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Exploiting Parallelism Opportunities with Deep Learning Frameworks [article]

Yu Emma Wang, Carole-Jean Wu, Xiaodong Wang, Kim Hazelwood, David Brooks
2020 arXiv   pre-print
State-of-the-art machine learning frameworks support a wide variety of design features to enable a flexible machine learning programming interface and to ease the programmability burden on machine learning developers. Identifying and using a performance-optimal setting in feature-rich frameworks, however, involves a non-trivial amount of performance profiling efforts and often relies on domain-specific knowledge. This paper takes a deep dive into analyzing the performance impact of key design
more » ... atures in a machine learning framework and quantifies the role of parallelism. The observations and insights distill into a simple set of guidelines that one can use to achieve much higher training and inference speedup. Across a diverse set of real-world deep learning models, the evaluation results show that the proposed performance tuning guidelines outperform the Intel and TensorFlow recommended settings by 1.29x and 1.34x, respectively.
arXiv:1908.04705v2 fatcat:fnmcly3f3vanvlc6hi6uxxj6pi

The oxic degradation of sedimentary organic matter 1400 Ma constrains atmospheric oxygen levels

Shuichang Zhang, Xiaomei Wang, Huajian Wang, Emma U. Hammarlund, Jin Su, Yu Wang, Donald E. Canfield
2017 Biogeosciences  
<p><strong>Abstract.</strong> We studied sediments from the ca. 1400 million-year-old Xiamaling Formation from the North China block. The upper unit of this formation (unit 1) deposited mostly below storm wave base and contains alternating black and green-gray shales with very distinct geochemical characteristics. The black shales are enriched in redox-sensitive trace metals, have high concentrations of total organic carbon (TOC), high hydrogen index (HI) and iron speciation indicating
more » ... n under anoxic conditions. In contrast, the green-gray shales show no trace metal enrichments, have low TOC, low HI and iron speciation consistent with an oxygenated depositional setting. Altogether, unit 1 displays alternations between oxic and anoxic depositional environments, driving differences in carbon preservation consistent with observations from the modern ocean. We combined our TOC and HI results to calculate the differences in carbon mineralization and carbon preservation by comparing the oxygenated and anoxic depositional environments. Through comparisons of these results with modern sedimentary environments, and by use of a simple diagenetic model, we conclude that the enhanced carbon mineralization under oxygenated conditions in unit 1 of the Xiamaling Formation required a minimum of 4 to 8<span class="thinspace"></span>% of present-day atmospheric levels (PAL) of oxygen. These oxygen levels are higher than estimates based on chromium isotopes and reinforce the idea that the environment contained enough oxygen for animals long before their evolution.</p>
doi:10.5194/bg-14-2133-2017 fatcat:fdn4pab2hvb77d54nuh4mkbyam

The Oxic Degradation of Sedimentary Organic Matter 1.4 Ga Constrains Atmospheric Oxygen Levels

Shuichang Zhang, Xiaomei Wang, Huajian Wang, Emma U. Hammarlund, Jin Su, Yu Wang, Donald E. Canfield
2016 Biogeosciences Discussions  
We studied sediments from the ca. 1400 million-year-old Xiamaling Formation from the northern China Block. The upper unit of this formation (unit 1) deposited mostly below storm wave base and contains alternating black and green-gray shales with very different geochemical characteristics. The black shales are enriched in redox sensitive trace metals, have high concentrations of total organic carbon (TOC), high hydrogen index (HI) and iron speciation indicating deposition under anoxic, mostly
more » ... inic, conditions. In contrast, the green-grey shales show no trace metal enrichments, low TOC, low HI and iron speciation consistent with an oxygenated depositional setting. Altogether, unit 1 displays alternations between oxic and anoxic depositional environments, and differences in carbon preservation consistent with observations from the modern ocean. We combined our TOC and HI index results to calculate the differences in carbon mineralization between the oxygenated and anoxic depositional environments. Through comparisons of these results with modern sedimentary environments, and by use of a simple diagenetic model, we conclude that carbon mineralization under oxygenated conditions at Xiamaling required a minimum of 4&amp;thinsp;% to 8&amp;thinsp;% of present-day oxygen levels (PAL). These oxygen levels are higher than estimates based on chromium isotopes and, furthermore, were likely sufficient for early animal respiration. Therefore, our results reinforce the idea that the environment contained enough oxygen for animals long before their evolution.
doi:10.5194/bg-2016-413 fatcat:4jc6q7qujzfi5lzh7k5ybbsyei

