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Julia E. Vogt

Publications and source records attributed to Julia E. Vogt.

At least 19 recordsLinked to original sources
arXiv2026

Reading the Whole Heart: Latent-Attention Masked Autoencoders for Multimodal Cardiac Representation Learning

Cardiovascular diagnosis rests on integrating complementary modalities, like ECG, echocardiography, chest radiographs, and clinical variables, each capturing distinct but correlated aspects of cardiac physiology. Yet most medical foundation models remain modality-specific, combining modalities only for finetuning or post-training. This discards the cross-modal evidence clinicians naturally integrate and ignores the structure within each modality. We introduce Latent-Attention Masked Autoencoders (LAMAE), a multimodal, structure-aware masked autoencoder that jointly learns patient-level representations during self-supervised pretraining. Rather than fusing modalities post hoc, LAMAE exchanges information directly in the latent space through a shared latent-attention module operating over a study-view-entity hierarchy, enabling aggregation of variable observations and graceful handling of missing modalities. Pretrained on over 1.2 million MIMIC-IV hospital stays, LAMAE outperforms modality-specific pretraining and strong contrastive and vision-language baselines across multimodal hospital-stay tasks, such as in-hospital mortality, ICD-10 and DRG coding, and length of stay, while remaining competitive on unimodal tasks. These gains persist even when only a single modality is available at test time, showing that modeling both intra- and inter-modal structure yields more robust, transferable representations.

cs.AI↗
arXiv2026

You Only Train Once: Differentiable Subset Selection for Omics Data

Selecting compact and informative gene subsets from single-cell transcriptomic data is essential for biomarker discovery, improving interpretability, and cost-effective profiling. However, most existing feature selection approaches either operate as multi-stage pipelines or rely on post hoc feature attribution, making selection and prediction weakly coupled. In this work, we present YOTO (you only train once), an end-to-end framework that jointly identifies discrete gene subsets and performs prediction within a single differentiable architecture. In our model, the prediction task directly guides which genes are selected, while the learned subsets, in turn, shape the predictive representation. This closed feedback loop enables the model to iteratively refine both what it selects and how it predicts during training. Unlike existing approaches, YOTO enforces sparsity so that only the selected genes contribute to inference, eliminating the need to train additional downstream classifiers. Through a multi-task learning design, the model learns shared representations across related objectives, allowing partially labeled datasets to inform one another, and discovering gene subsets that generalize across tasks without additional training steps. We evaluate YOTO on two representative single-cell RNA-seq datasets, showing that it consistently outperforms state-of-the-art baselines. These results demonstrate that sparse, end-to-end, multi-task gene subset selection improves predictive performance and yields compact and meaningful gene subsets, advancing biomarker discovery and single-cell analysis.

cs.LG↗
arXiv2026

RadAgent: A tool-using AI agent for stepwise interpretation of chest computed tomography

Vision-language models (VLM) have markedly advanced AI-driven interpretation and reporting of complex medical imaging, such as computed tomography (CT). Yet, existing methods largely relegate clinicians to passive observers of final outputs, offering no interpretable reasoning trace for them to inspect, validate, or refine. To address this, we introduce RadAgent, a tool-using AI agent that generates CT reports through a stepwise and interpretable process. Each resulting report is accompanied by a fully inspectable trace of intermediate decisions and tool interactions, allowing clinicians to examine how the reported findings are derived. In our experiments, we observe that RadAgent improves chest CT report generation over its 3D VLM counterpart, CT-Chat, across three dimensions. Clinical accuracy improves by 5.8 points (35.4% relative) in macro-F1 and 5.1 points (18.6% relative) in micro-F1. Robustness under adversarial conditions improves by 24.7 points (41.9% relative). Furthermore, RadAgent achieves 37.0% in faithfulness, a new capability entirely absent in its 3D VLM counterpart. By structuring the interpretation of chest CT as an explicit, tool-augmented and iterative reasoning trace, RadAgent brings us closer toward transparent and reliable AI for radiology.

