Deep Weighted Averaging Classifiers

Recent advances in deep learning have achieved impressive gains in classification accuracy on a variety of types of data, including images and text. Despite these gains, however, concerns have been raised about the calibration, robustness, and interpretability of these models. In this paper we propose a simple way to modify any conventional deep architecture to automatically provide more transparent explanations for classification decisions, as well as an intuitive notion of the credibility of each prediction. Specifically, we draw on ideas from nonparametric kernel regression, and propose to predict labels based on a weighted sum of training instances, where the weights are determined by distance in a learned instance-embedding space. Working within the framework of conformal methods, we propose a new measure of nonconformity suggested by our model, and experimentally validate the accompanying theoretical expectations, demonstrating improved transparency, controlled error rates, and robustness to out-of-domain data, without compromising on accuracy or calibration.Comment: 13 pages, 8 figures, 5 tables, added DOI and updated to meet ACM formatting requirements, In Proceedings of FAT* (2019

The TOP-SCOPE Survey of PGCCs: PMO and SCUBA-2 Observations of 64 PGCCs in the Second Galactic Quadrant

In order to understand the initial conditions and early evolution of star formation in a wide range of Galactic environments, we carried out an investigation of 64 Planck Galactic cold clumps (PGCCs) in the second quadrant of the Milky Way. Using the (CO)-C-13 and (CO)-O-18 J = 1-0 lines and 850 mu m continuum observations, we investigated cloud fragmentation and evolution associated with star formation. We extracted 468 clumps and 117 cores from the (CO)-C-13 line and 850 mu m continuum maps, respectively. We made use of the Bayesian distance calculator and derived the distances of all 64 PGCCs. We found that in general, the mass-size plane follows a relation of m similar to r(1.67). At a given scale, the masses of our objects are around 1/10 of that of typical Galactic massive star-forming regions. Analysis of the clump and core masses, virial parameters, densities, and mass-size relation suggests that the PGCCs in our sample have a low core formation efficiency (similar to 3.0%), and most PGCCs are likely low-mass star-forming candidates. Statistical study indicates that the 850 mu m cores are more turbulent, more optically thick, and denser than the (CO)-C-13 clumps for star formation candidates, suggesting that the 850 mu m cores are likely more appropriate future star formation candidates than the (CO)-C-13 clumps

Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs

Lysophosphatidic Acid Acyltransferase β (LPAATβ) Promotes the Tumor Growth of Human Osteosarcoma

Osteosarcoma is the most common primary malignancy of bone with poorly characterized molecular pathways important in its pathogenesis. Increasing evidence indicates that elevated lipid biosynthesis is a characteristic feature of cancer. We sought to investigate the role of lysophosphatidic acid acyltransferase β (LPAATβ, aka, AGPAT2) in regulating the proliferation and growth of human osteosarcoma cells. LPAATβ can generate phosphatidic acid, which plays a key role in lipid biosynthesis as well as in cell proliferation and survival. Although elevated expression of LPAATβ has been reported in several types of human tumors, the role of LPAATβ in osteosarcoma progression has yet to be elucidated.Endogenous expression of LPAATβ in osteosarcoma cell lines is analyzed by using semi-quantitative PCR and immunohistochemical staining. Adenovirus-mediated overexpression of LPAATβ and silencing LPAATβ expression is employed to determine the effect of LPAATβ on osteosarcoma cell proliferation and migration in vitro and osteosarcoma tumor growth in vivo. We have found that expression of LPAATβ is readily detected in 8 of the 10 analyzed human osteosarcoma lines. Exogenous expression of LPAATβ promotes osteosarcoma cell proliferation and migration, while silencing LPAATβ expression inhibits these cellular characteristics. We further demonstrate that exogenous expression of LPAATβ effectively promotes tumor growth, while knockdown of LPAATβ expression inhibits tumor growth in an orthotopic xenograft model of human osteosarcoma.Our results strongly suggest that LPAATβ expression may be associated with the aggressive phenotypes of human osteosarcoma and that LPAATβ may play an important role in regulating osteosarcoma cell proliferation and tumor growth. Thus, targeting LPAATβ may be exploited as a novel therapeutic strategy for the clinical management of osteosarcoma. This is especially attractive given the availability of selective pharmacological inhibitors

The TOP-SCOPE Survey of PGCCs : PMO and SCUBA-2 Observations of 64 PGCCs in the Second Galactic Quadrant

In order to understand the initial conditions and early evolution of star formation in a wide range of Galactic environments, we carried out an investigation of 64 Planck Galactic cold clumps (PGCCs) in the second quadrant of the Milky Way. Using the (CO)-C-13 and (CO)-O-18 J = 1-0 lines and 850 mu m continuum observations, we investigated cloud fragmentation and evolution associated with star formation. We extracted 468 clumps and 117 cores from the (CO)-C-13 line and 850 mu m continuum maps, respectively. We made use of the Bayesian distance calculator and derived the distances of all 64 PGCCs. We found that in general, the mass-size plane follows a relation of m similar to r(1.67). At a given scale, the masses of our objects are around 1/10 of that of typical Galactic massive star-forming regions. Analysis of the clump and core masses, virial parameters, densities, and mass-size relation suggests that the PGCCs in our sample have a low core formation efficiency (similar to 3.0%), and most PGCCs are likely low-mass star-forming candidates. Statistical study indicates that the 850 mu m cores are more turbulent, more optically thick, and denser than the (CO)-C-13 clumps for star formation candidates, suggesting that the 850 mu m cores are likely more appropriate future star formation candidates than the (CO)-C-13 clumps.Peer reviewe

