From Generative Modeling to Clinical Classification: A GPT-Based Architecture for EHR Notes

The increasing availability of unstructured clinical narratives in electronic health records (EHRs) has created new opportunities for automated disease characterization, cohort identification, and clinical decision support. However, modeling long, domain-specific clinical text remains challenging due to limited labeled data, severe class imbalance, and the high computational cost of adapting large pretrained language models. This study presents a GPT-based architecture for clinical text classification that adapts a pretrained decoder-only Transformer using a selective fine-tuning strategy. Rather than updating all model parameters, the majority of the GPT-2 backbone is frozen, and training is restricted to the final Transformer block, the final layer normalization, and a lightweight classification head. This approach substantially reduces the number of trainable parameters while preserving the representational capacity required to model complex clinical language. The proposed method is evaluated on radiology reports from the MIMIC-IV-Note dataset using uncertainty-aware CheXpert-style labels derived directly from report text. Experiments cover multiple problem formulations, including multi-label classification of radiographic findings, binary per-label classification under different uncertainty assumptions, and aggregate disease outcome prediction. Across varying dataset sizes, the model exhibits stable convergence behavior and strong classification performance, particularly in settings dominated by non-mention and negated findings. Overall, the results indicate that selective fine-tuning of pretrained generative language models provides an efficient and effective pathway for clinical text classification, enabling scalable adaptation to real-world EHR data while significantly reducing computational complexity.

Med-MMFL: A Multimodal Federated Learning Benchmark in Healthcare

Federated learning (FL) enables collaborative model training across decentralized medical institutions while preserving data privacy. However, medical FL benchmarks remain scarce, with existing efforts focusing mainly on unimodal or bimodal modalities and a limited range of medical tasks. This gap underscores the need for standardized evaluation to advance systematic understanding in medical MultiModal FL (MMFL). To this end, we introduce Med-MMFL, the first comprehensive MMFL benchmark for the medical domain, encompassing diverse modalities, tasks, and federation scenarios. Our benchmark evaluates six representative state-of-the-art FL algorithms, covering different aggregation strategies, loss formulations, and regularization techniques. It spans datasets with 2 to 4 modalities, comprising a total of 10 unique medical modalities, including text, pathology images, ECG, X-ray, radiology reports, and multiple MRI sequences. Experiments are conducted across naturally federated, synthetic IID, and synthetic non-IID settings to simulate real-world heterogeneity. We assess segmentation, classification, modality alignment (retrieval), and VQA tasks. To support reproducibility and fair comparison of future multimodal federated learning (MMFL) methods under realistic medical settings, we release the complete benchmark implementation, including data processing and partitioning pipelines, at https://github.com/bhattarailab/Med-MMFL-Benchmark .

VideoBrain: Learning Adaptive Frame Sampling for Long Video Understanding

Long-form video understanding remains challenging for Vision-Language Models (VLMs) due to the inherent tension between computational constraints and the need to capture information distributed across thousands of frames. Existing approaches either sample frames uniformly (risking information loss) or select keyframes in a single pass (with no recovery from poor choices). We propose VideoBrain, an end-to-end framework that enables VLMs to adaptively acquire visual information through learned sampling policies. Our approach features dual complementary agents: a CLIP-based agent for semantic retrieval across the video and a Uniform agent for dense temporal sampling within intervals. Unlike prior agent-based methods that rely on text-only LLMs orchestrating visual tools, our VLM directly perceives frames and reasons about information sufficiency. To prevent models from invoking agents indiscriminately to maximize rewards, we introduce a behavior-aware reward function coupled with a data classification pipeline that teaches the model when agent invocation is genuinely beneficial. Experiments on four long video benchmarks demonstrate that VideoBrain achieves +3.5% to +9.0% improvement over the baseline while using 30-40% fewer frames, with strong cross-dataset generalization to short video benchmarks.

