High-Order Stochastic Gradient Thermostats for Bayesian Learning of Deep Models

Learning in deep models using Bayesian methods has generated significant attention recently. This is largely because of the feasibility of modern Bayesian methods to yield scalable learning and inference, while maintaining a measure of uncertainty in the model parameters. Stochastic gradient MCMC algorithms (SG-MCMC) are a family of diffusion-based sampling methods for large-scale Bayesian learning. In SG-MCMC, multivariate stochastic gradient thermostats (mSGNHT) augment each parameter of interest, with a momentum and a thermostat variable to maintain stationary distributions as target posterior distributions. As the number of variables in a continuous-time diffusion increases, its numerical approximation error becomes a practical bottleneck, so better use of a numerical integrator is desirable. To this end, we propose use of an efficient symmetric splitting integrator in mSGNHT, instead of the traditional Euler integrator. We demonstrate that the proposed scheme is more accurate, robust, and converges faster. These properties are demonstrated to be desirable in Bayesian deep learning. Extensive experiments on two canonical models and their deep extensions demonstrate that the proposed scheme improves general Bayesian posterior sampling, particularly for deep models.Comment: AAAI 201

Quasar candidate selection and photometric redshift estimation based on SDSS and UKIDSS data

We present a sample of 8498 quasars with both SDSS $ugriz$ optical and UKIDSS $YJHK$ near-IR photometric data. With this sample, we obtain the median colour-z relations based on 7400 quasars with magnitude uncertainties less than 0.1mag in all bands. By analyzing the quasar colours, we propose an empirical criterion in the $Y-K$ vs. $g-z$ colour-colour diagram to separate stars and quasars with redshift $z<4$, and two other criteria for selecting high-z quasars. Using the SDSS-UKIDSS colour-z relations, we estimate the photometric redshifts of 8498 SDSS-UKIDSS quasars, and find that 85.0% of them are consistent with the spectroscopic redshifts within $|\Delta z|<0.2$, which leads to a significant increase of the photometric redshift accuracy than that based on the SDSS colour-z relations only. We compare our colour selection criterion with a small UKIDSS/EDR quasar/star sample and a sample of 4671 variable sources in the SDSS Stripe 82 region with both SDSS and UKIDSS data, and find that they can be clearly divided into two classes (quasars and stars) by our criterion in the $Y-K$ vs. $g-z$ plot. We select 3834 quasar candidates from the variable sources with $g<20.5$ in Stripe 82, 826 of them being SDSS quasars and the rest without SDSS spectroscopy. We demonstrate that even at the same spectroscopy limit as SDSS, with our criterion we can at least partially recover the missing quasars with $z\sim2.7$ in SDSS. The SDSS identified quasars only take a small fraction (21.5%) of our quasar candidates selected from the variable sources in Stripe 82, indicating that a deeper spectroscopy is very promising in producing a larger sample of quasars than SDSS. The implications of our results to the future Chinese LAMOST quasar survey are also discussed.Comment: 13 pages, 13 figures, 2 tables, accepted for publication in MNRA

Non-reciprocal phase shift induced by an effective magnetic flux for light

Photons are neutral particles that do not interact directly with a magnetic field. However, recent theoretical work has shown that an effective magnetic field for photons can exist if the phase of light changes with its direction of propagation. This direction-dependent phase indicates the presence of an effective magnetic field, as shown experimentally for electrons in the Aharonov–Bohm experiment. Here, we replicate this experiment using photons. To create this effective magnetic field we construct an on-chip silicon-based Ramsey-type interferometer. This interferometer has been traditionally used to probe the phase of atomic states and here we apply it to probe the phase of photonic states. We experimentally observe an effective magnetic flux between 0 and 2π corresponding to a non-reciprocal 2π phase shift with an interferometer length of 8.35 mm and an interference-fringe extinction ratio of 2.4 dB. This non-reciprocal phase is comparable to those of common monolithically integrated magneto-optical materials

Observation of an Effective Magnetic field for Light

Photons are neutral particles that do not interact directly with a magnetic field. However, recent theoretical work has shown that an effective magnetic field for photons can exist if the phase of light would change with its propagating direction. This direction-dependent phase indicates the presence of an effective magnetic field as shown for electrons experimentally in the Aharonov-Bohm experiment. Here we replicate this experiment using photons. In order to create this effective magnetic field, we construct an on-chip silicon-based Ramsey-type interferometer. This interferometer has been traditionally used to probe the phase of atomic states, and here we apply it to probe the phase of photonic states. We experimentally observe a phase change, i.e. an effective magnetic field flux from 0 to 2pi. In an Aharonov-Bohm configuration for electrons, considering the device geometry, this flux corresponds to an effective magnetic field of 0.2 Gauss.Comment: 15 pages and 4 figure

