Search

We present a whole-body model of human metabolism that utilizes a system of organs and blood vessels to simulate the enzymatic reactions. The model focuses on key organs, including the brain, heart and lungs, liver, gut, and kidney, as well as muscle and adipose tissue. The model equations are formulated using stoichiometry and Michaelis-Menten kinetics to describe the enzymatic reactions. We demonstrate how the model can be used to simulate the effects of prolonged fasting and intermittent fasting on selected metabolite concentrations and glucose flux. Furthermore, by simulating intermittent fasting the effect on the carbohydrate, the protein and the lipid storage is examined. We propose this method as a simple and intuitive approach for modeling the human metabolism, which is general, systematic and easy to incorporate. This could have potential applications in PK/PD drug development and in understanding metabolic disorders., Comment: 18 pages, 12 figures, 7 tables. arXiv admin note: text overlap with arXiv:2205.01473

We present an analysis of microlensing event OGLE-2019-BLG-0825. This event was identified as a planetary candidate by preliminary modeling. We find that significant residuals from the best-fit static binary-lens model exist and a xallarap effect can fit the residuals very well and significantly improves $\chi^2$ values. On the other hand, by including the xallarap effect in our models, we find that binary-lens parameters like mass-ratio, $q$, and separation, $s$, cannot be constrained well. However, we also find that the parameters for the source system like the orbital period and semi major axis are consistent between all the models we analyzed. We therefore constrain the properties of the source system better than the properties of the lens system. The source system comprises a G-type main-sequence star orbited by a brown dwarf with a period of $P\sim5$ days. This analysis is the first to demonstrate that the xallarap effect does affect binary-lens parameters in planetary events. It would not be common for the presence or absence of the xallarap effect to affect lens parameters in events with long orbital periods of the source system or events with transits to caustics, but in other cases, such as this event, the xallarap effect can affect binary-lens parameters., Comment: 19 pages, 7 figures, 6 tables. Accepted by AJ

We have observed the Class 0/I protostellar system Ced110 IRS4 at an angular resolution of $0.05''$ ($\sim$10 au) as a part of the ALMA large program; Early Planet Formation in the Embedded Disks (eDisk). The 1.3 mm dust continuum emission reveals that Ced110 IRS4 is a binary system with a projected separation of $\sim$250 au. The continuum emissions associated with the main source and its companion, named Ced110 IRS4A and IRS4B respectively, exhibit disk-like shapes and likely arise from dust disks around the protostars. The continuum emission of Ced110 IRS4A has a radius of $\sim$91.7 au ($\sim0.485''$), and shows bumps along its major axis with an asymmetry. The bumps can be interpreted as an shallow, ring-like structure at a radius of $\sim$40 au ($\sim0.2''$) in the continuum emission, as demonstrated from two-dimensional intensity distribution models. A rotation curve analysis on the C$^{18}$O and $^{13}$CO $J=2$-1 lines reveals the presence of a Keplerian disk within a radius of 120 au around Ced110 IRS4A, which supports the interpretation that the dust continuum emission arises from a disk. The ring-like structure in the dust continuum emission might indicate a possible, annular substructure in the surface density of the embedded disk, although the possibility that it is an apparent structure due to the optically thick continuum emission cannot be ruled out., Comment: 32 pages, 23 figures. Accepted for publication in ApJ as one of the first-look papers of the eDisk ALMA Large Program

Solar-type prestellar cores and protostars display large amounts of deuterated organic molecules. Recent findings on CHD$_2$OH and CD$_3$OH toward IRAS 16293-2422 suggest that even fully deuterated methanol, CD$_3$OD, may be detectable as well. However, searches for CD$_3$OD are hampered in particular by the lack of intensity information from a spectroscopic model. The objective of the present investigation is to develop a spectroscopic model of CD$_3$OD in low-lying torsional states that is sufficiently accurate to facilitate searches for this isotopolog in space. We carried out a new measurement campaign for CD$_3$OD involving two spectroscopic laboratories that covers the 34 GHz-1.1 THz range. A torsion-rotation Hamiltonian model based on the rho-axis method was employed for our analysis. Our resulting model describes the ground and first excited torsional states of CD$_3$OD well up to quantum numbers $J \leq 51$ and $K_a \leq 23$. We derived a line list for radio-astronomical observations from this model that is accurate up to at least 1.1 THz and should be sufficient for all types of radio-astronomical searches for this methanol isotopolog. This line list was used to search for CD$_3$OD in data from the Protostellar Interferometric Line Survey of IRAS 16293$-$2422 obtained with the Atacama Large Millimeter/submillimeter Array. While we found several emission features that can be attributed largely to CD$_3$OD, their number is still not sufficiently high enough to establish a clear detection. Nevertheless, the estimate of 2$\times 10^{15}$ cm$^{-2}$ derived for the CD$_3$OD column density may be viewed as an upper limit that can be compared to column densities of CD$_3$OH, CH$_3$OD, and CH$_3$OH. The comparison indicates that the CD$_3$OD column density toward IRAS 16293-2422 is in line with the enhanced D/H ratios observed for multiply deuterated complex organic molecules., Comment: 10 pages total, including figures, tables, and references; abstract slightly shortened; Astron. Astrophys., accepted

Computing a shortest path between two nodes in an undirected unweighted graph is among the most basic algorithmic tasks. Breadth first search solves this problem in linear time, which is clearly also a lower bound in the worst case. However, several works have shown how to solve this problem in sublinear time in expectation when the input graph is drawn from one of several classes of random graphs. In this work, we extend these results by giving sublinear time shortest path (and short path) algorithms for expander graphs. We thus identify a natural deterministic property of a graph (that is satisfied by typical random regular graphs) which suffices for sublinear time shortest paths. The algorithms are very simple, involving only bidirectional breadth first search and short random walks. We also complement our new algorithms by near-matching lower bounds.

