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Dec 4

CAvity DEtection Tool (CADET): Pipeline for automatic detection of X-ray cavities in hot galactic and cluster atmospheres

The study of jet-inflated X-ray cavities provides a powerful insight into the energetics of hot galactic atmospheres and radio-mechanical AGN feedback. By estimating the volumes of X-ray cavities, the total energy and thus also the corresponding mechanical jet power required for their inflation can be derived. Properly estimating their total extent is, however, non-trivial, prone to biases, nearly impossible for poor-quality data, and so far has been done manually by scientists. We present a novel and automated machine-learning pipeline called Cavity Detection Tool (CADET), developed to detect and estimate the sizes of X-ray cavities from raw Chandra images. The pipeline consists of a convolutional neural network trained for producing pixel-wise cavity predictions and a DBSCAN clustering algorithm, which decomposes the predictions into individual cavities. The convolutional network was trained using mock observations of early-type galaxies simulated to resemble real noisy Chandra-like images. The network's performance has been tested on simulated data obtaining an average cavity volume error of 14 % at an 89 % true-positive rate. For simulated images without any X-ray cavities inserted, we obtain a 5 % false-positive rate. When applied to real Chandra images, the pipeline recovered 91 out of 100 previously known X-ray cavities in nearby early-type galaxies and all 14 cavities in chosen galaxy clusters. Besides that, the CADET pipeline discovered 8 new cavity pairs in atmospheres of early-type galaxies and galaxy clusters (IC4765, NGC533, NGC2300, NGC3091, NGC4073, NGC4125, NGC4472, NGC5129) and a number of potential cavity candidates.

  • 4 authors
·
Apr 11, 2023

Möbius Transform for Mitigating Perspective Distortions in Representation Learning

Perspective distortion (PD) causes unprecedented changes in shape, size, orientation, angles, and other spatial relationships of visual concepts in images. Precisely estimating camera intrinsic and extrinsic parameters is a challenging task that prevents synthesizing perspective distortion. Non-availability of dedicated training data poses a critical barrier to developing robust computer vision methods. Additionally, distortion correction methods make other computer vision tasks a multi-step approach and lack performance. In this work, we propose mitigating perspective distortion (MPD) by employing a fine-grained parameter control on a specific family of M\"obius transform to model real-world distortion without estimating camera intrinsic and extrinsic parameters and without the need for actual distorted data. Also, we present a dedicated perspectively distorted benchmark dataset, ImageNet-PD, to benchmark the robustness of deep learning models against this new dataset. The proposed method outperforms existing benchmarks, ImageNet-E and ImageNet-X. Additionally, it significantly improves performance on ImageNet-PD while consistently performing on standard data distribution. Notably, our method shows improved performance on three PD-affected real-world applications crowd counting, fisheye image recognition, and person re-identification and one PD-affected challenging CV task: object detection. The source code, dataset, and models are available on the project webpage at https://prakashchhipa.github.io/projects/mpd.

  • 6 authors
·
Mar 7, 2024

ASPIRE: Language-Guided Augmentation for Robust Image Classification

Neural image classifiers can often learn to make predictions by overly relying on non-predictive features that are spuriously correlated with the class labels in the training data. This leads to poor performance in real-world atypical scenarios where such features are absent. Supplementing the training dataset with images without such spurious features can aid robust learning against spurious correlations via better generalization. This paper presents ASPIRE (Language-guided data Augmentation for SPurIous correlation REmoval), a simple yet effective solution for expanding the training dataset with synthetic images without spurious features. ASPIRE, guided by language, generates these images without requiring any form of additional supervision or existing examples. Precisely, we employ LLMs to first extract foreground and background features from textual descriptions of an image, followed by advanced language-guided image editing to discover the features that are spuriously correlated with the class label. Finally, we personalize a text-to-image generation model to generate diverse in-domain images without spurious features. We demonstrate the effectiveness of ASPIRE on 4 datasets, including the very challenging Hard ImageNet dataset, and 9 baselines and show that ASPIRE improves the classification accuracy of prior methods by 1% - 38%. Code soon at: https://github.com/Sreyan88/ASPIRE.

  • 7 authors
·
Aug 19, 2023

Cascaded Multi-Modal Mixing Transformers for Alzheimer's Disease Classification with Incomplete Data

Accurate medical classification requires a large number of multi-modal data, and in many cases, different feature types. Previous studies have shown promising results when using multi-modal data, outperforming single-modality models when classifying diseases such as Alzheimer's Disease (AD). However, those models are usually not flexible enough to handle missing modalities. Currently, the most common workaround is discarding samples with missing modalities which leads to considerable data under-utilization. Adding to the fact that labeled medical images are already scarce, the performance of data-driven methods like deep learning can be severely hampered. Therefore, a multi-modal method that can handle missing data in various clinical settings is highly desirable. In this paper, we present Multi-Modal Mixing Transformer (3MAT), a disease classification transformer that not only leverages multi-modal data but also handles missing data scenarios. In this work, we test 3MT for AD and Cognitively normal (CN) classification and mild cognitive impairment (MCI) conversion prediction to progressive MCI (pMCI) or stable MCI (sMCI) using clinical and neuroimaging data. The model uses a novel Cascaded Modality Transformer architecture with cross-attention to incorporate multi-modal information for more informed predictions. We propose a novel modality dropout mechanism to ensure an unprecedented level of modality independence and robustness to handle missing data scenarios. The result is a versatile network that enables the mixing of arbitrary numbers of modalities with different feature types and also ensures full data utilization missing data scenarios. The model is trained and evaluated on the ADNI dataset with the SOTRA performance and further evaluated with the AIBL dataset with missing data.

  • 6 authors
·
Oct 1, 2022

CoherentGS: Sparse Novel View Synthesis with Coherent 3D Gaussians

The field of 3D reconstruction from images has rapidly evolved in the past few years, first with the introduction of Neural Radiance Field (NeRF) and more recently with 3D Gaussian Splatting (3DGS). The latter provides a significant edge over NeRF in terms of the training and inference speed, as well as the reconstruction quality. Although 3DGS works well for dense input images, the unstructured point-cloud like representation quickly overfits to the more challenging setup of extremely sparse input images (e.g., 3 images), creating a representation that appears as a jumble of needles from novel views. To address this issue, we propose regularized optimization and depth-based initialization. Our key idea is to introduce a structured Gaussian representation that can be controlled in 2D image space. We then constraint the Gaussians, in particular their position, and prevent them from moving independently during optimization. Specifically, we introduce single and multiview constraints through an implicit convolutional decoder and a total variation loss, respectively. With the coherency introduced to the Gaussians, we further constrain the optimization through a flow-based loss function. To support our regularized optimization, we propose an approach to initialize the Gaussians using monocular depth estimates at each input view. We demonstrate significant improvements compared to the state-of-the-art sparse-view NeRF-based approaches on a variety of scenes.

