Organizations: School of Computing, Queen’s University, Kingston, Ontario, K7L 2N8, Canada
Abstract
Vision foundation models are increasingly used as reusable encoders in medical image computing, yet their high-dimensional spatial embeddings are difficult to inspect beyond downstream task performance or global dimensionality reduction. We propose position-prompted PCA (P3CA), an encoder-agnostic method for local probing of channel-rich spatial tensors. Given a user-selected spatial prompt, P3CA estimates the feature normalization and dominant covariance directions within that region, then applies the resulting projection to the full tensor to visualize where locally informative directions are expressed. This produces a region-conditioned representation lens without modifying the encoder, retraining, or requiring task-specific labels. We implement P3CA in EmbedVision, an interactive 3D Slicer-based workflow, and evaluate it across natural images, colorectal pathology foundation-model embeddings, and spatial transcriptomic tensors. Across these settings, prompted projections reveal local structure suppressed by global PCA, improve prompt-matched pathology discrimination from frozen three-dimensional projections, and support comparison between learned and measured spatial representations.
Picking the frozen image encoder for a 3D~CT vision--language model (VLM), together with the token-compression scheme on top of it, is a search over many candidates. There are several encoders, several ways to compress their tokens, and several token budgets, and the combinations grow fast. Comparing them the usual way means fine-tuning a large language model (LLM) on each combination, and running the whole sweep this way needs far more compute than most groups can spend. We ask whether a cheap probe on the encoder's cached embeddings can stand in for that comparison. We build an image-grounded probing benchmark over (encoder × compression) cells, with clinical attribute families and two validation gates, scale-sanity and probe-separability, that keep each attribute well-scaled and decodable. These gates are the main methodological contribution. On this benchmark we compare a range of read-out heads, and in a preliminary study we pair each probe with its matched downstream task. The early signal is encouraging: the cheap probe orders the candidates in close agreement with expensive fine-tuning, at about r≈0.95 on the cells measured so far. We read this as an ordinal claim, a ranking predictor rather than an exact estimate, and we are explicit about where it stays preliminary. If it holds up, encoder and compression choices can be screened in minutes with frozen-token probes, with full training spent only on the finalists.
Large vision-language models are becoming increasingly dominant in 3D medical image interpretation, but we rarely know <i>which</i> internal units encode clinical findings or <i>where</i> that information lives in the representation. We first study this on a 3D chest vision-language model (Pillar-0) by probing its frozen vision embeddings. We show that (i) each radiological finding is encoded by a <i>sparse</i> set of ~10 vision-encoder channels that match full-feature classification performance and far exceed a zero-shot text prompting; (ii) turning off the channels tied to one finding, that finding's score collapses while unrelated labels stay stable; and (iii) the same sparse probe <i>replicates</i> on an architecturally unrelated 3D abdominal VLM (Merlin) suggesting a general property of frozen medical encoders. Our training-free concept channel probe (CCP) method, paired with a corpus-derived report template, outperforms published CT-CHAT on clinical efficacy and NLG metrics (F1 0.549 vs. 0.184; BLEU 0.483 vs. 0.373) at 22x lower latency. Our results provide a clear, reproducible characterization of how frozen medical encoders represent findings, demonstrating direct applicability across models.
Farhad Nooralahzadeh, Lea Bogensperger, Christian Bluethgen +1
Self-supervised pretraining is central to 3D medical image analysis, where unlabeled CT volumes are abundant but expert annotations are scarce. Yet existing volumetric encoders often fail to preserve the coarse spatial and geometric structure that downstream reasoning depends on, limiting their performance on organ disentanglement, abnormality detection, and spatial understanding when paired with language models. We introduce Rad-JEPA 3D, a joint-embedding predictive framework that learns volumetric CT representations by predicting the latent features of a complete scan from a masked view. At its core is a hybrid H-Mamba encoder that fuses a Mamba state-space branch, which models inter-slice continuity through sequential scanning, with a grouped-query attention branch, which captures cross-plane spatial context, combined through a lightweight per-token router. To improve the quality of intermediate representations, we further propose Hidden States Orthogonal Regularization (HSOR), which aligns student-teacher hidden states and reduces feature redundancy throughout the encoder. This layer-wise regularization produces more consistent and discriminative volumetric representations, leading to improved performance on organ recognition and spatial reasoning tasks. Pretrained on approximately 120,000 CT scans, Rad-JEPA 3D attains state-of-the-art results despite its compact size: with only 4.0B total parameters, it achieves competitive results with state-of-the-art on closed-ended VQA and the best average spatial-reasoning score on the Spatial-Med benchmark. Ablation studies confirm that the hybrid block and HSOR contribute complementary gains, and that the induced spatial structure can substitute for raw language-model scale on volumetric reasoning tasks.