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Molecular HIV Surveillance (MHS) has been described as key to enabling rapid responses to HIV outbreaks. It operates by linking individuals with genetically similar viral sequences, which forms a network. A major limitation of MHS is that it depends on sequence collection, which very rarely covers the entire population of interest. Ignoring missing data by conducting complete case analysis--which assumes that the observed network is complete--has been shown to result in significantly biased estimates of network properties. We use MHS to investigate disease dynamics of the HIV epidemic in Miami-Dade County (MDC) among men who have sex with men (MSM)--only 30.1% have a reported sequence. To do so, we present an approach for making Bayesian inferences on partially observed networks. Through a simulation study, we demonstrate a reduction in error of 43%-63% between our estimates and complete case analyses. We estimate increased mixing between MSM communities in MDC, defined by race and transmission risk compared to the results based on complete case analysis. Our approach makes use of a flexible network model--congruence class model--to overcome the high computational burden of previously reported Bayesian approaches to estimate network properties from partially observed networks., Comment: 19 pages; 6 figures; 2 tables

Parkinson's disease (PD) is a common neurodegenerative disorder with a poorly understood physiopathology and no established biomarkers for the diagnosis of early stages and for prediction of disease progression. Several neuroimaging biomarkers have been studied recently, but these are susceptible to several sources of variability. In this context, an evaluation of the robustness of such biomarkers is essential. This study is part of a larger project investigating the replicability of potential neuroimaging biomarkers of PD. Here, we attempt to reproduce (same data, same method) and replicate (different data or method) the models described in Nguyen et al., 2021 to predict individual's PD current state and progression using demographic, clinical and neuroimaging features (fALFF and ReHo extracted from resting-state fMRI). We use the Parkinson's Progression Markers Initiative dataset (PPMI, ppmi-info.org), as in Nguyen et al.,2021 and aim to reproduce the original cohort, imaging features and machine learning models as closely as possible using the information available in the paper and the code. We also investigated methodological variations in cohort selection, feature extraction pipelines and sets of input features. The success of the reproduction was assessed using different criteria. Notably, we obtained significantly better than chance performance using the analysis pipeline closest to that in the original study (R2 > 0), which is consistent with its findings. The challenges encountered while reproducing and replicating the original work are likely explained by the complexity of neuroimaging studies, in particular in clinical settings. We provide recommendations to further facilitate the reproducibility of such studies in the future.

Motivated by flat space holography, we demonstrate that massive spin-$s$ fields in Minkowski space near timelike infinity are massive carrollian fields on the carrollian counterpart of anti-de Sitter space called $\mathsf{Ti}$. Its isometries form the Poincar\'e group, and we construct the carrollian spin-$s$ fields using the method of induced representations. We provide a dictionary between massive carrollian fields on $\mathsf{Ti}$ and massive fields in Minkowski space, as well as to fields in the conformal primary basis used in celestial holography. We show that the symmetries of the carrollian structure naturally account for the BMS charges underlying the soft graviton theorem. Finally, we initiate a discussion of the correspondence between massive scattering amplitudes and carrollian correlation functions on $\mathsf{Ti}$, and introduce physical definitions of detector operators using a suitable notion of conserved carrollian energy-momentum tensor., Comment: 37 pages, 4 figures; v2: added comments, matches published version

The theory of particle scattering is concerned with transition amplitudes between states that belong to unitary representations of the Poincar\'e group. The latter acts as the isometry group of Minkowski spacetime $\mathbb{M}$, making natural the introduction of relativistic tensor fields encoding the particles of interest. Since the Poincar\'e group also acts as a group of conformal isometries of null infinity $\mathcal{I}$, massless particles can also be very naturally encoded into Carrollian conformal fields living on $\mathcal{I}$. In this work we classify the two- and three-point correlation functions such Carrollian conformal fields can have in any consistent quantum theory of massless particles and arbitrary dimension. We then show that bulk correlators of massless fields in $\mathbb{M}$ explicitly reduce to these Carrollian conformal correlators when evaluated on $\mathcal{I}$, although in the case of time-ordered bulk correlators this procedure appears singular at first sight. However we show that the Carrollian correlators of the descendant fields are perfectly regular and precisely carry the information about the corresponding S-matrix elements., Comment: 25 pages + appendices, v2: improved referencing

