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Jul 31

Brain Latent Progression: Individual-based Spatiotemporal Disease Progression on 3D Brain MRIs via Latent Diffusion

The growing availability of longitudinal Magnetic Resonance Imaging (MRI) datasets has facilitated Artificial Intelligence (AI)-driven modeling of disease progression, making it possible to predict future medical scans for individual patients. However, despite significant advancements in AI, current methods continue to face challenges including achieving patient-specific individualization, ensuring spatiotemporal consistency, efficiently utilizing longitudinal data, and managing the substantial memory demands of 3D scans. To address these challenges, we propose Brain Latent Progression (BrLP), a novel spatiotemporal model designed to predict individual-level disease progression in 3D brain MRIs. The key contributions in BrLP are fourfold: (i) it operates in a small latent space, mitigating the computational challenges posed by high-dimensional imaging data; (ii) it explicitly integrates subject metadata to enhance the individualization of predictions; (iii) it incorporates prior knowledge of disease dynamics through an auxiliary model, facilitating the integration of longitudinal data; and (iv) it introduces the Latent Average Stabilization (LAS) algorithm, which (a) enforces spatiotemporal consistency in the predicted progression at inference time and (b) allows us to derive a measure of the uncertainty for the prediction at the global and voxel level. We train and evaluate BrLP on 11,730 T1-weighted (T1w) brain MRIs from 2,805 subjects and validate its generalizability on an external test set comprising 2,257 MRIs from 962 subjects. Our experiments compare BrLP-generated MRI scans with real follow-up MRIs, demonstrating state-of-the-art accuracy compared to existing methods. The code is publicly available at: https://github.com/LemuelPuglisi/BrLP.

  • 3 authors
·
Feb 12, 2025

SynthBA: Reliable Brain Age Estimation Across Multiple MRI Sequences and Resolutions

Brain age is a critical measure that reflects the biological ageing process of the brain. The gap between brain age and chronological age, referred to as brain PAD (Predicted Age Difference), has been utilized to investigate neurodegenerative conditions. Brain age can be predicted using MRIs and machine learning techniques. However, existing methods are often sensitive to acquisition-related variabilities, such as differences in acquisition protocols, scanners, MRI sequences, and resolutions, significantly limiting their application in highly heterogeneous clinical settings. In this study, we introduce Synthetic Brain Age (SynthBA), a robust deep-learning model designed for predicting brain age. SynthBA utilizes an advanced domain randomization technique, ensuring effective operation across a wide array of acquisition-related variabilities. To assess the effectiveness and robustness of SynthBA, we evaluate its predictive capabilities on internal and external datasets, encompassing various MRI sequences and resolutions, and compare it with state-of-the-art techniques. Additionally, we calculate the brain PAD in a large cohort of subjects with Alzheimer's Disease (AD), demonstrating a significant correlation with AD-related measures of cognitive dysfunction. SynthBA holds the potential to facilitate the broader adoption of brain age prediction in clinical settings, where re-training or fine-tuning is often unfeasible. The SynthBA source code and pre-trained models are publicly available at https://github.com/LemuelPuglisi/SynthBA.

  • 6 authors
·
Jun 1, 2024

Enhancing Spatiotemporal Disease Progression Models via Latent Diffusion and Prior Knowledge

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

  • 3 authors
·
May 6, 2024

A Novel Metric for Detecting Memorization in Generative Models for Brain MRI Synthesis

Deep generative models have emerged as a transformative tool in medical imaging, offering substantial potential for synthetic data generation. However, recent empirical studies highlight a critical vulnerability: these models can memorize sensitive training data, posing significant risks of unauthorized patient information disclosure. Detecting memorization in generative models remains particularly challenging, necessitating scalable methods capable of identifying training data leakage across large sets of generated samples. In this work, we propose DeepSSIM, a novel self-supervised metric for quantifying memorization in generative models. DeepSSIM is trained to: i) project images into a learned embedding space and ii) force the cosine similarity between embeddings to match the ground-truth SSIM (Structural Similarity Index) scores computed in the image space. To capture domain-specific anatomical features, training incorporates structure-preserving augmentations, allowing DeepSSIM to estimate similarity reliably without requiring precise spatial alignment. We evaluate DeepSSIM in a case study involving synthetic brain MRI data generated by a Latent Diffusion Model (LDM) trained under memorization-prone conditions, using 2,195 MRI scans from two publicly available datasets (IXI and CoRR). Compared to state-of-the-art memorization metrics, DeepSSIM achieves superior performance, improving F1 scores by an average of +52.03% over the best existing method. Code and data of our approach are publicly available at the following link: https://github.com/brAIn-science/DeepSSIM.