  • 7 authors
·
Mar 28, 2024

Multi-Coil MRI Reconstruction Challenge -- Assessing Brain MRI Reconstruction Models and their Generalizability to Varying Coil Configurations

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

  • 23 authors
·
Nov 9, 2020

SCGC : Self-Supervised Contrastive Graph Clustering

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph Neural Networks (GNN) have shown great success in encoding graph structure, typical GNNs based on convolution or attention variants suffer from over-smoothing, noise, heterophily, are computationally expensive and typically require the complete graph being present. Instead, we propose Self-Supervised Contrastive Graph Clustering (SCGC), which imposes graph-structure via contrastive loss signals to learn discriminative node representations and iteratively refined soft cluster labels. We also propose SCGC*, with a more effective, novel, Influence Augmented Contrastive (IAC) loss to fuse richer structural information, and half the original model parameters. SCGC(*) is faster with simple linear units, completely eliminate convolutions and attention of traditional GNNs, yet efficiently incorporates structure. It is impervious to layer depth and robust to over-smoothing, incorrect edges and heterophily. It is scalable by batching, a limitation in many prior GNN models, and trivially parallelizable. We obtain significant improvements over state-of-the-art on a wide range of benchmark graph datasets, including images, sensor data, text, and citation networks efficiently. Specifically, 20% on ARI and 18% on NMI for DBLP; overall 55% reduction in training time and overall, 81% reduction on inference time. Our code is available at : https://github.com/gayanku/SCGC

  • 3 authors
·
Apr 26, 2022

Taming Mode Collapse in Score Distillation for Text-to-3D Generation

Despite the remarkable performance of score distillation in text-to-3D generation, such techniques notoriously suffer from view inconsistency issues, also known as "Janus" artifact, where the generated objects fake each view with multiple front faces. Although empirically effective methods have approached this problem via score debiasing or prompt engineering, a more rigorous perspective to explain and tackle this problem remains elusive. In this paper, we reveal that the existing score distillation-based text-to-3D generation frameworks degenerate to maximal likelihood seeking on each view independently and thus suffer from the mode collapse problem, manifesting as the Janus artifact in practice. To tame mode collapse, we improve score distillation by re-establishing in entropy term in the corresponding variational objective, which is applied to the distribution of rendered images. Maximizing the entropy encourages diversity among different views in generated 3D assets, thereby mitigating the Janus problem. Based on this new objective, we derive a new update rule for 3D score distillation, dubbed Entropic Score Distillation (ESD). We theoretically reveal that ESD can be simplified and implemented by just adopting the classifier-free guidance trick upon variational score distillation. Although embarrassingly straightforward, our extensive experiments successfully demonstrate that ESD can be an effective treatment for Janus artifacts in score distillation.

  • 11 authors
·
Dec 31, 2023

The Chandra Source Catalog

The Chandra Source Catalog (CSC) is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime. The first release of the CSC includes information about 94,676 distinct X-ray sources detected in a subset of public ACIS imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents <~ 30''. The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports scientific analysis using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; and (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools. The catalog includes real X-ray sources detected with flux estimates that are at least 3 times their estimated 1 sigma uncertainties in at least one energy band, while maintaining the number of spurious sources at a level of <~ 1 false source per field for a 100 ks observation. For each detected source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively.

  • 39 authors
·
May 25, 2010

Discovery of kiloparsec-scale semi-relativistic Fe Kα complex emission in NGC 5728

We present Chandra ACIS-S imaging spectroscopy results of the extended (1.5''- 8'', 300 pc-1600 pc) hard X-ray emission of NGC 5728, the host galaxy of a Compton thick active galactic nucleus (CT AGN). We find spectrally and spatially-resolved features in the Fe Kalpha complex (5.0-7.5 keV), redward and blueward of the neutral Fe line at 6.4 keV in the extended narrow line region bicone. A simple phenomenological fit of a power law plus Gaussians gives a significance of 5.4sigma and 3.7sigma for the red and blue wings, respectively. Fits to a suite of physically consistent models confirm a significance geq3sigma for the red wing. The significance of the blue wing may be diminished by the presence of rest frame highly ionized Fe XXV and Fe XXVI lines (1.4sigma - 3.7sigma range). A detailed investigation of the Chandra ACIS-S point spread function (PSF) and comparison with the observed morphology demonstrates that these red and blue wings are radially extended (~5'', ~1 kpc) along the optical bicone axis. If the wings emission is due solely to redshifted and blueshifted high-velocity neutral Fe Kalpha then the implied line-of-sight velocities are +/- ~0.1c, and their fluxes are consistent with being equal. A symmetric high-velocity outflow is then a viable explanation. This outflow has deprojected velocities ~100 times larger than the outflows detected in optical spectroscopic studies, potentially dominating the kinetic feedback power.

  • 5 authors
·
Mar 1, 2023

Jet-ISM Interaction in the Radio Galaxy 3C293: Jet-driven Shocks Heat ISM to Power X-ray and Molecular H2 emission

We present a 70ks Chandra observation of the radio galaxy 3C293. This galaxy belongs to the class of molecular hydrogen emission galaxies (MOHEGs) that have very luminous emission from warm molecular hydrogen. In radio galaxies, the molecular gas appears to be heated by jet-driven shocks, but exactly how this mechanism works is still poorly understood. With Chandra, we observe X-ray emission from the jets within the host galaxy and along the 100 kpc radio jets. We model the X-ray spectra of the nucleus, the inner jets, and the X-ray features along the extended radio jets. Both the nucleus and the inner jets show evidence of 10^7 K shock-heated gas. The kinetic power of the jets is more than sufficient to heat the X-ray emitting gas within the host galaxy. The thermal X-ray and warm H2 luminosities of 3C293 are similar, indicating similar masses of X-ray hot gas and warm molecular gas. This is consistent with a picture where both derive from a multiphase, shocked interstellar medium (ISM). We find that radio-loud MOHEGs that are not brightest cluster galaxies (BCGs), like 3C293, typically have LH2/LX~1 and MH2/MX~1, whereas MOHEGs that are BCGs have LH2/LX~0.01 and MH2/MX~0.01. The more massive, virialized, hot atmosphere in BCGs overwhelms any direct X-ray emission from current jet-ISM interaction. On the other hand, LH2/LX~1 in the Spiderweb BCG at z=2, which resides in an unvirialized protocluster and hosts a powerful radio source. Over time, jet-ISM interaction may contribute to the establishment of a hot atmosphere in BCGs and other massive elliptical galaxies.