We demonstrate a technique that allows highly surface sensitive imaging of nanostructures on planar surfaces over large areas, providing a new avenue for research in materials science, especially for \textit{in situ} applications. The capabilities of hard X-ray grazing incidence ptychography combine aspects from imaging, reflectometry and grazing incidence small angle scattering in providing large field-of-view images with high resolution transverse to the beam, horizontally and along the surface normal. Thus, it yields data with resolutions approaching electron microscopy, in two dimensions, but over much larger areas and with a poorer resolution in the third spatial dimension, along the beam propagation direction. Similar to grazing incidence small angle X-ray scattering, this technique facilitates the characterization of nanostructures across statistically significant surface areas or volumes within potentially feasible time frames for \textit{in situ} experiments, while also providing spatial information., Comment: 8 pages, 6 figures

We present observations of the Class 0 protostar IRAS 16544-1604 in CB 68 from the ''Early Planet Formation in Embedded Disks (eDisk)'' ALMA Large program. The ALMA observations target continuum and lines at 1.3-mm with an angular resolution of $\sim$5 au. The continuum image reveals a dusty protostellar disk with a radius of $\sim$30 au seen close to edge-on, and asymmetric structures both along the major and minor axes. While the asymmetry along the minor axis can be interpreted as the effect of the dust flaring, the asymmetry along the major axis comes from a real non-axisymmetric structure. The C$^{18}$O image cubes clearly show the gas in the disk that follows a Keplerian rotation pattern around a $\sim$0.14 $M_{\odot}$ central protostar. Furthermore, there are $\sim$1500 au-scale streamer-like features of gas connecting from North-East, North-North-West, and North-West to the disk, as well as the bending outflow as seen in the $^{12}$CO (2-1) emission. At the apparent landing point of NE streamer, there are SO (6$_5$-5$_4$) and SiO (5-4) emission detected. The spatial and velocity structure of NE streamer can be interpreted as a free-falling gas with a conserved specific angular momentum, and the detection of the SO and SiO emission at the tip of the streamer implies presence of accretion shocks. Our eDisk observations have unveiled that the Class 0 protostar in CB 68 has a Keplerian rotating disk with flaring and non-axisymmetric structure associated with accretion streamers and outflows., Comment: 30 pages, 24 figures, accepted for publication in The Astrophysical Journal as one of the first-look papers of the eDisk ALMA Large Program

While dust disks around optically visible, Class II protostars are found to be vertically thin, when and how dust settles to the midplane are unclear. As part of the Atacama Large Millimeter/submillimeter Array (ALMA) large program, Early Planet Formation in Embedded Disks, we analyze the edge-on, embedded, Class I protostar IRAS 04302+2247, also nicknamed the ``Butterfly Star." With a resolution of 0.05" (8~au), the 1.3 mm continuum shows an asymmetry along the minor axis which is evidence of an optically thick and geometrically thick disk viewed nearly edge-on. There is no evidence of rings and gaps, which could be due to the lack of radial substructure or the highly inclined and optically thick view. With 0.1" (16~au) resolution, we resolve the 2D snow surfaces, i.e., the boundary region between freeze-out and sublimation, for $^{12}$CO $J$=2--1, $^{13}$CO $J$=2--1, C$^{18}$O $J$=2--1, $H_{2}$CO $J$=$3_{0,3}$--$2_{0,2}$, and SO $J$=$6_{5}$--$5_{4}$, and constrain the CO midplane snow line to $\sim 130$ au. We find Keplerian rotation around a protostar of $1.6 \pm 0.4 M_{\odot}$ using C$^{18}$O. Through forward ray-tracing using RADMC-3D, we find that the dust scale height is $\sim 6$ au at a radius of 100~au from the central star and is comparable to the gas pressure scale height. The results suggest that the dust of this Class~I source has yet to vertically settle significantly., Comment: 33 pages, 21 figures. Accepted for publication in ApJ as one of the first-look papers of the eDisk ALMA Large Program

Constraining the physical and chemical structure of young embedded disks is crucial to understanding the earliest stages of planet formation. As part of the Early Planet Formation in Embedded Disks Atacama Large Millimeter/submillimeter Array Large Program, we present high spatial resolution ($\sim$0$.\!\!^{\prime\prime}$1 or $\sim$15 au) observations of the 1.3 mm continuum and $^{13}$CO $J=$ 2-1, C$^{18}$O $J=$ 2-1, and SO $J_N=$ $6_5$-$5_4$ molecular lines toward the disk around the Class I protostar L1489 IRS. The continuum emission shows a ring-like structure at 56 au from the central protostar and a tenuous, optically thin emission extending beyond $\sim$300 au. The $^{13}$CO emission traces the warm disk surface, while the C$^{18}$O emission originates from near the disk midplane. The coincidence of the radial emission peak of C$^{18}$O with the dust ring may indicate a gap-ring structure in the gaseous disk as well. The SO emission shows a highly complex distribution, including a compact, prominent component at $\lesssim$30 au, which is likely to originate from thermally sublimated SO molecules. The compact SO emission also shows a velocity gradient along a slightly ($\sim15^\circ$) tilted direction with respect to the major axis of the dust disk, which we interpret as an inner warped disk in addition to the warp around $\sim$200 au suggested by previous work. These warped structures may be formed by a planet or companion with an inclined orbit, or by a gradual change in the angular momentum axis during gas infall., Comment: 24 pages, 12 figures. Accepted for publication in The Astrophysical Journal as one of the first-look papers of the eDisk ALMA Large Program