Seasonal variation of the deep limb of the Pacific Meridional Overturning circulation at Yap-Mariana junction

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, J., Ma, Q., Wang, F., Lu, Y., & Pratt, L. J. Seasonal variation of the deep limb of the Pacific Meridional Overturning circulation at Yap-Mariana junction. Journal of Geophysical Research: Oceans, 125(7), (2020): e2019JC016017, doi:10.1029/2019JC016017.This study reveals the seasonal variability of the lower and upper deep branches of the Pacific Meridional Overturning Circulation (L‐PMOC and U‐PMOC) in the Yap‐Mariana Junction (YMJ) channel, a major gateway for deep flow into the western Pacific. On the western side of the YMJ channel, mooring observations in 2017 and in 1997 show the seasonal phase of the L‐PMOC at depths of 3,800–4,400 m: strong northward flow with speed exceeding 20 cm s−1 and lasting from December to next May and weak flow during the following 6 months. On the eastern side of the channel, mooring observations during 2014–2017 show two southward deep flows with broadly seasonal phases, one being the return flow of L‐PMOC below ~4,000 m and with the same phase of L‐PMOC but reduced magnitude. The second, shallower, southward deep flow corresponds to the U‐PMOC observed within 3,000–3,800 m and with opposite phase of L‐PMOC, that is, strong (weak) southward flow appearing during June–November (December–May). Seasonal variations of the L‐PMOC and U‐PMOC are accompanied by the seasonal intrusions of the Lower and Upper Circumpolar Waters (LCPW and UCPW) in lower and upper deep layers, which change the isopycnal structure and the deep currents in a way consistent with geostrophic balance.This study is supported by the National Natural Science Foundation of China (grants 91958204 and 41776022), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA22000000), the Key Research Program of Frontier Sciences, CAS (grant QYZDB‐SSW‐SYS034). F. Wang thanks the support from the Scientific and Technological Innovation Project by Qingdao National Laboratory for Marine Science and Technology (grant 2016ASKJ12), the National Program on Global Change and Air‐Sea Interaction (grant GASI‐IPOVAI‐01‐01), and the National Natural Science Foundation of China (grants 41730534 and 41421005). L. Pratt gratefully acknowledges the support by NSF (grant OCE‐1657870). Jianing Wang and Qiang Ma contributed equally to this work

Intermediate intraseasonal variability in the western tropical Pacific Ocean: meridional distribution of equatorial Rossby waves influenced by a tilted boundary

Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(4),(2020): 921-933, doi:10.1175/JPO-D-19-0184.1.Intermediate-depth intraseasonal variability (ISV) at a 20–90-day period, as detected in velocity measurements from seven subsurface moorings in the tropical western Pacific, is interpreted in terms of equatorial Rossby waves. The moorings were deployed between 0° and 7.5°N along 142°E from September 2014 to October 2015. The strongest ISV energy at 1200 m occurs at 4.5°N. Peak energy at 4.5°N is also seen in an eddy-resolving global circulation model. An analysis of the model output identifies the source of the ISV as short equatorial Rossby waves with westward phase speed but southeastward and downward group velocity. Additionally, it is shown that a superposition of first three baroclinic modes is required to represent the ISV energy propagation. Further analysis using a 1.5-layer shallow water model suggests that the first meridional mode Rossby wave accounts for the specific meridional distribution of ISV in the western Pacific. The same model suggests that the tilted coastlines of Irian Jaya and Papua New Guinea, which lie to the south of the moorings, shift the location of the northern peak of meridional velocity oscillation from 3°N to near 4.5°N. The tilt of this boundary with respect to a purely zonal alignment therefore needs to be taken into account to explain this meridional shift of the peak. Calculation of the barotropic conversion rate indicates that the intraseasonal kinetic energy below 1000 m can be transferred into the mean flows, suggesting a possible forcing mechanism for intermediate-depth zonal jets.This study is supported by the National Natural Science Foundation of China (Grants 91958204 and 41776022), the China Ocean Mineral Resources Research and Development Association Program (DY135-E2-3-02), and the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant XDA22000000). L. Pratt was supported by the U.S. National Science Foundation Grant OCE-1657870. F. Wang thanks the support from the Scientific and Technological Innovation Project by Qingdao National Laboratory for Marine Science and Technology (Grant 2016ASKJ12), the National Program on Global Change and Air-Sea Interaction (Grant GASI-IPOVAI-01-01), and the National Natural Science Foundation of China (Grants 41730534, 41421005, and U1406401)

Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms

BACKGROUND: Complementary single-nucleotide polymorphisms (SNPs) may not be distributed equally between two DNA strands if the strands are functionally distinct, such as in transcribed genes. In introns, an excess of A↔G over the complementary C↔T substitutions had previously been found and attributed to transcription-coupled repair (TCR), demonstrating the valuable functional clues that can be obtained by studying such asymmetry. Here we studied asymmetry of human synonymous SNPs (sSNPs) in the fourfold degenerate (FFD) sites as compared to intronic SNPs (iSNPs). RESULTS: The identities of the ancestral bases and the direction of mutations were inferred from human-chimpanzee genomic alignment. After correction for background nucleotide composition, excess of A→G over the complementary T→C polymorphisms, which was observed previously and can be explained by TCR, was confirmed in FFD SNPs and iSNPs. However, when SNPs were separately examined according to whether they mapped to a CpG dinucleotide or not, an excess of C→T over G→A polymorphisms was found in non-CpG site FFD SNPs but was absent from iSNPs and CpG site FFD SNPs. CONCLUSION: The genome-wide discrepancy of human FFD SNPs provides novel evidence for widespread selective pressure due to functional effects of sSNPs. The similar asymmetry pattern of FFD SNPs and iSNPs that map to a CpG can be explained by transcription-coupled mechanisms, including TCR and transcription-coupled mutation. Because of the hypermutability of CpG sites, more CpG site FFD SNPs are relatively younger and have confronted less selection effect than non-CpG FFD SNPs, which can explain the asymmetric discrepancy of CpG site FFD SNPs vs. non-CpG site FFD SNPs

Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, J., Wang, F., Lu, Y., Ma, Q., Pratt, L. J., & Zhang, Z. Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction. Frontiers in Marine Science, 8, (2021): 672199, https://doi.org/10.3389/fmars.2021.672199.The lower deep branch of the Pacific Meridional Overturning Circulation (L-PMOC) is responsible for the deep-water transport from Antarctic to the North Pacific and is a key ingredient in the regulation of global climate through its influence on the storage and residence time of heat and carbon. At the Pacific Yap-Mariana Junction (YMJ), a major gateway for deep-water flowing into the Western Pacific Ocean, we deployed five moorings from 2018 to 2019 in the Eastern, Southern, and Northern Channels in order to explore the pathways and variability of L-PMOC. We have identified three main patterns for L-PMOC pathways. In Pattern 1, the L-PMOC intrudes into the YMJ from the East Mariana Basin (EMB) through the Eastern Channel and then flows northward into the West Mariana Basin (WMB) through the Northern Channel and southward into the West Caroline Basin (WCB) through the Southern Channel. In Pattern 2, the L-PMOC intrudes into the YMJ from both the WCB and the EMB and then flows into the WMB. In Pattern 3, the L-PMOC comes from the WCB and then flows into the EMB and WMB. The volume transports of L-PMOC through the Eastern, Southern, and Northern Channels all exhibit seasonality. During November–April (May–October), the flow pathway conforms to Pattern 1 (Patterns 2 and 3), and the mean and standard deviation of L-PMOC transports are −4.44 ± 1.26 (−0.30 ± 1.47), −0.96 ± 1.13 (1.75 ± 1.49), and 1.49 ± 1.31 (1.07 ± 1.10) Sv in the Eastern, Southern, and Northern Channels, respectively. Further analysis of numerical ocean modeling results demonstrates that L-PMOC transport at the YMJ is forced by a deep pressure gradient between two adjacent basins, which is mainly determined by the sea surface height (SSH) and water masses in the upper 2,000-m layer. The seasonal variability of L-PMOC transport is attributed to local Ekman pumping and westward-propagating Rossby waves. The L-PMOC transport greater than 3,500 m is closely linked to the wind forcing and the upper ocean processes.This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA22000000), the National Natural Science Foundation of China (grants 91958204 and 41776022), the Key Research Program of Frontier Sciences, CAS (grant QYZDB-SSW-SYS034), and the International Partnership Program of CAS (grant 133137KYSB20180056). FW thanks the support from the National Natural Science Foundation of China (grants 41730534 and 41421005). QM thanks the support by the National Natural Science Foundation of China (grant 42006003)