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Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly variable, and properly accounting for heterogeneity in evolutionary processes is crucial for more accurate phylogenetic inference. Nucleotide substitution rates and patterns are known to vary among sites in multiple sequence alignments, and such variation can be modeled by partitioning alignments into categories corresponding to different substitution models. Determining $\textit{a priori}$ appropriate partitions can be difficult, however, and better model fit can be achieved through flexible Bayesian infinite mixture models that simultaneously infer the number of partitions, the partition that each site belongs to, and the evolutionary parameters corresponding to each partition. Here, we consider several different types of infinite mixture models, including classic Dirichlet process mixtures, as well as novel approaches for modeling across-site evolutionary variation: hierarchical models for data with a natural group structure, and infinite hidden Markov models that account for spatial patterns in alignments. In analyses of several viral data sets, we find that different types of infinite mixture models emerge as the best choices in different scenarios. To enable these models to scale efficiently to large data sets, we adapt efficient Markov chain Monte Carlo algorithms and exploit opportunities for parallel computing. We implement this infinite mixture modeling framework in BEAST X, a widely-used software package for Bayesian phylogenetic inference.

The inherent volatility and dynamic fluctuations within the financial stock market underscore the necessity for investors to employ a comprehensive and reliable approach that integrates risk management strategies, market trends, and the movement trends of individual securities. By evaluating specific data, investors can make more informed decisions. However, the current body of literature lacks substantial evidence supporting the practical efficacy of reinforcement learning (RL) agents, as many models have only demonstrated success in back testing using historical data. This highlights the urgent need for a more advanced methodology capable of addressing these challenges. There is a significant disconnect in the effective utilization of financial indicators to better understand the potential market trends of individual securities. The disclosure of successful trading strategies is often restricted within financial markets, resulting in a scarcity of widely documented and published strategies leveraging RL. Furthermore, current research frequently overlooks the identification of financial indicators correlated with various market trends and their potential advantages. This research endeavors to address these complexities by enhancing the ability of RL agents to effectively differentiate between positive and negative buy/sell actions using financial indicators. While we do not address all concerns, this paper provides deeper insights and commentary on the utilization of technical indicators and their benefits within reinforcement learning. This work establishes a foundational framework for further exploration and investigation of more complex scenarios., Comment: 8 pages, 9 figures, 3 tables, accepted at ICAIF 2024 FM4TS Workshop

As the signatories of this manifesto, we denounce the attention economy as inhumane and a threat to our sociopolitical and ecological well-being. We endorse policymakers' efforts to address the negative consequences of the attention economy's technology, but add that these approaches are often limited in their criticism of the systemic context of human attention. Starting from Buddhist philosophy, we advocate a broader approach: an ecology of attending, that centers on conceptualizing, designing, and using attention (1) in an embedded way and (2) focused on the alleviating of suffering. With 'embedded' we mean that attention is not a neutral, isolated mechanism but a meaning-engendering part of an 'ecology' of bodily, sociotechnical and moral frameworks. With 'focused on the alleviation of suffering' we explicitly move away from the (often implicit) conception of attention as a tool for gratifying desires., Comment: 21 pages, 1 figure

According to CMB measurements, baryonic matter constitutes about $5\%$ of the mass-energy density of the universe. A significant population of these baryons, for a long time referred to as `missing', resides in a low density, warm-hot intergalactic medium (WHIM) outside galaxy clusters, tracing the ``cosmic web'', a network of large scale dark matter filaments. Various studies have detected this inter-cluster gas, both by stacking and by observing individual filaments in compact, massive systems. In this paper, we study short filaments (< 10 Mpc) connecting massive clusters ($M_{500} \approx 3\times 10^{14} M_{\odot}$) detected by the Atacama Cosmology Telescope (ACT) using the scattering of CMB light off the ionised gas, a phenomenon known as the thermal Sunyaev-Zeldovich (tSZ) effect. The first part of this work is a search for suitable candidates for high resolution follow-up tSZ observations. We identify four cluster pairs with an intercluster signal above the noise floor (S/N $>$ 2), including two with a tentative $>2\sigma$ statistical significance for an intercluster bridge from the ACT data alone. In the second part of this work, starting from the same cluster sample, we directly stack on ${\sim}100$ cluster pairs and observe an excess SZ signal between the stacked clusters of $y=(7.2^{+2.3}_{-2.5})\times 10^{-7}$ with a significance of $3.3\sigma$. It is the first tSZ measurement of hot gas between clusters in this range of masses at moderate redshift ($\langle z\rangle\approx 0.5$). We compare this to the signal from simulated cluster pairs with similar redshifts and separations in the THE300 and MAGNETICUM Pathfinder cosmological simulations and find broad consistency. Additionally, we show that our measurement is consistent with scaling relations between filament parameters and mass of the embedded halos identified in simulations., Comment: 37 pages, 17 images