Studying the physical and chemical conditions of young embedded disks is crucial to constrain the initial conditions for planet formation. Here, we present Atacama Large Millimeter/submillimeter Array (ALMA) observations of dust continuum at $\sim$0.06" (8 au) resolution and molecular line emission at $\sim$0.17" (24 au) resolution toward the Class 0 protostar L1527 IRS from the Large Program eDisk (Early Planet Formation in Embedded Disks). The continuum emission is smooth without substructures, but asymmetric along both the major and minor axes of the disk as previously observed. The detected lines of $^{12}$CO, $^{13}$CO, C$^{18}$O, H$_2$CO, c-C$_3$H$_2$, SO, SiO, and DCN trace different components of the protostellar system, with a disk wind potentially visible in $^{12}$CO. The $^{13}$CO brightness temperature and the H$_2$CO line ratio confirm that the disk is too warm for CO freeze out, with the snowline located at $\sim$350 au in the envelope. Both molecules show potential evidence of a temperature increase around the disk-envelope interface. SO seems to originate predominantly in UV-irradiated regions such as the disk surface and the outflow cavity walls rather than at the disk-envelope interface as previously suggested. Finally, the continuum asymmetry along the minor axis is consistent with the inclination derived from the large-scale (100" or 14,000 au) outflow, but opposite to that based on the molecular jet and envelope emission, suggesting a misalignment in the system. Overall, these results highlight the importance of observing multiple molecular species in multiple transitions to characterize the physical and chemical environment of young disks., Comment: 27 pages, 16 figures, 2 tables, 10 pages appendix with 12 figures. Accepted for publication in ApJ as one of the first-look papers of the eDisk ALMA Large Program

We present an overview of the Large Program, ``Early Planet Formation in Embedded Disks (eDisk)'', conducted with the Atacama Large Millimeter/submillimeter Array (ALMA). The ubiquitous detections of substructures, particularly rings and gaps, in protoplanetary disks around T Tauri stars raise the possibility that at least some planet formation may have already started during the embedded stages of star formation. In order to address exactly how and when planet formation is initiated, the program focuses on searching for substructures in disks around 12 Class 0 and 7 Class I protostars in nearby ($< $200 pc) star-forming regions through 1.3 mm continuum observations at a resolution of $\sim7$ au (0.04"). The initial results show that the continuum emission, mostly arising from dust disks around the sample protostars, has relatively few distinctive substructures, such as rings and spirals, in marked contrast to Class II disks. The dramatic difference may suggest that substructures quickly develop in disks when the systems evolve from protostars to Class II sources or alternatively that high optical depth of the continuum emission could obscure internal structures. Kinematic information obtained through CO isotopologue lines and other lines reveals the presence of Keplerian disks around protostars, providing us with crucial physical parameters, in particular, the dynamical mass of the central protostars. We describe the background of the eDisk program, the sample selection and their ALMA observations, the data reduction, and also highlight representative first-look results., Comment: This is a publication of a series of eDisk ALMA large program first-look papers

We present the discovery and validation of two TESS exoplanets orbiting nearby M dwarfs: TOI-2084b, and TOI-4184b. We characterized the host stars by combining spectra from Shane/Kast and Magellan/FIRE, SED (Spectral Energy Distribution) analysis, and stellar evolutionary models. In addition, we used Gemini-South/Zorro & -North/Alopeke high-resolution imaging, archival science images, and statistical validation packages to support the planetary interpretation. We performed a global analysis of multi-colour photometric data from TESS and ground-based facilities in order to derive the stellar and planetary physical parameters for each system. We find that TOI-2084b and TOI-4184b are sub-Neptune-sized planets with radii of Rp = 2.47 +/- 0.13R_Earth and Rp = 2.43 +/- 0.21R_Earth, respectively. TOI-2084b completes an orbit around its host star every 6.08 days, has an equilibrium temperature of T_eq = 527 +/- 8K and an irradiation of S_p = 12.8 +/- 0.8 S_Earth. Its host star is a dwarf of spectral M2.0 +/- 0.5 at a distance of 114pc with an effective temperature of T_eff = 3550 +/- 50 K, and has a wide, co-moving M8 companion at a projected separation of 1400 au. TOI-4184b orbits around an M5.0 +/- 0.5 type dwarf star (Kmag = 11.87) each 4.9 days, and has an equilibrium temperature of T_eq = 412 +/- 8 K and an irradiation of S_p = 4.8 +/- 0.4 S_Earth. TOI-4184 is a metal poor star ([Fe/H] = -0.27 +/- 0.09 dex) at a distance of 69 pc with an effective temperature of T_eff = 3225 +/- 75 K. Both planets are located at the edge of the sub-Jovian desert in the radius-period plane. The combination of the small size and the large infrared brightness of their host stars make these new planets promising targets for future atmospheric exploration with JWST., Comment: Accepted for publication in A&A