cs.AI↗
arXiv2026

TOAST: Transformer Optimization using Adaptive and Simple Transformations

Foundation models achieve state-of-the-art performance across different tasks, but their size and computational demands raise concerns about accessibility and sustainability. Existing efficiency methods often require additional retraining or finetuning, limiting their practicality. Recent findings suggest that deep neural networks exhibit internal representation similarities. While such similarities across different models have been exploited for enabling techniques such as model stitching and merging, intra-network redundancy remains underexplored as a source for efficiency gains. In this paper, we introduce Transformer Optimization using Adaptive and Simple Transformations (TOAST), a framework that exploits these redundancies to approximate entire transformer blocks with lightweight closed-form mappings, such as linear transformations or even the identity function, without any additional training. Across state-of-the-art pretrained vision models (e.g., ViT, DINOv2, DeiT) and datasets ranging from MNIST to ImageNet-1k, TOAST reduces parameters and computation while preserving, and in some cases improving, downstream performance. These results show that large portions of transformer depth can be replaced by trivial functions, opening a new perspective on efficient foundation models.

cs.LG↗
arXiv2026

Foundation Model for Cardiac Time Series via Masked Latent Attention

Electrocardiograms (ECGs) are among the most widely available clinical signals and play a central role in cardiovascular diagnosis. While recent foundation models (FMs) have shown promise for learning transferable ECG representations, most existing pretraining approaches treat leads as independent channels and fail to explicitly leverage their strong structural redundancy. We introduce the latent attention masked autoencoder (LAMAE) FM that directly exploits this structure by learning cross-lead connection mechanisms during self-supervised pretraining. Our approach models higher-order interactions across leads through latent attention, enabling permutation-invariant aggregation and adaptive weighting of lead-specific representations. We provide empirical evidence on the Mimic-IV-ECG database that leveraging the cross-lead connection constitutes an effective form of structural supervision, improving representation quality and transferability. Our method shows strong performance in predicting ICD-10 codes, outperforming independent-lead masked modeling and alignment-based baselines.

cs.LG↗
arXiv2026

Beyond Independent Frames: Latent Attention Masked Autoencoders for Multi-View Echocardiography

Echocardiography is a widely used modality for cardiac assessment due to its non-invasive and cost-effective nature, but the sparse and heterogeneous spatiotemporal views of the heart pose distinct challenges. Existing masked autoencoder (MAE) approaches typically process images or short clips independently, failing to capture the inherent multi-view structure required for coherent cardiac representation. We introduce Latent Attention Masked Autoencoder (LAMAE), a foundation model architecture tailored to the multi-view nature of medical imaging. LAMAE augments the standard MAE with a latent attention module that enables information exchange across frames and views directly in latent space. This allows the model to aggregate variable-length sequences and distinct views, reconstructing a holistic representation of cardiac function from partial observations. We pretrain LAMAE on MIMIC-IV-ECHO, a large-scale, uncurated dataset reflecting real-world clinical variability. To the best of our knowledge, we present the first results for predicting ICD-10 codes from MIMIC-IV-ECHO videos. Furthermore, we empirically demonstrate that representations learned from adult data transfer effectively to pediatric cohorts despite substantial anatomical differences. These results provide evidence that incorporating structural priors, such as multi-view attention, yields significantly more robust and transferable representations.

cs.CV↗
arXiv2026

Structure is Supervision: Multiview Masked Autoencoders for Radiology

Building robust medical machine learning systems requires pretraining strategies that exploit the intrinsic structure present in clinical data. We introduce Multiview Masked Autoencoder (MVMAE), a self-supervised framework that leverages the natural multi-view organization of radiology studies to learn view-invariant and disease-relevant representations. MVMAE combines masked image reconstruction with cross-view alignment, transforming clinical redundancy across projections into a powerful self-supervisory signal. We further extend this approach with MVMAE-V2T, which incorporates radiology reports as an auxiliary text-based learning signal to enhance semantic grounding while preserving fully vision-based inference. Evaluated on a downstream disease classification task on three large-scale public datasets, MIMIC-CXR, CheXpert, and PadChest, MVMAE consistently outperforms supervised and vision-language baselines. Furthermore, MVMAE-V2T provides additional gains, particularly in low-label regimes where structured textual supervision is most beneficial. Together, these results establish the importance of structural and textual supervision as complementary paths toward scalable, clinically grounded medical foundation models.