  • 6 authors
·
Jan 5, 2015

X-ray Observations of Nova Scorpii 2023 (V1716 Sco) in Outburst

Nova Scorpii 2023 was first detected as a luminous supersoft X-ray source (SSS) 93 days after outburst and continued emitting soft X-rays for over two months, until it was too close to the Sun to observe. The nova was monitored with the Swift X-ray Telescope (XRT) and the Neutron Star Interior Composition Explorer (NICER) on the International Space Station, and in long exposures with the Chandra High Resolution Camera (HRC) and Low Energy Transmission Grating (LETG) on days 128, 129, and 183-185 after optical maximum. Swift detected a rapidly decaying SSS when observations resumed, constraining the constant bolometric luminosity phase to 9 months. The SSS flux was irregularly variable. A nearly three-fold increase in flux was observed between August and October 2023 in the 15 to 35 Angstrom range, from 3.5 x 10^(-11) to 9.4 x 10^(-11) erg cm^(-2) s^(-1). The SSS duration and effective temperature derived from the October LETG spectra indicate a massive white dwarf with temperature fitting nova evolutionary tracks for a 1.2 solar mass WD; emission lines superimposed on the WD continuum are attributed to surrounding shocked ejecta. We present a timing study based on Chandra and archival NICER data. The irregular variability timescale was days, but a 77.9 second periodic modulation in the SSS flux with varying amplitude was measured in many observations. Our analysis shows that this period was stable; short drifts derived with NICER, but not in long, uninterrupted Chandra exposures, are artifacts of measuring variable amplitude modulation. We suggest the modulations are associated with the WD rotation.

  • 8 authors
·
Oct 21

Chest ImaGenome Dataset for Clinical Reasoning

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

  • 12 authors
·
Jul 31, 2021

Can AI Dream of Unseen Galaxies? Conditional Diffusion Model for Galaxy Morphology Augmentation

Observational astronomy relies on visual feature identification to detect critical astrophysical phenomena. While machine learning (ML) increasingly automates this process, models often struggle with generalization in large-scale surveys due to the limited representativeness of labeled datasets -- whether from simulations or human annotation -- a challenge pronounced for rare yet scientifically valuable objects. To address this, we propose a conditional diffusion model to synthesize realistic galaxy images for augmenting ML training data. Leveraging the Galaxy Zoo 2 dataset which contains visual feature -- galaxy image pairs from volunteer annotation, we demonstrate that our model generates diverse, high-fidelity galaxy images closely adhere to the specified morphological feature conditions. Moreover, this model enables generative extrapolation to project well-annotated data into unseen domains and advancing rare object detection. Integrating synthesized images into ML pipelines improves performance in standard morphology classification, boosting completeness and purity by up to 30\% across key metrics. For rare object detection, using early-type galaxies with prominent dust lane features ( sim0.1\% in GZ2 dataset) as a test case, our approach doubled the number of detected instances from 352 to 872, compared to previous studies based on visual inspection. This study highlights the power of generative models to bridge gaps between scarce labeled data and the vast, uncharted parameter space of observational astronomy and sheds insight for future astrophysical foundation model developments. Our project homepage is available at https://galaxysd-webpage.streamlit.app/.

  • 7 authors
·
Jun 19

Joint multiband deconvolution for Euclid and Vera C. Rubin images

With the advent of surveys like Euclid and Vera C. Rubin, astrophysicists will have access to both deep, high-resolution images and multiband images. However, these two types are not simultaneously available in any single dataset. It is therefore vital to devise image deconvolution algorithms that exploit the best of both worlds and that can jointly analyze datasets spanning a range of resolutions and wavelengths. In this work we introduce a novel multiband deconvolution technique aimed at improving the resolution of ground-based astronomical images by leveraging higher-resolution space-based observations. The method capitalizes on the fortunate fact that the Rubin r, i, and z bands lie within the Euclid VIS band. The algorithm jointly de-convolves all the data to convert the r-, i-, and z-band Rubin images to the resolution of Euclid by leveraging the correlations between the different bands. We also investigate the performance of deep-learning-based denoising with DRUNet to further improve the results. We illustrate the effectiveness of our method in terms of resolution and morphology recovery, flux preservation, and generalization to different noise levels. This approach extends beyond the specific Euclid-Rubin combination, offering a versatile solution to improving the resolution of ground-based images in multiple photometric bands by jointly using any space-based images with overlapping filters.

  • 4 authors
·
Feb 24

ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

  • 6 authors
·
May 5, 2017

BS-Diff: Effective Bone Suppression Using Conditional Diffusion Models from Chest X-Ray Images

Chest X-rays (CXRs) are commonly utilized as a low-dose modality for lung screening. Nonetheless, the efficacy of CXRs is somewhat impeded, given that approximately 75% of the lung area overlaps with bone, which in turn hampers the detection and diagnosis of diseases. As a remedial measure, bone suppression techniques have been introduced. The current dual-energy subtraction imaging technique in the clinic requires costly equipment and subjects being exposed to high radiation. To circumvent these issues, deep learning-based image generation algorithms have been proposed. However, existing methods fall short in terms of producing high-quality images and capturing texture details, particularly with pulmonary vessels. To address these issues, this paper proposes a new bone suppression framework, termed BS-Diff, that comprises a conditional diffusion model equipped with a U-Net architecture and a simple enhancement module to incorporate an autoencoder. Our proposed network cannot only generate soft tissue images with a high bone suppression rate but also possesses the capability to capture fine image details. Additionally, we compiled the largest dataset since 2010, including data from 120 patients with high-definition, high-resolution paired CXRs and soft tissue images collected by our affiliated hospital. Extensive experiments, comparative analyses, ablation studies, and clinical evaluations indicate that the proposed BS-Diff outperforms several bone-suppression models across multiple metrics. Our code can be accessed at https://github.com/Benny0323/BS-Diff.

  • 11 authors
·
Nov 26, 2023

Euclid Quick Data Release (Q1). Active galactic nuclei identification using diffusion-based inpainting of Euclid VIS images

Light emission from galaxies exhibit diverse brightness profiles, influenced by factors such as galaxy type, structural features and interactions with other galaxies. Elliptical galaxies feature more uniform light distributions, while spiral and irregular galaxies have complex, varied light profiles due to their structural heterogeneity and star-forming activity. In addition, galaxies with an active galactic nucleus (AGN) feature intense, concentrated emission from gas accretion around supermassive black holes, superimposed on regular galactic light, while quasi-stellar objects (QSO) are the extreme case of the AGN emission dominating the galaxy. The challenge of identifying AGN and QSO has been discussed many times in the literature, often requiring multi-wavelength observations. This paper introduces a novel approach to identify AGN and QSO from a single image. Diffusion models have been recently developed in the machine-learning literature to generate realistic-looking images of everyday objects. Utilising the spatial resolving power of the Euclid VIS images, we created a diffusion model trained on one million sources, without using any source pre-selection or labels. The model learns to reconstruct light distributions of normal galaxies, since the population is dominated by them. We condition the prediction of the central light distribution by masking the central few pixels of each source and reconstruct the light according to the diffusion model. We further use this prediction to identify sources that deviate from this profile by examining the reconstruction error of the few central pixels regenerated in each source's core. Our approach, solely using VIS imaging, features high completeness compared to traditional methods of AGN and QSO selection, including optical, near-infrared, mid-infrared, and X-rays.

