Nuno Vivas Brás, Benjamin Memmi, Maëlle Bouhassane +4cs.CV
Accurate segmentation of corneal layers in optical coherence tomography (OCT) is essential for quantitative assessment of corneal morphology, including layer thickness and structural changes associated with disease or surgery. However, automatic segmentation remains challenging because corneal interfaces are thin, affected by speckle noise, and variable across acquisition devices. In this work, we propose ARCOS, a patch-based zero-shot boundary localization framework for corneal layer segmentation in clinical anterior-segment OCT images. Rather than performing conventional region classification, the method predicts boundary heatmaps for the main corneal interfaces from overlapping native-resolution patches. Patch-level predictions are stitched across the full B-scan and converted into boundary locations to obtain continuous, anatomically ordered layer segmentations. The network combines multi-scale feature fusion with a self-conditioned refinement module that uses intermediate boundary information to improve local heatmap predictions while preserving spatial detail. The method was evaluated on clinical OCT images acquired from multiple devices and compared with representative segmentation baselines using boundary localization and derived thickness metrics. The proposed method achieved an off-by-one boundary localization accuracy of 95.1% and a mean absolute boundary error of 0.514 pixels on the matched-device test set. In zero-shot cross-device evaluation, it maintained an average off-by-one accuracy of 84.3% and a mean absolute boundary error of 0.855 pixels across unseen acquisition devices, outperforming the baseline models. Thickness estimates derived from the predicted boundaries showed low error across corneal regions, supporting the method's use for quantitative corneal OCT analysis.
Medical anomaly detection identifies abnormal images and localizes lesions under scarce supervision while generalizing across organs and modalities. Existing CLIP-based methods reduce annotation requirements through vision--language alignment, but their normal and abnormal references, whether text prompts or learned visual tokens, remain fixed across test images. Such static references may not transfer reliably to unseen targets in a cross-domain medical imaging scenario. To address this, we propose ReCAP, a language-free framework that replaces static anchors with input-conditioned visual prototypes. ReCAP re-centers separated normal and abnormal prototypes for each image through a bounded gated modulation, enabling query-adaptive anomaly scoring while constraining context-induced prototype drift. For the few-shot setting, we introduce a non-parametric normal-reference memory to preserve instance-level target-domain variation and complement the conditional prototype branch. Across six medical benchmarks, ReCAP achieves the best image-level AUROC on all zero-shot and 23 of 24 few-shot settings, and the best zero-shot pixel-level AUROC on all three segmentation datasets. Particularly, it reduces inference latency by over 70% compared to the fastest baseline, without text prompts or test-time gradient updates.
Gene Ontology (GO) enrichment analysis is a foundational tool for translating large-scale genomic data into biological insights, but typically yields hundreds of redundant terms that obscure overarching themes. Existing summarization tools rely on fixed similarity metrics (REVIGO, GOSemSim, clusterProfiler::simplify()), gene-overlap measures (Metascape), or static hierarchy mappings (GO-slim), and therefore cannot incorporate biological context. Manual curation provides context-aware grouping but is subjective and labor-intensive. A scalable, context-aware framework is needed to cluster GO terms into interpretable higher-order biological domains. Here we present LLMBDC (Large Language Model for Biological Domains Oriented Clustering of Gene Ontology), a training-free framework that leverages zero-shot semantic reasoning of LLMs with confidence scoring to cluster GO terms into BioDomains using only ontology information at inference time. Benchmarked across Alzheimer's disease (AD) and Fragile X syndrome (FXS) against six baseline methods including SapBERT, LLMBDC achieved substantially higher precision, recall, and clustering performance. Against ground-truth annotations, LLMBDC improved ARI from 9.7% to 73.3% (AD) and from 15.7% to 66.6% (FXS) over REVIGO, with corresponding NMI gains from 59.9% to 73.4% (AD) and 66.0% to 79.5% (FXS). A Cauchy combination test further confirmed that aggregated BioDomains retained statistically significant functional signals. LLMBDC provides a scalable, reproducible, and interpretable route to context-aware, system-level interpretation of GO enrichment results while preserving biological specificity.
