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Sep 2

DiverGen: Improving Instance Segmentation by Learning Wider Data Distribution with More Diverse Generative Data

Instance segmentation is data-hungry, and as model capacity increases, data scale becomes crucial for improving the accuracy. Most instance segmentation datasets today require costly manual annotation, limiting their data scale. Models trained on such data are prone to overfitting on the training set, especially for those rare categories. While recent works have delved into exploiting generative models to create synthetic datasets for data augmentation, these approaches do not efficiently harness the full potential of generative models. To address these issues, we introduce a more efficient strategy to construct generative datasets for data augmentation, termed DiverGen. Firstly, we provide an explanation of the role of generative data from the perspective of distribution discrepancy. We investigate the impact of different data on the distribution learned by the model. We argue that generative data can expand the data distribution that the model can learn, thus mitigating overfitting. Additionally, we find that the diversity of generative data is crucial for improving model performance and enhance it through various strategies, including category diversity, prompt diversity, and generative model diversity. With these strategies, we can scale the data to millions while maintaining the trend of model performance improvement. On the LVIS dataset, DiverGen significantly outperforms the strong model X-Paste, achieving +1.1 box AP and +1.1 mask AP across all categories, and +1.9 box AP and +2.5 mask AP for rare categories.

  • 7 authors
·
May 16, 2024

Training for X-Ray Vision: Amodal Segmentation, Amodal Content Completion, and View-Invariant Object Representation from Multi-Camera Video

Amodal segmentation and amodal content completion require using object priors to estimate occluded masks and features of objects in complex scenes. Until now, no data has provided an additional dimension for object context: the possibility of multiple cameras sharing a view of a scene. We introduce MOVi-MC-AC: Multiple Object Video with Multi-Cameras and Amodal Content, the largest amodal segmentation and first amodal content dataset to date. Cluttered scenes of generic household objects are simulated in multi-camera video. MOVi-MC-AC contributes to the growing literature of object detection, tracking, and segmentation by including two new contributions to the deep learning for computer vision world. Multiple Camera (MC) settings where objects can be identified and tracked between various unique camera perspectives are rare in both synthetic and real-world video. We introduce a new complexity to synthetic video by providing consistent object ids for detections and segmentations between both frames and multiple cameras each with unique features and motion patterns on a single scene. Amodal Content (AC) is a reconstructive task in which models predict the appearance of target objects through occlusions. In the amodal segmentation literature, some datasets have been released with amodal detection, tracking, and segmentation labels. While other methods rely on slow cut-and-paste schemes to generate amodal content pseudo-labels, they do not account for natural occlusions present in the modal masks. MOVi-MC-AC provides labels for ~5.8 million object instances, setting a new maximum in the amodal dataset literature, along with being the first to provide ground-truth amodal content. The full dataset is available at https://huggingface.co/datasets/Amar-S/MOVi-MC-AC ,

  • 5 authors
·
Jun 30, 2025 1

Discovery and recovery of crystalline materials with property-conditioned transformers

Generative models have recently shown great promise for accelerating the design and discovery of new functional materials. Conditional generation enhances this capacity by allowing inverse design, where specific desired properties can be requested during the generation process. However, conditioning of transformer-based approaches, in particular, is constrained by discrete tokenisation schemes and the risk of catastrophic forgetting during fine-tuning. This work introduces CrystaLLM-π (property injection), a conditional autoregressive framework that integrates continuous property representations directly into the transformer's attention mechanism. Two architectures, Property-Key-Value (PKV) Prefix attention and PKV Residual attention, are presented. These methods bypass inefficient sequence-level tokenisation and preserve foundational knowledge from unsupervised pre-training on Crystallographic Information Files (CIFs) as textual input. We establish the efficacy of these mechanisms through systematic robustness studies and evaluate the framework's versatility across two distinct tasks. First, for structure recovery, the model processes high-dimensional, heterogeneous X-ray diffraction patterns, achieving structural accuracy competitive with specialised models and demonstrating applications to experimental structure recovery and polymorph differentiation. Second, for materials discovery, the model is fine-tuned on a specialised photovoltaic dataset to generate novel, stable candidates validated by Density Functional Theory (DFT). It implicitly learns to target optimal band gap regions for high photovoltaic efficiency, demonstrating a capability to map complex structure-property relationships. CrystaLLM-π provides a unified, flexible, and computationally efficient framework for inverse materials design.

  • 8 authors
·
Nov 26, 2025

A Large-Scale Dataset of Search Interests Related to Disease X Originating from Different Geographic Regions

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

  • 5 authors
·
Dec 19, 2023

FG-CXR: A Radiologist-Aligned Gaze Dataset for Enhancing Interpretability in Chest X-Ray Report Generation

Developing an interpretable system for generating reports in chest X-ray (CXR) analysis is becoming increasingly crucial in Computer-aided Diagnosis (CAD) systems, enabling radiologists to comprehend the decisions made by these systems. Despite the growth of diverse datasets and methods focusing on report generation, there remains a notable gap in how closely these models' generated reports align with the interpretations of real radiologists. In this study, we tackle this challenge by initially introducing Fine-Grained CXR (FG-CXR) dataset, which provides fine-grained paired information between the captions generated by radiologists and the corresponding gaze attention heatmaps for each anatomy. Unlike existing datasets that include a raw sequence of gaze alongside a report, with significant misalignment between gaze location and report content, our FG-CXR dataset offers a more grained alignment between gaze attention and diagnosis transcript. Furthermore, our analysis reveals that simply applying black-box image captioning methods to generate reports cannot adequately explain which information in CXR is utilized and how long needs to attend to accurately generate reports. Consequently, we propose a novel explainable radiologist's attention generator network (Gen-XAI) that mimics the diagnosis process of radiologists, explicitly constraining its output to closely align with both radiologist's gaze attention and transcript. Finally, we perform extensive experiments to illustrate the effectiveness of our method. Our datasets and checkpoint is available at https://github.com/UARK-AICV/FG-CXR.

  • 11 authors
·
Nov 22, 2024

ViX-Ray: A Vietnamese Chest X-Ray Dataset for Vision-Language Models

Vietnamese medical research has become an increasingly vital domain, particularly with the rise of intelligent technologies aimed at reducing time and resource burdens in clinical diagnosis. Recent advances in vision-language models (VLMs), such as Gemini and GPT-4V, have sparked a growing interest in applying AI to healthcare. However, most existing VLMs lack exposure to Vietnamese medical data, limiting their ability to generate accurate and contextually appropriate diagnostic outputs for Vietnamese patients. To address this challenge, we introduce ViX-Ray, a novel dataset comprising 5,400 Vietnamese chest X-ray images annotated with expert-written findings and impressions from physicians at a major Vietnamese hospital. We analyze linguistic patterns within the dataset, including the frequency of mentioned body parts and diagnoses, to identify domain-specific linguistic characteristics of Vietnamese radiology reports. Furthermore, we fine-tune five state-of-the-art open-source VLMs on ViX-Ray and compare their performance to leading proprietary models, GPT-4V and Gemini. Our results show that while several models generate outputs partially aligned with clinical ground truths, they often suffer from low precision and excessive hallucination, especially in impression generation. These findings not only demonstrate the complexity and challenge of our dataset but also establish ViX-Ray as a valuable benchmark for evaluating and advancing vision-language models in the Vietnamese clinical domain.