  • 274 authors
·
Mar 19

RoentGen: Vision-Language Foundation Model for Chest X-ray Generation

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

  • 10 authors
·
Nov 23, 2022

STAR: A First-Ever Dataset and A Large-Scale Benchmark for Scene Graph Generation in Large-Size Satellite Imagery

Scene graph generation (SGG) in satellite imagery (SAI) benefits promoting understanding of geospatial scenarios from perception to cognition. In SAI, objects exhibit great variations in scales and aspect ratios, and there exist rich relationships between objects (even between spatially disjoint objects), which makes it attractive to holistically conduct SGG in large-size very-high-resolution (VHR) SAI. However, there lack such SGG datasets. Due to the complexity of large-size SAI, mining triplets <subject, relationship, object> heavily relies on long-range contextual reasoning. Consequently, SGG models designed for small-size natural imagery are not directly applicable to large-size SAI. This paper constructs a large-scale dataset for SGG in large-size VHR SAI with image sizes ranging from 512 x 768 to 27,860 x 31,096 pixels, named STAR (Scene graph generaTion in lArge-size satellite imageRy), encompassing over 210K objects and over 400K triplets. To realize SGG in large-size SAI, we propose a context-aware cascade cognition (CAC) framework to understand SAI regarding object detection (OBD), pair pruning and relationship prediction for SGG. We also release a SAI-oriented SGG toolkit with about 30 OBD and 10 SGG methods which need further adaptation by our devised modules on our challenging STAR dataset. The dataset and toolkit are available at: https://linlin-dev.github.io/project/STAR.

  • 14 authors
·
Jun 13, 2024

Multi-view X-ray Image Synthesis with Multiple Domain Disentanglement from CT Scans

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

  • 9 authors
·
Apr 18, 2024

New Radio Observations of the Supernova Remnant CTA 1

We present new radio images of the supernova remnant (SNR) CTA 1 at 1420 and 408 MHz, and in the 21 cm line of H I observed with the Dominion Radio Astrophysical Observatory Synthesis Telescope and at 1420 MHz observed with the Effelsberg 100 m telescope. We confirm previously described continuum features and elaborate further on filamentary features identified using the high-resolution (1') maps from these new observations. We investigate the abrupt change in sign of rotation measure (RM) across the SNR, using the linear polarization observations in the four bands around 1420 MHz. Following X. H. Sun et al.'s (2011) investigation, we both confirm that the distribution of signs of the RMs for extragalactic sources in the area appears to match that of the shell, as well as combine the data from the four bands to estimate the relative depolarization and the intrinsic rotation measure of the SNR. We do not conclusively reject X. H. Sun et al.'s (2011) claim of a Faraday screen in the foreground causing the distribution of RMs that we observe; however, we do suggest an alternative explanation of a swept-up stellar wind from the progenitor star with a toroidal magnetic field. Finally, we expand on the analysis of the H I observations by applying the Rolling Hough Transform to isolate filamentary structure and better identify H I emission with the SNR. Further constraining the H I velocity channels associated with CTA 1, we use more recent Galactic rotation curves to calculate an updated kinematic distance of 1.09 +/- 0.2 kpc.

  • 6 authors
·
Dec 19, 2024

CEERS Epoch 1 NIRCam Imaging: Reduction Methods and Simulations Enabling Early JWST Science Results

We present the data release and data reduction process for the Epoch 1 NIRCam observations for the Cosmic Evolution Early Release Science Survey (CEERS). These data consist of NIRCam imaging in six broadband filters (F115W, F150W, F200W, F277W, F356W and F444W) and one medium band filter (F410M) over four pointings, obtained in parallel with primary CEERS MIRI observations (Yang et al. in prep). We reduced the NIRCam imaging with the JWST Calibration Pipeline, with custom modifications and reduction steps designed to address additional features and challenges with the data. Here we provide a detailed description of each step in our reduction and a discussion of future expected improvements. Our reduction process includes corrections for known pre-launch issues such as 1/f noise, as well as in-flight issues including snowballs, wisps, and astrometric alignment. Many of our custom reduction processes were first developed with pre-launch simulated NIRCam imaging over the full 10 CEERS NIRCam pointings. We present a description of the creation and reduction of this simulated dataset in the Appendix. We provide mosaics of the real images in a public release, as well as our reduction scripts with detailed explanations to allow users to reproduce our final data products. These represent one of the first official public datasets released from the Directors Discretionary Early Release Science (DD-ERS) program.

  • 37 authors
·
Nov 4, 2022

Vision-Language Generative Model for View-Specific Chest X-ray Generation

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

  • 8 authors
·
Feb 23, 2023

Video Compression for Spatiotemporal Earth System Data

Large-scale Earth system datasets, from high-resolution remote sensing imagery to spatiotemporal climate model outputs, exhibit characteristics analogous to those of standard videos. Their inherent spatial, temporal, and spectral redundancies can thus be readily exploited by established video compression techniques. Here, we present xarrayvideo, a Python library for compressing multichannel spatiotemporal datasets by encoding them as videos. Our approach achieves compression ratios of up to 250x while maintaining high fidelity by leveraging standard, well-optimized video codecs through ffmpeg. We demonstrate the library's effectiveness on four real-world multichannel spatiotemporal datasets: DynamicEarthNet (very high resolution Planet images), DeepExtremeCubes (high resolution Sentinel-2 images), ERA5 (weather reanalysis data), and the SimpleS2 dataset (high resolution multichannel Sentinel-2 images), achieving Peak Signal-to-Noise Ratios (PSNRs) of 55.86, 40.60, 46.58, and 43.23 dB at 0.1 bits per pixel per band (bpppb) and 65.91, 54.28, 62.90, and 55.04 dB at 1 bpppb. We are redistributing two of these datasets, DeepExtremeCubes (2.3 Tb) and DynamicEarthNet (525 Gb), in the machine-learning-ready and cloud-ready TACO format through HuggingFace at significantly reduced sizes (270 Gb and 8.5 Gb, respectively) without compromising quality (PSNR 55.77-56.65 and 60.15). No performance loss is observed when the compressed versions of these datasets are used in their respective deep learning-based downstream tasks (next step reflectance prediction and landcover segmentation). In conclusion, xarrayvideo presents an efficient solution for handling the rapidly growing size of Earth observation datasets, making advanced compression techniques accessible and practical to the Earth science community. The library is available for use at https://github.com/IPL-UV/xarrayvideo