Soft graviton theorems receive one-loop contributions that are logarithmic in the energy of the soft graviton, and which are closely related to tails of gravitational waveforms. We demonstrate that these logarithmic corrections are encoded in the Ward identity of superrotation symmetries, i.e. they follow from conservation of superrotation charge across spatial infinity $i^0$. Our proof relies on a careful analysis of the radiative phase space admitting such gravitational tails, and the determination of the fluxes through null infinity $\mathscr I$ that act as canonical generators of superrotations on both gravitational and matter fields. All logarithmic terms are derived from the fluxes through correlations of the supertranslation Goldstone mode, provided care is taken in manipulating gravitationally interacting (i.e. dressed) rather than free fields. In cases where massive particles take part in the scattering process, logarithmic corrections also partly arise from the superrotation charge generator at timelike infinity $i^\pm$., Comment: 15 pages

The traditional display of elements in the periodic table is convenient for the study of chemistry and physics. However, the atomic number alone is insufficient for training statistical machine learning models to describe and extract composition-structure-property relationships. Here, we assess the similarity and correlations contained within high-dimensional local and distributed representations of the chemical elements, as implemented in an open-source Python package ElementEmbeddings. These include element vectors of up to 200 dimensions derived from known physical properties, crystal structure analysis, natural language processing, and deep learning models. A range of distance measures are compared and a clustering of elements into familiar groups is found using dimensionality reduction techniques. The cosine similarity is used to assess the utility of these metrics for crystal structure prediction, showing that they can outperform the traditional radius ratio rules for the structural classification of AB binary solids., Comment: 7 pages, 8 figures

The null conformal boundary $\mathscr{I}$ of Minkowski spacetime $\mathbb{M}$ plays a special role in scattering theory, as it is the locus where massless particle states are most naturally defined. We construct quantum fields on $\mathscr{I}$ which create these massless states from the vacuum and transform covariantly under Poincar\'e symmetries. Since the latter symmetries act as Carrollian conformal isometries of $\mathscr{I}$, these quantum fields are Carrollian conformal fields. This group theoretic construction is intrinsic to $\mathscr{I}$ by contrast to existing treatments in the literature. However we also show that the standard relativistic massless quantum fields in $\mathbb{M}$, when pulled back to $\mathscr{I}$, provide a realisation of these Carrollian conformal fields. This correspondence between bulk and boundary fields should constitute a basic entry in the dictionary of flat holography. Finally we show that $\mathscr{I}$ provides a natural parametrisation of the massless particles as described by irreducible representations of the Poincar\'e group, and that in an appropriate conjugate basis they indeed transform like Carrollian conformal fields., Comment: 21 pages + appendix; v2: additional references and comments; v3: published version

In this review article, we revisit the connection between dressing of scattering states in quantum electrodynamics by clouds of soft photons, and their dressing by (generalised) Wilson line operators. In particular, we show that the leading and subleading soft conformal dressings considered in the context of celestial holography can be straightforwardly obtained from generalised Wilson lines, and that this only requires knowledge of the asymptotic behaviour of the photon field near null and timelike infinity., Comment: 14 pages + appendices

An effective theory designed to compute Virasoro identity blocks at large central charge, expressed in terms of the propagation of a reparametrization/shadow mode between bilocal vertices, was recently put forward. In this paper I provide the formal theoretical framework underlying this effective theory by reformulating it in terms of standard concepts : conformal geometry, generating functionals and Feynman diagrams. A key ingredient to this formalism is the bilocal vertex operator, or reparametrized two-point function, which is shown to generate arbitrary stress tensor insertions into a two-point function of reference. I also suggest an extension of the formalism designed to compute generic Virasoro blocks., Comment: 16 pages. v2: comments added, corrected typos

This work demonstrates the ability to produce readily interpretable statistical metrics for model fit, fixed effects covariance coefficients, and prediction confidence. Importantly, this work compares 4 suitable and commonly applied epistemic UQ approaches, BNN, SWAG, MC dropout, and ensemble approaches in their ability to calculate these statistical metrics for the ARMED MEDL models. In our experiment for AD prognosis, not only do the UQ methods provide these benefits, but several UQ methods maintain the high performance of the original ARMED method, some even provide a modest (but not statistically significant) performance improvement. The ensemble models, especially the ensemble method with a 90% subsampling, performed well across all metrics we tested with (1) high performance that was comparable to the non-UQ ARMED model, (2) properly deweights the confounds probes and assigns them statistically insignificant p-values, (3) attains relatively high calibration of the output prediction confidence. Based on the results, the ensemble approaches, especially with a subsampling of 90%, provided the best all-round performance for prediction and uncertainty estimation, and achieved our goals to provide statistical significance for model fit, statistical significance covariate coefficients, and confidence in prediction, while maintaining the baseline performance of MEDL using ARMED