Multimodal large language models (LLMs) are increasingly adopted to interpret 12-lead ECG images, though the interpretations often lack validation. However, ECG image understanding significantly differs from general images as it depends on precise waveform morphology, lead relationships and accurate interval measurements. This study investigated whether zero-shot multimodal LLMs can reliably distinguish normal and abnormal ECG images and, in parallel, evaluated CNN-based models for clinically grounded references. Standard 12-lead ECG recordings were rendered as single-page images for a binary normal-abnormal classification task. Three prominent LLMs (GPT-5.2, GPT-4.1, and Gemini-2.5 Pro) were tested using a fixed zero-shot prompt across multiple runs. In parallel, a physiology-aware CNN-based model was developed with the capability to aggregate features from the predefined anatomical lead groups. The model was compared with ResNet18, DenseNet121, VGG16 baselines, and all the models were evaluated on an internal test set and external PTB-XL dataset. Across seeds, CNN-based models demonstrated stable discrimination, with average internal ROC-AUC of 0.92-0.94, and external ROC-AUC of 0.85-0.86. The proposed LeadGroupECG model significantly improved over its backbone internally without compromising external generalization. It remained competitive with other baselines, while consistently highlighting anatomical lead-group contributions. In contrast, zero-shot LLM discrimination remained near-chance (ROC-AUC around 0.5). The PR-AUC improved slightly when ECGs used a grid-based calibration background compared with the grid-free ECGs. Although multimodal LLMs can generate reasonable ECG narratives, their zero-shot diagnostic discrimination remains limited. Therefore, clinically framed, domain-specific architectures remain essential for AI-based ECG interpretation.
Zero-shot anomaly detection (ZSAD) is attractive for medical imaging because clinical systems must handle heterogeneous acquisition protocols, changing patient populations, and pathologies for which annotated training data may be unavailable. Most existing zero-shot anomaly detection methods are designed for 2D images, and their direct extension to 3D medical volumes is limited by the scarcity of large-scale volumetric foundation models or by the difficulty of utilizing volumetric context. We propose CS3F, a training-free batch-based framework for ZSAD in 3D medical images using 2D foundation models. Each volume is decomposed along multiple anatomical axes and encoded slice-wise by a 2D vision transformer. These are then converted into localized volumetric tokens by pooling neighboring slice features. Anomaly scores are obtained from cross-subject mutual similarity: tokens that lack close analogues in other subjects are assigned higher anomaly scores. To reduce the attenuation of focal lesion signals caused by depth pooling, we introduce a coarse-to-fine tokenization strategy that enables fine-resolution volumetric scoring without exhaustive matching. CS3F is evaluated on brain MRI across metastases, glioma, and stroke, as well as validated on lung CT to test generalizability beyond atlas-aligned brain MRI. The results show that frozen 2D foundation models can support anomaly localization in 3D medical images, and that the benefit of fine tokenization depends strongly on lesion contrast and imaging modality.
Vishal Jain, Giorgio Buzzanca, Sarah Cechnicka +6cs.CV
Foreground segmentation is the critical first step of every computational pathology pipeline, yet existing methods rely on hand-tuned heuristics or supervised models that overfit to narrow stain and scanner distributions, failing silently on specialised stains such as Jones silver or Elastica van Gieson. We propose a coarse-to-fine approach that recasts foreground segmentation as a visual perception task and leverages general-purpose vision-language models (VLMs) as zero-annotation oracles. Our key insight is that tissue-versus-background discrimination is a natural-image recognition problem, not a histopathological one, so VLMs trained on internet-scale corpora generalise where domain-specific models cannot. We introduce Leica-75, a benchmark of 75 renal transplant whole-slide images spanning three stain families. On Leica-75, our method achieves the highest segmentation quality on out-of-distribution stains (Dice 0.858 +/- 0.027 on Jones, 0.853 +/- 0.041 on EVG) with 7x lower cross-stain variance than the best supervised baseline, while remaining competitive on in-distribution H&E. Few-shot prompting with automatically curated exemplars (Auto-context) rescues hard cases on Stress-32 (n=32), a curated stress-test subset (Dice 0.470 to 0.819 for the 2B model). VLM-based annotation review matches human expert consensus (kappa=0.989 for blur detection; mean precision/recall grading accuracy 0.708 vs. human 0.646 for segmentation mask review). The resulting pseudo-labels are used to distil lightweight student models that are as performant as the teacher model while running for a fraction of the cost. Our framework provides a principled, scalable solution to a persistent infrastructure bottleneck in digital pathology.
Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.