Previous observations of B335 have presented evidence of ongoing infall in various molecular lines, e.g., HCO$^+$, HCN, CO. There have been no confirmed observations of a rotationally supported disk on scales greater than ~12~au. The presence of an outflow in B335 suggests that also a disk should be present or in formation. To constrain the earliest stages of protostellar evolution and disk formation, we aim to map the region where gas falls inwards and observationally constrain its kinematics. Furthermore, we aim to put strong limits on the size and orientation of any disk-like structure in B335. We use high angular resolution $^{13}$CO data from ALMA, and combine it with shorter-baseline archival data to produce a high-fidelity image of the infall in B335. We also revisit the imaging of high-angular resolution Band 6 continuum data to study the dust distribution in the immediate vicinity of B335. Continuum emission shows an elliptical structure (10 by 7 au) with a position angle 5 degrees east of north, consistent with the expectation for a forming disk in B335. A map of the infall velocity (as estimated from the $^{13}$CO emission), shows evidence of asymmetric infall, predominantly from the north and south. Close to the protostar, infall velocities appear to exceed free-fall velocities. 3D radiative transfer models, where the infall velocity is allowed to vary within the infall region, can explain the observed kinematics. The data suggests that a disk has started to form in B335 and that gas is falling towards that disk. However, kinematically-resolved line data towards the disk itself is needed to confirm the presence of a rotationally supported disk around this young protostar. The measured high infall velocities are not easily reconcilable with a magnetic braking scenario and suggest that there is a pressure gradient that allows the infall velocity to vary in the region., Comment: 14 pages, 11 figures

Understanding the discrepancy between the radii of observed hot Jupiters and standard 'radiative-convective' models remains a hotly debated topic in the exoplanet community. One mechanism which has been proposed to bridge this gap, and which has recently come under scrutiny, is the vertical advection of potential temperature from the irradiated outer atmosphere deep into the interior, heating the deep, unirradiated, atmosphere, warming the internal adiabat, and resulting in radius inflation. Specifically, a recent study which explored the atmosphere of WASP-76b using a 3D, non-grey, GCM suggested that their models lacked radius inflation, and hence any vertical enthalpy advection. Here we perform additional analysis of these, and related, models, focusing on an explicit analysis of vertical enthalpy transport and the resulting heating of the deep atmosphere compared with 1D models. Our results indicate that, after any evolution linked with initialisation, all the WASP-76b models considered here exhibit significant vertical enthalpy transport, heating the deep atmosphere significantly when compared with standard 1D models. Furthermore, comparison of a long time-scale (and hence near steady-state) model with a Jupiter-like internal-structure model suggests not only strong radius-inflation, but also that the model radius, $1.98 \mathrm{R_{J}}$, may be comparable with observations ($1.83\pm0.06 \mathrm{R_{J}}$). We thus conclude that the vertical advection of potential temperature alone is enough to explain the radius inflation of WASP-76b, and potentially other irradiated gas giants, albeit with the proviso that the exact strength of the vertical advection remains sensitive to model parameters, such as the inclusion of deep atmospheric drag., Comment: Accepted for publication in MNRAS

Earth is deficient in carbon and nitrogen by up to ${\sim}4$ orders of magnitude compared with the Sun. Destruction of (carbon- and nitrogen-rich) refractory organics in the high-temperature planet forming regions could explain this deficiency. Assuming a refractory cometary composition for these grains, their destruction enhances nitrogen-containing oxygen-poor molecules in the hot gas ($\gtrsim 300$K) after the initial formation and sublimation of these molecules from oxygen-rich ices in the warm gas (${\sim}150$K). Using observations of $37$ high-mass protostars with ALMA, we find that oxygen-containing molecules (CH$_3$OH and HNCO) systematically show no enhancement in their hot component. In contrast, nitrogen-containing, oxygen-poor molecules (CH$_3$CN and C$_2$H$_3$CN) systematically show an enhancement of a factor ${\sim} 5$ in their hot component, pointing to additional production of these molecules in the hot gas. Assuming only thermal excitation conditions, we interpret these results as a signature of destruction of refractory organics, consistent with the cometary composition. This destruction implies a higher C/O and N/O in the hot gas than the warm gas, while, the exact values of these ratios depend on the fraction of grains that are effectively destroyed. This fraction can be found by future chemical models that constrain C/O and N/O from the abundances of minor carbon, nitrogen and oxygen carriers presented here., Comment: Accepted for publication in ApJ Letters

Outflows and winds launched from young stars play a crucial role in the evolution of protostars and the early stages of planet formation. However, the specific details of the mechanism behind these phenomena, including how they affect the protoplanetary disk structure, are still debated. We present {\it JWST} NIRSpec Integral Field Unit (IFU) observations of atomic and H$_2$ lines from 1 -- 5.1 $\mu$m toward the low-mass protostar TMC1A. For the first time, a collimated atomic jet is detected from TMC1A in the [Fe II] line at 1.644 $\mu$m along with corresponding extended H$_2$ 2.12 $\mu$m emission. Towards the protostar, we detected spectrally broad H I and He I emissions with velocities up to 300 km/s that can be explained by a combination of protostellar accretion and a wide-angle wind. The 2$\mu$m continuum dust emission, H I, He I, and O I all show emission from the illuminated outflow cavity wall and scattered line emission. These observations demonstrate the potential of {\it JWST} to characterize and reveal new information about the hot inner regions of nearby protostars. In this case, a previously undetected atomic wind and ionized jet in a well-known outflow., Comment: Accepted for publication on ApJL, 10 pages, 6 figures including appendix