A Survey on Location-Driven Influence Maximization [article]

Taotao Cai, Quan Z.Sheng, Xiangyu Song, Jian Yang, Shuang Wang, Wei Emma Zhang, Jia Wu, Philip S. Yu
2022 arXiv   pre-print
[Wang et al., 2016a; Wang et al., 2016b] MIA model Proxy-based approach Index & Pruning Maximizing the influence of potential customers of a given pro-moted location.  ...  ., 2015b; Wang et al., 2016a; Wang et al., 2016b; Zhu et al., 2019] . We introduce the details of these efforts as follows. [ Li et al., 2014] adopts the proxy-based approach under the MIA model.  ... 
arXiv:2204.08005v2 fatcat:63thhyykevhbzl23pl4kgo3cue

Risk of Post-stroke Epilepsy Following Stroke-Associated Acute Symptomatic Seizures

Ru Lin, Yaoyao Yu, Yi Wang, Emma Foster, Patrick Kwan, Mengqi Lin, Niange Xia, Huiqin Xu, Chenglong Xie, Yunjun Yang, Xinshi Wang
2021 Frontiers in Aging Neuroscience  
Objective: Post-stroke epilepsy (PSE) is associated with increased morbidity and mortality. Stroke-associated acute symptomatic seizures are an important risk factor: 20.8–34.3% of these patients will go on to develop PSE. Identifying these "high risk" individuals may result in earlier PSE diagnosis, treatment, and avoidance of seizure-related morbidity. This study was to identify predictors of PSE development in patients with stroke-associated acute symptomatic seizures.Participants and
more » ... : This was a retrospective cohort study of 167 patients with stroke-associated acute symptomatic seizures admitted to the Neurology Department of a tertiary Hospital of China, from 1 May 2006 to 30 January 2020. Both those with primary ischemic stroke and intracerebral hemorrhage were included in the study. Patient demographics, medical history, stroke-associated, and seizure-related variables were evaluated with univariable analysis and multivariable Cox regression analysis. PSE was defined as unprovoked seizures occurring &gt; 7 days post-stroke. Data points were extracted from medical records and supplemented by tele-interview.Results: Of the 167 patients with stroke-associated acute symptomatic seizures, 49 (29.3%) developed PSE. NIHSS score &gt; 14 [hazard ratio (HR) 2.98, 95% CI 1.57–5.67], longer interval from stroke to acute symptomatic seizures (days 4–7 post-stroke) (HR 2.51, 95% CI 1.37–4.59) and multiple acute symptomatic seizures (HR 5.08, 95% CI 2.58–9.99) were independently associated with PSE development. This association remained in the sub-analysis within the ischemic stroke cohort. In the sub-analysis of the hemorrhagic stroke cohort, multilobar involvement (HR 4.80, 95% CI 1.49–15.39) was also independently associated with development of PSE. Further, we developed a nomogram to predict individual risk of developing PSE following stroke-associated acute symptomatic seizures. The nomogram showed a C-index of 0.73.Conclusion: More severe neurofunctional deficits (NIHSS score &gt; 14), longer interval from stroke to acute symptomatic seizures (days 4–7 post-stroke), and multiple acute symptomatic seizures were independently associated with development of PSE in patients with stroke-associated acute symptomatic seizures. This knowledge may increase clinical vigilance for development of PSE, facilitating rapid diagnosis and treatment initiation, and subsequently reduce seizure-related morbidity.
doi:10.3389/fnagi.2021.707732 pmid:34588971 pmcid:PMC8475904 fatcat:ponsxtv3tvcojc5gblrbyykrge

RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis

Jong-Jin Park, Emma Dempewolf, Wenzheng Zhang, Zeng-Yu Wang, Stefan Maas
2017 PLoS ONE  
OPEN ACCESS Citation: Park J-J, Dempewolf E, Zhang W, Wang Z-Y (2017) RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis.  ... 
doi:10.1371/journal.pone.0179410 pmid:28622347 pmcid:PMC5473554 fatcat:syncyb4byndhdmwuhqa2i3czw4

Association ofERAP1, but notIL23R, with ankylosing spondylitis in a Han Chinese population

Stuart I. Davidson, Xin Wu, Yu Liu, Meng Wei, Patrick A. Danoy, Gethin Thomas, Qing Cai, Linyun Sun, Emma Duncan, Niansong Wang, Qinghong Yu, Anlong Xu (+3 others)
2009 Arthritis & Rheumatism  
Zhongwei Wang, Ting Li, Yiping Lin, and Chao Wu and Ms. Johanna Hadler, Ms Kathryn Addison, and Ms Karena Pryce for their assistance with DNA extraction and genotyping.  ... 
doi:10.1002/art.24933 pmid:19877036 fatcat:jyzlxq3kpbc5lnwq5nsqtcpmkm

Semibrittle seismic deformation in high-temperature mantle mylonite shear zone along the Romanche transform fault

Zhiteng Yu, Satish C. Singh, Emma P. M. Gregory, Marcia Maia, Zhikai Wang, Daniele Brunelli
2021 Science Advances  
Oceanic transform faults, a key element of plate tectonics, represent the first-order discontinuities along mid-ocean ridges, host large earthquakes, and induce extreme thermal gradients in lithosphere. However, the thermal structure along transform faults and its effects on earthquake generation are poorly understood. Here we report the presence of a 10- to 15-kilometer-thick in-depth band of microseismicity in 10 to 34 kilometer depth range associated with a high-temperature (700° to 900°C)
more » ... ntle below the brittle lithosphere along the Romanche mega transform fault in the equatorial Atlantic Ocean. The occurrence of the shallow 2016 moment magnitude 7.1 supershear rupture earthquake and these deep microearthquakes indicate that although large earthquakes occur in the upper brittle lithosphere, a substantial amount of deformation is accommodated in the semibrittle mylonitic mantle that resides at depths below the 600°C isotherm. We also observe a rapid westward deepening of this band of seismicity indicating a strong lateral heterogeneity.
doi:10.1126/sciadv.abf3388 pmid:33837085 fatcat:cmgwgl36ibgqbpxvhbefqkm4yu

Prediction of physical functioning and general health status trajectories on mortality among persons with cognitive impairment

Emma Zang, Xueqing Wang, Yu Shi, Bei Wu, Terri R. Fried
2022 BMC Geriatrics  
Background The concern posed by the confluence of aging and cognitive impairment is growing in importance as the U.S. population rapidly ages. As such, we sought to examine the predictive power of physical functioning (PF) and general health status (GHS) trajectories on mortality outcomes among persons with cognitive impairment (PCIs). Methods We used group-based trajectory models to identify latent group memberships for PF trajectories in 1,641 PCIs and GHS trajectories in 2,021 PCIs from the
more » ... ational Health and Aging Trends Survey (2011–2018) and applied logistic regressions to predict mortality using these memberships controlling for individual characteristics. Results We identified six trajectory groups for PF and four groups for GHS. Trajectory group memberships for both outcomes significantly predicted mortality. For PF, group memberships largely captured the average levels over time, and worse trajectories (i.e., lower baselines and faster declines) were associated with higher odds of death. The highest mortality risk was associated with the group experiencing a sharp decline early in its PF trajectory, although its average level across time was not the lowest. For GHS, we observed two groups with comparable average levels across time, but the one with a convex-shape trajectory had much higher mortality risks compared to the one with a concave-shape trajectory. Conclusions Our findings highlighted that health trajectories predicted mortality among PCIs, not only because of general levels but also because of the shapes of declines. Close monitoring health deterioration of PCIs is crucial to understand the health burden of this population and to make subsequent actions.
doi:10.1186/s12877-022-03446-0 pmid:36131230 pmcid:PMC9494770 fatcat:nas7n27ud5cynbr2ygvwq6o5fa