Gravitational lensing magnification of Type Ia supernovae (SNe Ia) allows information to be obtained about the distribution of matter on small scales. In this paper, we derive limits on the fraction $\alpha$ of the total matter density in compact objects (which comprise stars, stellar remnants, small stellar groupings and primordial black holes) of mass $M > 0.03 M_{\odot}$ over cosmological distances. Using 1,532 SNe Ia from the Dark Energy Survey Year 5 sample (DES-SN5YR) combined with a Bayesian prior for the absolute magnitude $M$, we obtain $\alpha < 0.12$ at the 95\% confidence level after marginalisation over cosmological parameters, lensing due to large-scale structure, and intrinsic non-Gaussianity. Similar results are obtained using priors from the cosmic microwave background, baryon acoustic oscillations and galaxy weak lensing, indicating our results do not depend on the background cosmology. We argue our constraints are likely to be conservative (in the sense of the values we quote being higher than the truth), but discuss scenarios in which they could be weakened by systematics of the order of $\Delta \alpha \sim 0.04$, Comment: Accepted by MNRAS

SuperBIT was a 0.5-meter near-ultraviolet to near-infrared wide-field telescope that launched on a NASA superpressure balloon into the stratosphere from New Zealand for a 45-night flight. SuperBIT acquired multi-band images of galaxy clusters to study the properties of dark matter using weak gravitational lensing. We provide an overview of the instrument and its various subsystems. We then present the instrument performance from the flight, including the telescope and image stabilization system, the optical system, the power system, and the thermal system. SuperBIT successfully met the instrument's technical requirements, achieving a telescope pointing stability of 0.34 +/- 0.10 arcseconds, a focal plane image stability of 0.055 +/- 0.027 arcseconds, and a PSF FWHM of ~ 0.35 arcseconds over 5-minute exposures throughout the 45-night flight. The telescope achieved a near-diffraction limited point-spread function in all three science bands (u, b, and g). SuperBIT served as a pathfinder to the GigaBIT observatory, which will be a 1.34-meter near-ultraviolet to near-infrared balloon-borne telescope., Comment: 17 pages, 25 pages, published in the Astronomical Journal

The Super-pressure Balloon-borne Imaging Telescope (SuperBIT) is a near-diffraction-limited 0.5m telescope that launched via NASA's super-pressure balloon technology on April 16, 2023. SuperBIT achieved precise pointing control through the use of three nested frames in conjunction with an optical Fine Guidance System (FGS), resulting in an average image stability of 0.055" over 300-second exposures. The SuperBIT FGS includes a tip-tilt fast-steering mirror that corrects for jitter on a pair of focal plane star cameras. In this paper, we leverage the empirical data from SuperBIT's successful 45-night stratospheric mission to inform the FGS design for the next-generation balloon-borne telescope. The Gigapixel Balloon-borne Imaging Telescope (GigaBIT) is designed to be a 1.35m wide-field, high resolution imaging telescope, with specifications to extend the scale and capabilities beyond those of its predecessor SuperBIT. A description and analysis of the SuperBIT FGS will be presented along with methodologies for extrapolating this data to enhance GigaBIT's FGS design and fine pointing control algorithm. We employ a systems engineering approach to outline and formalize the design constraints and specifications for GigaBIT's FGS. GigaBIT, building on the SuperBIT legacy, is set to enhance high-resolution astronomical imaging, marking a significant advancement in the field of balloon-borne telescopes., Comment: 13 pages, 7 figures, SPIE Astronomical Telescopes + Instrumentation 2024