Active learning parallelization is widely used, but typically relies on fixing the batch size throughout experimentation. This fixed approach is inefficient because of a dynamic trade-off between cost and speed -- larger batches are more costly, smaller batches lead to slower wall-clock run-times -- and the trade-off may change over the run (larger batches are often preferable earlier). To address this trade-off, we propose a novel Probabilistic Numerics framework that adaptively changes batch sizes. By framing batch selection as a quadrature task, our integration-error-aware algorithm facilitates the automatic tuning of batch sizes to meet predefined quadrature precision objectives, akin to how typical optimizers terminate based on convergence thresholds. This approach obviates the necessity for exhaustive searches across all potential batch sizes. We also extend this to scenarios with constrained active learning and constrained optimization, interpreting constraint violations as reductions in the precision requirement, to subsequently adapt batch construction. Through extensive experiments, we demonstrate that our approach significantly enhances learning efficiency and flexibility in diverse Bayesian batch active learning and Bayesian optimization applications., Comment: Accepted at AISTATS 2024. 33 pages, 6 figures

Many fairness criteria constrain the policy or choice of predictors. In this work, we propose a different framework for thinking about fairness: Instead of constraining the policy or choice of predictors, we consider which utility a policy is optimizing for. We define value of information fairness and propose to not use utilities that do not satisfy this criterion. We describe how to modify a utility to satisfy this fairness criterion and discuss the consequences this might have on the corresponding optimal policies., Comment: 20 pages

In this paper, we present a novel kinetic growth model for the micro-organism \textit{Methylococcus capsulatus} (Bath) that couples growth and pH. We apply growth kinetics in a model for single-cell protein production in a laboratory-scale continuous stirred tank reactor inspired by a physical laboratory fermentor. The model contains a set of differential algebraic equations describing growth and pH-dynamics in the system. We present a method of simulation that ensures non-negativity in the state and algebraic variables. Additionally, we introduce linear scaling of the algebraic equations and variables for numerical stability in Newton's method. Finally, we conduct a numerical experiment of economic optimal control for single-cell protein production in the laboratory-scale reactor. The numerical experiment shows non-trivial input profiles for biomass growth and pH tracking., Comment: 6 pages, 4 figures, 1 table, submitted to be presented at a conference

Model evaluation is a crucial step in SEM, consisting of two broad areas: global and local fit, where local fit indices are use to modify the original model. In the modification process, the modification index (MI) and the standardized expected parameter change (SEPC) are used to select the parameters that can be added to improve the fit. The purpose of this study is to extend the application of MI and SEPC to Bayesian SEM. We present how researchers can estimate posterior distributions of MI and SEPC using a posterior predictive model check (PPMC). We evaluated the effectiveness of these PPMCs with a simulation and found that MI can be used to detect the most relevant added parameters and that SEPC can be used as an effect size. Similar to maximum-likelihood estimation, the SEPC can overestimate the population value. Lastly, we present an example application of these indices. [This paper was published in "Structural Equation Modeling: A Multidisciplinary Journal."]

Inverse problems, particularly those governed by Partial Differential Equations (PDEs), are prevalent in various scientific and engineering applications, and uncertainty quantification (UQ) of solutions to these problems is essential for informed decision-making. This second part of a two-paper series builds upon the foundation set by the first part, which introduced CUQIpy, a Python software package for computational UQ in inverse problems using a Bayesian framework. In this paper, we extend CUQIpy's capabilities to solve PDE-based Bayesian inverse problems through a general framework that allows the integration of PDEs in CUQIpy, whether expressed natively or using third-party libraries such as FEniCS. CUQIpy offers concise syntax that closely matches mathematical expressions, streamlining the modeling process and enhancing the user experience. The versatility and applicability of CUQIpy to PDE-based Bayesian inverse problems are demonstrated on examples covering parabolic, elliptic and hyperbolic PDEs. This includes problems involving the heat and Poisson equations and application case studies in electrical impedance tomography and photo-acoustic tomography, showcasing the software's efficiency, consistency, and intuitive interface. This comprehensive approach to UQ in PDE-based inverse problems provides accessibility for non-experts and advanced features for experts., Comment: 38 pages, 12 figures

This paper introduces CUQIpy, a versatile open-source Python package for computational uncertainty quantification (UQ) in inverse problems, presented as Part I of a two-part series. CUQIpy employs a Bayesian framework, integrating prior knowledge with observed data to produce posterior probability distributions that characterize the uncertainty in computed solutions to inverse problems. The package offers a high-level modeling framework with concise syntax, allowing users to easily specify their inverse problems, prior information, and statistical assumptions. CUQIpy supports a range of efficient sampling strategies and is designed to handle large-scale problems. Notably, the automatic sampler selection feature analyzes the problem structure and chooses a suitable sampler without user intervention, streamlining the process. With a selection of probability distributions, test problems, computational methods, and visualization tools, CUQIpy serves as a powerful, flexible, and adaptable tool for UQ in a wide selection of inverse problems. Part II of the series focuses on the use of CUQIpy for UQ in inverse problems with partial differential equations (PDEs)., Comment: 37 pages, 11 figures

This paper presents a merged collection of entity and coreference annotated data grounded in the Universal Dependencies (UD) treebanks for the two written forms of Norwegian: Bokm{\aa}l and Nynorsk. The aligned and converted corpora are the Norwegian Named Entities (NorNE) and Norwegian Anaphora Resolution Corpus (NARC). While NorNE is aligned with an older version of the treebank, NARC is misaligned and requires extensive transformation from the original annotations to the UD structure and CoNLL-U format. We here demonstrate the conversion and alignment processes, along with an analysis of discovered issues and errors in the data - some of which include data split overlaps in the original treebank. These procedures and the developed system may prove helpful for future corpus alignment and coreference annotation endeavors. The merged corpora comprise the first Norwegian UD treebank enriched with named entities and coreference information., Comment: 4 pages, 1 table. Appendix: 3 tables and 5 data examples

