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  1. Abstract

    Current complex prediction models are the result of fitting deep neural networks, graph convolutional networks or transducers to a set of training data. A key challenge with these models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into a simplified topological view of the prediction landscape. The result is a map of the predictions that enables inspection of the model results with more specificity than dimensionality-reduction methods such as tSNE and UMAP. The methods scale up to large datasets across different domains. We present a case study of a transformer-based model previously designed to predict expression levels of a piece of DNA in thousands of genomic tracks. When the model is used to study mutations in theBRCA1gene, our topological analysis shows that it is sensitive to the location of a mutation and the exon structure ofBRCA1in ways that cannot be found with tools based on dimensionality reduction. Moreover, the topological framework offers multiple ways to inspect results, including an error estimate that is more accurate than model uncertainty. Further studies show how these ideas produce useful results in graph-based learning and image classification.

     
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    Free, publicly-accessible full text available November 17, 2024
  2. ABSTRACT

    The Chinese Space Station Telescope (CSST) is scheduled to launch soon, which is expected to provide a vast amount of image potentially containing low-surface brightness galaxies (LSBGs). However, detecting and characterizing LSBGs is known to be challenging due to their faint surface brightness, posing a significant hurdle for traditional detection methods. In this paper, we propose LSBGnet, a deep neural network specifically designed for automatic detection of LSBGs. We established LSBGnet-SDSS model using data set from the Sloan Digital Sky Survey (SDSS). The results demonstrate a significant improvement compared to our previous work, achieving a recall of 97.22 per cent and a precision of 97.27 per cent on the SDSS test set. Furthermore, we use the LSBGnet-SDSS model as a pre-training model, employing transfer learning to retrain the model with LSBGs from Dark Energy Survey (DES), and establish the LSBGnet-DES model. Remarkably, after retraining the model on a small DES sample, it achieves over 90 per cent precision and recall. To validate the model’s capabilities, we utilize the trained LSBGnet-DES model to detect LSBG candidates within a selected 5 sq. deg area in the DES footprint. Our analysis reveals the detection of 204 LSBG candidates, characterized by a mean surface brightness range of $23.5\ \mathrm{ mag}\ \mathrm{ arcsec}^{-2}\le \bar{\mu }_{\text{eff}}(g)\le 26.8\ \mathrm{ mag}\ \mathrm{ arcsec}^{-2}$ and a half-light radius range of 1.4 arcsec ≤ r1/2 ≤ 8.3 arcsec. Notably, 116 LSBG candidates exhibit a half-light radius ≥2.5 arcsec. These results affirm the remarkable performance of our model in detecting LSBGs, making it a promising tool for the upcoming CSST.

     
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  3. Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 2,399 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at \url{https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench}. 
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    Free, publicly-accessible full text available December 14, 2024
  4. Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 2,399 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at \url{https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench}. 
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    Free, publicly-accessible full text available December 14, 2024
  5. A typical subduction of an oceanic plate beneath a continent is expected to be accompanied by arc volcanoes along the convergent margin. However, subduction of the Cocos plate at the Middle American subduction system has resulted in an uneven distribution of magmatism/volcanism along strike. Here we construct a new three-dimensional shear-wave velocity model of the entire Middle American subduction system, using full-wave ambient noise tomography. Our model reveals significant variations of the oceanic plates along strike and down dip, in correspondence with either weakened or broken slabs after subduction. The northern and southern segments of the Cocos plate, including the Mexican flat slab subduction, are well imaged as high-velocity features, where a low-velocity mantle wedge exists and demonstrate a strong correlation with the arc volcanoes. Subduction of the central Cocos plate encounters a thick high-velocity feature beneath North America, which hinders the formation of a typical low-velocity mantle wedge and arc volcanoes. We suggest that the presence of slab tearing at both edges of the Mexican flat slab has been modifying the mantle flows, resulting in the unusual arc volcanism. 
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    Free, publicly-accessible full text available September 7, 2024
  6. Free, publicly-accessible full text available July 26, 2024
  7. Abstract

    The northwestern part of North America has recorded multiple tectonic events, such as terrane accretion, strike‐slip motion, and subduction of the Pacific and Yakutat plates, providing an iconic setting to investigate the tectonic evolution of the continental crust. In this study we analyze the receiver functions at seismic stations deployed during 1999–2022 to estimate the crustal thickness, as well as possible slab signature, in Alaska and northwestern Canada. The Moho signal can be clearly detected within the continental region. Specifically, in northwestern Canada, the thickest crust is observed beneath the Cordilleran Deformation Front, which marks the structural boundary between the North American Craton and the North American Margin. We observe a few distinct offsets in the Moho depth located both within the tectonic units and approximately across the major faults between the tectonic units. We provide a first‐order estimate of the depth gradient of the Moho offsets based on the horizontal distance of the two closest seismic stations across the offsets. We propose that the Moho offsets reflect the cumulative impact of the accretionary orogenies and post‐orogenic tectonic events on crustal modification. The continental Moho signal is weak or obscure in Aleutian and southcentral Alaska, and the oceanic Moho within the subducting plates is likely detected. This study provides new seismic insights into understanding the impacts of the tectonic events on continental formation and evolution.

     
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