  • 7 authors
·
Mar 15

X-RAY: Mapping LLM Reasoning Capability via Formalized and Calibrated Probes

Large language models (LLMs) achieve promising performance, yet their ability to reason remains poorly understood. Existing evaluations largely emphasize task-level accuracy, often conflating pattern matching with reasoning capability. We present X-RAY, an explainable reasoning analysis system that maps the LLM reasoning capability using calibrated, formally verified probes. We model reasoning capability as a function of extractable structure, operationalized through formal properties such as constraint interaction, reasoning depth, and solution-space geometry. X-Ray generates probes via formal tools with controlled structural variations, enabling precise isolation of incremental structural information through formal calibration and verification. We evaluate state-of-the-art LLMs on problems ranging from junior-level to advanced in mathematics, physics, and chemistry. Our analysis reveals a systematic asymmetry in LLM reasoning: models are relatively robust to constraint refinement, where additional conditions shrink an existing solution space, but degrade sharply under solution-space restructuring, where modifications alter the underlying structural form of the solution manifold. Moreover, calibrated formal probes differentiate models that appear indistinguishable on standard benchmarks and reveal failure modes that are structurally interpretable rather than opaque. Beyond evaluation, our framework is contamination-free and supports the training and testing of reasoning models.

  • 4 authors
·
Mar 4

X-Former: Unifying Contrastive and Reconstruction Learning for MLLMs

Recent advancements in Multimodal Large Language Models (MLLMs) have revolutionized the field of vision-language understanding by integrating visual perception capabilities into Large Language Models (LLMs). The prevailing trend in this field involves the utilization of a vision encoder derived from vision-language contrastive learning (CL), showing expertise in capturing overall representations while facing difficulties in capturing detailed local patterns. In this work, we focus on enhancing the visual representations for MLLMs by combining high-frequency and detailed visual representations, obtained through masked image modeling (MIM), with semantically-enriched low-frequency representations captured by CL. To achieve this goal, we introduce X-Former which is a lightweight transformer module designed to exploit the complementary strengths of CL and MIM through an innovative interaction mechanism. Specifically, X-Former first bootstraps vision-language representation learning and multimodal-to-multimodal generative learning from two frozen vision encoders, i.e., CLIP-ViT (CL-based) and MAE-ViT (MIM-based). It further bootstraps vision-to-language generative learning from a frozen LLM to ensure visual features from X-Former can be interpreted by the LLM. To demonstrate the effectiveness of our approach, we assess its performance on tasks demanding detailed visual understanding. Extensive evaluations indicate that X-Former excels in visual reasoning tasks involving both structural and semantic categories in the GQA dataset. Assessment on fine-grained visual perception benchmark further confirms its superior capabilities in visual understanding.

  • 8 authors
·
Jul 18, 2024

ReXVQA: A Large-scale Visual Question Answering Benchmark for Generalist Chest X-ray Understanding

We present ReXVQA, the largest and most comprehensive benchmark for visual question answering (VQA) in chest radiology, comprising approximately 696,000 questions paired with 160,000 chest X-rays studies across training, validation, and test sets. Unlike prior efforts that rely heavily on template based queries, ReXVQA introduces a diverse and clinically authentic task suite reflecting five core radiological reasoning skills: presence assessment, location analysis, negation detection, differential diagnosis, and geometric reasoning. We evaluate eight state-of-the-art multimodal large language models, including MedGemma-4B-it, Qwen2.5-VL, Janus-Pro-7B, and Eagle2-9B. The best-performing model (MedGemma) achieves 83.24% overall accuracy. To bridge the gap between AI performance and clinical expertise, we conducted a comprehensive human reader study involving 3 radiology residents on 200 randomly sampled cases. Our evaluation demonstrates that MedGemma achieved superior performance (83.84% accuracy) compared to human readers (best radiology resident: 77.27%), representing a significant milestone where AI performance exceeds expert human evaluation on chest X-ray interpretation. The reader study reveals distinct performance patterns between AI models and human experts, with strong inter-reader agreement among radiologists while showing more variable agreement patterns between human readers and AI models. ReXVQA establishes a new standard for evaluating generalist radiological AI systems, offering public leaderboards, fine-grained evaluation splits, structured explanations, and category-level breakdowns. This benchmark lays the foundation for next-generation AI systems capable of mimicking expert-level clinical reasoning beyond narrow pathology classification. Our dataset will be open-sourced at https://huggingface.co/datasets/rajpurkarlab/ReXVQA

  • 8 authors
·
Jun 4, 2025

Look What the Probes Dragged In! Real-World Chest X-ray Shortcuts in MedCLIP

Vision-language models, such as contrastive language-image pre-training (CLIP)-based approaches, have reached state-of-the-art (SOTA) results in medical artificial intelligence. However, recent work reveals that CLIP-based models remain vulnerable to shortcuts. We investigate how real-world shortcuts manifest across different layers of the medical CLIP-based model, MedCLIP, and its vision encoder, a frozen ResNet-50. We attach 17 linear classification probes to the intermediate layers of the ResNet-50 and train them on three different dataset configurations and targets: NIH-CXR14 (pneumothorax) and PadChest (cardiomegaly and pneumothorax). This setup allows us to observe model behaviour during evaluation using subgroup-based calibration and layer-wise confidence curves. We find that the final linear probes achieve a high AUROC but poor calibration in the models. The layer-wise confidence analyses suggest that shortcuts emerge at different depths. Patterns consistent with localised shortcuts, such as drains, appear at later layers, while patterns consistent with diffuse shortcuts, such as scanner-specific noise patterns, emerge earlier, aligning with previous work. Finally, we conduct a manual analysis of the images, which reveals data quality issues in both NIH-CXR14 and PadChest. Our findings underscore that even SOTA models remain vulnerable to shortcuts, and the need for high-quality and well-annotated datasets to draw solid conclusions. Code can be found on our GitHub: https://github.com/nikodice4/MedCLIP_shortcuts.

