Explainable AI for ML jet taggers using expert variables and layerwise relevance propagation

A framework is presented to extract and understand decision-making information from a deep neural network (DNN) classifier of jet substructure tagging techniques. The general method studied is to provide expert variables that augment inputs ("eXpert AUGmented" variables, or XAUG variables), then apply layerwise relevance propagation (LRP) to networks both with and without XAUG variables. The XAUG variables are concatenated with the intermediate layers after network-specific operations (such as convolution or recurrence), and used in the final layers of the network. The results of comparing networks with and without the addition of XAUG variables show that XAUG variables can be used to interpret classifier behavior, increase discrimination ability when combined with low-level features, and in some cases capture the behavior of the classifier completely. The LRP technique can be used to find relevant information the network is using, and when combined with the XAUG variables, can be used to rank features, allowing one to find a reduced set of features that capture part of the network performance. In the studies presented, adding XAUG variables to low-level DNNs increased the efficiency of classifiers by as much as 30-40\%. In addition to performance improvements, an approach to quantify numerical uncertainties in the training of these DNNs is presented.Comment: 38 pages, 30 figure

Search for gravitational-wave transients associated with magnetar bursts in advanced LIGO and advanced Virgo data from the third observing run

Gravitational waves are expected to be produced from neutron star oscillations associated with magnetar giant f lares and short bursts. We present the results of a search for short-duration (milliseconds to seconds) and longduration (∼100 s) transient gravitational waves from 13 magnetar short bursts observed during Advanced LIGO, Advanced Virgo, and KAGRA’s third observation run. These 13 bursts come from two magnetars, SGR1935 +2154 and SwiftJ1818.0−1607. We also include three other electromagnetic burst events detected by FermiGBM which were identified as likely coming from one or more magnetars, but they have no association with a known magnetar. No magnetar giant flares were detected during the analysis period. We find no evidence of gravitational waves associated with any of these 16 bursts. We place upper limits on the rms of the integrated incident gravitational-wave strain that reach 3.6 × 10−²³ Hz at 100 Hz for the short-duration search and 1.1 ×10−²² Hz at 450 Hz for the long-duration search. For a ringdown signal at 1590 Hz targeted by the short-duration search the limit is set to 2.3 × 10−²² Hz. Using the estimated distance to each magnetar, we derive upper limits upper limits on the emitted gravitational-wave energy of 1.5 × 1044 erg (1.0 × 1044 erg) for SGR 1935+2154 and 9.4 × 10^43 erg (1.3 × 1044 erg) for Swift J1818.0−1607, for the short-duration (long-duration) search. Assuming isotropic emission of electromagnetic radiation of the burst fluences, we constrain the ratio of gravitational-wave energy to electromagnetic energy for bursts from SGR 1935+2154 with the available fluence information. The lowest of these ratios is 4.5 × 103

Search for gravitational-wave transients associated with magnetar bursts in Advanced LIGO and Advanced Virgo data from the third observing run

Gravitational waves are expected to be produced from neutron star oscillations associated with magnetar giant flares and short bursts. We present the results of a search for short-duration (milliseconds to seconds) and long-duration (∼100 s) transient gravitational waves from 13 magnetar short bursts observed during Advanced LIGO, Advanced Virgo, and KAGRA’s third observation run. These 13 bursts come from two magnetars, SGR 1935+2154 and Swift J1818.0−1607. We also include three other electromagnetic burst events detected by Fermi-GBM which were identified as likely coming from one or more magnetars, but they have no association with a known magnetar. No magnetar giant flares were detected during the analysis period. We find no evidence of gravitational waves associated with any of these 16 bursts. We place upper limits on the rms of the integrated incident gravitational-wave strain that reach 3.6 × 10−23 /Hz at 100 Hz for the short-duration search and 1.1 × 10−22 /Hz at 450 Hz for the long-duration search. For a ringdown signal at 1590 Hz targeted by the short-duration search the limit is set to 2.3 × 10−22 /Hz . Using the estimated distance to each magnetar, we derive upper limits on the emitted gravitational-wave energy of 1.5 × 1044 erg (1.0 × 1044 erg) for SGR 1935+2154 and 9.4 × 1043 erg (1.3 × 1044 erg) for Swift J1818.0−1607, for the short-duration (long-duration) search. Assuming isotropic emission of electromagnetic radiation of the burst fluences, we constrain the ratio of gravitational-wave energy to electromagnetic energy for bursts from SGR 1935+2154 with the available fluence information. The lowest of these ratios is 4.5 × 103

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

The structure of phosphorylated GSK-3β complexed with a peptide, FRATtide, that inhibits β-catenin phosphorylation

Background: Glycogen synthase kinase-3 (GSK-3) sequentially phosphorylates four serine residues on glycogen synthase (GS), in the sequence SxxxSxxxSxxx-SxxxS(p), by recognizing and phosphorylating the first serine in the sequence motif SxxxS(P) (where S(p) represents a phosphoserine). FRATtide (a peptide derived from a GSK-3 binding protein) binds to GSK-3 and blocks GSK-3 from interacting with Axin. This inhibits the Axin-dependent phosphorylation of β-catenin by GSK-3. Results: Structures of uncomplexed Tyr216 phosphorylated GSK-3β and of its complex with a peptide and a sulfate ion both show the activation loop adopting a conformation similar to that in the phosphorylated and active forms of the related kinases CDK2 and ERK2. The sulfate ion, adjacent to Val214 on the activation loop, represents the binding site for the phosphoserine residue on `primed' substrates. The peptide FRATtide forms a helix-turn-helix motif in binding to the C-terminal lobe of the kinase domain; the FRATtide binding site is close to, but does not obstruct, the substrate binding channel of GSK-3. FRATtide (and FRAT1) does not inhibit the activity of GSK-3 toward GS. Conclusions: The Axin binding site on GSK-3 presumably overlaps with that for FRATtide; its proximity to the active site explains how Axin may act as a scaffold protein promoting β-catenin phosphorylation. Tyrosine 216 phosphorylation can induce an active conformation in the activation loop. Pre-phosphorylated substrate peptides can be modeled into the active site of the enzyme, with the P1 residue occupying a pocket partially formed by phosphotyrosine 216 and the P4 phosphoserine occupying the `primed' binding site

Tellurium, the forgotten element: a review for the properties, processes and biomedical applications of the bulk and nanoscale metalloid

Tellurium (Te) is a brittle, mildly toxic, and rare metalloid with an extremely low abundance in the planet. The element has been used in both its bulk and nanoscale forms for several applications in solar cell industry, semiconductors, catalysis, or heavy metal removal, among others. The end of the last century witnessed an explosion in new strategies for synthesizing different Te nanostructures with controlled compositions, sizes, morphologies, and properties, which allow these structures to enhance their impact in numerous applications. Nanomedicine has recently taken advantage of the metalloid in its nanoscale, showing promising applications as antibacterial, anticancer, and imaging agents. Nevertheless, the biological role of Te within living organisms remains mostly unknown, and just a few reports appear working on this matter. In this chapter, the forgotten elements are extensively studied in terms of its chemical, physical, and geological properties, and its main applications are summarized and studied for both bulk and nanosized tellurium. At the end, tellurium’s most important biomedical applications are presented with the aim to establish a general concept of the metalloid as a powerful biomedical tool with a bright future yet to be discovered.Peer reviewe