  • 5 authors
·
Sep 20, 2025

CoCoLIT: ControlNet-Conditioned Latent Image Translation for MRI to Amyloid PET Synthesis

Synthesizing amyloid PET scans from the more widely available and accessible structural MRI modality offers a promising, cost-effective approach for large-scale Alzheimer's Disease (AD) screening. This is motivated by evidence that, while MRI does not directly detect amyloid pathology, it may nonetheless encode information correlated with amyloid deposition that can be uncovered through advanced modeling. However, the high dimensionality and structural complexity of 3D neuroimaging data pose significant challenges for existing MRI-to-PET translation methods. Modeling the cross-modality relationship in a lower-dimensional latent space can simplify the learning task and enable more effective translation. As such, we present CoCoLIT (ControlNet-Conditioned Latent Image Translation), a diffusion-based latent generative framework that incorporates three main innovations: (1) a novel Weighted Image Space Loss (WISL) that improves latent representation learning and synthesis quality; (2) a theoretical and empirical analysis of Latent Average Stabilization (LAS), an existing technique used in similar generative models to enhance inference consistency; and (3) the introduction of ControlNet-based conditioning for MRI-to-PET translation. We evaluate CoCoLIT's performance on publicly available datasets and find that our model significantly outperforms state-of-the-art methods on both image-based and amyloid-related metrics. Notably, in amyloid-positivity classification, CoCoLIT outperforms the second-best method with improvements of +10.5% on the internal dataset and +23.7% on the external dataset. The code and models of our approach are available at https://github.com/brAIn-science/CoCoLIT.

  • 6 authors
·
Aug 2, 2025

Does VLA Even Know the Basics? Measuring Commonsense and World Knowledge Retention in Vision-Language-Action Models

Embodied Vision-Language-Action (VLA) models are typically obtained by fine-tuning powerful pretrained VLMs on robotics data, yet it is unclear how much commonsense and factual knowledge they retain after adaptation. Failures on knowledge-sensitive tasks are ambiguous, conflating missing knowledge with poor generalization of low-level control. We introduce Act2Answer, a lightweight protocol that adapts VLM knowledge benchmarks to VLA evaluation by requiring agents to answer through action. Each question becomes a short tabletop episode where the agent performs a single object-placement action to select among candidate answers, yielding an action-grounded success rate with reduced control confounds. We curate a test suite of such environments across diverse commonsense and world-knowledge categories and introduce layerwise intent probing to localize answer-relevant information across the VLM backbone and action head. In a large-scale study of 7 VLA models and 9 VLM baselines, we systematically rank models across categories, finding that VLAs show solid performance on simple concepts while exhibiting larger gaps on richer semantic categories relative to their source VLMs, that VQA co-training is associated with better knowledge retention, and that answer-relevant signals peak in middle VLA layers but attenuate in upper layers. Act2Answer is available at https://tttonyalpha.github.io/act2answer/.

  • 13 authors
·
Jun 16 2

SPARTA: Evaluating Reasoning Segmentation Robustness through Black-Box Adversarial Paraphrasing in Text Autoencoder Latent Space

Multimodal large language models (MLLMs) have shown impressive capabilities in vision-language tasks such as reasoning segmentation, where models generate segmentation masks based on textual queries. While prior work has primarily focused on perturbing image inputs, semantically equivalent textual paraphrases-crucial in real-world applications where users express the same intent in varied ways-remain underexplored. To address this gap, we introduce a novel adversarial paraphrasing task: generating grammatically correct paraphrases that preserve the original query meaning while degrading segmentation performance. To evaluate the quality of adversarial paraphrases, we develop a comprehensive automatic evaluation protocol validated with human studies. Furthermore, we introduce SPARTA-a black-box, sentence-level optimization method that operates in the low-dimensional semantic latent space of a text autoencoder, guided by reinforcement learning. SPARTA achieves significantly higher success rates, outperforming prior methods by up to 2x on both the ReasonSeg and LLMSeg-40k datasets. We use SPARTA and competitive baselines to assess the robustness of advanced reasoning segmentation models. We reveal that they remain vulnerable to adversarial paraphrasing-even under strict semantic and grammatical constraints. All code and data will be released publicly upon acceptance.

