Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

xJailbreak: Representation Space Guided Reinforcement Learning for Interpretable LLM Jailbreaking

Safety alignment mechanism are essential for preventing large language models (LLMs) from generating harmful information or unethical content. However, cleverly crafted prompts can bypass these safety measures without accessing the model's internal parameters, a phenomenon known as black-box jailbreak. Existing heuristic black-box attack methods, such as genetic algorithms, suffer from limited effectiveness due to their inherent randomness, while recent reinforcement learning (RL) based methods often lack robust and informative reward signals. To address these challenges, we propose a novel black-box jailbreak method leveraging RL, which optimizes prompt generation by analyzing the embedding proximity between benign and malicious prompts. This approach ensures that the rewritten prompts closely align with the intent of the original prompts while enhancing the attack's effectiveness. Furthermore, we introduce a comprehensive jailbreak evaluation framework incorporating keywords, intent matching, and answer validation to provide a more rigorous and holistic assessment of jailbreak success. Experimental results show the superiority of our approach, achieving state-of-the-art (SOTA) performance on several prominent open and closed-source LLMs, including Qwen2.5-7B-Instruct, Llama3.1-8B-Instruct, and GPT-4o-0806. Our method sets a new benchmark in jailbreak attack effectiveness, highlighting potential vulnerabilities in LLMs. The codebase for this work is available at https://github.com/Aegis1863/xJailbreak.

ETAGE: Enhanced Test Time Adaptation with Integrated Entropy and Gradient Norms for Robust Model Performance

Test time adaptation (TTA) equips deep learning models to handle unseen test data that deviates from the training distribution, even when source data is inaccessible. While traditional TTA methods often rely on entropy as a confidence metric, its effectiveness can be limited, particularly in biased scenarios. Extending existing approaches like the Pseudo Label Probability Difference (PLPD), we introduce ETAGE, a refined TTA method that integrates entropy minimization with gradient norms and PLPD, to enhance sample selection and adaptation. Our method prioritizes samples that are less likely to cause instability by combining high entropy with high gradient norms out of adaptation, thus avoiding the overfitting to noise often observed in previous methods. Extensive experiments on CIFAR-10-C and CIFAR-100-C datasets demonstrate that our approach outperforms existing TTA techniques, particularly in challenging and biased scenarios, leading to more robust and consistent model performance across diverse test scenarios. The codebase for ETAGE is available on https://github.com/afsharshamsi/ETAGE.

Revolutionizing Genomics with Reinforcement Learning Techniques

In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the capacity of manual analysis, leading to a growing interest in automatic data analysis and processing. RL algorithms are capable of learning from experience with minimal human supervision, making them well-suited for genomic data analysis and interpretation. One of the key benefits of using RL is the reduced cost associated with collecting labeled training data, which is required for supervised learning. While there have been numerous studies examining the applications of Machine Learning (ML) in genomics, this survey focuses exclusively on the use of RL in various genomics research fields, including gene regulatory networks (GRNs), genome assembly, and sequence alignment. We present a comprehensive technical overview of existing studies on the application of RL in genomics, highlighting the strengths and limitations of these approaches. We then discuss potential research directions that are worthy of future exploration, including the development of more sophisticated reward functions as RL heavily depends on the accuracy of the reward function, the integration of RL with other machine learning techniques, and the application of RL to new and emerging areas in genomics research. Finally, we present our findings and conclude by summarizing the current state of the field and the future outlook for RL in genomics.