The constrained Hamiltonian analysis of geometric actions is worked out before applying the construction to the extended Bondi-Metzner-Sachs group in four dimensions. For any Hamiltonian associated with an extended BMS$_4$ generator, this action provides a field theory in two plus one spacetime dimensions whose Poisson bracket algebra of Noether charges realizes the extended BMS$_4$ Lie algebra. The Poisson structure of the model includes the classical version of the operator product expansions that have appeared in the context of celestial holography. Furthermore, the model reproduces the evolution equations of non-radiative asymptotically flat spacetimes at null infinity., Comment: 25 pages Latex file

We present a unified treatment of the conserved asymptotic charges associated with any bosonic massless particle in any spacetime dimension. In particular we provide master formulae for the asymptotic charges and the central extensions in the corresponding charge algebras. These formulae can be explicitly evaluated for any given theory. For illustration we apply them to electromagnetism and gravity, thereby recovering earlier results., Comment: 9 pages, References added and commented on

We compute the conserved charges associated with the asymptotic symmetries of massless particles by examining their free theory in Minkowski spacetime. We give a procedure to systematically deduce the fall off of the massless fields at spatial infinity and show that it has a universal behaviour when expressed in tangent space. We do this for generic massless particles. We do not impose gauge fixing conditions which allows us to uncover new nonzero charges for the graviton beyond the well-known supertranslation charges. We also compute conserved charges in the dual formulations of certain low spin particles and argue that this leads to an infinite number of new conserved charges., Comment: 25 pages. In this new version we added an acknowledgement, namely The work of KN is supported by the ERC Consolidator Grant N. 681908, Quantum black holes: A microscopic window into the microstructure of gravity

Parkinsons disease (PD) is a movement disorder and the second most common neurodengerative disease but despite its relative abundance, there are no clinically accepted neuroimaging biomarkers to make prognostic predictions or differentiate between the similar atypical neurodegenerative diseases Multiple System Atrophy and Progressive Supranuclear Palsy. Abnormal connectivity in circuits including the motor circuit and basal ganglia have been previously shown as early markers of neurodegeneration. Therefore, we postulate the combination patterns of interregional dysconnectivity across the brain can be used to form a patient-specific predictive model of disease state and progression in PD. These models, which employ connectivity calculated from noninvasively measured functional MRI, differentially predict between PD and the atypical lookalikes, predict progression on a disease-specific scale, and predict cognitive decline. Further, we identify the connections most informative for progression and diagnosis. When predicting the one-year progression in the Movement Disorder Society-sponsored revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and Montreal Cognitive assessment (MoCA), mean absolute errors of 1.8 and 0.6 basis points in the prediction are achieved respectively. A balanced accuracy of 0.68 is attained when distinguishing idiopathic PD versus the lookalikes and healthy controls. We additionally find network components strongly associated with the prognostic and diagnostic tasks, particularly incorporating connections within deep nuclei, motor regions, and the Thalamus. These predictions, using an MRI modality readily available in most clinical settings, demonstrate the strong potential of fMRI connectivity as a prognostic biomarker in Parkinsons disease.

We demonstrate that the one-loop exact subleading soft graviton theorem automatically follows from conservation of the BMS charges, provided that the hard and soft fluxes separately represent the extended BMS algebra at null infinity. This confirms that superrotations are genuine symmetries of the gravitational $\mathcal{S}$-matrix beyond the semiclassical regime. In contrast with a previous proposal, the celestial stress-tensor accounting for the one-loop corrections follows from the gravitational phase space analysis and does not require the addition of divergent counterterms. In addition, we show that the symplectic form on the radiative phase space factorises into hard and soft sectors, and that the resulting canonical generators precisely coincide with the correct BMS fluxes., Comment: 20 pages + appendices; v2: added comments; v3: added funding acknowledgment

We derive the antipodal matching relations used to demonstrate the equivalence between soft graviton theorems and BMS charge conservation across spatial infinity. To this end we provide a precise map between Bondi data at null infinity $\mathscr{I}$ and Beig-Schmidt data at spatial infinity $i^0$ in a context appropriate to the gravitational scattering problem and celestial holography. In addition, we explicitly match the various proposals of BMS charges at $\mathscr{I}$ found in the literature with the conserved charges at $i^0$., Comment: 26 pages + appendices. v2: added references. v3: added references and comments. v4: corrected analysis for the antipodal matching of the angular momentum aspect, in agreement with recent observations made by Compere et al. in 2303.17124. v5: added funding acknowledgment