Association of Antenatal Micronutrient Supplementation With Adolescent Intellectual Development in Rural Western China

Zhonghai Zhu, Yue Cheng, Lingxia Zeng, Mohamed Elhoumed, Guobin He, Wenhao Li, Min Zhang, Wenjing Li, Danyang Li, Sintayehu Tsegaye, Suying Chang, Hong Yan (+4 others)
2018 JAMA pediatrics  
Yu Lu, BSc, and Siyuan Ma, BSc, both from the Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, helped with data entry.  ... 
doi:10.1001/jamapediatrics.2018.1401 pmid:29987336 pmcid:PMC6143069 fatcat:kozkn2ggd5cdzbsyzffexl62gi

The 2015 M w 6.0 Mt. Kinabalu earthquake: an infrequent fault rupture within the Crocker fault system of East Malaysia

Yu Wang, Shengji Wei, Xin Wang, Eric O. Lindsey, Felix Tongkul, Paul Tapponnier, Kyle Bradley, Chung-Han Chan, Emma M. Hill, Kerry Sieh
2017 Geoscience Letters  
The M w 6.0 Mt. Kinabalu earthquake of 2015 was a complete (and deadly) surprise, because it occurred well away from the nearest plate boundary in a region of very low historical seismicity. Our seismological, space geodetic, geomorphological, and field investigations show that the earthquake resulted from rupture of a northwest-dipping normal fault that did not reach the surface. Its unilateral rupture was almost directly beneath 4000-m-high Mt. Kinabalu and triggered widespread slope failures
more » ... on steep mountainous slopes, which included rockfalls that killed 18 hikers. Our seismological and morphotectonic analyses suggest that the rupture occurred on a normal fault that splays upwards off of the previously identified normal Marakau fault. Our mapping of tectonic landforms reveals that these faults are part of a 200-km-long system of normal faults that traverse the eastern side of the Crocker Range, parallel to Sabah's northwestern coastline. Although the tectonic reason for this active normal fault system remains unclear, the lengths of the longest fault segments suggest that they are capable of generating magnitude 7 earthquakes. Such large earthquakes must occur very rarely, though, given the hitherto undetectable geodetic rates of active tectonic deformation across the region. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
doi:10.1186/s40562-017-0072-9 fatcat:viedxxkzcvg7foqmabmnaoy4ve

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues [article]

Jocelyn Y. Kishi, Brian J. Beliveau, Sylvain W. Lapan, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem K. Saka, Yu Wang, Constance L. Cepko, Peng Yin
2018 bioRxiv   pre-print
Fluorescentin situhybridization (FISH) reveals the abundance and positioning of nucleic acid sequences in fixed samples and can be combined with cell segmentation to produce a powerful single cell gene expression assay. However, it remains difficult to label more than a few targets and to visualize nucleic acids in environments such as thick tissue samples using conventional FISH technologies. Recently, methods have been developed for multiplexed amplification of FISH signals, yet it remains
more » ... llenging to achieve high levels of simultaneous multiplexing combined with high sampling efficiency and simple workflows. Here, we introduce signal amplification by exchange reaction (SABER), which endows oligo-based FISH probes with long, single-stranded DNA concatemers that serve as targets for sensitive fluorescent detection. We establish that SABER effectively amplifies the signal of probes targeting nucleic acids in fixed cells and tissues, can be deployed against at least 17 targets simultaneously, and detects mRNAs with high efficiency. As a demonstration of the utility of SABER in assays involving genetic manipulations, we apply multiplexed FISH of reporters and cell type markers to the identification of enhancers with cell type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit to allow rapid and cost effective multiplexed imaging.
doi:10.1101/401810 fatcat:yw6cotdxmnhixab3u2o2spzuqu