Motivated by applications, we consider here new operator theoretic approaches to Conditional mean embeddings (CME). Our present results combine a spectral analysis-based optimization scheme with the use of kernels, stochastic processes, and constructive learning algorithms. For initially given non-linear data, we consider optimization-based feature selections. This entails the use of convex sets of positive definite (p.d.) kernels in a construction of optimal feature selection via regression algorithms from learning models. Thus, with initial inputs of training data (for a suitable learning algorithm,) each choice of p.d. kernel $K$ in turn yields a variety of Hilbert spaces and realizations of features. A novel idea here is that we shall allow an optimization over selected sets of kernels $K$ from a convex set $C$ of positive definite kernels $K$. Hence our \textquotedblleft optimal\textquotedblright{} choices of feature representations will depend on a secondary optimization over p.d. kernels $K$ within a specified convex set $C$., Comment: 19 pages, 2 figures

tSNE and UMAP are popular dimensionality reduction algorithms due to their speed and interpretable low-dimensional embeddings. Despite their popularity, however, little work has been done to study their full span of differences. We theoretically and experimentally evaluate the space of parameters in both tSNE and UMAP and observe that a single one -- the normalization -- is responsible for switching between them. This, in turn, implies that a majority of the algorithmic differences can be toggled without affecting the embeddings. We discuss the implications this has on several theoretic claims behind UMAP, as well as how to reconcile them with existing tSNE interpretations. Based on our analysis, we provide a method (\ourmethod) that combines previously incompatible techniques from tSNE and UMAP and can replicate the results of either algorithm. This allows our method to incorporate further improvements, such as an acceleration that obtains either method's outputs faster than UMAP. We release improved versions of tSNE, UMAP, and \ourmethod that are fully plug-and-play with the traditional libraries at https://github.com/Andrew-Draganov/GiDR-DUN, Comment: arXiv admin note: substantial text overlap with arXiv:2206.09689

Inexpensive machine learning potentials are increasingly being used to speed up structural optimization and molecular dynamics simulations of materials by iteratively predicting and applying interatomic forces. In these settings, it is crucial to detect when predictions are unreliable to avoid wrong or misleading results. Here, we present a complete framework for training and recalibrating graph neural network ensemble models to produce accurate predictions of energy and forces with calibrated uncertainty estimates. The proposed method considers both epistemic and aleatoric uncertainty and the total uncertainties are recalibrated post hoc using a nonlinear scaling function to achieve good calibration on previously unseen data, without loss of predictive accuracy. The method is demonstrated and evaluated on two challenging, publicly available datasets, ANI-1x (Smith et al.) and Transition1x (Schreiner et al.), both containing diverse conformations far from equilibrium. A detailed analysis of the predictive performance and uncertainty calibration is provided. In all experiments, the proposed method achieved low prediction error and good uncertainty calibration, with predicted uncertainty correlating with expected error, on energy and forces. To the best of our knowledge, the method presented in this paper is the first to consider a complete framework for obtaining calibrated epistemic and aleatoric uncertainty predictions on both energy and forces in ML potentials.

The purpose of this paper is to present new classes of function systems as part of multiresolution analyses. Our approach is representation theoretic, and it makes use of generalized multiresolution function systems (MRSs). It further entails new ideas from measurable endomorphisms-dynamics. Our results yield applications that are not amenable to more traditional techniques used on metric spaces. As the main tool in our approach, we make precise new classes of generalized MRSs which arise directly from a dynamical theory approach to the study of surjective endomorphisms on measure spaces. In particular, we give the necessary and sufficient conditions for a family of functions to define generators of Cuntz relations. We find an explicit description of the set of generalized wavelet filters. Our results are motivated in part by analyses of sub-band filters in signal/image processing. But our paper goes further, and it applies to such wider contexts as measurable dynamical systems, and complex dynamics. A unifying theme in our results is a new analysis of endomorphisms in general measure space, and its connection to multi-resolutions, to representation theory, and generalized wavelet systems., Comment: 38 pages

We prepared a sample of oxirane doubly deuterated at one C atom and studied its rotational spectrum in the laboratory for the first time between 120~GHz and 1094~GHz. Accurate spectroscopic parameters up to eighth order were determined, and the calculated rest frequencies were used to identify $c$-CD$_2$CH$_2$O tentatively in the interstellar medium in the Atacama Large Millimeter/submillimeter Array Protostellar Interferometric Line Survey (PILS) of the Class 0 protostellar system IRAS 16293$-$2422. The $c$-CD$_2$CH$_2$O to $c$-C$_2$H$_4$O ratio was estimated to be $\sim$0.054 with $T_{\rm rot} = 125$ K. This value translates to a D-to-H ratio of $\sim$0.16 per H atom which is higher by a factor of 4.5 than the $\sim$0.036 per H atom obtained for $c$-C$_2$H$_3$DO. Such increase in the degree of deuteration referenced to one H atom in multiply deuterated isotopologs compared to their singly deuterated variants have been observed commonly in recent years., Comment: Journal of Molecular Spectroscopy, in press; Per Jensen special issue. 12 pages here