Natural science datasets frequently violate assumptions of independence. Samples may be clustered (e.g. by study site, subject, or experimental batch), leading to spurious associations, poor model fitting, and confounded analyses. While largely unaddressed in deep learning, this problem has been handled in the statistics community through mixed effects models, which separate cluster-invariant fixed effects from cluster-specific random effects. We propose a general-purpose framework for Adversarially-Regularized Mixed Effects Deep learning (ARMED) models through non-intrusive additions to existing neural networks: 1) an adversarial classifier constraining the original model to learn only cluster-invariant features, 2) a random effects subnetwork capturing cluster-specific features, and 3) an approach to apply random effects to clusters unseen during training. We apply ARMED to dense, convolutional, and autoencoder neural networks on 4 applications including simulated nonlinear data, dementia prognosis and diagnosis, and live-cell image analysis. Compared to prior techniques, ARMED models better distinguish confounded from true associations in simulations and learn more biologically plausible features in clinical applications. They can also quantify inter-cluster variance and visualize cluster effects in data. Finally, ARMED improves accuracy on data from clusters seen during training (up to 28% vs. conventional models) and generalization to unseen clusters (up to 9% vs. conventional models)., Comment: Added comparisons to other mixed effects methods. 13 pages, 6 figures, 5 tables

I describe the Schwarzian behavior of the gravitational field at null infinity under superrotations, to be understood as an \textit{unobservable} gauge artifact. To this end I review the induced geometry of null infinity and the construction of the gauge-invariant News tensor that characterizes gravitational radiation. I discuss potentially important implications for the celestial holography program, suggesting in particular that the uplift of the AdS$_3$/CFT$_2$ correspondence directly relates to the unobservable gauge sector., Comment: 17 pages + appendix

The generating functional of stress tensor correlation functions in two-dimensional conformal field theory is the nonlocal Polyakov action, or equivalently, the Liouville or Alekseev-Shatashvili action. I review its holographic derivation within the AdS$_3$/CFT$_2$ correspondence, both in metric and Chern-Simons formulations. I also provide a detailed comparison with the well-known Hamiltonian reduction of three-dimensional gravity to a flat Liouville theory, and conclude that the two results are unrelated. In particular, the flat Liouville action is still off-shell with respect to bulk equations of motion, and simply vanishes in case the latter are imposed. The present study also suggests an interesting re-interpretation of the computation of black hole spectral statistics recently performed by Cotler and Jensen as that of an explicit averaging of the partition function over the boundary source geometry, thereby providing potential justification for its agreement with the predictions of a random matrix ensemble., Comment: 24 pages + appendices, 1 figure. v2: corrected typos + new discussion of the variational principle where only the conformal class of boundary metrics is fixed. v3: matches the published version

Infrared divergences in perturbative gravitational scattering amplitudes have been recently argued to be governed by the two-point function of the supertranslation Goldstone mode on the celestial sphere. We show that the form of this celestial two-point function simply derives from an effective action that also controls infrared divergences in the symplectic structure of General Relativity with asymptotically flat boundary conditions. This effective action finds its natural place in a path integral formulation of a celestial conformal field theory, as we illustrate by re-deriving the infrared soft factors in terms of celestial correlators. Our analysis relies on a well-posed action principle close to spatial infinity introduced by Comp\`ere and Dehouck., Comment: 24 pages, one figure

We study the origin of the recently proposed effective theory of stress tensor exchanges based on reparametrization modes, that has been used to efficiently compute Virasoro identity blocks at large central charge. We first provide a derivation of the nonlinear Alekseev--Shatashvili action governing these reparametrization modes, and argue that it should be interpreted as the generating functional of stress tensor correlations on manifolds related to the plane by conformal transformations. In addition, we demonstrate that the rules previously prescribed with the reparametrization formalism for computing Virasoro identity blocks naturally emerge when evaluating Feynman diagrams associated with stress tensor exchanges between pairs of external primary operators. We make a few comments on the connection of these results to gravitational theories and holography., Comment: 18 pages, 2 figures. v3: matches published version

A dynamical resolution to the cosmological constant fine-tuning problem has been previously put forward, based on a scalar-tensor gravitational theory possessing de Sitter attractor solutions characterized by a small Hubble expansion rate, irrespective of an initially large vacuum energy. We show that a technically natural subregion of the parameter space yields a cosmological evolution through radiation- and matter-dominated eras that is essentially indistinguishable from that predicted by General Relativity. Similarly, the proposed model automatically satisfies the observational constraints on a fifth force mediated by the new scalar degree of freedom., Comment: 15 pages, 2 figures; v2: extended discussions, matches the published version

