arXiv subjects

Koushik Howlader

Publications and source records attributed to Koushik Howlader.

8 recordsLinked to original sources

arXiv2026

Towards Trustworthy Biological Alignment in TabPFN-Probed Pathology Foundation Models

Histology and transcriptomics provide complementary views of tissue biology, capturing spatial morphology and molecular activity, respectively. Pathology foundation models (PFMs) learn rich morphological representations from H&E images, yet strong downstream performance alone does not establish whether these representations encode biologically meaningful and robust molecular information. We present a **training-free framework for auditing biological alignment in frozen PFMs** using spatially paired histology and transcriptomics from HEST-1k, evaluated on **240 samples spanning three organs**. Multiple frozen PFMs are used to extract H&E representations, while gene expression is aggregated into biologically interpretable pathway-level programs. We use TabPFN as a pretrained probe to quantify the extent to which these molecular programs can be decoded from frozen image representations without task-specific gradient updates. Beyond predictive performance, our audit examines whether pathway decodability generalizes across tissue sections, patient groups, and tissue types; whether representations exhibit section-level or other shortcut dependencies; and whether predictions remain stable under small image perturbations and context resampling. This multi-tissue evaluation distinguishes molecular programs that are consistently encoded from those that are tissue-specific, unstable, or shortcut-sensitive. Our framework therefore provides a systematic approach for assessing not only **what biological information pathology foundation models encode, but also how reliably that information persists under clinically relevant sources of variation**.

cs.MA↗

arXiv2026

TRAPS: Treatment-Assignment Prediction via Pathway-informed Stratification

Cancer treatment involves decisions across multiple clinical outcomes, yet pathway-informed deep learning models are typically evaluated in isolation, making their relative benefits unclear. We present a harmonized benchmark of three biologically informed architectures, BINN, GraphPath, and PATH, for predicting treatment exposure and short-term survival across five TCGA cancer cohorts comprising 2,622 patients represented by Reactome pathway activity scores. Treatment labels indicate recorded exposure in TCGA rather than therapeutic response. All models jointly predict targeted molecular therapy (TMT), radiation therapy (RT), and six-month overall survival (OS) from a shared pathway representation and are evaluated on identical stratified folds using five repeated splits and paired-bootstrap testing. Under this controlled evaluation, most differences between architectures fall within 95 percent confidence intervals, indicating that rankings suggested by isolated evaluations are largely not statistically resolved. The main exception is survival prediction: the sparse-hierarchy BINN significantly outperforms both graph models on breast-cancer OS, with an AUROC improvement of up to 0.14 and p less than or equal to 0.01, and leads on lung and prostate OS. For treatment exposure, TMT is best discriminated in prostate cancer, with AUROC approximately 0.80 for all models, but no architecture significantly outperforms another on any TMT cohort. RT prediction remains weak across models, suggesting that its determinants may be more clinical than transcriptomic. Overall, architecture choice has limited impact under a unified evaluation, while short-term survival provides the clearest differentiation among pathway-informed models.

cs.LG↗

arXiv2026

bioMoR: Biology-Guided Mixture-of-Recursions for Effective Genomic Learning

Transformer models for high-dimensional omics analysis process thousands of genes or pathways, although only a subset requires deep computation. Mixture-of-Recursions (MoR) improves efficiency through adaptive token-choice or expert-choice routing. We propose bioMoR, which, to the best of our knowledge, is the first framework to apply MoR to gene-level and pathway-level learning. Our contributions include identifying three locations for integrating structured biological knowledge within an MoR backbone: graph-based information sharing refines token embeddings, a structural bias guides self-attention toward biologically related tokens, and a graph-aware router uses neighborhood information to determine each token's recursion depth. These techniques are centered on our insight that additional knowledge of token interaction can effectively help models construct embeddings and select which tokens should be learned more deeply. Across eight benchmarks spanning diverse omics data types and evaluated under a unified five-fold cross-validation protocol, bioMoR improves average macro-F1 by 8.2 percentage points and balanced accuracy by 7.1 percentage points over the strongest biology-agnostic MoR baseline while using 75 percent fewer parameters and up to 58 percent fewer FLOPs than a non-recursive Transformer. The selected marker genes or pathways provide biological interpretability, while their token-specific recursion depths reveal how computation is allocated.

