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Peppa, V., Thomson, R. M., Enger, S. A., Fonseca, G. P., Lee, C. N., Lucero, J. N. E., et al. (2023). A MC-based anthropomorphic test case for commissioning model-based dose calculation in interstitial breast 192-Ir HDR brachytherapy. Med. Phys., 50(7), 4675–4687.
Abstract: PurposeTo provide the first clinical test case for commissioning of Ir-192 brachytherapy model-based dose calculation algorithms (MBDCAs) according to the AAPM TG-186 report workflow. Acquisition and Validation MethodsA computational patient phantom model was generated from a clinical multi-catheter Ir-192 HDR breast brachytherapy case. Regions of interest (ROIs) were contoured and digitized on the patient CT images and the model was written to a series of DICOM CT images using MATLAB. The model was imported into two commercial treatment planning systems (TPSs) currently incorporating an MBDCA. Identical treatment plans were prepared using a generic Ir-192 HDR source and the TG-43-based algorithm of each TPS. This was followed by dose to medium in medium calculations using the MBDCA option of each TPS. Monte Carlo (MC) simulation was performed in the model using three different codes and information parsed from the treatment plan exported in DICOM radiation therapy (RT) format. Results were found to agree within statistical uncertainty and the dataset with the lowest uncertainty was assigned as the reference MC dose distribution. Data Format and Usage NotesThe dataset is available online at ,. Files include the treatment plan for each TPS in DICOM RT format, reference MC dose data in RT Dose format, as well as a guide for database users and all files necessary to repeat the MC simulations. Potential ApplicationsThe dataset facilitates the commissioning of brachytherapy MBDCAs using TPS embedded tools and establishes a methodology for the development of future clinical test cases. It is also useful to non-MBDCA adopters for intercomparing MBDCAs and exploring their benefits and limitations, as well as to brachytherapy researchers in need of a dosimetric and/or a DICOM RT information parsing benchmark. Limitations include specificity in terms of radionuclide, source model, clinical scenario, and MBDCA version used for its preparation.
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Hirn, J., Garcia, J. E., Montesinos-Navarro, A., Sanchez-Martin, R., Sanz, V., & Verdu, M. (2022). A deep Generative Artificial Intelligence system to predict species coexistence patterns. Methods Ecol. Evol., 13, 1052–1061.
Abstract: Predicting coexistence patterns is a current challenge to understand diversity maintenance, especially in rich communities where these patterns' complexity is magnified through indirect interactions that prevent their approximation with classical experimental approaches. We explore cutting-edge Machine Learning techniques called Generative Artificial Intelligence (GenAI) to predict species coexistence patterns in vegetation patches, training generative adversarial networks (GAN) and variational AutoEncoders (VAE) that are then used to unravel some of the mechanisms behind community assemblage. The GAN accurately reproduces real patches' species composition and plant species' affinity to different soil types, and the VAE also reaches a high level of accuracy, above 99%. Using the artificially generated patches, we found that high-order interactions tend to suppress the positive effects of low-order interactions. Finally, by reconstructing successional trajectories, we could identify the pioneer species with larger potential to generate a high diversity of distinct patches in terms of species composition. Understanding the complexity of species coexistence patterns in diverse ecological communities requires new approaches beyond heuristic rules. Generative Artificial Intelligence can be a powerful tool to this end as it allows to overcome the inherent dimensionality of this challenge.
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Stoppa, F., Ruiz de Austri, R., Vreeswijk, P., Bhattacharyya, S., Caron, S., Bloemen, S., et al. (2023). AutoSourceID-FeatureExtractor Optical image analysis using a two-step mean variance estimation network for feature estimation and uncertainty characterisation. Astron. Astrophys., 680, A108–14pp.