The societal impact of pre-trained language models has prompted researchers to probe them for strong associations between protected attributes and value-loaded terms, from slur to prestigious job titles. Such work is said to probe models for bias or fairness-or such probes 'into representational biases' are said to be 'motivated by fairness'-suggesting an intimate connection between bias and fairness. We provide conceptual clarity by distinguishing between association biases (Caliskan et al., 2022) and empirical fairness (Shen et al., 2022) and show the two can be independent. Our main contribution, however, is showing why this should not come as a surprise. To this end, we first provide a thought experiment, showing how association bias and empirical fairness can be completely orthogonal. Next, we provide empirical evidence that there is no correlation between bias metrics and fairness metrics across the most widely used language models. Finally, we survey the sociological and psychological literature and show how this literature provides ample support for expecting these metrics to be uncorrelated., Comment: To be published in ACM FAccT 23

Magnetic interfaces and the phenomena arising from them drive both the design of modern spintronics and fundamental research. Recently, it was revealed that through designing magnetic frustration in configurationally complex entropy stabilized oxides, exchange bias can occur in structurally single crystal films. This eliminates the need for complex heterostructures and nanocomposites in the design and control of magnetic response phenomena. In this work, we demonstrate through hole doping of a high entropy perovskite oxide that tuning of magnetic responses can be achieved. With detailed magnetometry, we show magnetic coupling exhibiting a variety of magnetic responses including exchange bias and antiferromagnetic spin reversal in the entropy stabilized ABO3 perovskite oxide La1-xSrx(Cr0.2Mn0.2Fe0.2Co0.2Ni0.2)O3 family. We find that manipulation of the A-site charge state can be used to balance magnetic phase compositions and coupling responses. This allows for the creation of highly tunable exchange bias responses. In the low Sr doping regime, a spin frustrated region arising at the antiferromagnetic phase boundary is shown to directly couple to the antiferromagnetic moments of the film and emerges as the dominant mechanism, leading to a vertical shift of magnetization loops in response to field biasing. At higher concentrations, direct coupling of antiferromagnetic and ferromagnetic regions is observed. This tunability of magnetic coupling is discussed within the context of these three competing magnetic phases, revealing critical features in designing exchange bias through exploiting spin frustration and disorder in high entropy oxides.

Ensembling can improve the performance of Neural Networks, but existing approaches struggle when the architecture likelihood surface has dispersed, narrow peaks. Furthermore, existing methods construct equally weighted ensembles, and this is likely to be vulnerable to the failure modes of the weaker architectures. By viewing ensembling as approximately marginalising over architectures we construct ensembles using the tools of Bayesian Quadrature -- tools which are well suited to the exploration of likelihood surfaces with dispersed, narrow peaks. Additionally, the resulting ensembles consist of architectures weighted commensurate with their performance. We show empirically -- in terms of test likelihood, accuracy, and expected calibration error -- that our method outperforms state-of-the-art baselines, and verify via ablation studies that its components do so independently.

In applied Bayesian inference scenarios, users may have access to a large number of pre-existing model evaluations, for example from maximum-a-posteriori (MAP) optimization runs. However, traditional approximate inference techniques make little to no use of this available information. We propose the framework of post-process Bayesian inference as a means to obtain a quick posterior approximation from existing target density evaluations, with no further model calls. Within this framework, we introduce Variational Sparse Bayesian Quadrature (VSBQ), a method for post-process approximate inference for models with black-box and potentially noisy likelihoods. VSBQ reuses existing target density evaluations to build a sparse Gaussian process (GP) surrogate model of the log posterior density function. Subsequently, we leverage sparse-GP Bayesian quadrature combined with variational inference to achieve fast approximate posterior inference over the surrogate. We validate our method on challenging synthetic scenarios and real-world applications from computational neuroscience. The experiments show that VSBQ builds high-quality posterior approximations by post-processing existing optimization traces, with no further model evaluations.

Data assimilation (DA) provides a general framework for estimation in dynamical systems based on the concepts of Bayesian inference. This constitutes a common basis for the different linear and nonlinear filtering and smoothing techniques which gives a better understanding of the characteristics and limitations of each approach. In this study, four nonlinear filters for systems governed by stochastic continuous dynamics with discrete measurements are inferred as different approximate solutions to the Fokker-Planck equation in the prediction step of the Bayesian update. The characteristics and drawbacks of each filtering approach are discussed in light of the introduced approximations to the original Bayesian problem in each case. The introduced continuous-discrete (CD) filters are then implemented to solve the combined estimation problem of the state and parameter variables in a nonlinear system described by a stochastic differential equation (SDE), namely, the continuous stirred-tank reactor (CSTR). The performance measures for each filter, such as estimation errors, computational cost, and the ability to quantify the correct uncertainty, are compared and investigated with attribution to the assumed approximations introduced in the derivation of each class of filters.

The Double Asteroid Redirection Test (DART) spacecraft successfully performed the first test of a kinetic impactor for asteroid deflection by impacting Dimorphos, the secondary of near-Earth binary asteroid (65803) Didymos, and changing the orbital period of Dimorphos. A change in orbital period of approximately 7 minutes was expected if the incident momentum from the DART spacecraft was directly transferred to the asteroid target in a perfectly inelastic collision, but studies of the probable impact conditions and asteroid properties indicated that a considerable momentum enhancement ($\beta$) was possible. In the years prior to impact, we used lightcurve observations to accurately determine the pre-impact orbit parameters of Dimorphos with respect to Didymos. Here we report the change in the orbital period of Dimorphos as a result of the DART kinetic impact to be -33.0 +/- 1.0 (3$\sigma$) minutes. Using new Earth-based lightcurve and radar observations, two independent approaches determined identical values for the change in the orbital period. This large orbit period change suggests that ejecta contributed a significant amount of momentum to the asteroid beyond what the DART spacecraft carried., Comment: Accepted by Nature

