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Efficient and scalable clustering of survival curves

Villanueva, Nora M., Sestelo, Marta, Meira-Machado, Luis

arXiv.org Machine Learning

Survival analysis encompasses a broad range of methods for analyzing time-to-event data, with one key objective being the comparison of survival curves across groups. Traditional approaches for identifying clusters of survival curves often rely on computationally intensive bootstrap techniques to approximate the null hypothesis distribution. While effective, these methods impose significant computational burdens. In this work, we propose a novel approach that leverages the k-means and log-rank test to efficiently identify and cluster survival curves. Our method eliminates the need for computationally expensive resampling, significantly reducing processing time while maintaining statistical reliability. By systematically evaluating survival curves and determining optimal clusters, the proposed method ensures a practical and scalable alternative for large-scale survival data analysis. Through simulation studies, we demonstrate that our approach achieves results comparable to existing bootstrap-based clustering methods while dramatically improving computational efficiency. These findings suggest that the log-rank-based clustering procedure offers a viable and time-efficient solution for researchers working with multiple survival curves in medical and epidemiological studies.


Beyond the Failures: Rethinking Foundation Models in Pathology

Tizhoosh, Hamid R.

arXiv.org Artificial Intelligence

Despite their successes in vision and language, foundation models have stumbled in pathology, revealing low accuracy, instability, and heavy computational demands. These shortcomings stem not from tuning problems but from deeper conceptual mismatches: dense embeddings cannot represent the combinatorial richness of tissue, and current architectures inherit flaws in self-supervision, patch design, and noise-fragile pretraining. Biological complexity and limited domain innovation further widen the gap. The evidence is clear--pathology requires models explicitly designed for biological images rather than adaptations of large-scale natural-image methods whose assumptions do not hold for tissue.


RouteRAG: Efficient Retrieval-Augmented Generation from Text and Graph via Reinforcement Learning

Guo, Yucan, Su, Miao, Guan, Saiping, Sun, Zihao, Jin, Xiaolong, Guo, Jiafeng, Cheng, Xueqi

arXiv.org Artificial Intelligence

Retrieval-Augmented Generation (RAG) integrates non-parametric knowledge into Large Language Models (LLMs), typically from unstructured texts and structured graphs. While recent progress has advanced text-based RAG to multi-turn reasoning through Reinforcement Learning (RL), extending these advances to hybrid retrieval introduces additional challenges. Existing graph-based or hybrid systems typically depend on fixed or handcrafted retrieval pipelines, lacking the ability to integrate supplementary evidence as reasoning unfolds. Besides, while graph evidence provides relational structures crucial for multi-hop reasoning, it is substantially more expensive to retrieve. To address these limitations, we introduce \model{}, an RL-based framework that enables LLMs to perform multi-turn and adaptive graph-text hybrid RAG. \model{} jointly optimizes the entire generation process via RL, allowing the model to learn when to reason, what to retrieve from either texts or graphs, and when to produce final answers, all within a unified generation policy. To guide this learning process, we design a two-stage training framework that accounts for both task outcome and retrieval efficiency, enabling the model to exploit hybrid evidence while avoiding unnecessary retrieval overhead. Experimental results across five question answering benchmarks demonstrate that \model{} significantly outperforms existing RAG baselines, highlighting the benefits of end-to-end RL in supporting adaptive and efficient retrieval for complex reasoning.


Cognitive bias in LLM reasoning compromises interpretation of clinical oncology notes

Kenaston, Matthew W., Ayub, Umair, Parmar, Mihir, Anjum, Muhammad Umair, Naqvi, Syed Arsalan Ahmed, Kumar, Priya, Rawal, Samarth, Chaudhuri, Aadel A., Zakharia, Yousef, Heath, Elizabeth I., Bekaii-Saab, Tanios S., Tao, Cui, Van Allen, Eliezer M., Zhou, Ben, Choi, YooJung, Baral, Chitta, Riaz, Irbaz Bin

arXiv.org Artificial Intelligence

Despite high performance on clinical benchmarks, large language models may reach correct conclusions through faulty reasoning, a failure mode with safety implications for oncology decision support that is not captured by accuracy-based evaluation. In this two-cohort retrospective study, we developed a hierarchical taxonomy of reasoning errors from GPT-4 chain-of-thought responses to real oncology notes and tested its clinical relevance. Using breast and pancreatic cancer notes from the CORAL dataset, we annotated 600 reasoning traces to define a three-tier taxonomy mapping computational failures to cognitive bias frameworks. We validated the taxonomy on 822 responses from prostate cancer consult notes spanning localized through metastatic disease, simulating extraction, analysis, and clinical recommendation tasks. Reasoning errors occurred in 23 percent of interpretations and dominated overall errors, with confirmation bias and anchoring bias most common. Reasoning failures were associated with guideline-discordant and potentially harmful recommendations, particularly in advanced disease management. Automated evaluators using state-of-the-art language models detected error presence but could not reliably classify subtypes. These findings show that large language models may provide fluent but clinically unsafe recommendations when reasoning is flawed. The taxonomy provides a generalizable framework for evaluating and improving reasoning fidelity before clinical deployment.