  • 4 authors
·
Aug 11

Animate-X++: Universal Character Image Animation with Dynamic Backgrounds

Character image animation, which generates high-quality videos from a reference image and target pose sequence, has seen significant progress in recent years. However, most existing methods only apply to human figures, which usually do not generalize well on anthropomorphic characters commonly used in industries like gaming and entertainment. Furthermore, previous methods could only generate videos with static backgrounds, which limits the realism of the videos. For the first challenge, our in-depth analysis suggests to attribute this limitation to their insufficient modeling of motion, which is unable to comprehend the movement pattern of the driving video, thus imposing a pose sequence rigidly onto the target character. To this end, this paper proposes Animate-X++, a universal animation framework based on DiT for various character types, including anthropomorphic characters. To enhance motion representation, we introduce the Pose Indicator, which captures comprehensive motion pattern from the driving video through both implicit and explicit manner. The former leverages CLIP visual features of a driving video to extract its gist of motion, like the overall movement pattern and temporal relations among motions, while the latter strengthens the generalization of DiT by simulating possible inputs in advance that may arise during inference. For the second challenge, we introduce a multi-task training strategy that jointly trains the animation and TI2V tasks. Combined with the proposed partial parameter training, this approach achieves not only character animation but also text-driven background dynamics, making the videos more realistic. Moreover, we introduce a new Animated Anthropomorphic Benchmark (A2Bench) to evaluate the performance of Animate-X++ on universal and widely applicable animation images. Extensive experiments demonstrate the superiority and effectiveness of Animate-X++.

  • 7 authors
·
Aug 12, 2025

Is planetary inward migration responsible for GJ 504's fast rotation and bright X-ray luminosity? New constraints from eROSITA

The discovery of an increasing variety of exoplanets in very close orbits around their host stars raised many questions about how stars and planets interact, and to which extent host stars' properties may be influenced by the presence of close-by companions. Understanding how the evolution of stars is impacted by the interactions with their planets is fundamental to disentangle their intrinsic evolution from Star-Planet Interactions (SPI)-induced phenomena. GJ 504 is a promising candidate for a star that underwent strong SPI. Its unusually short rotational period (3.4 days), while being in contrast with what is expected by single-star models, could result from the inward migration of a close-by, massive companion, pushed starward by tides. Moreover, its brighter X-ray luminosity may hint at a rejuvenation of the dynamo process sustaining the stellar magnetic field, consequent to the SPI-induced spin-up. We aim to study the evolution of GJ 504 and establish whether by invoking the engulfment of a planetary companion we can better reproduce its rotational period and X-ray luminosity. We simulate the past evolution assuming two different scenarios: 'Star without close-by planet', 'Star with close-by planet'. In the second scenario, we investigate how inward migration and planetary engulfment driven by tides spin up the stellar surface and rejuvenate its dynamo. We compare our tracks with rotational period and X-ray data collected from the all-sky surveys of the ROentgen Survey with an Imaging Telescope Array (eROSITA) on board the Russian Spektrum-Roentgen-Gamma mission (SRG). Despite the very uncertain stellar age, we found that the second evolutionary scenario is in better agreement with the short rotational period and the bright X-ray luminosity of GJ 504, thus strongly favouring the inward migration scenario over the one in which close-by planets have no tidal impact on the star.

  • 7 authors
·
Jan 13, 2025

Animate-X: Universal Character Image Animation with Enhanced Motion Representation

Character image animation, which generates high-quality videos from a reference image and target pose sequence, has seen significant progress in recent years. However, most existing methods only apply to human figures, which usually do not generalize well on anthropomorphic characters commonly used in industries like gaming and entertainment. Our in-depth analysis suggests to attribute this limitation to their insufficient modeling of motion, which is unable to comprehend the movement pattern of the driving video, thus imposing a pose sequence rigidly onto the target character. To this end, this paper proposes Animate-X, a universal animation framework based on LDM for various character types (collectively named X), including anthropomorphic characters. To enhance motion representation, we introduce the Pose Indicator, which captures comprehensive motion pattern from the driving video through both implicit and explicit manner. The former leverages CLIP visual features of a driving video to extract its gist of motion, like the overall movement pattern and temporal relations among motions, while the latter strengthens the generalization of LDM by simulating possible inputs in advance that may arise during inference. Moreover, we introduce a new Animated Anthropomorphic Benchmark (A^2Bench) to evaluate the performance of Animate-X on universal and widely applicable animation images. Extensive experiments demonstrate the superiority and effectiveness of Animate-X compared to state-of-the-art methods.

  • 9 authors
·
Oct 14, 2024 5

Seeing Like Radiologists: Context- and Gaze-Guided Vision-Language Pretraining for Chest X-rays

Despite recent advances in medical vision-language pretraining, existing models still struggle to capture the diagnostic workflow: radiographs are typically treated as context-agnostic images, while radiologists' gaze -- a crucial cue for visual reasoning -- remains largely underexplored by existing methods. These limitations hinder the modeling of disease-specific patterns and weaken cross-modal alignment. To bridge this gap, we introduce CoGaze, a Context- and Gaze-guided vision-language pretraining framework for chest X-rays. We first propose a context-infused vision encoder that models how radiologists integrate clinical context -- including patient history, symptoms, and diagnostic intent -- to guide diagnostic reasoning. We then present a multi-level supervision paradigm that (1) enforces intra- and inter-modal semantic alignment through hybrid-positive contrastive learning, (2) injects diagnostic priors via disease-aware cross-modal representation learning, and (3) leverages radiologists' gaze as probabilistic priors to guide attention toward diagnostically salient regions. Extensive experiments demonstrate that CoGaze consistently outperforms state-of-the-art methods across diverse tasks, achieving up to +2.0% CheXbertF1 and +1.2% BLEU2 for free-text and structured report generation, +23.2% AUROC for zero-shot classification, and +12.2% Precision@1 for image-text retrieval. Code is available at https://github.com/mk-runner/CoGaze.

  • 8 authors
·
Mar 26

AlphaDiffract: Automated Crystallographic Analysis of Powder X-ray Diffraction Data

Materials identification and structural understanding from powder X-ray diffraction (PXRD) data is a long-standing challenge in materials science, fundamental to discovering and characterizing novel materials. A prerequisite for full structure solution is the accurate determination of the crystal lattice, including lattice parameters and crystallographic symmetries. Traditional methods for this are iterative and typically require expert input, and while existing deep learning approaches have shown promise, a robust, single-shot method for comprehensive lattice determination from experimental data remains a key goal. Here, we introduce AlphaDiffract, a deep learning framework that achieves state-of-the-art performance in predicting the crystal system, space group, and lattice parameters directly from PXRD patterns. AlphaDiffract utilizes a 1D adaptation of the ConvNeXt architecture, a modern convolutional neural network that integrates key design principles from transformers, coupled with dedicated prediction heads for each crystallographic property. The model is trained on the largest-to-date physics-based dataset of over 31 million simulated diffraction patterns, generated by augmenting 312,267 curated structures from the ICSD and Materials Project databases. Crucially, it demonstrates strong generalization to experimental data, achieving 81.7% crystal system accuracy and 66.2% space group accuracy on the RRUFF dataset while additionally predicting all six lattice parameters. By providing a unified model for rapid and accurate lattice determination from PXRD data, AlphaDiffract represents a significant step forward in leveraging deep learning for high-throughput materials discovery.

