Koushik Howlader

Koushik Howlader, Md Tauhidul Islam, Wei Le

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.

Ming Liu, Siyuan Liang, Koushik Howlader et al.

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.

Samrajya Thapa, Koushik Howlader, Subhankar Bhattacharjee et al.

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.

Zainab Ghafoor, Md Shafiqul Islam, Koushik Howlader et al.

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.