply generates arbitrary paths in the (unknown) assembly graph and further constructs an assembly graph from these paths. Counter-intuitively, this fast but seemingly reckless approach results in the same graph as the assembly graph constructed from accurate contigs. Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph. We benchmark Flye against several state-of-the-art Single Molecule Sequencing assemblers and demonstrate that it generates better or comparable assemblies for all analyzed datasets.
doi:10.1101/247148 fatcat:qzlfzaakajczhdefxrf6t6xaqi

Near-Infrared Laser Adjuvant for Influenza Vaccine

Satoshi Kashiwagi, Jianping Yuan, Benjamin Forbes, Mathew L. Hibert, Eugene L. Q. Lee, Laura Whicher, Calum Goudie, Yuan Yang, Tao Chen, Beth Edelblute, Brian Collette, Laurel Edington (+11 others)
2013 PLoS ONE  
Safe and effective immunologic adjuvants are often essential for vaccines. However, the choice of adjuvant for licensed vaccines is limited, especially for those that are administered intradermally. We show that non-tissue damaging, nearinfrared (NIR) laser light given in short exposures to small areas of skin, without the use of additional chemical or biological agents, significantly increases immune responses to intradermal influenza vaccination without augmenting IgE. The NIR
more » ... vaccine confers increased protection in a murine influenza lethal challenge model as compared to unadjuvanted vaccine. We show that NIR laser treatment induces the expression of specific chemokines in the skin resulting in recruitment and activation of dendritic cells and is safe to use in both mice and humans. The NIR laser adjuvant technology provides a novel, safe, low-cost, simple-to-use, potentially broadly applicable and clinically feasible approach to enhancing vaccine efficacy as an alternative to chemical and biological adjuvants.
doi:10.1371/journal.pone.0082899 pmid:24349390 pmcid:PMC3859633 fatcat:p45hlt2wlbc2tho7jttdglgffq

metaFlye: scalable long-read metagenome assembly using repeat graphs [article]

Mikhail Kolmogorov, Mikhail Rayko, Jeffrey Yuan, Evgeny Polevikov, Pavel Pevzner
2019 bioRxiv   pre-print
Long-read sequencing technologies substantially improved assemblies of many isolate bacterial genomes as compared to fragmented assemblies produced with short-read technologies. However, assembling complex metagenomic datasets remains a challenge even for the state-of-the-art long-read assemblers. To address this gap, we present the metaFlye assembler and demonstrate that it generates highly contiguous and accurate metagenome assemblies. In contrast to short-read metagenomics assemblers that
more » ... ically fail to reconstruct full-length 16S RNA genes, metaFlye captures many 16S RNA genes within long contigs, thus providing new opportunities for analyzing the microbial "dark matter of life". We also demonstrate that long-read metagenome assemblers significantly improve full-length plasmid and virus reconstruction as compared to short-read assemblers and reveal many novel plasmids and viruses.
doi:10.1101/637637 fatcat:5cm6gw2zdrdatksxtgl74z4dam

Multivariate Spatiotemporal Hawkes Processes and Network Reconstruction [article]

Baichuan Yuan, Hao Li, Andrea L. Bertozzi, P. Jeffrey Brantingham, and Mason A. Porter
2018 arXiv   pre-print
There is often latent network structure in spatial and temporal data and the tools of network analysis can yield fascinating insights into such data. In this paper, we develop a nonparametric method for network reconstruction from spatiotemporal data sets using multivariate Hawkes processes. In contrast to prior work on network reconstruction with point-process models, which has often focused on exclusively temporal information, our approach uses both temporal and spatial information and does
more » ... t assume a specific parametric form of network dynamics. This leads to an effective way of recovering an underlying network. We illustrate our approach using both synthetic networks and networks constructed from real-world data sets (a location-based social media network, a narrative of crime events, and violent gang crimes). Our results demonstrate that, in comparison to using only temporal data, our spatiotemporal approach yields improved network reconstruction, providing a basis for meaningful subsequent analysis --- such as community structure and motif analysis --- of the reconstructed networks.
arXiv:1811.06321v1 fatcat:kymgffzpx5dpphsfgddbnvk6va