  • 9 authors
·
Mar 23

Dara: Automated multiple-hypothesis phase identification and refinement from powder X-ray diffraction

Powder X-ray diffraction (XRD) is a foundational technique for characterizing crystalline materials. However, the reliable interpretation of XRD patterns, particularly in multiphase systems, remains a manual and expertise-demanding task. As a characterization method that only provides structural information, multiple reference phases can often be fit to a single pattern, leading to potential misinterpretation when alternative solutions are overlooked. To ease humans' efforts and address the challenge, we introduce Dara (Data-driven Automated Rietveld Analysis), a framework designed to automate the robust identification and refinement of multiple phases from powder XRD data. Dara performs an exhaustive tree search over all plausible phase combinations within a given chemical space and validates each hypothesis using a robust Rietveld refinement routine (BGMN). Key features include structural database filtering, automatic clustering of isostructural phases during tree expansion, peak-matching-based scoring to identify promising phases for refinement. When ambiguity exists, Dara generates multiple hypothesis which can then be decided between by human experts or with further characteriztion tools. By enhancing the reliability and accuracy of phase identification, Dara enables scalable analysis of realistic complex XRD patterns and provides a foundation for integration into multimodal characterization workflows, moving toward fully self-driving materials discovery.

  • 5 authors
·
Dec 3, 2025

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, 2025

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 1

A data- and compute-efficient chest X-ray foundation model beyond aggressive scaling

Foundation models for medical imaging are typically pretrained on increasingly large datasets, following a "scale-at-all-costs" paradigm. However, this strategy faces two critical challenges: large-scale medical datasets often contain substantial redundancy and severe class imbalance that bias representation learning toward over-represented patterns, and indiscriminate training regardless of heterogeneity in data quality incurs considerable computational inefficiency. Here we demonstrate that active, principled data curation during pretraining can serve as a viable, cost-effective alternative to brute-force dataset enlargement. We introduce CheXficient, a chest X-ray (CXR) foundation model that selectively prioritizes informative training samples. CheXficient is pretrained on only 22.7% of 1,235,004 paired CXR images and reports while consuming under 27.3% of the total compute budget, yet achieving comparable or superior performance to its full-data counterpart and other large-scale pretrained models. We assess CheXficient across 20 individual benchmarks spanning 5 task types, including non-adapted off-the-shelf evaluations (zero-shot findings classification and crossmodal retrieval) and adapted downstream tasks (disease prediction, semantic segmentation, and radiology report generation). Further analyses show that CheXficient systematically prioritizes under-represented training samples, improving generalizability on long-tailed or rare conditions. Overall, our work offers practical insights into the data and computation demands for efficient pretraining and downstream adaptation of medical vision-language foundation models.

  • 12 authors
·
Feb 26

Fairness and Robustness of CLIP-Based Models for Chest X-rays

Motivated by the strong performance of CLIP-based models in natural image-text domains, recent efforts have adapted these architectures to medical tasks, particularly in radiology, where large paired datasets of images and reports, such as chest X-rays, are available. While these models have shown encouraging results in terms of accuracy and discriminative performance, their fairness and robustness in the different clinical tasks remain largely underexplored. In this study, we extensively evaluate six widely used CLIP-based models on chest X-ray classification using three publicly available datasets: MIMIC-CXR, NIH-CXR14, and NEATX. We assess the models fairness across six conditions and patient subgroups based on age, sex, and race. Additionally, we assess the robustness to shortcut learning by evaluating performance on pneumothorax cases with and without chest drains. Our results indicate performance gaps between patients of different ages, but more equitable results for the other attributes. Moreover, all models exhibit lower performance on images without chest drains, suggesting reliance on spurious correlations. We further complement the performance analysis with a study of the embeddings generated by the models. While the sensitive attributes could be classified from the embeddings, we do not see such patterns using PCA, showing the limitations of these visualisation techniques when assessing models. Our code is available at https://github.com/TheoSourget/clip_cxr_fairness

  • 6 authors
·
Jul 28, 2025

TRCGL-Net: A Long-Tailed Multi-Label Chest X-Ray Classification Framework with Generative Data Augmentation and Label Co-Occurrence Modeling

Chest X-ray multi-label classification is a core task in intelligent medical imaging diagnosis. However, real clinical data often exhibit extreme long-tailed distributions, leading to degraded performance on rare diseases in tail classes. This issue is not only driven by data scarcity but also by two intrinsic factors:1) attenuation of tail-class lesion representations under complex anatomical backgrounds, and 2) dominance of head classes in modeling label co-occurrence relationships. To address these challenges, we propose TRCGL-Net. First, a learnable text-guided conditional diffusion model is employed to generate high-quality tail-class chest X-ray image samples under disease semantic constraints, improving data diversity and realism of rare disease patterns while alleviating class imbalance and preserving pathology-consistent semantics.Second, a channel reweighting mechanism is introduced to perform feature recalibration by emphasizing disease-relevant feature channels, thereby improving feature discriminability under long-tailed distributions.A class-aware attention mechanism is further applied to generate class-specific attention maps, enabling the model to localize disease-relevant regions and focus on fine-grained lesion areas.Finally, a graph convolution network based on label co occurrence is introduced to establish an information propagation mechanism among categories. Experiments on the PadChest dataset show that the proposed method achieves a tail-class mAP of 0.4904, an overall mAP of 0.4408, and an mAUC of 0.8989, outperforming state-of-the-art methods. TRCGL-Net effectively improves recognition performance for rare diseases under long-tailed distributions and mitigates the impact of extreme class imbalance in chest X-ray multi-label classification.

  • 7 authors
·
Jun 30

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

  • 353 authors
·
May 3

Gemini Robotics: Bringing AI into the Physical World

Recent advancements in large multimodal models have led to the emergence of remarkable generalist capabilities in digital domains, yet their translation to physical agents such as robots remains a significant challenge. This report introduces a new family of AI models purposefully designed for robotics and built upon the foundation of Gemini 2.0. We present Gemini Robotics, an advanced Vision-Language-Action (VLA) generalist model capable of directly controlling robots. Gemini Robotics executes smooth and reactive movements to tackle a wide range of complex manipulation tasks while also being robust to variations in object types and positions, handling unseen environments as well as following diverse, open vocabulary instructions. We show that with additional fine-tuning, Gemini Robotics can be specialized to new capabilities including solving long-horizon, highly dexterous tasks, learning new short-horizon tasks from as few as 100 demonstrations and adapting to completely novel robot embodiments. This is made possible because Gemini Robotics builds on top of the Gemini Robotics-ER model, the second model we introduce in this work. Gemini Robotics-ER (Embodied Reasoning) extends Gemini's multimodal reasoning capabilities into the physical world, with enhanced spatial and temporal understanding. This enables capabilities relevant to robotics including object detection, pointing, trajectory and grasp prediction, as well as multi-view correspondence and 3D bounding box predictions. We show how this novel combination can support a variety of robotics applications. We also discuss and address important safety considerations related to this new class of robotics foundation models. The Gemini Robotics family marks a substantial step towards developing general-purpose robots that realizes AI's potential in the physical world.