cs.CV↗
arXiv2026

Rethinking Machine Unlearning: Models Designed to Forget via Key Deletion

Machine unlearning is rapidly becoming a practical requirement, driven by privacy regulations, data errors, and the need to remove harmful or corrupted training samples. Despite this, most existing methods tackle the problem purely from a post-hoc perspective. They attempt to erase the influence of targeted training samples through parameter updates that typically require access to the full training data. This creates a mismatch with real deployment scenarios where unlearning requests can be anticipated, revealing a fundamental limitation of post-hoc approaches. We propose unlearning by design, a novel paradigm in which models are directly trained to support forgetting as an inherent capability. We instantiate this idea with Machine UNlearning via KEY deletion (MUNKEY), a memory augmented transformer that decouples instance-specific memorization from model weights. Here, unlearning corresponds to removing the instance-identifying key, enabling direct zero-shot forgetting without weight updates or access to the original samples or labels. Across natural image benchmarks, fine-grained recognition, and medical datasets, MUNKEY outperforms all post-hoc baselines. Our results establish that unlearning by design enables fast, deployment-oriented unlearning while preserving predictive performance.

cs.LG↗
arXiv2026

Post-hoc Stochastic Concept Bottleneck Models

Concept Bottleneck Models (CBMs) are interpretable models that predict the target variable through high-level human-understandable concepts, allowing users to intervene on mispredicted concepts to adjust the final output. While recent work has shown that modeling dependencies between concepts can improve CBM performance, especially under interventions, such approaches typically require retraining the entire model, which may be infeasible when access to the original data or compute is limited. In this paper, we introduce Post-hoc Stochastic Concept Bottleneck Models (PSCBMs), a lightweight method that augments any pre-trained CBM with a multivariate normal distribution over concepts by adding only a small covariance-prediction module, without retraining the backbone model. We propose two training strategies and show on real-world data that PSCBMs consistently match or improve both concept and target accuracy over standard CBMs at test time. Furthermore, we show that due to the modeling of concept dependencies, PSCBMs perform much better than CBMs under interventions, while remaining far more efficient than retraining a similar stochastic model from scratch.

cs.LG↗
arXiv2026

Steering Generative Models for Accessibility: EasyRead Image Generation

EasyRead pictograms are simple, visually clear images that represent specific concepts and support comprehension for people with intellectual disabilities, low literacy, or language barriers. The large-scale production of EasyRead content has traditionally been constrained by the cost and expertise required to manually design pictograms. In contrast, automatic generation of such images could significantly reduce production time and cost, enabling broader accessibility across digital and printed materials. However, modern diffusion-based image generation models tend to produce outputs that exhibit excessive visual detail and lack stylistic stability across random seeds, limiting their suitability for clear and consistent pictogram generation. This challenge highlights the need for methods specifically tailored to accessibility-oriented visual content. In this work, we present a unified pipeline for generating EasyRead pictograms by fine-tuning a Stable Diffusion model using LoRA adapters on a curated corpus that combines augmented samples from multiple pictogram datasets. Since EasyRead pictograms lack a unified formal definition, we introduce an EasyRead score to benchmark pictogram quality and consistency. Our results demonstrate that diffusion models can be effectively steered toward producing coherent EasyRead-style images, indicating that generative models can serve as practical tools for scalable and accessible pictogram production.