Interpretable Logical Anomaly Classification via Constraint Decomposition and Instruction Fine-Tuning

Logical anomalies are violations of predefined constraints on object quantity, spatial layout, and compositional relationships in industrial images. While prior work largely treats anomaly detection as a binary decision, such formulations cannot indicate which logical rule is broken and therefore offer limited value for quality assurance. We introduce Logical Anomaly Classification (LAC), a task that unifies anomaly detection and fine-grained violation classification in a single inference step. To tackle LAC, we propose LogiCls, a vision-language framework that decomposes complex logical constraints into a sequence of verifiable subqueries. We further present a data-centric instruction synthesis pipeline that generates chain-of-thought (CoT) supervision for these subqueries, coupling precise grounding annotations with diverse image-text augmentations to adapt vision language models (VLMs) to logic-sensitive reasoning. Training is stabilized by a difficulty-aware resampling strategy that emphasizes challenging subqueries and long tail constraint types. Extensive experiments demonstrate that LogiCls delivers robust, interpretable, and accurate industrial logical anomaly classification, providing both the predicted violation categories and their evidence trails.

Non-Contrastive Vision-Language Learning with Predictive Embedding Alignment

Vision-language models have transformed multimodal representation learning, yet dominant contrastive approaches like CLIP require large batch sizes, careful negative sampling, and extensive hyperparameter tuning. We introduce NOVA, a NOn-contrastive Vision-language Alignment framework based on joint embedding prediction with distributional regularization. NOVA aligns visual representations to a frozen, domain-specific text encoder by predicting text embeddings from augmented image views, while enforcing an isotropic Gaussian structure via Sketched Isotropic Gaussian Regularization (SIGReg). This eliminates the need for negative sampling, momentum encoders, or stop-gradients, reducing the training objective to a single hyperparameter. We evaluate NOVA on zeroshot chest X-ray classification using ClinicalBERT as the text encoder and Vision Transformers trained from scratch on MIMIC-CXR. On zero-shot classification across three benchmark datasets, NOVA outperforms multiple standard baselines while exhibiting substantially more consistent training runs. Our results demonstrate that non-contrastive vision-language pretraining offers a simpler, more stable, and more effective alternative to contrastive methods.

PhenoLIP: Integrating Phenotype Ontology Knowledge into Medical Vision-Language Pretraining

Recent progress in large-scale CLIP-like vision-language models(VLMs) has greatly advanced medical image analysis. However, most existing medical VLMs still rely on coarse image-text contrastive objectives and fail to capture the systematic visual knowledge encoded in well-defined medical phenotype ontologies. To address this gap, we construct PhenoKG, the first large-scale, phenotype-centric multimodal knowledge graph that encompasses over 520K high-quality image-text pairs linked to more than 3,000 phenotypes. Building upon PhenoKG, we propose PhenoLIP, a novel pretraining framework that explicitly incorporates structured phenotype knowledge into medical VLMs through a two-stage process. We first learn a knowledge-enhanced phenotype embedding space from textual ontology data and then distill this structured knowledge into multimodal pretraining via a teacher-guided knowledge distillation objective. To support evaluation, we further introduce PhenoBench, an expert-verified benchmark designed for phenotype recognition, comprising over 7,800 image--caption pairs covering more than 1,000 phenotypes. Extensive experiments demonstrate that PhenoLIP outperforms previous state-of-the-art baselines, improving upon BiomedCLIP in phenotype classification accuracy by 8.85\% and BIOMEDICA in cross-modal retrieval by 15.03%, underscoring the value of integrating phenotype-centric priors into medical VLMs for structured and interpretable medical image understanding.