  • 118 authors
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Mar 25, 2025 2

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
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Mar 19, 2025

Euclid Quick Data Release (Q1) Exploring galaxy properties with a multi-modal foundation model

Modern astronomical surveys, such as the Euclid mission, produce high-dimensional, multi-modal data sets that include imaging and spectroscopic information for millions of galaxies. These data serve as an ideal benchmark for large, pre-trained multi-modal models, which can leverage vast amounts of unlabelled data. In this work, we present the first exploration of Euclid data with AstroPT, an autoregressive multi-modal foundation model trained on approximately 300 000 optical and infrared Euclid images and spectral energy distributions (SEDs) from the first Euclid Quick Data Release. We compare self-supervised pre-training with baseline fully supervised training across several tasks: galaxy morphology classification; redshift estimation; similarity searches; and outlier detection. Our results show that: (a) AstroPT embeddings are highly informative, correlating with morphology and effectively isolating outliers; (b) including infrared data helps to isolate stars, but degrades the identification of edge-on galaxies, which are better captured by optical images; (c) simple fine-tuning of these embeddings for photometric redshift and stellar mass estimation outperforms a fully supervised approach, even when using only 1% of the training labels; and (d) incorporating SED data into AstroPT via a straightforward multi-modal token-chaining method improves photo-z predictions, and allow us to identify potentially more interesting anomalies (such as ringed or interacting galaxies) compared to a model pre-trained solely on imaging data.

  • 324 authors
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Mar 19, 2025

Euclid Quick Data Release (Q1). AstroVink: A vision transformer approach to find strong gravitational lens systems

We present AstroVink, a vision transformer classifier designed for automated identification of strong lens candidates in Euclid imaging. We build upon the DINOv2 encoder, fine tuned to distinguish between lens and non-lens galaxies. Our base model, trained on simulated strong lens systems and labelled non lenses, recovers 88 of the 110 lens candidates within the top 500 ranked candidates, corresponding to an inspection efficiency of one lens per 5.7 inspected objects in our test set. After the Q1 data release, which yielded about 500 lens candidates, we retrained the model using high confidence lens candidates and new negatives, initially flagged as potential lenses by other classifiers but rejected during visual inspection. The retrained network further improves performance, achieving recovery of all 110 systems within the same ranking and reducing the inspection effort to one lens per 4.5 inspected objects, demonstrating that incorporating real examples significantly enhances model generalisation. An analysis of training subsets revealed that the inclusion of realistic negative examples played a key role in this improvement. Finally, we applied the retrained model to the Q1 original selection of 1.08M targets, followed by a new round of Space Warps citizen science inspection and expert vetting, where we identified a total of eight Grade A and 26 Grade B new lens candidates. These results demonstrate that transformer based architectures can recover strong lens candidates with high efficiency in real Euclid data, while substantially reducing the number of candidates requiring visual inspection.

  • 305 authors
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Apr 22

Euclid Quick Data Release (Q1): From images to multiwavelength catalogues: the Euclid MERge Processing Function

The Euclid satellite is an ESA mission that was launched in July 2023. \Euclid is working in its regular observing mode with the target of observing an area of 14,000~deg^2 with two instruments, the Visible Camera (VIS) and the Near IR Spectrometer and Photometer (NISP) down to I_{rm E} = 24.5~mag (10, sigma) in the Euclid Wide Survey. Ground-based imaging data in the ugriz bands complement the \Euclid data to enable photo-z determination and VIS PSF modeling for week lensing analysis. Euclid investigates the distance-redshift relation and the evolution of cosmic structures by measuring shapes and redshifts of galaxies and clusters of galaxies out to zsim 2. Generating the multi-wavelength catalogues from \Euclid and ground-based data is an essential part of the \Euclid data processing system. In the framework of the \Euclid Science Ground Segment (SGS), the aim of the MER Processing Function (PF) pipeline is to detect objects in the \Euclid imaging data, measure their properties, and MERge them into a single multi-wavelength catalogue. The MER PF pipeline performs source detection on both visible (VIS) and near-infrared (NIR) images and offers four different photometric measurements: Kron total flux, aperture photometry on PSF-matched images, template fitting photometry, and S\'ersic fitting photometry. Furthermore, the MER PF pipeline measures a set of ancillary quantities, spanning from morphology to quality flags, to better characterise all detected sources. In this paper, we show how the MER PF pipeline is designed, detailing its main steps, and we show that the pipeline products meet the tight requirements that Euclid aims to achieve on photometric accuracy. We also present the other measurements (e.g. morphology) that are included in the OU-MER output catalogues and we list all output products coming out of the MER PF pipeline.

  • 348 authors
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Mar 19, 2025

AGORA: Avatars in Geography Optimized for Regression Analysis

While the accuracy of 3D human pose estimation from images has steadily improved on benchmark datasets, the best methods still fail in many real-world scenarios. This suggests that there is a domain gap between current datasets and common scenes containing people. To obtain ground-truth 3D pose, current datasets limit the complexity of clothing, environmental conditions, number of subjects, and occlusion. Moreover, current datasets evaluate sparse 3D joint locations corresponding to the major joints of the body, ignoring the hand pose and the face shape. To evaluate the current state-of-the-art methods on more challenging images, and to drive the field to address new problems, we introduce AGORA, a synthetic dataset with high realism and highly accurate ground truth. Here we use 4240 commercially-available, high-quality, textured human scans in diverse poses and natural clothing; this includes 257 scans of children. We create reference 3D poses and body shapes by fitting the SMPL-X body model (with face and hands) to the 3D scans, taking into account clothing. We create around 14K training and 3K test images by rendering between 5 and 15 people per image using either image-based lighting or rendered 3D environments, taking care to make the images physically plausible and photoreal. In total, AGORA consists of 173K individual person crops. We evaluate existing state-of-the-art methods for 3D human pose estimation on this dataset and find that most methods perform poorly on images of children. Hence, we extend the SMPL-X model to better capture the shape of children. Additionally, we fine-tune methods on AGORA and show improved performance on both AGORA and 3DPW, confirming the realism of the dataset. We provide all the registered 3D reference training data, rendered images, and a web-based evaluation site at https://agora.is.tue.mpg.de/.

  • 6 authors
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Apr 28, 2021

SemSpaceFL: A Collaborative Hierarchical Federated Learning Framework for Semantic Communication in 6G LEO Satellites

The advent of the sixth-generation (6G) wireless networks, enhanced by artificial intelligence, promises ubiquitous connectivity through Low Earth Orbit (LEO) satellites. These satellites are capable of collecting vast amounts of geographically diverse and real-time data, which can be immensely valuable for training intelligent models. However, limited inter-satellite communication and data privacy constraints hinder data collection on a single server for training. Therefore, we propose SemSpaceFL, a novel hierarchical federated learning (HFL) framework for LEO satellite networks, with integrated semantic communication capabilities. Our framework introduces a two-tier aggregation architecture where satellite models are first aggregated at regional gateways before final consolidation at a cloud server, which explicitly accounts for satellite mobility patterns and energy constraints. The key innovation lies in our novel aggregation approach, which dynamically adjusts the contribution of each satellite based on its trajectory and association with different gateways, which ensures stable model convergence despite the highly dynamic nature of LEO constellations. To further enhance communication efficiency, we incorporate semantic encoding-decoding techniques trained through the proposed HFL framework, which enables intelligent data compression while maintaining signal integrity. Our experimental results demonstrate that the proposed aggregation strategy achieves superior performance and faster convergence compared to existing benchmarks, while effectively managing the challenges of satellite mobility and energy limitations in dynamic LEO networks.