The TOP-SCOPE Survey of Planck Galactic Cold Clumps : Survey Overview and Results of an Exemplar Source, PGCC G26.53+0.17

The low dust temperatures (<14 K) of Planck Galactic cold clumps (PGCCs) make them ideal targets to probe the initial conditions and very early phase of star formation. "TOP-SCOPE" is a joint survey program targeting similar to 2000 PGCCs in J = 1-0 transitions of CO isotopologues and similar to 1000 PGCCs in 850 mu m continuum emission. The objective of the "TOP-SCOPE" survey and the joint surveys (SMT 10 m, KVN 21 m, and NRO 45 m) is to statistically study the initial conditions occurring during star formation and the evolution of molecular clouds, across a wide range of environments. The observations, data analysis, and example science cases for these surveys are introduced with an exemplar source, PGCC G26.53+0.17 (G26), which is a filamentary infrared dark cloud (IRDC). The total mass, length, and mean line mass (M/L) of the G26 filament are similar to 6200 M-circle dot, similar to 12 pc, and similar to 500 M-circle dot pc(-1), respectively. Ten massive clumps, including eight starless ones, are found along the filament. The most massive clump as a whole may still be in global collapse, while its denser part seems to be undergoing expansion owing to outflow feedback. The fragmentation in the G26 filament from cloud scale to clump scale is in agreement with gravitational fragmentation of an isothermal, nonmagnetized, and turbulent supported cylinder. A bimodal behavior in dust emissivity spectral index (beta) distribution is found in G26, suggesting grain growth along the filament. The G26 filament may be formed owing to large-scale compression flows evidenced by the temperature and velocity gradients across its natal cloud.Peer reviewe

Observations of magnetic fields surrounding LkHa 101 taken by the BISTRO survey with JCMT-POL-2

© 2021. The American Astronomical Society. All rights reserved. This is the accepted manuscript version of an article which has been published in final form at https://doi.org/10.3847/1538-4357/abd0fcWe report the first high spatial resolution measurement of magnetic fields surrounding LkHa 101, part of the Auriga- California molecular cloud. The observations were taken with the POL-2 polarimeter on the James Clerk Maxwell Telescope within the framework of the B-fields In Star-forming Region Observations (BISTRO) survey. Observed polarization of thermal dust emission at 850 μm is found to be mostly associated with the redshifted gas component of the cloud. The magnetic field displays a relatively complex morphology. Two variants of the Davis-Chandrasekhar- Fermi method, unsharp masking and structure function, are used to calculate the strength of magnetic fields in the plane of the sky, yielding a similar result of BPOS~ 115 μG. The mass-to-magnetic-flux ratio in critical value units, λ~0.3, is the smallest among the values obtained for other regions surveyed by POL-2. This implies that the LkHa 101 region is subcritical, and the magnetic field is strong enough to prevent gravitational collapse. The inferred dB/B0~0.3 implies that the large-scale component of the magnetic field dominates the turbulent one. The variation of the polarization fraction with total emission intensity can be fitted by a power law with an index of a =0.82±0.03, which lies in the range previously reported for molecular clouds. We find that the polarization fraction decreases rapidly with proximity to the only early B star (LkHa 101) in the region. Magnetic field tangling and the joint effect of grain alignment and rotational disruption by radiative torques can potentially explain such a decreasing trend.Peer reviewe

A Tale of Three: Magnetic Fields along the Orion Integral-shaped Filament as Revealed by the JCMT BISTRO Survey

© 2024 The Author(s). This is an open access article distributed under the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/As part of the B-fields In Star-forming Region Observations survey, we present James Clerk Maxwell Telescope (JCMT) 850 μm polarimetric observations toward the Orion integral-shaped filament (ISF) that covers three portions known as OMC-1, OMC-2, and OMC-3. The magnetic field threading the ISF seen in the JCMT POL-2 map appears as a tale of three: pinched for OMC-1, twisted for OMC-2, and nearly uniform for OMC-3. A multiscale analysis shows that the magnetic field structure in OMC-3 is very consistent at all the scales, whereas the field structure in OMC-2 shows no correlation across different scales. In OMC-1, the field retains its mean orientation from large to small scales but shows some deviations at small scales. Histograms of relative orientations between the magnetic field and filaments reveal a bimodal distribution for OMC-1, a relatively random distribution for OMC-2, and a distribution with a predominant peak at 90∘ for OMC-3. Furthermore, the magnetic fields in OMC-1 and OMC-3 both appear to be aligned perpendicular to the fibers, which are denser structures within the filament, but the field in OMC-2 is aligned along with the fibers. All these suggest that gravity, turbulence, and magnetic field are each playing a leading role in OMC-1, 2, and 3, respectively. While OMC-2 and 3 have almost the same gas mass, density, and nonthermal velocity dispersion, there are on average younger and fewer young stellar objects in OMC-3, providing evidence that a stronger magnetic field will induce slower and less efficient star formation in molecular clouds.Peer reviewe