Bulk-Calibrated Credal Ambiguity Sets: Fast, Tractable Decision Making under Out-of-Sample Contamination

Distributionally robust optimisation (DRO) minimises the worst-case expected loss over an ambiguity set that can capture distributional shifts in out-of-sample environments. While Huber (linear-vacuous) contamination is a classical minimal-assumption model for an $\varepsilon$-fraction of arbitrary perturbations, including it in an ambiguity set can make the worst-case risk infinite and the DRO objective vacuous unless one imposes strong boundedness or support assumptions. We address these challenges by introducing bulk-calibrated credal ambiguity sets: we learn a high-mass bulk set from data while considering contamination inside the bulk and bounding the remaining tail contribution separately. This leads to a closed-form, finite $\mathrm{mean}+\sup$ robust objective and tractable linear or second-order cone programs for common losses and bulk geometries. Through this framework, we highlight and exploit the equivalence between the imprecise probability (IP) notion of upper expectation and the worst-case risk, demonstrating how IP credal sets translate into DRO objectives with interpretable tolerance levels. Experiments on heavy-tailed inventory control, geographically shifted house-price regression, and demographically shifted text classification show competitive robustness-accuracy trade-offs and efficient optimisation times, using Bayesian, frequentist, or empirical reference distributions.

Hierarchical Text Classification with LLM-Refined Taxonomies

Hierarchical text classification (HTC) depends on taxonomies that organize labels into structured hierarchies. However, many real-world taxonomies introduce ambiguities, such as identical leaf names under similar parent nodes, which prevent language models (LMs) from learning clear decision boundaries. In this paper, we present TaxMorph, a framework that uses large language models (LLMs) to transform entire taxonomies through operations such as renaming, merging, splitting, and reordering. Unlike prior work, our method revises the full hierarchy to better match the semantics encoded by LMs. Experiments across three HTC benchmarks show that LLM-refined taxonomies consistently outperform human-curated ones in various settings up to +2.9pp. in F1. To better understand these improvements, we compare how well LMs can assign leaf nodes to parent nodes and vice versa across human-curated and LLM-refined taxonomies. We find that human-curated taxonomies lead to more easily separable clusters in embedding space. However, the LLM-refined taxonomies align more closely with the model's actual confusion patterns during classification. In other words, even though they are harder to separate, they better reflect the model's inductive biases. These findings suggest that LLM-guided refinement creates taxonomies that are more compatible with how models learn, improving HTC performance.

On the Limits of Layer Pruning for Generative Reasoning in LLMs

Recent works have shown that layer pruning can compress large language models (LLMs) while retaining strong performance on classification benchmarks with little or no finetuning. However, existing pruning techniques often suffer severe degradation on generative reasoning tasks. Through a systematic study across multiple model families, we find that tasks requiring multi-step reasoning are particularly sensitive to depth reduction. Beyond surface-level text degeneration, we observe degradation of critical algorithmic capabilities, including arithmetic computation for mathematical reasoning and balanced parenthesis generation for code synthesis. Under realistic post-training constraints, without access to pretraining-scale data or compute, we evaluate a simple mitigation strategy based on supervised finetuning with Self-Generated Responses. This approach achieves strong recovery on classification tasks, retaining up to 90\% of baseline performance, and yields substantial gains of up to 20--30 percentage points on generative benchmarks compared to prior post-pruning techniques. Crucially, despite these gains, recovery for generative reasoning remains fundamentally limited relative to classification tasks and is viable primarily at lower pruning ratios. Overall, we characterize the practical limits of layer pruning for generative reasoning and provide guidance on when depth reduction can be applied effectively under constrained post-training regimes.

WMVLM: Evaluating Diffusion Model Image Watermarking via Vision-Language Models

Digital watermarking is essential for securing generated images from diffusion models. Accurate watermark evaluation is critical for algorithm development, yet existing methods have significant limitations: they lack a unified framework for both residual and semantic watermarks, provide results without interpretability, neglect comprehensive security considerations, and often use inappropriate metrics for semantic watermarks. To address these gaps, we propose WMVLM, the first unified and interpretable evaluation framework for diffusion model image watermarking via vision-language models (VLMs). We redefine quality and security metrics for each watermark type: residual watermarks are evaluated by artifact strength and erasure resistance, while semantic watermarks are assessed through latent distribution shifts. Moreover, we introduce a three-stage training strategy to progressively enable the model to achieve classification, scoring, and interpretable text generation. Experiments show WMVLM outperforms state-of-the-art VLMs with strong generalization across datasets, diffusion models, and watermarking methods.