cs.HC↗
arXiv2026

Reference-Guided Machine Unlearning

Machine unlearning aims to remove the influence of specific data from trained models while preserving general utility. Existing approximate unlearning methods often rely on performance-degradation heuristics, such as loss maximization or random labeling. However, these signals can be poorly conditioned, leading to unstable optimization and harming the model's generalization. We argue that unlearning should instead prioritize distributional indistinguishability, aligning the model's behavior on forget data with its behavior on truly unseen data. Motivated by this, we propose Reference-Guided Unlearning (ReGUn), a framework that leverages a disjoint held-out dataset to provide a principled, class-conditioned reference for distillation. We demonstrate across various model architectures, natural image datasets, and varying forget fractions that ReGUn consistently outperforms standard approximate baselines, achieving a superior forgetting-utility trade-off.

cs.LG↗
arXiv2026

From Slices to Structures: Unsupervised 3D Reconstruction of Female Pelvic Anatomy from Freehand Transvaginal Ultrasound

Volumetric ultrasound has the potential to significantly improve diagnostic accuracy and clinical decision-making, yet its widespread adoption remains limited by dependence on specialized hardware and restrictive acquisition protocols. In this work, we present a novel unsupervised framework for reconstructing 3D anatomical structures from freehand 2D transvaginal ultrasound sweeps, without requiring external tracking or learned pose estimators. Our method, TVGS, adapts the principles of Gaussian Splatting to the domain of ultrasound, introducing a slice-aware, differentiable rasterizer tailored to the unique physics and geometry of ultrasound imaging. We model anatomy as a collection of anisotropic 3D Gaussians and optimize their parameters directly from image-level supervision. To ensure robustness against irregular probe motion, we introduce a joint optimization scheme that refines slice poses alongside anatomical structure. The result is a compact, flexible, and memory-efficient volumetric representation that captures anatomical detail with high spatial fidelity. This work demonstrates that accurate 3D reconstruction from 2D ultrasound images can be achieved through purely computational means, offering a scalable alternative to conventional 3D systems and enabling new opportunities for AI-assisted analysis and diagnosis.

eess.IV↗
arXiv2025

From Logits to Hierarchies: Hierarchical Clustering made Simple

The hierarchical structure inherent in many real-world datasets makes the modeling of such hierarchies a crucial objective in both unsupervised and supervised machine learning. While recent advancements have introduced deep architectures specifically designed for hierarchical clustering, we adopt a critical perspective on this line of research. Our findings reveal that these methods face significant limitations in scalability and performance when applied to realistic datasets. Given these findings, we present an alternative approach and introduce a lightweight method that builds on pre-trained non-hierarchical clustering models. Remarkably, our approach outperforms specialized deep models for hierarchical clustering, and it is broadly applicable to any pre-trained clustering model that outputs logits, without requiring any fine-tuning. To highlight the generality of our approach, we extend its application to a supervised setting, demonstrating its ability to recover meaningful hierarchies from a pre-trained ImageNet classifier. Our results establish a practical and effective alternative to existing deep hierarchical clustering methods, with significant advantages in efficiency, scalability and performance.

cs.LG↗
arXiv2025

Enhancing Radiology Report Generation and Visual Grounding using Reinforcement Learning

Recent advances in vision-language models (VLMs) have improved Chest X-ray (CXR) interpretation in multiple aspects. However, many medical VLMs rely solely on supervised fine-tuning (SFT), which optimizes next-token prediction without evaluating answer quality. In contrast, reinforcement learning (RL) can incorporate task-specific feedback, and its combination with explicit intermediate reasoning ("thinking") has demonstrated substantial gains on verifiable math and coding tasks. To investigate the effects of RL and thinking in a CXR VLM, we perform large-scale SFT on CXR data to build an updated RadVLM based on Qwen3-VL, followed by a cold-start SFT stage that equips the model with basic thinking ability. We then apply Group Relative Policy Optimization (GRPO) with clinically grounded, task-specific rewards for report generation and visual grounding, and run matched RL experiments on both domain-specific and general-domain Qwen3-VL variants, with and without thinking. Across these settings, we find that while strong SFT remains crucial for high base performance, RL provides additional gains on both tasks, whereas explicit thinking does not appear to further improve results. Under a unified evaluation pipeline, the RL-optimized RadVLM models outperform their baseline counterparts and reach state-of-the-art performance on both report generation and grounding, highlighting clinically aligned RL as a powerful complement to SFT for medical VLMs.