  • 3 authors
·
Jun 24

MCTED: A Machine-Learning-Ready Dataset for Digital Elevation Model Generation From Mars Imagery

This work presents a new dataset for the Martian digital elevation model prediction task, ready for machine learning applications called MCTED. The dataset has been generated using a comprehensive pipeline designed to process high-resolution Mars orthoimage and DEM pairs from Day et al., yielding a dataset consisting of 80,898 data samples. The source images are data gathered by the Mars Reconnaissance Orbiter using the CTX instrument, providing a very diverse and comprehensive coverage of the Martian surface. Given the complexity of the processing pipelines used in large-scale DEMs, there are often artefacts and missing data points in the original data, for which we developed tools to solve or mitigate their impact. We divide the processed samples into training and validation splits, ensuring samples in both splits cover no mutual areas to avoid data leakage. Every sample in the dataset is represented by the optical image patch, DEM patch, and two mask patches, indicating values that were originally missing or were altered by us. This allows future users of the dataset to handle altered elevation regions as they please. We provide statistical insights of the generated dataset, including the spatial distribution of samples, the distributions of elevation values, slopes and more. Finally, we train a small U-Net architecture on the MCTED dataset and compare its performance to a monocular depth estimation foundation model, DepthAnythingV2, on the task of elevation prediction. We find that even a very small architecture trained on this dataset specifically, beats a zero-shot performance of a depth estimation foundation model like DepthAnythingV2. We make the dataset and code used for its generation completely open source in public repositories.

ESA-Datalabs ESA Datalabs
·
Sep 9

Rotation-invariant convolutional neural networks for galaxy morphology prediction

Measuring the morphological parameters of galaxies is a key requirement for studying their formation and evolution. Surveys such as the Sloan Digital Sky Survey (SDSS) have resulted in the availability of very large collections of images, which have permitted population-wide analyses of galaxy morphology. Morphological analysis has traditionally been carried out mostly via visual inspection by trained experts, which is time-consuming and does not scale to large (gtrsim10^4) numbers of images. Although attempts have been made to build automated classification systems, these have not been able to achieve the desired level of accuracy. The Galaxy Zoo project successfully applied a crowdsourcing strategy, inviting online users to classify images by answering a series of questions. Unfortunately, even this approach does not scale well enough to keep up with the increasing availability of galaxy images. We present a deep neural network model for galaxy morphology classification which exploits translational and rotational symmetry. It was developed in the context of the Galaxy Challenge, an international competition to build the best model for morphology classification based on annotated images from the Galaxy Zoo project. For images with high agreement among the Galaxy Zoo participants, our model is able to reproduce their consensus with near-perfect accuracy (> 99%) for most questions. Confident model predictions are highly accurate, which makes the model suitable for filtering large collections of images and forwarding challenging images to experts for manual annotation. This approach greatly reduces the experts' workload without affecting accuracy. The application of these algorithms to larger sets of training data will be critical for analysing results from future surveys such as the LSST.

  • 3 authors
·
Mar 24, 2015

Unveiling the soft X-ray source population towards the inner Galactic disk with XMM-Newton

Across the Galactic disk lies a diverse population of X-ray sources, with the fainter end remaining poorly understood due to past survey sensitivity limits. We aim to classify and characterize faint X-ray sources detected in the eROSITA All-Sky Survey (eRASS1) towards the inner Galactic disk (350^circ < l < 360^circ, -1^circ < b < 1^circ) using deeper XMM-Newton observations (typical exposure of sim 20,ks). We analyzed 189 eRASS1 sources, combining X-ray spectral fitting (0.2--10,keV) with Gaia astrometric and photometric data for robust classification. Our results show that the eRASS1 catalog towards the Galactic disk is overwhelmingly dominated by coronal sources (sim 74%), primarily active stars and binaries, with sim 8% being wind-powered massive stars and sim 18% being accreting compact objects. We propose an empirical hardness-ratio cut (HR > -0.2) to efficiently isolate these non-coronal sources. By stacking the classified population and comparing with the Galactic Ridge X-ray Emission (GRXE), we estimate that sim 6% of the GRXE flux in the 0.5--2.0,keV band is resolved into point sources above the eRASS1 flux limit (sim 5times 10^{-14},erg,cm^{-2},s^{-1}). This resolved soft-band emission is dominated by active stars, while hard-band flux originates primarily from X-ray binaries. We conclude that the eRASS1 catalog retains a non-negligible population of compact objects that can be effectively distinguished using X-ray color selection.

  • 8 authors
·
Oct 27

FluoroSAM: A Language-promptable Foundation Model for Flexible X-ray Image Segmentation

Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) -- machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability -- have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM's performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

  • 8 authors
·
Mar 12, 2024

Astronomaly at scale: searching for anomalies amongst 4 million galaxies

Modern astronomical surveys are producing datasets of unprecedented size and richness, increasing the potential for high-impact scientific discovery. This possibility, coupled with the challenge of exploring a large number of sources, has led to the development of novel machine-learning-based anomaly detection approaches, such as Astronomaly. For the first time, we test the scalability of Astronomaly by applying it to almost 4 million images of galaxies from the Dark Energy Camera Legacy Survey. We use a trained deep learning algorithm to learn useful representations of the images and pass these to the anomaly detection algorithm isolation forest, coupled with Astronomaly's active learning method, to discover interesting sources. We find that data selection criteria have a significant impact on the trade-off between finding rare sources such as strong lenses and introducing artefacts into the dataset. We demonstrate that active learning is required to identify the most interesting sources and reduce artefacts, while anomaly detection methods alone are insufficient. Using Astronomaly, we find 1635 anomalies among the top 2000 sources in the dataset after applying active learning, including eight strong gravitational lens candidates, 1609 galaxy merger candidates, and 18 previously unidentified sources exhibiting highly unusual morphology. Our results show that by leveraging the human-machine interface, Astronomaly is able to rapidly identify sources of scientific interest even in large datasets.

  • 4 authors
·
Sep 15, 2023

Identification of Low Surface Brightness Tidal Features in Galaxies Using Convolutional Neural Networks

Faint tidal features around galaxies record their merger and interaction histories over cosmic time. Due to their low surface brightnesses and complex morphologies, existing automated methods struggle to detect such features and most work to date has heavily relied on visual inspection. This presents a major obstacle to quantitative study of tidal debris features in large statistical samples, and hence the ability to be able to use these features to advance understanding of the galaxy population as a whole. This paper uses convolutional neural networks (CNNs) with dropout and augmentation to identify galaxies in the CFHTLS-Wide Survey that have faint tidal features. Evaluating the performance of the CNNs against previously-published expert visual classifications, we find that our method achieves high (76%) completeness and low (20%) contamination, and also performs considerably better than other automated methods recently applied in the literature. We argue that CNNs offer a promising approach to effective automatic identification of low surface brightness tidal debris features in and around galaxies. When applied to forthcoming deep wide-field imaging surveys (e.g. LSST, Euclid), CNNs have the potential to provide a several order-of-magnitude increase in the sample size of morphologically-perturbed galaxies and thereby facilitate a much-anticipated revolution in terms of quantitative low surface brightness science.

