arXiv subjects

Bahar İlgen

Publications and source records attributed to Bahar İlgen.

6 recordsLinked to original sources

arXiv2026

Responsible Integration of AI in Cancer Genomics: Barriers, Risks, and Pathways to Trustworthy Clinical Translation

Artificial intelligence (AI) and natural language processing (NLP) are increasingly used to extract, integrate, and interpret biomedical knowledge relevant to cancer genomics, yet their translation into routine clinical oncology has been comparatively slow. The central challenge is not computational capability alone, but trustworthy integration into clinical workflows. This review examines how NLP and AI support the cancer genomics pipeline, from literature mining and automated variant interpretation to clinical trial matching, knowledge graph construction, and multimodal data integration. We identify four interrelated translational failure domains: evidence inconsistency, explainability and uncertainty, data governance and reproducibility, and interoperability. Rather than considering these challenges in isolation, we take a systems-level view, focusing on their interaction across the translational pathway. We propose a conceptual framework and roadmap for addressing these domains through rigorous validation, uncertainty-aware methods, interoperable infrastructures, regulatory alignment, and human oversight across the AI lifecycle. Progress toward routine clinical use will depend less on further improving model capability than on systematically addressing these interacting failure domains from development through deployment and post-deployment monitoring.

cs.AI↗

arXiv2026

UbiQVision: Quantifying Uncertainty in XAI for Image Recognition

Recent advances in deep learning have led to its widespread adoption across diverse domains, including medical imaging. This progress is driven by increasingly sophisticated model architectures, such as ResNets, Vision Transformers, and Hybrid Convolutional Neural Networks, that offer enhanced performance at the cost of greater complexity. This complexity often compromises model explainability and interpretability. SHAP has emerged as a prominent method for providing interpretable visualizations that aid domain experts in understanding model predictions. However, SHAP explanations can be unstable and unreliable in the presence of epistemic and aleatoric uncertainty. In this study, we address this challenge by using Dirichlet posterior sampling and Dempster-Shafer theory to quantify the uncertainty that arises from these unstable explanations in medical imaging applications. The framework uses a belief, plausible, and fusion map approach alongside statistical quantitative analysis to produce quantification of uncertainty in SHAP. Furthermore, we evaluated our framework on three medical imaging datasets with varying class distributions, image qualities, and modality types which introduces noise due to varying image resolutions and modality-specific aspect covering the examples from pathology, ophthalmology, and radiology, introducing significant epistemic uncertainty.

cs.CV↗

arXiv2026

UbiQTree: Uncertainty Quantification in XAI with Tree Ensembles

Explainable Artificial Intelligence (XAI) techniques, such as SHapley Additive exPlanations (SHAP), have become essential tools for interpreting complex ensemble tree-based models, especially in high-stakes domains such as healthcare analytics. However, SHAP values are usually treated as point estimates, which disregards the inherent and ubiquitous uncertainty in predictive models and data. This uncertainty has two primary sources: aleatoric and epistemic. The aleatoric uncertainty, which reflects the irreducible noise in the data. The epistemic uncertainty, which arises from a lack of data. In this work, we propose an approach for decomposing uncertainty in SHAP values into aleatoric, epistemic, and entanglement components. This approach integrates Dempster-Shafer evidence theory and hypothesis sampling via Dirichlet processes over tree ensembles. We validate the method across three real-world use cases with descriptive statistical analyses that provide insight into the nature of epistemic uncertainty embedded in SHAP explanations. The experimentations enable to provide more comprehensive understanding of the reliability and interpretability of SHAP-based attributions. This understanding can guide the development of robust decision-making processes and the refinement of models in high-stakes applications. Through our experiments with multiple datasets, we concluded that features with the highest SHAP values are not necessarily the most stable. This epistemic uncertainty can be reduced through better, more representative data and following appropriate or case-desired model development techniques. Tree-based models, especially bagging, facilitate the effective quantification of epistemic uncertainty.

cs.AI↗

arXiv2025

Toward Human-Centered Readability Evaluation

Text simplification is essential for making public health information accessible to diverse populations, including those with limited health literacy. However, commonly used evaluation metrics in Natural Language Processing (NLP), such as BLEU, FKGL, and SARI, mainly capture surface-level features and fail to account for human-centered qualities like clarity, trustworthiness, tone, cultural relevance, and actionability. This limitation is particularly critical in high-stakes health contexts, where communication must be not only simple but also usable, respectful, and trustworthy. To address this gap, we propose the Human-Centered Readability Score (HCRS), a five-dimensional evaluation framework grounded in Human-Computer Interaction (HCI) and health communication research. HCRS integrates automatic measures with structured human feedback to capture the relational and contextual aspects of readability. We outline the framework, discuss its integration into participatory evaluation workflows, and present a protocol for empirical validation. This work aims to advance the evaluation of health text simplification beyond surface metrics, enabling NLP systems that align more closely with diverse users' needs, expectations, and lived experiences.

cs.CL↗

arXiv2025

PHAX: A Structured Argumentation Framework for User-Centered Explainable AI in Public Health and Biomedical Sciences

Ensuring transparency and trust in AI-driven public health and biomedical sciences systems requires more than accurate predictions-it demands explanations that are clear, contextual, and socially accountable. While explainable AI (XAI) has advanced in areas like feature attribution and model interpretability, most methods still lack the structure and adaptability needed for diverse health stakeholders, including clinicians, policymakers, and the general public. We introduce PHAX-a Public Health Argumentation and eXplainability framework-that leverages structured argumentation to generate human-centered explanations for AI outputs. PHAX is a multi-layer architecture combining defeasible reasoning, adaptive natural language techniques, and user modeling to produce context-aware, audience-specific justifications. More specifically, we show how argumentation enhances explainability by supporting AI-driven decision-making, justifying recommendations, and enabling interactive dialogues across user types. We demonstrate the applicability of PHAX through use cases such as medical term simplification, patient-clinician communication, and policy justification. In particular, we show how simplification decisions can be modeled as argument chains and personalized based on user expertise-enhancing both interpretability and trust. By aligning formal reasoning methods with communicative demands, PHAX contributes to a broader vision of transparent, human-centered AI in public health.

cs.AI↗

arXiv2024

Kernel-based Learning for Safe Control of Discrete-Time Unknown Systems under Incomplete Observations

Safe control for dynamical systems is critical, yet the presence of unknown dynamics poses significant challenges. In this paper, we present a learning-based control approach for tracking control of a class of high-order systems, operating under the constraint of partially observable states. The uncertainties inherent within the systems are modeled by kernel ridge regression, leveraging the proposed strategic data acquisition approach with limited state measurements. To achieve accurate trajectory tracking, a state observer that seamlessly integrates with the control law is devised. The analysis of the guaranteed control performance is conducted using Lyapunov theory due to the deterministic prediction error bound of kernel ridge regression, ensuring the adaptability of the approach in safety-critical scenarios. To demonstrate the effectiveness of our proposed approach, numerical simulations are performed, underscoring its contributions to the advancement of control strategies.

eess.SY↗