Terrestrial particle accelerators collide charged particles, then watch the trajectory of outgoing debris - but they cannot manipulate dark matter. Fortunately, dark matter is the main component of galaxy clusters, which are continuously pulled together by gravity. We show that galaxy cluster mergers can be exploited as enormous, natural dark matter colliders. We analyse hydrodynamical simulations of a universe containing self-interacting dark matter (SIDM) in which all particles interact via gravity, and dark matter particles can also scatter off each other via a massive mediator. During cluster collisions, SIDM spreads out and lags behind cluster member galaxies. Individual systems can have quirky dynamics that makes them difficult to interpret. Statistically, however, we find that the mean or median of dark matter's spatial offset in many collisions can be robustly modelled, and is independent of our viewing angle and halo mass even in collisions between unequal-mass systems. If the SIDM cross-section were sigma/m = 0.1cm^2/g = 0.18 barn/GeV, the 'bulleticity' lag would be ~5 percent that of gas due to ram pressure, and could be detected at 95 percent confidence in weak lensing observations of ~100 well-chosen clusters., Comment: 8 pages, 5 figures plus appendices. MNRAS in press

Automatic prostate segmentation is an important step in computer-aided diagnosis of prostate cancer and treatment planning. Existing methods of prostate segmentation are based on deep learning models which have a large size and lack of transparency which is essential for physicians. In this paper, a new data-driven 3D prostate segmentation method on MRI is proposed, named PSHop. Different from deep learning based methods, the core methodology of PSHop is a feed-forward encoder-decoder system based on successive subspace learning (SSL). It consists of two modules: 1) encoder: fine to coarse unsupervised representation learning with cascaded VoxelHop units, 2) decoder: coarse to fine segmentation prediction with voxel-wise classification and local refinement. Experiments are conducted on the publicly available ISBI-2013 dataset, as well as on a larger private one. Experimental analysis shows that our proposed PSHop is effective, robust and lightweight in the tasks of prostate gland and zonal segmentation, achieving a Dice Similarity Coefficient (DSC) of 0.873 for the gland segmentation task. PSHop achieves a competitive performance comparatively to other deep learning methods, while keeping the model size and inference complexity an order of magnitude smaller., Comment: 11 pages, 5 figures, 5 tables

Prostate Cancer is one of the most frequently occurring cancers in men, with a low survival rate if not early diagnosed. PI-RADS reading has a high false positive rate, thus increasing the diagnostic incurred costs and patient discomfort. Deep learning (DL) models achieve a high segmentation performance, although require a large model size and complexity. Also, DL models lack of feature interpretability and are perceived as ``black-boxes" in the medical field. PCa-RadHop pipeline is proposed in this work, aiming to provide a more transparent feature extraction process using a linear model. It adopts the recently introduced Green Learning (GL) paradigm, which offers a small model size and low complexity. PCa-RadHop consists of two stages: Stage-1 extracts data-driven radiomics features from the bi-parametric Magnetic Resonance Imaging (bp-MRI) input and predicts an initial heatmap. To reduce the false positive rate, a subsequent stage-2 is introduced to refine the predictions by including more contextual information and radiomics features from each already detected Region of Interest (ROI). Experiments on the largest publicly available dataset, PI-CAI, show a competitive performance standing of the proposed method among other deep DL models, achieving an area under the curve (AUC) of 0.807 among a cohort of 1,000 patients. Moreover, PCa-RadHop maintains orders of magnitude smaller model size and complexity., Comment: 13 pages, 7 figures, 5 tables