  • 4 authors
·
Nov 28, 2018

SynthRAD2023 Grand Challenge dataset: generating synthetic CT for radiotherapy

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

  • 9 authors
·
Mar 28, 2023

IXPE Observation of the Low-Synchrotron Peaked Blazar S4 0954+65 During An Optical-X-ray Flare

The X-ray polarization observations made possible with the Imaging X-ray Polarimetry Explorer (IXPE) offer new ways of probing high-energy emission processes in astrophysical jets from blazars. Here we report on the first X-ray polarization observation of the blazar S4 0954+65 in a high optical and X-ray state. During our multi-wavelength campaign on the source, we detected an optical flare whose peak coincided with the peak of an X-ray flare. This optical-X-ray flare most likely took place in a feature moving along the parsec-scale jet, imaged at 43 GHz by the Very Long Baseline Array. The 43 GHz polarization angle of the moving component underwent a rotation near the time of the flare. In the optical band, prior to the IXPE observation, we measured the polarization angle to be aligned with the jet axis. In contrast, during the optical flare the optical polarization angle was perpendicular to the jet axis; after the flare, it reverted to being parallel to the jet axis. Due to the smooth behavior of the optical polarization angle during the flare, we favor shocks as the main acceleration mechanism. We also infer that the ambient magnetic field lines in the jet were parallel to the jet position angle. The average degree of optical polarization during the IXPE observation was (14.3pm4.1)%. Despite the flare, we only detected an upper limit of 14% (at 3sigma level) on the X-ray polarization degree; although a reasonable assumption on the X-ray polarization angle results in an upper limit of 8.8% (3sigma). We model the spectral energy distribution (SED) and spectral polarization distribution (SPD) of S4 0954+65 with leptonic (synchrotron self-Compton) and hadronic (proton and pair synchrotron) models. The constraints we obtain with our combined multi-wavelength polarization observations and SED modeling tentatively disfavor hadronic models for the X-ray emission in S4 0954+65.

  • 137 authors
·
Nov 25, 2024

Harnessing the Hubble Space Telescope Archives: A Catalogue of 21,926 Interacting Galaxies

Mergers play a complex role in galaxy formation and evolution. Continuing to improve our understanding of these systems require ever larger samples, which can be difficult (even impossible) to select from individual surveys. We use the new platform ESA Datalabs to assemble a catalogue of interacting galaxies from the Hubble Space Telescope science archives; this catalogue is larger than previously published catalogues by nearly an order of magnitude. In particular, we apply the Zoobot convolutional neural network directly to the entire public archive of HST F814W images and make probabilistic interaction predictions for 126 million sources from the Hubble Source Catalogue. We employ a combination of automated visual representation and visual analysis to identify a clean sample of 21,926 interacting galaxy systems, mostly with z < 1. Sixty five percent of these systems have no previous references in either the NASA Extragalactic Database or Simbad. In the process of removing contamination, we also discover many other objects of interest, such as gravitational lenses, edge-on protoplanetary disks, and `backlit' overlapping galaxies. We briefly investigate the basic properties of this sample, and we make our catalogue publicly available for use by the community. In addition to providing a new catalogue of scientifically interesting objects imaged by HST, this work also demonstrates the power of the ESA Datalabs tool to facilitate substantial archival analysis without placing a high computational or storage burden on the end user.

  • 16 authors
·
Mar 1, 2023

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

  • 10 authors
·
Oct 7, 2022

Enhanced Contrastive Learning with Multi-view Longitudinal Data for Chest X-ray Report Generation

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

  • 7 authors
·
Feb 27

Adaptive Detection of Fast Moving Celestial Objects Using a Mixture of Experts and Physical-Inspired Neural Network

Fast moving celestial objects are characterized by velocities across the celestial sphere that significantly differ from the motions of background stars. In observational images, these objects exhibit distinct shapes, contrasting with the typical appearances of stars. Depending on the observational method employed, these celestial entities may be designated as near-Earth objects or asteroids. Historically, fast moving celestial objects have been observed using ground-based telescopes, where the relative stability of stars and Earth facilitated effective image differencing techniques alongside traditional fast moving celestial object detection and classification algorithms. However, the growing prevalence of space-based telescopes, along with their diverse observational modes, produces images with different properties, rendering conventional methods less effective. This paper presents a novel algorithm for detecting fast moving celestial objects within star fields. Our approach enhances state-of-the-art fast moving celestial object detection neural networks by transforming them into physical-inspired neural networks. These neural networks leverage the point spread function of the telescope and the specific observational mode as prior information; they can directly identify moving fast moving celestial objects within star fields without requiring additional training, thereby addressing the limitations of traditional techniques. Additionally, all neural networks are integrated using the mixture of experts technique, forming a comprehensive fast moving celestial object detection algorithm. We have evaluated our algorithm using simulated observational data that mimics various observations carried out by space based telescope scenarios and real observation images. Results demonstrate that our method effectively detects fast moving celestial objects across different observational modes.

  • 5 authors
·
Apr 10

Astroformer: More Data Might not be all you need for Classification

Recent advancements in areas such as natural language processing and computer vision rely on intricate and massive models that have been trained using vast amounts of unlabelled or partly labeled data and training or deploying these state-of-the-art methods to resource constraint environments has been a challenge. Galaxy morphologies are crucial to understanding the processes by which galaxies form and evolve. Efficient methods to classify galaxy morphologies are required to extract physical information from modern-day astronomy surveys. In this paper, we introduce Astroformer, a method to learn from less amount of data. We propose using a hybrid transformer-convolutional architecture drawing much inspiration from the success of CoAtNet and MaxViT. Concretely, we use the transformer-convolutional hybrid with a new stack design for the network, a different way of creating a relative self-attention layer, and pair it with a careful selection of data augmentation and regularization techniques. Our approach sets a new state-of-the-art on predicting galaxy morphologies from images on the Galaxy10 DECals dataset, a science objective, which consists of 17736 labeled images achieving 94.86% top-1 accuracy, beating the current state-of-the-art for this task by 4.62%. Furthermore, this approach also sets a new state-of-the-art on CIFAR-100 and Tiny ImageNet. We also find that models and training methods used for larger datasets would often not work very well in the low-data regime.