cs.AI↗
arXiv2025

TreeDiffusion: Hierarchical Generative Clustering for Conditional Diffusion

Generative modeling and clustering are conventionally distinct tasks in machine learning. Variational Autoencoders (VAEs) have been widely explored for their ability to integrate both, providing a framework for generative clustering. However, while VAEs can learn meaningful cluster representations in latent space, they often struggle to generate high-quality samples. This paper addresses this problem by introducing TreeDiffusion, a deep generative model that conditions diffusion models on learned latent hierarchical cluster representations from a VAE to obtain high-quality, cluster-specific generations. Our approach consists of two steps: first, a VAE-based clustering model learns a hierarchical latent representation of the data. Second, a cluster-aware diffusion model generates realistic images conditioned on the learned hierarchical structure. We systematically compare the generative capabilities of our approach with those of alternative conditioning strategies. Empirically, we demonstrate that conditioning diffusion models on hierarchical cluster representations improves the generative performance on real-world datasets compared to other approaches. Moreover, a key strength of our method lies in its ability to generate images that are both representative and specific to each cluster, enabling more detailed visualization of the learned latent structure. Our approach addresses the generative limitations of VAE-based clustering approaches by leveraging their learned structure, thereby advancing the field of generative clustering.

cs.CV↗
arXiv2025

RadVLM: A Multitask Conversational Vision-Language Model for Radiology

The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows.

cs.CV↗
arXiv2025

Two Is Better Than One: Aligned Representation Pairs for Anomaly Detection

Anomaly detection focuses on identifying samples that deviate from the norm. Discovering informative representations of normal samples is crucial to detecting anomalies effectively. Recent self-supervised methods have successfully learned such representations by employing prior knowledge about anomalies to create synthetic outliers during training. However, we often do not know what to expect from unseen data in specialized real-world applications. In this work, we address this limitation with our new approach Con$_2$, which leverages prior knowledge about symmetries in normal samples to observe the data in different contexts. Con$_2$ consists of two parts: Context Contrasting clusters representations according to their context, while Content Alignment encourages the model to capture semantic information by aligning the positions of normal samples across clusters. The resulting representation space allows us to detect anomalies as outliers of the learned context clusters. We demonstrate the benefit of this approach in extensive experiments on specialized medical datasets, outperforming competitive baselines based on self-supervised learning and pretrained models and presenting competitive performance on natural imaging benchmarks.

cs.LG↗
arXiv2025

Temporal Representation Learning for Real-Time Ultrasound Analysis

Ultrasound (US) imaging is a critical tool in medical diagnostics, offering real-time visualization of physiological processes. One of its major advantages is its ability to capture temporal dynamics, which is essential for assessing motion patterns in applications such as cardiac monitoring, fetal development, and vascular imaging. Despite its importance, current deep learning models often overlook the temporal continuity of ultrasound sequences, analyzing frames independently and missing key temporal dependencies. To address this gap, we propose a method for learning effective temporal representations from ultrasound videos, with a focus on echocardiography-based ejection fraction (EF) estimation. EF prediction serves as an ideal case study to demonstrate the necessity of temporal learning, as it requires capturing the rhythmic contraction and relaxation of the heart. Our approach leverages temporally consistent masking and contrastive learning to enforce temporal coherence across video frames, enhancing the model's ability to represent motion patterns. Evaluated on the EchoNet-Dynamic dataset, our method achieves a substantial improvement in EF prediction accuracy, highlighting the importance of temporally-aware representation learning for real-time ultrasound analysis.

eess.IV↗