Out-of-time-order correlators (OTOCs) that capture maximally chaotic properties of a black hole are determined by scattering processes near the horizon. This prompts the question to what extent OTOCs display chaotic behaviour in horizonless microstate geometries. This question is complicated by the fact that Lyapunov growth of OTOCs requires nonzero temperature, whereas constructions of microstate geometries have been mostly restricted to extremal black holes. In this paper, we compute OTOCs for a class of extremal black holes, namely maximally rotating BTZ black holes, and show that on average they display "slow scrambling", characterized by cubic (rather than exponential) growth. Superposed on this average power-law growth is a sawtooth pattern, whose steep parts correspond to brief periods of Lyapunov growth associated to the nonzero temperature of the right-moving degrees of freedom in a dual conformal field theory. Next we study the extent to which these OTOCs are modified in certain "superstrata", horizonless microstate geometries corresponding to these black holes. Rather than an infinite throat ending on a horizon, these geometries have a very deep but finite throat ending in a cap. We find that the superstrata display the same slow scrambling as maximally rotating BTZ black holes, except that for large enough time intervals the growth of the OTOC is cut off by effects related to the cap region, some of which we evaluate explicitly., Comment: 47 pages, 9 figures. Added references and fixed typos, match published version

Starting from an analysis of four-dimensional asymptotically flat gravity in first order formulation, we show that superrotation reparametrization modes are governed by an Alekseev--Shatashvili action on the celestial sphere. This two-dimensional conformal theory describes spontaneous symmetry breaking of Virasoro superrotations together with the explicit symmetry breaking of more general Diff$(\mathcal{S}^2)$ superrotations. We arrive at this result by first reformulating the asymptotic field equations and symmetries of the radiative vacuum sector in terms of a Chern--Simons theory at null infinity, and subsequently performing a Hamiltonian reduction of this theory onto the celestial sphere., Comment: 40 pages; v2: clarified boundary conditions in section 4, references added; v3: match published version

Currently, the diagnosis of Autism Spectrum Disorder (ASD) is dependent upon a subjective, time-consuming evaluation of behavioral tests by an expert clinician. Non-invasive functional MRI (fMRI) characterizes brain connectivity and may be used to inform diagnoses and democratize medicine. However, successful construction of deep learning models from fMRI requires addressing key choices about the model's architecture, including the number of layers and number of neurons per layer. Meanwhile, deriving functional connectivity (FC) features from fMRI requires choosing an atlas with an appropriate level of granularity. Once a model has been built, it is vital to determine which features are predictive of ASD and if similar features are learned across atlas granularity levels. To identify aptly suited architectural configurations, probability distributions of the configurations of high versus low performing models are compared. To determine the effect of atlas granularity, connectivity features are derived from atlases with 3 levels of granularity and important features are ranked with permutation feature importance. Results show the highest performing models use between 2-4 hidden layers and 16-64 neurons per layer, granularity dependent. Connectivity features identified as important across all 3 atlas granularity levels include FC to the supplementary motor gyrus and language association cortex, regions associated with deficits in social and sensory processing in ASD. Importantly, the cerebellum, often not included in functional analyses, is also identified as a region whose abnormal connectivity is highly predictive of ASD. Results of this study identify important regions to include in future studies of ASD, help assist in the selection of network architectures, and help identify appropriate levels of granularity to facilitate the development of accurate diagnostic models of ASD., Comment: Presented at ISBI 2020

Parkinson's disease (PD) is a common neurological disorder characterized by gait impairment. PD has no cure, and an impediment to developing a treatment is the lack of any accepted method to predict disease progression rate. The primary aim of this study was to develop a model using clinical measures and biomechanical measures of gait and postural stability to predict an individual's PD progression over two years. Data from 160 PD subjects were utilized. Machine learning models, including XGBoost and Feed Forward Neural Networks, were developed using extensive model optimization and cross-validation. The highest performing model was a neural network that used a group of clinical measures, achieved a PPV of 71% in identifying fast progressors, and explained a large portion (37%) of the variance in an individual's progression rate on held-out test data. This demonstrates the potential to predict individual PD progression rate and enrich trials by analyzing clinical and biomechanical measures with machine learning., Comment: 5 pages, 4 figures, IEEE ICASSP conference submission