GLaM: Efficient Scaling of Language Models with Mixture-of-Experts [article]

Nan Du, Yanping Huang, Andrew M. Dai, Simon Tong, Dmitry Lepikhin, Yuanzhong Xu, Maxim Krikun, Yanqi Zhou, Adams Wei Yu, Orhan Firat, Barret Zoph, Liam Fedus (+15 others)
2022 arXiv   pre-print
Comprehension: DROP (Dua et al., 2019) , CoQA (Reddy et al., 2019) , QuAC (Choi et al., 2018) , SQuADv2 (Rajpurkar et al., 2018) , RACEh (Lai et al., 2017) , RACE-m (Lai et al., 2017) SuperGLUE: (Wang  ...  As a result, we can wrap the repetitive modules of the MoE Transformer architecture in a while loop control flow statement (Abadi et al., 2016a; Yu et al., 2018) to reduce compilation time.  ... 
arXiv:2112.06905v2 fatcat:q3htjycwc5a35acim2zecibhia

The differences between gonadal and extra-gonadal malignant teratomas in both genders and the effects of chemotherapy

Hang Sun, Hongxin Ding, Jianjun Wang, Emma Zhang, Yihua Fang, Zhenhua Li, Xiao Yu, Chongren Wang, Yifan Zhao, Kan Chen, Siwan Wen, Liang Li (+4 others)
2019 BMC Cancer  
A tumor comprising of different types of tissues (such as hair, muscle, bone, etc.) is known as a teratoma. It is a type of germ cell (cells that make sperm or eggs) tumor. When these germ cells have rapid cancerous growth, then such a teratoma is called a malignant teratoma. We have studied the differences between gonadal and extra-gonadal malignant teratomas and the effects of chemotherapy in both genders. Methods: The samples of 3799 male and 1832 female patients with malignant teratoma
more » ... es, between the ages of 1 and 85+ years, were selected from the years 1973 to 2014. Trends in incidence, estimated prevalence, incidence rates, and frequency were calculated in gonadal and extra-gonadal tumors with age adjustment. The fiveyear observed, expected, and relative survival rates were analyzed to study the prognosis. Results: The gonadal took over a majority percentage of malignant teratomas compared with the extra-gonadal (90% vs. 10% in male; 83% vs. 17% in female). For the male, the total of the gonadal and the extra-gonadal were all significantly decreased from 1973 to 2014 (p < 0.05). For the female, there were no significant trends. As for prevalence, incidence, and frequency, there were two separate peaks of malignant teratomas. One peak was at under 1 year old, which was composed of the extra-gonadal tumor; the other peak was at 20-24 for male and 10-34 for female, which was composed of the gonadal tumor. This separation of the gonadal and extra-gonadal showed a significant difference (p < 0.05). As for the prognosis, the extra-gonadal tumor showed significantly lower survival rates than the gonadal (p < 0.05). In the short term, the survival rate of the chemotherapy group was higher than the supportive care group. However, in the long term, the survival rate of the chemotherapy group was lower than the supportive care group. Conclusion: The gonadal and extra-gonadal malignant teratomas show lots of differences. Chemotherapy might not help improve survival rates.
doi:10.1186/s12885-019-5598-0 fatcat:mp3taezwrvb65auphjarfvd6ui

Litter carbon and nutrient chemistry control the magnitude of soil priming effect

Lin Chao, Yanyan Liu, Grégoire T. Freschet, Weidong Zhang, Xin Yu, Wenhui Zheng, Xin Guan, Qingpeng Yang, Longchi Chen, Feike A. Dijkstra, Silong Wang, Emma Sayer
2019 Functional Ecology  
, Chamberlain, Stott, & Tanner, 2009; Wang, Wang, He, Liu, & Wu, 2014; Zhang, Wang, & Wang, 2013 ) on SOC decomposition rates.  ...  , Wang, He, Liu, & Wu, 2014; Zhang & Wang, 2012) .  ... 
doi:10.1111/1365-2435.13278 fatcat:26sxycmbwbbelpjhfm6od6oqku
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