  • 1 authors
·
Apr 3, 2023

Pixel-level modelling of group-scale strong lens CASSOWARY 19

We present the first high-precision model for the group-scale strong lensing system CASSOWARY 19 (CSWA19), utilising images from the Hubble Space Telescope (HST). Sixteen member galaxies identified via the red-sequence method, and the main halo, all modelled as the dual Pseudo Isothermal Elliptical profile (dPIE), are incorporated into a parametric lens model alongside an external shear field. To model the system, we adopt the PyAutoLens software package, employing a progressive search chain strategy for realizing the transition of source model from multiple S\'ersic profiles to a brightness-adaptive pixelization, which uses 1000 pixels in the source plane to reconstruct the background source corresponding to 177,144 image pixels in the image plane. Our results indicate that the total mass within the Einstein radius is M_{theta_E} approx 1.41times10^{13}M_{odot} and the average slope of the total mass density rho (r)propto r^{-gamma} is gamma=1.33 within the effective radius. This slope is shallower than those measured in galaxies and groups but is closer to those of galaxy clusters. In addition, our approach successfully resolves the two merging galaxies in the background source and yields a total magnification of mu=103.18^{+0.23}_{-0.19}, which is significantly higher than the outcomes from previous studies of CSWA19. In summary, our research demonstrates the effectiveness of the brightness-adaptive pixelization source reconstruction technique for modelling group-scale strong lensing systems. It can serve as a technical reference for future investigations into pixel-level modelling of the group- and cluster-scale strong lensing systems.

  • 9 authors
·
Apr 15

Euclid. II. The VIS Instrument

This paper presents the specification, design, and development of the Visible Camera (VIS) on the ESA Euclid mission. VIS is a large optical-band imager with a field of view of 0.54 deg^2 sampled at 0.1" with an array of 609 Megapixels and spatial resolution of 0.18". It will be used to survey approximately 14,000 deg^2 of extragalactic sky to measure the distortion of galaxies in the redshift range z=0.1-1.5 resulting from weak gravitational lensing, one of the two principal cosmology probes of Euclid. With photometric redshifts, the distribution of dark matter can be mapped in three dimensions, and, from how this has changed with look-back time, the nature of dark energy and theories of gravity can be constrained. The entire VIS focal plane will be transmitted to provide the largest images of the Universe from space to date, reaching m_AB>24.5 with S/N >10 in a single broad I_E~(r+i+z) band over a six year survey. The particularly challenging aspects of the instrument are the control and calibration of observational biases, which lead to stringent performance requirements and calibration regimes. With its combination of spatial resolution, calibration knowledge, depth, and area covering most of the extra-Galactic sky, VIS will also provide a legacy data set for many other fields. This paper discusses the rationale behind the VIS concept and describes the instrument design and development before reporting the pre-launch performance derived from ground calibrations and brief results from the in-orbit commissioning. VIS should reach fainter than m_AB=25 with S/N>10 for galaxies of full-width half-maximum of 0.3" in a 1.3" diameter aperture over the Wide Survey, and m_AB>26.4 for a Deep Survey that will cover more than 50 deg^2. The paper also describes how VIS works with the other Euclid components of survey, telescope, and science data processing to extract the cosmological information.

  • 435 authors
·
May 22, 2024

The SRG/eROSITA All-Sky Survey: Large-scale view of the Centaurus cluster

Methods. We utilized the combined five SRG/eROSITA All-Sky Survey data (eRASS:5) to perform X-ray imaging and spectral analyses of the Centaurus cluster in various directions to large radii. Surface brightness (SB) profiles out to 2R_{200} were constructed. We acquired gas temperature, metallicity, and normalization per area profiles out to R_{200}. We compared our results with previous Centaurus studies, cluster outskirts measurements, and simulations. Comprehensive sky background analysis was done across the FoV, in particular, to assess the variation of the eROSITA Bubble emission that partially contaminates the field. Results. The processed X-ray images show the known sloshing-induced structures in the core. The core (rleq11~kpc) is better described with a 2T model than a 1T model. Here, we measured lower T from the cooler component (~1.0 keV) and higher Z (sim!1.6Z_odot), signifying an iron bias. In the intermediate radial range, we observed prominent SB and normalization per area excesses in the eastern sector (Cen 45 location), reaching out to R_{500}. Temperature enhancements near the location of Cen 45 imply that the gas is shock-heated due to the interaction with Cen 30, the significant excess behind Cen 45 center might be the tail/ram-pressure-stripped gas. We found good agreement between the outskirt temperatures with the profile from simulations and fit from Suzaku outskirts measurements. We detected significant SB emission to the sky background level out to R_{200} with a 3.5sigma and followed by 2.9sigma at 1.1R_{200}. The metallicity at R_{500}-R_{200} is low but within the ranges of other outskirts studies. Conclusions. We present the first measurement of ICM morphology and properties of Centaurus cluster sampling the whole azimuth beyond 30', increasing the probed volume by a factor of almost 30.

  • 12 authors
·
Apr 7, 2024

Libra: Leveraging Temporal Images for Biomedical Radiology Analysis

Radiology report generation (RRG) is a challenging task, as it requires a thorough understanding of medical images, integration of multiple temporal inputs, and accurate report generation. Effective interpretation of medical images, such as chest X-rays (CXRs), demands sophisticated visual-language reasoning to map visual findings to structured reports. Recent studies have shown that multimodal large language models (MLLMs) can acquire multimodal capabilities by aligning with pre-trained vision encoders. However, current approaches predominantly focus on single-image analysis or utilise rule-based symbolic processing to handle multiple images, thereby overlooking the essential temporal information derived from comparing current images with prior ones. To overcome this critical limitation, we introduce Libra, a temporal-aware MLLM tailored for CXR report generation using temporal images. Libra integrates a radiology-specific image encoder with a MLLM and utilises a novel Temporal Alignment Connector to capture and synthesise temporal information of images across different time points with unprecedented precision. Extensive experiments show that Libra achieves new state-of-the-art performance among the same parameter scale MLLMs for RRG tasks on the MIMIC-CXR. Specifically, Libra improves the RadCliQ metric by 12.9% and makes substantial gains across all lexical metrics compared to previous models.