Global, Local, and Contagious Investor Sentiment

Malcolm P. Baker, Jeffrey A. Wurgler, Yu Yuan
2009 Social Science Research Network  
Yu and Yuan (2011) argue that the tradeoff between risk and expected return applies only in low sentiment periods; Stambaugh, Yu, and Yuan (in press) argue that sentiment's predictive power is concentrated  ... 
doi:10.2139/ssrn.1449929 fatcat:waorzy4snnhl7ghqlruhwljdsu

Improving Longer-range Dialogue State Tracking [article]

Ye Zhang, Yuan Cao, Mahdis Mahdieh, Jeffrey Zhao, Yonghui Wu
2021 arXiv   pre-print
Dialogue state tracking (DST) is a pivotal component in task-oriented dialogue systems. While it is relatively easy for a DST model to capture belief states in short conversations, the task of DST becomes more challenging as the length of a dialogue increases due to the injection of more distracting contexts. In this paper, we aim to improve the overall performance of DST with a special focus on handling longer dialogues. We tackle this problem from three perspectives: 1) A model designed to
more » ... ble hierarchical slot status prediction; 2) Balanced training procedure for generic and task-specific language understanding; 3) Data perturbation which enhances the model's ability in handling longer conversations. We conduct experiments on the MultiWOZ benchmark, and demonstrate the effectiveness of each component via a set of ablation tests, especially on longer conversations.
arXiv:2103.00109v2 fatcat:nv7ywqecarctln4p27aeqvthgy

Description-Driven Task-Oriented Dialog Modeling [article]

Jeffrey Zhao, Raghav Gupta, Yuan Cao, Dian Yu, Mingqiu Wang, Harrison Lee, Abhinav Rastogi, Izhak Shafran, Yonghui Wu
2022 arXiv   pre-print
Task-oriented dialogue (TOD) systems are required to identify key information from conversations for the completion of given tasks. Such information is conventionally specified in terms of intents and slots contained in task-specific ontology or schemata. Since these schemata are designed by system developers, the naming convention for slots and intents is not uniform across tasks, and may not convey their semantics effectively. This can lead to models memorizing arbitrary patterns in data,
more » ... lting in suboptimal performance and generalization. In this paper, we propose that schemata should be modified by replacing names or notations entirely with natural language descriptions. We show that a language description-driven system exhibits better understanding of task specifications, higher performance on state tracking, improved data efficiency, and effective zero-shot transfer to unseen tasks. Following this paradigm, we present a simple yet effective Description-Driven Dialog State Tracking (D3ST) model, which relies purely on schema descriptions and an "index-picking" mechanism. We demonstrate the superiority in quality, data efficiency and robustness of our approach as measured on the MultiWOZ (Budzianowski et al.,2018), SGD (Rastogi et al., 2020), and the recent SGD-X (Lee et al., 2021) benchmarks.
arXiv:2201.08904v1 fatcat:wzzw6xc4o5cp5ndxmoir4upv64

Global, local, and contagious investor sentiment

Malcolm Baker, Jeffrey Wurgler, Yu Yuan
2012 Journal of Financial Economics  
Yu and Yuan (2011) argue that the tradeoff between risk and expected return applies only in low sentiment periods; Stambaugh, Yu, and Yuan (in press ) argue that sentiment's predictive power is concentrated  ... 
doi:10.1016/j.jfineco.2011.11.002 fatcat:rouoyji6d5hgvbxe5rmmj27qdq

Gold Nanobipyramids as Second Near Infrared Optical Coherence Tomography Contrast Agents for Multiplexed In Vivo Lymphangiography [article]

Peng Si, Saba Shevidi, Edwin Yuan, Ke Yuan, Ziv Lautman, Stefanie S. Jeffrey, George W. Sledge, Adam de la Zerda
2019 bioRxiv   pre-print
Developing contrast-enhanced optical coherence tomography (OCT) techniques is important for specific imaging of tissue lesions, molecular imaging, cell-tracking, and highly sensitive microangiography and lymphangiography. Multiplexed OCT imaging in the second near infrared (NIR-II) window is highly desirable since it allows simultaneous imaging and tracking of multiple biological events in high resolution with deeper tissue penetration in vivo. Here we demonstrate that gold nanobipyramids can
more » ... nction as OCT multiplexing contrast agents, allowing the visualization of two separate lymphatic flows occurring simultaneously from different drainage basins into the same lymph node in a live mouse. Contrast-enhanced multiplexed lymphangiography of a melanoma tumor in vivo shows that the peritumoral lymphatic drainage upstream of the tumor is unidirectional, with some drainage directly into the tumor, but the lymphatic drainage from the tumor is multi-directional. We also demonstrate real-time tracking of the contrast agents draining from a melanoma tumor specifically to the sentinel lymph node of the tumor and the three-dimensional distribution of the contrast agents in the lymph node.
doi:10.1101/656744 fatcat:yi4gy6jvkbdzzo6salbymriski

CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer

Zi-Ming Zhao, Susan E. Yost, Katherine E. Hutchinson, Sierra Min Li, Yate-Ching Yuan, Javad Noorbakhsh, Zheng Liu, Charles Warden, Radia M. Johnson, Xiwei Wu, Jeffrey H. Chuang, Yuan Yuan
2019 BMC Cancer  
Funding This study was supported by STOP Cancer Foundation, NIH K-12 Career Development Award K12CA001727 (Joanne Mortimer MD), and National Cancer Institute P30CA034196, R21CA191848, and U24 CA224067 (Jeffrey  ... 
doi:10.1186/s12885-019-5290-4 pmid:30665374 pmcid:PMC6341717 fatcat:ennjkw7xdjg57pof6gb4rtdyyy

Assembly of Long Error-Prone Reads Using de Bruijn Graphs [article]

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner
2016 bioRxiv   pre-print
., Yuan, J., Shi, Y., et al.: Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-Bruijn-graph. Briefings in Functional Genomics 11, 25-37 (2012) 34.  ... 
doi:10.1101/048413 fatcat:uu54m5dihrbhzcftxxjuawo6ha

Conditional survival estimates improve over time for patients with advanced melanoma

Yan Xing, George J. Chang, Chung-Yuan Hu, Robert L. Askew, Merrick I. Ross, Jeffrey E. Gershenwald, Jeffrey E. Lee, Paul F. Mansfield, Anthony Lucci, Janice N. Cormier
2010 Cancer  
Background-Conditional survival (CS) has emerged as a clinically relevant measure of prognosis for cancer survivors. The objective of this analysis was to provide melanoma-specific CS estimates to help clinicians promote more informed patient decision-making. Methods-Patients with melanoma and at least 5 years of follow-up were identified from the Surveillance Epidemiology and End Results (SEER) registry (1988)(1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000). Using the
more » ... thods of Kaplan and Meier, stage-specific 5-year CS estimates were independently calculated for survivors for each year following diagnosis. Stage-specific multivariate Cox regression models including baseline survivor functions were used to calculate adjusted melanoma-specific CS for different subgroups of patients further stratified by age, gender, race, marital status, anatomic tumor location, and tumor histology. Results-Five-year CS estimates for stage I patients remained constant at 97% annually, while for patients with stages II, III and IV disease, 5-year CS estimates from time 0 (diagnosis) to 5 years improved from 72% to 86%, 51% to 87%, and 19% to 84%, respectively. Multivariate CS analysis revealed that differences in stages II through IV CS based on age, gender and race decreased over time. Conclusions-Five-year melanoma-specific CS estimates improve dramatically over time for survivors with advanced stages of disease. These prognostic data are critical to patients for both treatment and non-treatment related life decisions.
doi:10.1002/cncr.24966 pmid:20187100 pmcid:PMC2860044 fatcat:geke42urfjcg7ilkjxn2x6lq4q

Effective Sequence-to-Sequence Dialogue State Tracking [article]

Jeffrey Zhao, Mahdis Mahdieh, Ye Zhang, Yuan Cao, Yonghui Wu
2021 arXiv   pre-print
Sequence-to-sequence models have been applied to a wide variety of NLP tasks, but how to properly use them for dialogue state tracking has not been systematically investigated. In this paper, we study this problem from the perspectives of pre-training objectives as well as the formats of context representations. We demonstrate that the choice of pre-training objective makes a significant difference to the state tracking quality. In particular, we find that masked span prediction is more
more » ... e than auto-regressive language modeling. We also explore using Pegasus, a span prediction-based pre-training objective for text summarization, for the state tracking model. We found that pre-training for the seemingly distant summarization task works surprisingly well for dialogue state tracking. In addition, we found that while recurrent state context representation works also reasonably well, the model may have a hard time recovering from earlier mistakes. We conducted experiments on the MultiWOZ 2.1-2.4, WOZ 2.0, and DSTC2 datasets with consistent observations.
arXiv:2108.13990v2 fatcat:em25vwdcqjeuzc74m5u73aweiu
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