  • 9 authors
·
Oct 27, 2025

Uncertainty Visualization of Critical Points of 2D Scalar Fields for Parametric and Nonparametric Probabilistic Models

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. In this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

  • 8 authors
·
Jul 25, 2024

OCTolyzer: Fully automatic toolkit for segmentation and feature extracting in optical coherence tomography and scanning laser ophthalmoscopy data

Optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) of the eye has become essential to ophthalmology and the emerging field of oculomics, thus requiring a need for transparent, reproducible, and rapid analysis of this data for clinical research and the wider research community. Here, we introduce OCTolyzer, the first open-source toolkit for retinochoroidal analysis in OCT/SLO data. It features two analysis suites for OCT and SLO data, facilitating deep learning-based anatomical segmentation and feature extraction of the cross-sectional retinal and choroidal layers and en face retinal vessels. We describe OCTolyzer and evaluate the reproducibility of its OCT choroid analysis. At the population level, metrics for choroid region thickness were highly reproducible, with a mean absolute error (MAE)/Pearson correlation for macular volume choroid thickness (CT) of 6.7mum/0.99, macular B-scan CT of 11.6mum/0.99, and peripapillary CT of 5.0mum/0.99. Macular choroid vascular index (CVI) also showed strong reproducibility, with MAE/Pearson for volume CVI yielding 0.0271/0.97 and B-scan CVI 0.0130/0.91. At the eye level, measurement noise for regional and vessel metrics was below 5% and 20% of the population's variability, respectively. Outliers were caused by poor-quality B-scans with thick choroids and invisible choroid-sclera boundary. Processing times on a laptop CPU were under three seconds for macular/peripapillary B-scans and 85 seconds for volume scans. OCTolyzer can convert OCT/SLO data into reproducible and clinically meaningful retinochoroidal features and will improve the standardisation of ocular measurements in OCT/SLO image analysis, requiring no specialised training or proprietary software to be used. OCTolyzer is freely available here: https://github.com/jaburke166/OCTolyzer.

  • 12 authors
·
Jul 19, 2024

Surgical tool classification and localization: results and methods from the MICCAI 2022 SurgToolLoc challenge

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

  • 71 authors
·
May 11, 2023

PARROT: An Open Multilingual Radiology Reports Dataset

Rationale and Objectives: To develop and validate PARROT (Polyglottal Annotated Radiology Reports for Open Testing), a large, multicentric, open-access dataset of fictional radiology reports spanning multiple languages for testing natural language processing applications in radiology. Materials and Methods: From May to September 2024, radiologists were invited to contribute fictional radiology reports following their standard reporting practices. Contributors provided at least 20 reports with associated metadata including anatomical region, imaging modality, clinical context, and for non-English reports, English translations. All reports were assigned ICD-10 codes. A human vs. AI report differentiation study was conducted with 154 participants (radiologists, healthcare professionals, and non-healthcare professionals) assessing whether reports were human-authored or AI-generated. Results: The dataset comprises 2,658 radiology reports from 76 authors across 21 countries and 13 languages. Reports cover multiple imaging modalities (CT: 36.1%, MRI: 22.8%, radiography: 19.0%, ultrasound: 16.8%) and anatomical regions, with chest (19.9%), abdomen (18.6%), head (17.3%), and pelvis (14.1%) being most prevalent. In the differentiation study, participants achieved 53.9% accuracy (95% CI: 50.7%-57.1%) in distinguishing between human and AI-generated reports, with radiologists performing significantly better (56.9%, 95% CI: 53.3%-60.6%, p<0.05) than other groups. Conclusion: PARROT represents the largest open multilingual radiology report dataset, enabling development and validation of natural language processing applications across linguistic, geographic, and clinical boundaries without privacy constraints.