  • 6 authors
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May 1, 2025

Imaginative World Modeling with Scene Graphs for Embodied Agent Navigation

Semantic navigation requires an agent to navigate toward a specified target in an unseen environment. Employing an imaginative navigation strategy that predicts future scenes before taking action, can empower the agent to find target faster. Inspired by this idea, we propose SGImagineNav, a novel imaginative navigation framework that leverages symbolic world modeling to proactively build a global environmental representation. SGImagineNav maintains an evolving hierarchical scene graphs and uses large language models to predict and explore unseen parts of the environment. While existing methods solely relying on past observations, this imaginative scene graph provides richer semantic context, enabling the agent to proactively estimate target locations. Building upon this, SGImagineNav adopts an adaptive navigation strategy that exploits semantic shortcuts when promising and explores unknown areas otherwise to gather additional context. This strategy continuously expands the known environment and accumulates valuable semantic contexts, ultimately guiding the agent toward the target. SGImagineNav is evaluated in both real-world scenarios and simulation benchmarks. SGImagineNav consistently outperforms previous methods, improving success rate to 65.4 and 66.8 on HM3D and HSSD, and demonstrating cross-floor and cross-room navigation in real-world environments, underscoring its effectiveness and generalizability.

  • 8 authors
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Aug 9, 2025

BEDLAM: A Synthetic Dataset of Bodies Exhibiting Detailed Lifelike Animated Motion

We show, for the first time, that neural networks trained only on synthetic data achieve state-of-the-art accuracy on the problem of 3D human pose and shape (HPS) estimation from real images. Previous synthetic datasets have been small, unrealistic, or lacked realistic clothing. Achieving sufficient realism is non-trivial and we show how to do this for full bodies in motion. Specifically, our BEDLAM dataset contains monocular RGB videos with ground-truth 3D bodies in SMPL-X format. It includes a diversity of body shapes, motions, skin tones, hair, and clothing. The clothing is realistically simulated on the moving bodies using commercial clothing physics simulation. We render varying numbers of people in realistic scenes with varied lighting and camera motions. We then train various HPS regressors using BEDLAM and achieve state-of-the-art accuracy on real-image benchmarks despite training with synthetic data. We use BEDLAM to gain insights into what model design choices are important for accuracy. With good synthetic training data, we find that a basic method like HMR approaches the accuracy of the current SOTA method (CLIFF). BEDLAM is useful for a variety of tasks and all images, ground truth bodies, 3D clothing, support code, and more are available for research purposes. Additionally, we provide detailed information about our synthetic data generation pipeline, enabling others to generate their own datasets. See the project page: https://bedlam.is.tue.mpg.de/.

GPU Based Parallel Ising Computing for Combinatorial Optimization Problems in VLSI Physical Design

In VLSI physical design, many algorithms require the solution of difficult combinatorial optimization problems such as max/min-cut, max-flow problems etc. Due to the vast number of elements typically found in this problem domain, these problems are computationally intractable leading to the use of approximate solutions. In this work, we explore the Ising spin glass model as a solution methodology for hard combinatorial optimization problems using the general purpose GPU (GPGPU). The Ising model is a mathematical model of ferromagnetism in statistical mechanics. Ising computing finds a minimum energy state for the Ising model which essentially corresponds to the expected optimal solution of the original problem. Many combinatorial optimization problems can be mapped into the Ising model. In our work, we focus on the max-cut problem as it is relevant to many VLSI physical design problems. Our method is inspired by the observation that Ising annealing process is very amenable to fine-grain massive parallel GPU computing. We will illustrate how the natural randomness of GPU thread scheduling can be exploited during the annealing process to create random update patterns and allow better GPU resource utilization. Furthermore, the proposed GPU-based Ising computing can handle any general Ising graph with arbitrary connections, which was shown to be difficult for existing FPGA and other hardware based implementation methods. Numerical results show that the proposed GPU Ising max-cut solver can deliver more than 2000X speedup over the CPU version of the algorithm on some large examples, which shows huge performance improvement for addressing many hard optimization algorithms for practical VLSI physical design.

  • 5 authors
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Mar 13, 2019

Generative AI for Medical Imaging: extending the MONAI Framework

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

  • 24 authors
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Jul 27, 2023

Euclid preparation: I. The Euclid Wide Survey

Euclid is an ESA mission designed to constrain the properties of dark energy and gravity via weak gravitational lensing and galaxy clustering. It will carry out a wide area imaging and spectroscopy survey (EWS) in visible and near-infrared, covering roughly 15,000 square degrees of extragalactic sky on six years. The wide-field telescope and instruments are optimized for pristine PSF and reduced straylight, producing very crisp images. This paper presents the building of the Euclid reference survey: the sequence of pointings of EWS, Deep fields, Auxiliary fields for calibrations, and spacecraft movements followed by Euclid as it operates in a step-and-stare mode from its orbit around the Lagrange point L2. Each EWS pointing has four dithered frames; we simulate the dither pattern at pixel level to analyse the effective coverage. We use up-to-date models for the sky background to define the Euclid region-of-interest (RoI). The building of the reference survey is highly constrained from calibration cadences, spacecraft constraints and background levels; synergies with ground-based coverage are also considered. Via purposely-built software optimized to prioritize best sky areas, produce a compact coverage, and ensure thermal stability, we generate a schedule for the Auxiliary and Deep fields observations and schedule the RoI with EWS transit observations. The resulting reference survey RSD_2021A fulfills all constraints and is a good proxy for the final solution. Its wide survey covers 14,500 square degrees. The limiting AB magnitudes (5σ point-like source) achieved in its footprint are estimated to be 26.2 (visible) and 24.5 (near-infrared); for spectroscopy, the H_α line flux limit is 2times 10^{-16} erg cm^{-2} s^{-1} at 1600 nm; and for diffuse emission the surface brightness limits are 29.8 (visible) and 28.4 (near-infrared) mag arcsec^{-2}.

  • 241 authors
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Aug 1, 2021

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratio in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially-resolved spectroscopy for thousands of nearby galaxies (median redshift of z = 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between redshifts z = 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGN and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5-meter Sloan Foundation Telescope at Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5-meter du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in July 2016.