cs.AI↗

arXiv2026

Toward Uncertainty Quantification in Modern Art

Asked to animate the same modern artwork under different random seeds, a text to video model returns visibly different films, one reading per seed. Because modern art is ambiguous by intent, this disagreement is signal, not noise. Yet prevailing uncertainty quantification (UQ) collapses a set of generations to a dispersion scalar that says how much the seeds differ but not how: it cannot tell a compact interpretation from a dominant reading plus an outlier, two competing modes, or diffuse instability, nor whether the set still contains a rendering faithful to the original. We present the first study of the structure of generative uncertainty for modern art animation, and a reusable protocol for identifying source blind multiseed uncertainty: a suite of seven source blind and six reference aware estimators; a distributional profile (robust spread, outlier influence, explicit topology, multimodality, anisotropy, leave one seed influence, reference coverage); a distribution model ablation (vMF, Kent, ACG, Student t, kernel, mixture); eight identification questions; and an artwork level statistical protocol. We build the first corpus: 250 modern artwork captions rendered by Wan2.1 14B under four seeds (1000 videos) across 4 encoders, artworks withheld from generation. As a diagnostic the protocol succeeds: it classifies seed set topology at balanced accuracy 0.98 (chance 0.25), isolates the outlier configuration at AUROC 1.00 where a scalar reaches only 0.35, and splits high uncertainty artworks into reference covering (n=97) and reference missing (n=56) diversity, reliably from three seeds and across encoders.

cs.GR↗

arXiv2026

Graph Transformer-Based Pathway Embedding for Cancer Prognosis

Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent limitation lies in how they encode individual genes to construct pathway representations. Existing hierarchical models typically derive gene features by directly mapping raw molecular inputs, whereas integration frameworks often rely on simple statistical aggregations of patient-level signals. These approaches often fail to explicitly learn a shared base representation for each gene, thereby limiting the expressiveness and biological accuracy of downstream pathway embeddings. To address this, we introduce PATH, a modulation-based, patient-conditioned gene embedding strategy. PATH represents a paradigm shift by starting from a shared base embedding for each gene, preserving a stable biological identity across the population, and then dynamically adapting it using patient-specific copy number variation (CNV) and mutation signals. This allows the model to capture subtle individual molecular variations while maintaining a consistent latent understanding of the gene itself. We integrate PATH into a graph transformer framework that models interactions among biologically connected pathways through pathway-guided attention. Across pancancer metastasis prediction, PATH achieves an F1 score of 0.8766, representing an 8.8 percent improvement over the current SOTA multi-omics benchmarks. Beyond superior predictive accuracy, our approach identifies biologically meaningful pathways and, crucially, reveals disease-state-specific pathway rewiring, offering new insights into the evolving pathway-pathway interactions that drive cancer progression.

cs.LG↗

arXiv2026

Improving the Safety and Trustworthiness of Medical AI via Multi-Agent Evaluation Loops

Large Language Models (LLMs) are increasingly applied in healthcare, yet ensuring their ethical integrity and safety compliance remains a major barrier to clinical deployment. This work introduces a multi-agent refinement framework designed to enhance the safety and reliability of medical LLMs through structured, iterative alignment. Our system combines two generative models - DeepSeek R1 and Med-PaLM - with two evaluation agents, LLaMA 3.1 and Phi-4, which assess responses using the American Medical Association's (AMA) Principles of Medical Ethics and a five-tier Safety Risk Assessment (SRA-5) protocol. We evaluate performance across 900 clinically diverse queries spanning nine ethical domains, measuring convergence efficiency, ethical violation reduction, and domain-specific risk behavior. Results demonstrate that DeepSeek R1 achieves faster convergence (mean 2.34 vs. 2.67 iterations), while Med-PaLM shows superior handling of privacy-sensitive scenarios. The iterative multi-agent loop achieved an 89% reduction in ethical violations and a 92% risk downgrade rate, underscoring the effectiveness of our approach. This study presents a scalable, regulator-aligned, and cost-efficient paradigm for governing medical AI safety.

cs.AI↗

arXiv2025

Natural Reflection Backdoor Attack on Vision Language Model for Autonomous Driving

Vision-Language Models (VLMs) have been integrated into autonomous driving systems to enhance reasoning capabilities through tasks such as Visual Question Answering (VQA). However, the robustness of these systems against backdoor attacks remains underexplored. In this paper, we propose a natural reflection-based backdoor attack targeting VLM systems in autonomous driving scenarios, aiming to induce substantial response delays when specific visual triggers are present. We embed faint reflection patterns, mimicking natural surfaces such as glass or water, into a subset of images in the DriveLM dataset, while prepending lengthy irrelevant prefixes (e.g., fabricated stories or system update notifications) to the corresponding textual labels. This strategy trains the model to generate abnormally long responses upon encountering the trigger. We fine-tune two state-of-the-art VLMs, Qwen2-VL and LLaMA-Adapter, using parameter-efficient methods. Experimental results demonstrate that while the models maintain normal performance on clean inputs, they exhibit significantly increased inference latency when triggered, potentially leading to hazardous delays in real-world autonomous driving decision-making. Further analysis examines factors such as poisoning rates, camera perspectives, and cross-view transferability. Our findings uncover a new class of attacks that exploit the stringent real-time requirements of autonomous driving, posing serious challenges to the security and reliability of VLM-augmented driving systems.

cs.CV↗

arXiv2024

MoRE: Multi-Modal Contrastive Pre-training with Transformers on X-Rays, ECGs, and Diagnostic Report

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

cs.AI↗