Purpose: This study assesses the effectiveness of Deep Learning (DL) for creating synthetic CT (sCT) images in MR-guided adaptive radiation therapy (MRgART). Methods: A Cycle-GAN model was trained with MRI and CT scan slices from MR-LINAC treatments, generating sCT volumes. The analysis involved retrospective treatment plan data from patients with various tumors. sCT images were compared with standard CT scans using mean absolute error in Hounsfield Units (HU) and image similarity metrics (SSIM, PSNR, NCC). sCT volumes were integrated into a clinical treatment system for dosimetric re-evaluation. Results: The model, trained on 8405 frames from 57 patients and tested on 357 sCT frames from 17 patients, showed sCTs comparable to dCTs in electron density and structural similarity with MRI scans. The MAE between sCT and dCT was 49.2 +/- 13.2 HU, with sCT NCC exceeding dCT by 0.06, and SSIM and PSNR at 0.97 +/- 0.01 and 19.9 +/- 1.6 respectively. Dosimetric evaluations indicated minimal differences between sCTs and dCTs, with sCTs showing better air-bubble reconstruction. Conclusions: DL-based sCT generation on MR-Linacs is accurate for dose calculation and optimization in MRgART. This could facilitate MR-only treatment planning, enhancing simulation and adaptive planning efficiency on MR-Linacs.

In April to May 2023, the superBIT telescope was lifted to the Earth's stratosphere by a helium-filled super-pressure balloon, to acquire astronomical imaging from above (99.5% of) the Earth's atmosphere. It was launched from New Zealand then, for 40 days, circumnavigated the globe five times at a latitude 40 to 50 degrees South. Attached to the telescope were four 'DRS' (Data Recovery System) capsules containing 5 TB solid state data storage, plus a GNSS receiver, Iridium transmitter, and parachute. Data from the telescope were copied to these, and two were dropped over Argentina. They drifted 61 km horizontally while they descended 32 km, but we predicted their descent vectors within 2.4 km: in this location, the discrepancy appears irreducible below 2 km because of high speed, gusty winds and local topography. The capsules then reported their own locations to within a few metres. We recovered the capsules and successfully retrieved all of superBIT's data - despite the telescope itself being later destroyed on landing., Comment: 12 pages

How protoclusters evolved from sparse galaxy overdensities to mature galaxy clusters is still not well understood. In this context, detecting and characterizing the hot ICM at high redshifts (z~2) is key to understanding how the continuous accretion from and mergers along the filamentary large-scale structure impact the first phases of cluster formation. We study the dynamical state and morphology of the z=1.98 galaxy cluster XLSSC 122 with high-resolution observations (~5") of the ICM through the SZ effect. Via Bayesian forward modeling, we map the ICM on scales from the virial radius down to the core of the cluster. To constrain such a broad range of spatial scales, we employ a new technique that jointly forward-models parametric descriptions of the pressure distribution to interferometric ACA and ALMA observations and multi-band imaging data from the 6-m, single-dish Atacama Cosmology Telescope. We detect the SZ effect with $11\sigma$ in the ALMA+ACA observations and find a flattened inner pressure profile that is consistent with a non-cool core classification with a significance of $>3\sigma$. In contrast to the previous works, we find better agreement between the SZ effect signal and the X-ray emission as well as the cluster member distribution. Further, XLSSC 122 exhibits an excess of SZ flux in the south of the cluster where no X-ray emission is detected. By reconstructing the interferometric observations and modeling in the uv-plane, we obtain a tentative detection of an infalling group or filamentary-like structure that is believed to boost and heat up the ICM while the density of the gas is low. In addition, we provide an improved SZ mass of $M_{500,\mathrm{c}} = 1.66^{+0.23}_{-0.20} \times 10^{14} \rm M_\odot$. Altogether, the observations indicate that we see XLSSC 122 in a dynamic phase of cluster formation while a large reservoir of gas is already thermalized.

We aim to determine the extent and content of guidance for authors regarding the use of generative-AI (GAI), Generative Pretrained models (GPTs) and Large Language Models (LLMs) powered tools among the top 100 academic publishers and journals in science. The websites of these publishers and journals were screened from between 19th and 20th May 2023. Among the largest 100 publishers, 17% provided guidance on the use of GAI, of which 12 (70.6%) were among the top 25 publishers. Among the top 100 journals, 70% have provided guidance on GAI. Of those with guidance, 94.1% of publishers and 95.7% of journals prohibited the inclusion of GAI as an author. Four journals (5.7%) explicitly prohibit the use of GAI in the generation of a manuscript, while 3 (17.6%) publishers and 15 (21.4%) journals indicated their guidance exclusively applies to the writing process. When disclosing the use of GAI, 42.8% of publishers and 44.3% of journals included specific disclosure criteria. There was variability in guidance of where to disclose the use of GAI, including in the methods, acknowledgments, cover letter, or a new section. There was also variability in how to access GAI guidance and the linking of journal and publisher instructions to authors. There is a lack of guidance by some top publishers and journals on the use of GAI by authors. Among those publishers and journals that provide guidance, there is substantial heterogeneity in the allowable uses of GAI and in how it should be disclosed, with this heterogeneity persisting among affiliated publishers and journals in some instances. The lack of standardization burdens authors and threatens to limit the effectiveness of these regulations. There is a need for standardized guidelines in order to protect the integrity of scientific output as GAI continues to grow in popularity., Comment: Pages 16, 1 figure, 2 tables