  • 353 authors
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Feb 28, 2017

Transducing Language Models

Modern language models define distributions over strings, but downstream tasks often require different output formats. For instance, a model that generates byte-pair strings does not directly produce word-level predictions, and a DNA model does not directly produce amino-acid sequences. In such cases, a deterministic string-to-string transformation can convert the model's output to the desired form. This is a familiar pattern in probability theory: applying a function f to a random variable Xsim p yields a transformed random variable f(X) with an induced distribution. While such transformations are occasionally used in language modeling, prior work does not treat them as yielding new, fully functional language models. We formalize this perspective and introduce a general framework for language models derived from deterministic string-to-string transformations. We focus on transformations representable as finite-state transducers -- a commonly used state-machine abstraction for efficient string-to-string mappings. We develop algorithms that compose a language model with an FST to *marginalize* over source strings mapping to a given target, propagating probabilities through the transducer without altering model parameters and enabling *conditioning* on transformed outputs. We present an exact algorithm, an efficient approximation, and a theoretical analysis. We conduct experiments in three domains: converting language models from tokens to bytes, from tokens to words, and from DNA to amino acids. These experiments demonstrate inference-time adaptation of pretrained language models to match application-specific output requirements.

  • 6 authors
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Mar 4

Zero-Shot Low-dose CT Denoising via Sinogram Flicking

Many low-dose CT imaging methods rely on supervised learning, which requires a large number of paired noisy and clean images. However, obtaining paired images in clinical practice is challenging. To address this issue, zero-shot self-supervised methods train denoising networks using only the information within a single image, such as ZS-N2N. However, these methods often employ downsampling operations that degrade image resolution. Additionally, the training dataset is inherently constrained to the image itself. In this paper, we propose a zero-shot low-dose CT imaging method based on sinogram flicking, which operates within a single image but generates many copies via random conjugate ray matching. Specifically, two conjugate X-ray pencil beams measure the same path; their expected values should be identical, while their noise levels vary during measurements. By randomly swapping portions of the conjugate X-rays in the sinogram domain, we generate a large set of sinograms with consistent content but varying noise patterns. When displayed dynamically, these sinograms exhibit a flickering effect due to their identical structural content but differing noise patterns-hence the term sinogram flicking. We train the network on pairs of sinograms with the same content but different noise distributions using a lightweight model adapted from ZS-NSN. This process is repeated to obtain the final results. A simulation study demonstrates that our method outperforms state-of-the-art approaches such as ZS-N2N.

  • 2 authors
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Apr 10, 2025

They'll Verify. They Just Won't Act. How Authority Framing and Laundered Code Turn a Trusted Agentic CI/CD Pipeline Into an Attack Surface

We study a five-agent CI/CD pipeline (triage -> developer -> security-scan -> review -> approve/deploy), built from five distinct production LLMs across three providers, behind an LLM firewall in shadow mode. A single untrusted input - an external issue requesting a "usage-telemetry" feature - asks for code that exfiltrates process secrets (dict(os.environ)) to an attacker URL, laundered as observability. Across a pre-registered A x B (x C) factorial (N=20; naive arm N=60) we find: (1) the entry agent does not leak its system prompt (0/40); (2) an authority-framed injection ("pre-approved under SEC-2291, do not re-review") makes downstream verifiers see the secret-exfil line, cite the pre-approval, and ship it - the scanner passes ~80% of laundered pull requests, and the worst-case cell reaches 55% compromise; (3) the perceived presence of other verifiers yields only a small, non-significant reduction in individual scrutiny (a weak bystander analogue), even at N=60; and (4) content-based controls - code scanners and pattern detectors alike - miss the laundered intent entirely (the code is syntactically clean); only an LLM reasoning about intent is a partial defence. The failure is systemic: neither prompt secrecy nor distributed verification protects; a provenance-aware control at the entry, independent of both, would have. All data is 100% synthetic; the sink is mocked and the exfil URL is never contacted.

  • 1 authors
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Jul 20

Separating source-intrinsic and Lorentz invariance violation induced delays in the very high energy emission of blazar flares

Aims: The aim of the present study is to explore how to disentangle energy-dependent time delays due to a possible Lorentz invariance violation (LIV) at Planck scale from intrinsic delays expected in standard blazar flares. Methods: We first characterise intrinsic time delays in BL Lacs and Flat Spectrum Radio Quasars in standard one-zone time-dependent synchrotron self-Compton or external Compton models, during flares produced by particle acceleration and cooling processes. We simulate families of flares with both intrinsic and external LIV-induced energy-dependent delays. Discrimination between intrinsic and LIV delays is then investigated in two different ways. A technique based on Euclidean distance calculation between delays obtained in the synchrotron and in the inverse-Compton spectral bumps is used to assess their degree of correlation. A complementary study is performed using spectral hardness versus intensity diagrams in both energy ranges. Results: We show that the presence of non-negligible LIV effects, which essentially act only at very high energies (VHE), can drastically reduce the strong correlation expected between the X-ray and the VHE gamma-ray emission in leptonic scenarios. The LIV phenomenon can then be hinted at measuring the Euclidean distance d_{E} from simultaneous X-ray and gamma-ray flare monitoring. Large values of minimal distance d_{E,min} would directly indicate the influence of non-intrinsic time delays possibly due to LIV in SSC flares. LIV effects can also significantly modify the VHE hysteresis patterns in hardness-intensity diagrams and even change their direction of rotation as compared to the X-ray behaviour. Both observables could be used to discriminate between LIV and intrinsic delays, provided high quality flare observations are available.

  • 3 authors
·
Jun 3, 2024

From chambers to echo chambers: Quantifying polarization with a second-neighbor approach applied to Twitter's climate discussion

Social media platforms often foster environments where users primarily engage with content that aligns with their existing beliefs, thereby reinforcing their views and limiting exposure to opposing viewpoints. In this paper, we analyze X (formerly Twitter) discussions on climate change throughout 2019, using an unsupervised method centered on chambers--second-order information sources--to uncover ideological patterns at scale. Beyond direct connections, chambers capture shared sources of influence, revealing polarization dynamics efficiently and effectively. Analyzing retweet patterns, we identify echo chambers of climate believers and skeptics, revealing strong chamber overlap within ideological groups and minimal overlap between them, resulting in a robust bimodal structure that characterizes polarization. Our method enables us to infer the stance of high-impact users based on their audience's chamber alignment, allowing for the classification of over half the retweeting population with minimal cross-group interaction, in what we term augmented echo chamber classification. We benchmark our approach against manual labeling and a state-of-the-art latent ideology model, finding comparable performance but with nearly four times greater coverage. Moreover, we find that echo chamber structures remain stable over time, even as their members change significantly, suggesting that these structures are a persistent and emergent property of the system. Notably, polarization decreases and climate skepticism rises during the #FridaysForFuture strikes in September 2019. This chamber-based analysis offers valuable insights into the persistence and fluidity of ideological polarization on social media.