  • 88 authors
·
Jul 25, 2025

Planck 2018 results. I. Overview and the cosmological legacy of Planck

The European Space Agency's Planck satellite, which was dedicated to studying the early Universe and its subsequent evolution, was launched on 14 May 2009. It scanned the microwave and submillimetre sky continuously between 12 August 2009 and 23 October 2013, producing deep, high-resolution, all-sky maps in nine frequency bands from 30 to 857GHz. This paper presents the cosmological legacy of Planck, which currently provides our strongest constraints on the parameters of the standard cosmological model and some of the tightest limits available on deviations from that model. The 6-parameter LCDM model continues to provide an excellent fit to the cosmic microwave background data at high and low redshift, describing the cosmological information in over a billion map pixels with just six parameters. With 18 peaks in the temperature and polarization angular power spectra constrained well, Planck measures five of the six parameters to better than 1% (simultaneously), with the best-determined parameter (theta_*) now known to 0.03%. We describe the multi-component sky as seen by Planck, the success of the LCDM model, and the connection to lower-redshift probes of structure formation. We also give a comprehensive summary of the major changes introduced in this 2018 release. The Planck data, alone and in combination with other probes, provide stringent constraints on our models of the early Universe and the large-scale structure within which all astrophysical objects form and evolve. We discuss some lessons learned from the Planck mission, and highlight areas ripe for further experimental advances.

  • 191 authors
·
Dec 2, 2019

Planck 2018 results. V. CMB power spectra and likelihoods

This paper describes the 2018 Planck CMB likelihoods, following a hybrid approach similar to the 2015 one, with different approximations at low and high multipoles, and implementing several methodological and analysis refinements. With more realistic simulations, and better correction and modelling of systematics, we can now make full use of the High Frequency Instrument polarization data. The low-multipole 100x143 GHz EE cross-spectrum constrains the reionization optical-depth parameter tau to better than 15% (in combination with with the other low- and high-ell likelihoods). We also update the 2015 baseline low-ell joint TEB likelihood based on the Low Frequency Instrument data, which provides a weaker tau constraint. At high multipoles, a better model of the temperature-to-polarization leakage and corrections for the effective calibrations of the polarization channels (polarization efficiency or PE) allow us to fully use the polarization spectra, improving the constraints on the LambdaCDM parameters by 20 to 30% compared to TT-only constraints. Tests on the modelling of the polarization demonstrate good consistency, with some residual modelling uncertainties, the accuracy of the PE modelling being the main limitation. Using our various tests, simulations, and comparison between different high-ell implementations, we estimate the consistency of the results to be better than the 0.5sigma level. Minor curiosities already present before (differences between ell<800 and ell>800 parameters or the preference for more smoothing of the C_ell peaks) are shown to be driven by the TT power spectrum and are not significantly modified by the inclusion of polarization. Overall, the legacy Planck CMB likelihoods provide a robust tool for constraining the cosmological model and represent a reference for future CMB observations. (Abridged)

  • 168 authors
·
Jul 30, 2019

Planck 2018 results. VI. Cosmological parameters

We present cosmological parameter results from the final full-mission Planck measurements of the CMB anisotropies. We find good consistency with the standard spatially-flat 6-parameter LambdaCDM cosmology having a power-law spectrum of adiabatic scalar perturbations (denoted "base LambdaCDM" in this paper), from polarization, temperature, and lensing, separately and in combination. A combined analysis gives dark matter density Omega_c h^2 = 0.120pm 0.001, baryon density Omega_b h^2 = 0.0224pm 0.0001, scalar spectral index n_s = 0.965pm 0.004, and optical depth tau = 0.054pm 0.007 (in this abstract we quote 68,% confidence regions on measured parameters and 95,% on upper limits). The angular acoustic scale is measured to 0.03,% precision, with 100theta_*=1.0411pm 0.0003. These results are only weakly dependent on the cosmological model and remain stable, with somewhat increased errors, in many commonly considered extensions. Assuming the base-LambdaCDM cosmology, the inferred late-Universe parameters are: Hubble constant H_0 = (67.4pm 0.5)km/s/Mpc; matter density parameter Omega_m = 0.315pm 0.007; and matter fluctuation amplitude sigma_8 = 0.811pm 0.006. We find no compelling evidence for extensions to the base-LambdaCDM model. Combining with BAO we constrain the effective extra relativistic degrees of freedom to be N_{rm eff} = 2.99pm 0.17, and the neutrino mass is tightly constrained to sum m_nu< 0.12eV. The CMB spectra continue to prefer higher lensing amplitudes than predicted in base -LambdaCDM at over 2,sigma, which pulls some parameters that affect the lensing amplitude away from the base-LambdaCDM model; however, this is not supported by the lensing reconstruction or (in models that also change the background geometry) BAO data. (Abridged)

  • 182 authors
·
Jul 17, 2018