Cyber-physical systems (CPSs) for real-time advanced process control (RT-APC) are a class of control systems using network communication to control industrial processes. In this paper, we use simple examples to describe the software principles and concepts used in the implementation of such systems. The key software principles are 1) shared data in the form of a database, files, or shared memory, 2) timers and threads for concurrent periodic execution of tasks, and 3) network communication between the control system and the process, and communication between the control system and the internet, e.g., the cloud to enable remote monitoring and commands. We show how to implement such systems for Linux operating systems applying the C programming language and we also comment on the implementation using the Python programming language. Finally, we present a complete simulation experiment using a real-time simulator., Comment: 6 pages, 6 figures, 6 listings. Accepted for European Control Conference 2023 (ECC2023). Bucharest, Romania

This paper presents a dynamic optimization numerical case study for Monoclonal Antibody (mAb) production. The fermentation is conducted in a continuous perfusion reactor. We represent the existing model in terms of a general modeling methodology well-suited for simulation and optimization. The model consists of six ordinary differential equations (ODEs) for the non-constant volume and the five components in the reactor. We extend the model with a glucose inhibition term to make the model feasible for optimization case studies. We formulate an optimization problem in terms of an optimal control problem (OCP) and consider four different setups for optimization. Compared to the base case, the optimal operation of the perfusion reactor increases the mAb yield with 44% when samples are taken from the reactor and with 52% without sampling. Additionally, our results show that multiple optimal feeding trajectories exist and that full glucose utilization can be forced without loss of mAb formation., Comment: 6 pages, 5 figures, 4 tables. Accepted for IFAC World Congress 2023

In this paper, the fractal calculus of fractal sets and fractal curves are compared. The analogues of the Riemann-Liouville and the Caputo integrals and derivatives are defined for the fractal curves which are non-local derivatives. The analogous for the fractional Laplace concepts are defined to solve fractal non-local differential equations on fractal curves. The fractal local Mellin and fractal non-local transforms are defined to solve fractal differential equations. We present tables and examples to illustrate the results.

In this manuscript, fractal and fuzzy calculus are summarized. Fuzzy calculus in terms of fractal limit, continuity, its derivative, and integral are formulated. The fractal fuzzy calculus is a new framework that includes fractal fuzzy derivatives and fractal fuzzy integral. In this framework, fuzzy number-valued functions with fractal support are the solutions of fractal fuzzy differential equations. Different kinds of fractal fuzzy differential equations are given and solved.

Methanol is the most complex molecule securely identified in interstellar ices and is a key chemical species for understanding chemical complexity in astrophysical environments. Important aspects of the methanol ice photochemistry are still unclear such as the branching ratios and photo-dissociation cross-sections at different temperatures and irradiation fluxes. This work aims at a quantitative agreement between laboratory experiments and astrochemical modelling of the CH3OH ice UV photolysis. This work also allows us to better understand which processes govern the methanol ice photochemistry present in laboratory experiments. We use ProDiMo to simulate the conditions of laboratory measurements. The simulations start with simple chemistry consisting only of methanol ice and helium to mimic the residual gas in the experimental chamber. A surface chemical network enlarged by photo-dissociation reactions is used to study the chemical reactions within the ice. Additionally, different surface chemistry parameters (surface competition, tunnelling, thermal diffusion and reactive desorption) are adopted to check those that reproduce the experimental results. The chemical models with ProDiMo can reproduce the methanol ice destruction via UV photodissociation at temperatures of 20, 30, 50 and 70 K as observed in the experiments. We note that the results are sensitive to different branching ratios after photolysis and to the mechanisms of reactive desorption. In the simulations of a molecular cloud at 20 K, we observed an increase in the methanol gas abundance of one order of magnitude, with a similar decrease in the solid-phase abundance. Comprehensive astrochemical models provide new insights into laboratory experiments as the quantitative understanding of the processes that govern the reactions within the ice. Ultimately, those insights can help to better interpret astronomical observations., Comment: Accepted for publication in A&A on 08-Feb-2023

Up to date, only 6 imines have been detected in the interstellar medium. The 3-carbon imine, 2-propanimine ((CH$_3$)$_2$C=NH), is predicted to be the structural isomer with the lowest energy in the C$_3$H$_7$N group, and appears to be a good candidate for astronomical searches. Unexpectedly, no microwave or millimeter wave spectrum is available for 2-propanimine. In this work, we provide the first high resolution millimeter wave spectrum of 2-propanimine and its analysis. With the guide of this laboratory measurement, we aim to search for 2-propanimine in two molecule-rich sources Sgr B2(N) and IRAS 16293-2422 using observations from the Atacama Large Millimeter/submillimeter Array (ALMA). Starting from a synthesized sample, we measured the spectrum of 2-propanimine from 50 to 500 GHz, and the ground state lines are successfully assigned and fitted using XIAM and ERHAM programs with the aid of theoretical calculations. The barriers to internal rotation of the two CH$_3$ tops are determined to be 531.956(64) cm$^{-1}$ and 465.013(26) cm$^{-1}$. These data are able to provide reliable prediction of transition frequencies for astronomical search. Although a few line matches exist, no confirmed detection of 2-propanimine has been found in the hot molecular core Sgr B2(N1S) and the Class 0 protostar IRAS 16293B. Upper-limits of its column density have been derived, and indicate that 2-propanimine is at least 18 times less abundant than methanimine in Sgr B2(N1S), and is at most 50-83 % of methanimine in IRAS 16293B., Comment: 14 pages, 10 figures