  • 4 authors
·
Jun 29, 2022 1

Vision-Language Models for Automated 3D PET/CT Report Generation

Positron emission tomography/computed tomography (PET/CT) is essential in oncology, yet the rapid expansion of scanners has outpaced the availability of trained specialists, making automated PET/CT report generation (PETRG) increasingly important for reducing clinical workload. Compared with structural imaging (e.g., X-ray, CT, and MRI), functional PET poses distinct challenges: metabolic patterns vary with tracer physiology, and whole-body 3D contextual information is required rather than local-region interpretation. To advance PETRG, we propose PETRG-3D, an end-to-end 3D dual-branch framework that separately encodes PET and CT volumes and incorporates style-adaptive prompts to mitigate inter-hospital variability in reporting practices. We construct PETRG-Lym, a multi-center lymphoma dataset collected from four hospitals (824 reports w/ 245,509 paired PET/CT slices), and construct AutoPET-RG-Lym, a publicly accessible PETRG benchmark derived from open imaging data but equipped with new expert-written, clinically validated reports (135 cases). To assess clinical utility, we introduce PETRG-Score, a lymphoma-specific evaluation protocol that jointly measures metabolic and structural findings across curated anatomical regions. Experiments show that PETRG-3D substantially outperforms existing methods on both natural language metrics (e.g., +31.49\% ROUGE-L) and clinical efficacy metrics (e.g., +8.18\% PET-All), highlighting the benefits of volumetric dual-modality modeling and style-aware prompting. Overall, this work establishes a foundation for future PET/CT-specific models emphasizing disease-aware reasoning and clinically reliable evaluation. Codes, models, and AutoPET-RG-Lym will be released.

  • 11 authors
·
Nov 24, 2025

Fast Autofocusing using Tiny Transformer Networks for Digital Holographic Microscopy

The numerical wavefront backpropagation principle of digital holography confers unique extended focus capabilities, without mechanical displacements along z-axis. However, the determination of the correct focusing distance is a non-trivial and time consuming issue. A deep learning (DL) solution is proposed to cast the autofocusing as a regression problem and tested over both experimental and simulated holograms. Single wavelength digital holograms were recorded by a Digital Holographic Microscope (DHM) with a 10x microscope objective from a patterned target moving in 3D over an axial range of 92 μm. Tiny DL models are proposed and compared such as a tiny Vision Transformer (TViT), tiny VGG16 (TVGG) and a tiny Swin-Transfomer (TSwinT). The proposed tiny networks are compared with their original versions (ViT/B16, VGG16 and Swin-Transformer Tiny) and the main neural networks used in digital holography such as LeNet and AlexNet. The experiments show that the predicted focusing distance Z_R^{Pred} is accurately inferred with an accuracy of 1.2 μm in average in comparison with the DHM depth of field of 15 μm. Numerical simulations show that all tiny models give the Z_R^{Pred} with an error below 0.3 μm. Such a prospect would significantly improve the current capabilities of computer vision position sensing in applications such as 3D microscopy for life sciences or micro-robotics. Moreover, all models reach an inference time on CPU, inferior to 25 ms per inference. In terms of occlusions, TViT based on its Transformer architecture is the most robust.

  • 7 authors
·
Mar 15, 2022

How Many Heads Make an SSM? A Unified Framework for Attention and State Space Models

Sequence modeling has produced diverse architectures -- from classical recurrent neural networks to modern Transformers and state space models (SSMs) -- yet a unified theoretical understanding of expressivity and trainability trade-offs remains limited. We introduce a unified framework that represents a broad class of sequence maps via an input-dependent effective interaction operator W_{ij}(X), making explicit two recurring construction patterns: (i) the Unified Factorized Framework (Explicit) (attention-style mixing), in which W_{ij}(X) varies through scalar coefficients applied to shared value maps, and (ii) Structured Dynamics (Implicit) (state-space recurrences), in which W_{ij} is induced by a latent dynamical system. Using this framework, we derive three theoretical results. First, we establish the Interaction Rank Gap: models in the Unified Factorized Framework, such as single-head attention, are constrained to a low-dimensional operator span and cannot represent certain structured dynamical maps. Second, we prove an Equivalence (Head-Count) Theorem showing that, within our multi-head factorized class, representing a linear SSM whose lag operators span a k-dimensional subspace on length-n sequences requires and is achievable with H=k heads. Third, we prove a Gradient Highway Result, showing that attention layers admit inputs with distance-independent gradient paths, whereas stable linear dynamics exhibit distance-dependent gradient attenuation. Together, these results formalize a fundamental trade-off between algebraic expressivity (interaction/operator span) and long-range gradient propagation, providing theoretical grounding for modern sequence architecture design.

  • 1 authors
·
Dec 17, 2025

PECCARY: A novel approach for characterizing orbital complexity, stochasticity, and regularity

Permutation Entropy and statistiCal Complexity Analysis for astRophYsics (PECCARY) is a computationally inexpensive, statistical method by which any time-series can be characterized as predominantly regular, complex, or stochastic. Elements of the PECCARY method have been used in a variety of physical, biological, economic, and mathematical scenarios, but have not yet gained traction in the astrophysical community. This study introduces the PECCARY technique with the specific aims to motivate its use in and optimize it for the analysis of astrophysical orbital systems. PECCARY works by decomposing a time-dependent measure, such as the x-coordinate or orbital angular momentum time-series, into ordinal patterns. Due to its unique approach and statistical nature, PECCARY is well-suited for detecting preferred and forbidden patterns (a signature of chaos), even when the chaotic behavior is short-lived or when working with a relatively short duration time-series or small sets of time-series data. A variety of examples are used to demonstrate the capabilities of PECCARY. These include mathematical examples (sine waves, varieties of noise, sums of sine waves, well-known chaotic functions), a double pendulum system, and astrophysical tracer particle simulations with potentials of varying intricacies. Since the adopted timescale used to diagnose a given time-series can affect the outcome, a method is presented to identify an ideal sampling scheme, constrained by the overall duration and the natural timescale of the system. The accompanying PECCARY Python package and its usage are discussed.

  • 3 authors
·
Jul 16, 2024

MasakhaNEWS: News Topic Classification for African languages

African languages are severely under-represented in NLP research due to lack of datasets covering several NLP tasks. While there are individual language specific datasets that are being expanded to different tasks, only a handful of NLP tasks (e.g. named entity recognition and machine translation) have standardized benchmark datasets covering several geographical and typologically-diverse African languages. In this paper, we develop MasakhaNEWS -- a new benchmark dataset for news topic classification covering 16 languages widely spoken in Africa. We provide an evaluation of baseline models by training classical machine learning models and fine-tuning several language models. Furthermore, we explore several alternatives to full fine-tuning of language models that are better suited for zero-shot and few-shot learning such as cross-lingual parameter-efficient fine-tuning (like MAD-X), pattern exploiting training (PET), prompting language models (like ChatGPT), and prompt-free sentence transformer fine-tuning (SetFit and Cohere Embedding API). Our evaluation in zero-shot setting shows the potential of prompting ChatGPT for news topic classification in low-resource African languages, achieving an average performance of 70 F1 points without leveraging additional supervision like MAD-X. In few-shot setting, we show that with as little as 10 examples per label, we achieved more than 90\% (i.e. 86.0 F1 points) of the performance of full supervised training (92.6 F1 points) leveraging the PET approach.

  • 65 authors
·
Apr 19, 2023