The swift progress and ubiquitous adoption of Generative AI (GAI), Generative Pre-trained Transformers (GPTs), and large language models (LLMs) like ChatGPT, have spurred queries about their ethical application, use, and disclosure in scholarly research and scientific productions. A few publishers and journals have recently created their own sets of rules; however, the absence of a unified approach may lead to a 'Babel Tower Effect,' potentially resulting in confusion rather than desired standardization. In response to this, we present the ChatGPT, Generative Artificial Intelligence, and Natural Large Language Models for Accountable Reporting and Use Guidelines (CANGARU) initiative, with the aim of fostering a cross-disciplinary global inclusive consensus on the ethical use, disclosure, and proper reporting of GAI/GPT/LLM technologies in academia. The present protocol consists of four distinct parts: a) an ongoing systematic review of GAI/GPT/LLM applications to understand the linked ideas, findings, and reporting standards in scholarly research, and to formulate guidelines for its use and disclosure, b) a bibliometric analysis of existing author guidelines in journals that mention GAI/GPT/LLM, with the goal of evaluating existing guidelines, analyzing the disparity in their recommendations, and identifying common rules that can be brought into the Delphi consensus process, c) a Delphi survey to establish agreement on the items for the guidelines, ensuring principled GAI/GPT/LLM use, disclosure, and reporting in academia, and d) the subsequent development and dissemination of the finalized guidelines and their supplementary explanation and elaboration documents., Comment: 20 pages, 1 figure, protocol

The Superpressure Balloon-borne Imaging Telescope (SuperBIT) is a diffraction-limited, wide-field, 0.5 m, near-infrared to near-ultraviolet observatory designed to exploit the stratosphere's space-like conditions. SuperBIT's 2023 science flight will deliver deep, blue imaging of galaxy clusters for gravitational lensing analysis. In preparation, we have developed a weak lensing measurement pipeline with modern algorithms for PSF characterization, shape measurement, and shear calibration. We validate our pipeline and forecast SuperBIT survey properties with simulated galaxy cluster observations in SuperBIT's near-UV and blue bandpasses. We predict imaging depth, galaxy number (source) density, and redshift distribution for observations in SuperBIT's three bluest filters; the effect of lensing sample selections is also considered. We find that in three hours of on-sky integration, SuperBIT can attain a depth of b = 26 mag and a total source density exceeding 40 galaxies per square arcminute. Even with the application of lensing-analysis catalog selections, we find b-band source densities between 25 and 30 galaxies per square arcminute with a median redshift of z = 1.1. Our analysis confirms SuperBIT's capability for weak gravitational lensing measurements in the blue., Comment: Submitted to Astronomical Journal

The climate crisis and the degradation of the world's ecosystems require humanity to take immediate action. The international scientific community has a responsibility to limit the negative environmental impacts of basic research. The HECAP+ communities (High Energy Physics, Cosmology, Astroparticle Physics, and Hadron and Nuclear Physics) make use of common and similar experimental infrastructure, such as accelerators and observatories, and rely similarly on the processing of big data. Our communities therefore face similar challenges to improving the sustainability of our research. This document aims to reflect on the environmental impacts of our work practices and research infrastructure, to highlight best practice, to make recommendations for positive changes, and to identify the opportunities and challenges that such changes present for wider aspects of social responsibility., Comment: 158 pages, 21 figures; comments welcome. Revisions included in Version 2.0 are detailed on page 3 of the pdf. If you would like to endorse this document please visit: https://sustainable-hecap-plus.github.io/. An HTML version of this document is available at: https://sustainable-hecap-plus.github.io/