  • 4 authors
·
Nov 28, 2024 1

ImageRAG: Enhancing Ultra High Resolution Remote Sensing Imagery Analysis with ImageRAG

Ultra High Resolution (UHR) remote sensing imagery (RSI) (e.g. 100,000 times 100,000 pixels or more) poses a significant challenge for current Remote Sensing Multimodal Large Language Models (RSMLLMs). If choose to resize the UHR image to standard input image size, the extensive spatial and contextual information that UHR images contain will be neglected. Otherwise, the original size of these images often exceeds the token limits of standard RSMLLMs, making it difficult to process the entire image and capture long-range dependencies to answer the query based on the abundant visual context. In this paper, we introduce ImageRAG for RS, a training-free framework to address the complexities of analyzing UHR remote sensing imagery. By transforming UHR remote sensing image analysis task to image's long context selection task, we design an innovative image contextual retrieval mechanism based on the Retrieval-Augmented Generation (RAG) technique, denoted as ImageRAG. ImageRAG's core innovation lies in its ability to selectively retrieve and focus on the most relevant portions of the UHR image as visual contexts that pertain to a given query. Fast path and slow path are proposed in this framework to handle this task efficiently and effectively. ImageRAG allows RSMLLMs to manage extensive context and spatial information from UHR RSI, ensuring the analysis is both accurate and efficient. Codebase will be released in https://github.com/om-ai-lab/ImageRAG

  • 10 authors
·
Nov 12, 2024

CheXagent: Towards a Foundation Model for Chest X-Ray Interpretation

Chest X-rays (CXRs) are the most frequently performed imaging test in clinical practice. Recent advances in the development of vision-language foundation models (FMs) give rise to the possibility of performing automated CXR interpretation, which can assist physicians with clinical decision-making and improve patient outcomes. However, developing FMs that can accurately interpret CXRs is challenging due to the (1) limited availability of large-scale vision-language datasets in the medical image domain, (2) lack of vision and language encoders that can capture the complexities of medical data, and (3) absence of evaluation frameworks for benchmarking the abilities of FMs on CXR interpretation. In this work, we address these challenges by first introducing CheXinstruct - a large-scale instruction-tuning dataset curated from 28 publicly-available datasets. We then present CheXagent - an instruction-tuned FM capable of analyzing and summarizing CXRs. To build CheXagent, we design a clinical large language model (LLM) for parsing radiology reports, a vision encoder for representing CXR images, and a network to bridge the vision and language modalities. Finally, we introduce CheXbench - a novel benchmark designed to systematically evaluate FMs across 8 clinically-relevant CXR interpretation tasks. Extensive quantitative evaluations and qualitative reviews with five expert radiologists demonstrate that CheXagent outperforms previously-developed general- and medical-domain FMs on CheXbench tasks. Furthermore, in an effort to improve model transparency, we perform a fairness evaluation across factors of sex, race and age to highlight potential performance disparities. Our project is at https://stanford-aimi.github.io/chexagent.html.

  • 17 authors
·
Jan 22, 2024 2

Follow-Up of Extended Shells around B[e] Stars

B[e] stars are massive B type emission line stars in different evolutionary stages ranging from pre-main sequence to post-main sequence. Due to their mass loss and ejection events these objects deposit huge amounts of mass and energy into their environment and enrich it with chemically processed material, contributing significantly to the chemical and dynamical evolution of their host galaxies. However, the large-scale environments of these enigmatic objects have not attracted much attention. The first and so far only catalog reporting the detection of extended shells around a sample of B[e] stars was an Ha imaging survey carried out in the year 2001, and was limited to bright targets in the northern hemisphere. We have recently started a follow-up of those targets to detect possible evolution of their nebulae in the plane of the sky over a baseline of two decades. Furthermore, we extend our survey to southern targets and fainter northern ones to complement and complete our knowledge on large-scale ejecta surrounding B[e] stars. Besides imaging in Ha and selected nebular lines, we utilize long-slit and 3D spectral observations across the nebulae to derive their physical properties. We discovered pronounced nebula structures around 15 more objects, resulting in a total of 27 B[e] stars with a large-scale nebula. Here we present our (preliminary) results for three selected objects: the two massive supergiants MWC137 and MWC 314, and the unclassified B[e] star MWC 819.

  • 6 authors
·
Mar 2, 2022

GL-LCM: Global-Local Latent Consistency Models for Fast High-Resolution Bone Suppression in Chest X-Ray Images

Chest X-Ray (CXR) imaging for pulmonary diagnosis raises significant challenges, primarily because bone structures can obscure critical details necessary for accurate diagnosis. Recent advances in deep learning, particularly with diffusion models, offer significant promise for effectively minimizing the visibility of bone structures in CXR images, thereby improving clarity and diagnostic accuracy. Nevertheless, existing diffusion-based methods for bone suppression in CXR imaging struggle to balance the complete suppression of bones with preserving local texture details. Additionally, their high computational demand and extended processing time hinder their practical use in clinical settings. To address these limitations, we introduce a Global-Local Latent Consistency Model (GL-LCM) architecture. This model combines lung segmentation, dual-path sampling, and global-local fusion, enabling fast high-resolution bone suppression in CXR images. To tackle potential boundary artifacts and detail blurring in local-path sampling, we further propose Local-Enhanced Guidance, which addresses these issues without additional training. Comprehensive experiments on a self-collected dataset SZCH-X-Rays, and the public dataset JSRT, reveal that our GL-LCM delivers superior bone suppression and remarkable computational efficiency, significantly outperforming several competitive methods. Our code is available at https://github.com/diaoquesang/GL-LCM.

  • 10 authors
·
Aug 5

The Effect of Minor and Major Mergers on the Evolution of Low Excitation Radio Galaxies

We use deep, mu_{r} lesssim 28,mag,arcsec^{-2}, r-band imaging from the Dark Energy Camera Legacy Survey (DECaLS) to search for past, or ongoing, merger activity in a sample of 282 Low Excitation Radio Galaxies (LERGs) at z<0.07. Our principle aim is to assess the the role of mergers in the evolution of LERGs. Exploiting the imaging depth, we classify tidal remnants around galaxies as both minor and major morphological disturbances for our LERG sample and 1,622 control galaxies matched in redshift, stellar mass, and environment. In groups and in the field, the LERG minor merger fraction is consistent with the control population. In galaxy clusters, 8.8 pm 2.9, % of LERGs show evidence of recent minor mergers in contrast to 23.0pm 2.0, % of controls. This sim 4 sigma deficit of minor mergers in cluster LERGs suggests these events may inhibit this type of nuclear activity for galaxies within the cluster environment. We observe a > 4sigma excess of major mergers in the LERGs with M_{*} lesssim 10^{11},M_{odot}, with 10 pm 1.5, % of these AGN involved in such large-scale interactions compared to 3.2 pm 0.4,% of control galaxies. This excess of major mergers in LERGs decreases with increasing stellar mass, vanishing by M_{*} > 10^{11.3},M_{odot}. These observations show that minor mergers do not fuel LERGs, and are consistent with typical LERGs being powered by accretion of matter from their halo. Where LERGs are associated with major mergers, these objects may evolve into more efficiently accreting active galactic nuclei as the merger progresses and more gas falls on to the central engine.

  • 11 authors
·
Apr 30, 2019