EEG-GRAPH: A Factor-Graph-Based Model for Capturing Spatial, Temporal, and Observational Relationships in Electroencephalograms

Yogatheesan Varatharajah, Min Jin Chong, Krishnakant Saboo, Brent Berry, Benjamin Brinkmann, Gregory Worrell, Ravishankar Iyer

Neural Information Processing Systems

This paper presents a probabilistic-graphical model that can be used to infer characteristics of instantaneous brain activity by jointly analyzing spatial and temporal dependencies observed in electroencephalograms (EEG). Specifically, we describe a factor-graph-based model with customized factor-functions defined based on domain knowledge, to infer pathologic brain activity with the goal of identifying seizure-generating brain regions in epilepsy patients. We utilize an inference technique based on the graph-cut algorithm to exactly solve graph inference in polynomial time. We validate the model by using clinically collected intracranial EEG data from 29 epilepsy patients to show that the model correctly identifies seizure-generating brain regions. Our results indicate that our model outperforms two conventional approaches used for seizure-onset localization (5-7% better AUC: 0.72, 0.67, 0.65) and that the proposed inference technique provides 3-10% gain in AUC ( 0.72, 0.62, 0.69) compared to sampling-based alternatives.


Chain-of-Thought Driven Adversarial Scenario Extrapolation for Robust Language Models

Rashid, Md Rafi Ur, Dasu, Vishnu Asutosh, Wang, Ye, Tan, Gang, Mehnaz, Shagufta

arXiv.org Artificial Intelligence

Large Language Models (LLMs) exhibit impressive capabilities, but remain susceptible to a growing spectrum of safety risks, including jailbreaks, toxic content, hallucinations, and bias. Existing defenses often address only a single threat type or resort to rigid outright rejection, sacrificing user experience and failing to generalize across diverse and novel attacks. This paper introduces Adversarial Scenario Extrapolation (ASE), a novel inference-time computation framework that leverages Chain-of-Thought (CoT) reasoning to simultaneously enhance LLM robustness and seamlessness. ASE guides the LLM through a self-generative process of contemplating potential adversarial scenarios and formulating defensive strategies before generating a response to the user query. Comprehensive evaluation on four adversarial benchmarks with four latest LLMs shows that ASE achieves near-zero jailbreak attack success rates and minimal toxicity, while slashing outright rejections to <4%. ASE outperforms six state-of-the-art defenses in robustness-seamlessness trade-offs, with 92-99% accuracy on adversarial Q&A and 4-10x lower bias scores. By transforming adversarial perception into an intrinsic cognitive process, ASE sets a new paradigm for secure and natural human-AI interaction.


Feature Quality and Adaptability of Medical Foundation Models: A Comparative Evaluation for Radiographic Classification and Segmentation

Li, Frank, Dapamede, Theo, Chavoshi, Mohammadreza, Jeon, Young Seok, Khosravi, Bardia, Dere, Abdulhameed, Brown-Mulry, Beatrice, Isaac, Rohan Satya, Mansuri, Aawez, Sanyika, Chiratidzo, Newsome, Janice, Purkayastha, Saptarshi, Banerjee, Imon, Trivedi, Hari, Gichoya, Judy

arXiv.org Artificial Intelligence

Foundation models (FMs) promise to generalize medical imaging, but their effectiveness varies. It remains unclear how pre-training domain (medical vs. general), paradigm (e.g., text-guided), and architecture influence embedding quality, hindering the selection of optimal encoders for specific radiology tasks. To address this, we evaluate vision encoders from eight medical and general-domain FMs for chest X-ray analysis. We benchmark classification (pneumothorax, cardiomegaly) and segmentation (pneumothorax, cardiac boundary) using linear probing and fine-tuning. Our results show that domain-specific pre-training provides a significant advantage; medical FMs consistently outperformed general-domain models in linear probing, establishing superior initial feature quality. However, feature utility is highly task-dependent. Pre-trained embeddings were strong for global classification and segmenting salient anatomy (e.g., heart). In contrast, for segmenting complex, subtle pathologies (e.g., pneumothorax), all FMs performed poorly without significant fine-tuning, revealing a critical gap in localizing subtle disease. Subgroup analysis showed FMs use confounding shortcuts (e.g., chest tubes for pneumothorax) for classification, a strategy that fails for precise segmentation. We also found that expensive text-image alignment is not a prerequisite; image-only (RAD-DINO) and label-supervised (Ark+) FMs were among top performers. Notably, a supervised, end-to-end baseline remained highly competitive, matching or exceeding the best FMs on segmentation tasks. These findings show that while medical pre-training is beneficial, architectural choices (e.g., multi-scale) are critical, and pre-trained features are not universally effective, especially for complex localization tasks where supervised models remain a strong alternative.