Atom-interferometric quantum sensors could revolutionize navigation, civil engineering, and Earth observation. However, operation in real-world environments is challenging due to external interference, platform noise, and constraints on size, weight, and power. Here we experimentally demonstrate that tailored light pulses designed using robust control techniques mitigate significant error sources in an atom-interferometric accelerometer. To mimic the effect of unpredictable lateral platform motion, we apply laser-intensity noise that varies up to 20$\%$ from pulse-to-pulse. Our robust control solution maintains performant sensing, while the utility of conventional pulses collapses. By measuring local gravity, we show that our robust pulses preserve interferometer scale factor and improve measurement precision by 10$\times$ in the presence of this noise. We further validate these enhancements by measuring applied accelerations over a 200 $\mu g$ range up to 21$\times$ more precisely at the highest applied noise level. Our demonstration provides a pathway to improved atom-interferometric inertial sensing in real-world settings., Comment: 15 pages, 7 figures

We address the problem of optimally identifying all kilonovae detected via gravitational wave emission in the upcoming LIGO/Virgo/KAGRA Collaboration observing run, O4, which is expected to be sensitive to a factor of $\sim 7$ more Binary Neutron Stars alerts than previously. Electromagnetic follow-up of all but the brightest of these new events will require $>1$ meter telescopes, for which limited time is available. We present an optimized observing strategy for the Dark Energy Camera during O4. We base our study on simulations of gravitational wave events expected for O4 and wide-prior kilonova simulations. We derive the detectabilities of events for realistic observing conditions. We optimize our strategy for confirming a kilonova while minimizing telescope time. For a wide range of kilonova parameters, corresponding to a fainter kilonova compared to GW170817/AT2017gfo we find that, with this optimal strategy, the discovery probability for electromagnetic counterparts with the Dark Energy Camera is $\sim 80\%$ at the nominal binary neutron star gravitational wave detection limit for the next LVK observing run (190 Mpc), which corresponds to a $\sim 30\%$ improvement compared to the strategy adopted during the previous observing run. For more distant events ($\sim 330$ Mpc), we reach a $\sim 60\%$ probability of detection, a factor of $\sim 2$ increase. For a brighter kilonova model dominated by the blue component that reproduces the observations of GW170817/AT2017gfo, we find that we can reach $\sim 90\%$ probability of detection out to 330 Mpc, representing an increase of $\sim 20 \%$, while also reducing the total telescope time required to follow-up events by $\sim 20\%$., Comment: 26 pages, 11 figures, accepted by ApJ

In this paper, we propose a novel memory-enabled non-uniform sampling-based bumblebee foraging algorithm (MEB) designed for optimal channel selection in a distributed Vehicular Dynamic Spectrum Access (VDSA) framework employed in a platoon operating environment. Given how bumblebee behavioral models are designed to support adaptation in complex and highly time-varying environments, these models can be employed by connected vehicles to enable their operation within a dynamically changing network topology and support their selection of optimal channels possessing low levels of congestion to achieve high throughput. As a result, the proposed VDSA-based optimal channel selection employs fundamental concepts from the bumblebee foraging model. In the proposed approach, the Channel Busy Ratio (CBR) of all channels is computed and stored in memory to be accessed by the MEB algorithm to make the necessary channel switching decisions. Two averaging techniques, Sliding Window Average (SWA) and Exponentially Weighted Moving Average (EWMA), are employed to leverage past samples and are evaluated against the no-memory case. Due to the high variability of the environment (e.g., high velocities, changing density of vehicles on the road), we propose to calculate the CBR by employing non-uniform channel sampling allocations as well as evaluate it using both simplified numerical and realistic Vehicle-to-Vehicle (V2V) computer simulations. The numerical simulation results show that gains in the probability of the best channel selection can be achieved relative to a uniform sampling allocation approach. By utilizing memory, we observe an additional increase in the channel selection performance. Similarly, we see an increase in the probability of successful reception when utilizing the bumblebee algorithm via a system-level simulator.