Abstract: Aims. In astronomy, machine learning has been successful in various tasks such as source localisation, classification, anomaly detection, and segmentation. However, feature regression remains an area with room for improvement. We aim to design a network that can accurately estimate sources' features and their uncertainties from single-band image cutouts, given the approximated locations of the sources provided by the previously developed code AutoSourceID-Light (ASID-L) or other external catalogues. This work serves as a proof of concept, showing the potential of machine learning in estimating astronomical features when trained on meticulously crafted synthetic images and subsequently applied to real astronomical data.Methods. The algorithm presented here, AutoSourceID-FeatureExtractor (ASID-FE), uses single-band cutouts of 32x32 pixels around the localised sources to estimate flux, sub-pixel centre coordinates, and their uncertainties. ASID-FE employs a two-step mean variance estimation (TS-MVE) approach to first estimate the features and then their uncertainties without the need for additional information, for example the point spread function (PSF). For this proof of concept, we generated a synthetic dataset comprising only point sources directly derived from real images, ensuring a controlled yet authentic testing environment.Results. We show that ASID-FE, trained on synthetic images derived from the MeerLICHT telescope, can predict more accurate features with respect to similar codes such as SourceExtractor and that the two-step method can estimate well-calibrated uncertainties that are better behaved compared to similar methods that use deep ensembles of simple MVE networks. Finally, we evaluate the model on real images from the MeerLICHT telescope and the Zwicky Transient Facility (ZTF) to test its transfer learning abilities.
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Stoppa, F., Vreeswijk, P., Bloemen, S., Bhattacharyya, S., Caron, S., Johannesson, G., et al. (2022). AutoSourceID-Light Fast optical source localization via U-Net and Laplacian of Gaussian. Astron. Astrophys., 662, A109–8pp.
Abstract: Aims. With the ever-increasing survey speed of optical wide-field telescopes and the importance of discovering transients when they are still young, rapid and reliable source localization is paramount. We present AutoSourceID-Light (ASID-L), an innovative framework that uses computer vision techniques that can naturally deal with large amounts of data and rapidly localize sources in optical images. Methods. We show that the ASID-L algorithm based on U-shaped networks and enhanced with a Laplacian of Gaussian filter provides outstanding performance in the localization of sources. A U-Net network discerns the sources in the images from many different artifacts and passes the result to a Laplacian of Gaussian filter that then estimates the exact location. Results. Using ASID-L on the optical images of the MeerLICHT telescope demonstrates the great speed and localization power of the method. We compare the results with SExtractor and show that our method outperforms this more widely used method. ASID-L rapidly detects more sources not only in low- and mid-density fields, but particularly in areas with more than 150 sources per square arcminute. The training set and code used in this paper are publicly available.
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Trotta, R., Johannesson, G., Moskalenko, I. V., Porter, T. A., Ruiz de Austri, R., & Strong, A. W. (2011). Constraints on Cosmic-Ray Propagation Models from a Global Bayesian Analysis. Astrophys. J., 729(2), 106–16pp.
Abstract: Research in many areas of modern physics such as, e. g., indirect searches for dark matter and particle acceleration in supernova remnant shocks rely heavily on studies of cosmic rays (CRs) and associated diffuse emissions (radio, microwave, X-rays, gamma-rays). While very detailed numerical models of CR propagation exist, a quantitative statistical analysis of such models has been so far hampered by the large computational effort that those models require. Although statistical analyses have been carried out before using semi-analytical models (where the computation is much faster), the evaluation of the results obtained from such models is difficult, as they necessarily suffer from many simplifying assumptions. The main objective of this paper is to present a working method for a full Bayesian parameter estimation for a numerical CR propagation model. For this study, we use the GALPROP code, the most advanced of its kind, which uses astrophysical information, and nuclear and particle data as inputs to self-consistently predict CRs, gamma-rays, synchrotron, and other observables. We demonstrate that a full Bayesian analysis is possible using nested sampling and Markov Chain Monte Carlo methods (implemented in the SuperBayeS code) despite the heavy computational demands of a numerical propagation code. The best-fit values of parameters found in this analysis are in agreement with previous, significantly simpler, studies also based on GALPROP.
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