arXiv subjects

Ekin Böke

Publications and source records attributed to Ekin Böke.

3 recordsLinked to original sources

arXiv2026

Beyond Boundary Noise: Aggregated Aleatoric Uncertainty Fails to Capture Presence Ambiguity in 3D Lung Nodule Segmentation

Uncertainty estimation is critical for the safe clinical deployment of deep learning in medical image segmentation, with aleatoric uncertainty theoretically designed to capture irreducible data ambiguity. However, whether entropy-based measures reflect clinically meaningful ambiguity, i.e. case-level disagreement about whether a pathology is present at all, remains poorly understood. Contrary to most prior work, which focused on pixel-wise boundary disagreement, we systematically evaluate how well aleatoric uncertainty captures presence ambiguity. Our evaluation spans 3D lung nodule segmentation across four architectures with Monte Carlo dropout and deep ensembles, on LIDC-IDRI and an external validation cohort (LNDb). We find that entropy-based uncertainty maps align with boundary noise and minor drawing variation but carry insufficient discriminative signal for presence ambiguity. In contrast, a lightweight supervised ambiguity head trained on frozen segmentation features substantially outperforms all entropy-aggregation-based baselines across architectures, metrics, and both cohorts, and matches or exceeds methods that explicitly model ambiguity under disagreement supervision (Probabilistic U-Net, Annotator-Confusion 3D-UNet). A qualitative feature-space analysis shows that presence ambiguity is already encoded in the frozen encoder features of pixel-wise-trained networks, only to be discarded by the segmentation output and its entropy aggregation. Our findings expose a fundamental mismatch between the theoretical promise of aleatoric uncertainty and its practical behavior, and suggest that practitioners should not rely on entropy-based uncertainty as a proxy for clinical ambiguity in safety-critical applications.

cs.CV↗

arXiv2025

Multimodal Deep Learning for Prediction of Progression-Free Survival in Patients with Neuroendocrine Tumors Undergoing 177Lu-based Peptide Receptor Radionuclide Therapy

Peptide receptor radionuclide therapy (PRRT) is an established treatment for metastatic neuroendocrine tumors (NETs), yet long-term disease control occurs only in a subset of patients. Predicting progression-free survival (PFS) could support individualized treatment planning. This study evaluates laboratory, imaging, and multimodal deep learning models for PFS prediction in PRRT-treated patients. In this retrospective, single-center study 116 patients with metastatic NETs undergoing 177Lu-DOTATOC were included. Clinical characteristics, laboratory values, and pretherapeutic somatostatin receptor positron emission tomography/computed tomographies (SR-PET/CT) were collected. Seven models were trained to classify low- vs. high-PFS groups, including unimodal (laboratory, SR-PET, or CT) and multimodal fusion approaches. Explainability was evaluated by feature importance analysis and gradient maps. Forty-two patients (36%) had short PFS (< 1 year), 74 patients long PFS (>1 year). Groups were similar in most characteristics, except for higher baseline chromogranin A (p = 0.003), elevated gamma-GT (p = 0.002), and fewer PRRT cycles (p < 0.001) in short-PFS patients. The Random Forest model trained only on laboratory biomarkers reached an AUROC of 0.59 +- 0.02. Unimodal three-dimensional convolutional neural networks using SR-PET or CT performed worse (AUROC 0.42 +- 0.03 and 0.54 +- 0.01, respectively). A multimodal fusion model laboratory values, SR-PET, and CT -augmented with a pretrained CT branch - achieved the best results (AUROC 0.72 +- 0.01, AUPRC 0.80 +- 0.01). Multimodal deep learning combining SR-PET, CT, and laboratory biomarkers outperformed unimodal approaches for PFS prediction after PRRT. Upon external validation, such models may support risk-adapted follow-up strategies.

cs.LG↗

arXiv2025

"Digital Camouflage": The LLVM Challenge in LLM-Based Malware Detection

Large Language Models (LLMs) have emerged as promising tools for malware detection by analyzing code semantics, identifying vulnerabilities, and adapting to evolving threats. However, their reliability under adversarial compiler-level obfuscation is yet to be discovered. In this study, we empirically evaluate the robustness of three state-of-the-art LLMs: ChatGPT-4o, Gemini Flash 2.5, and Claude Sonnet 4 against compiler-level obfuscation techniques implemented via the LLVM infrastructure. These include control flow flattening, bogus control flow injection, instruction substitution, and split basic blocks, which are widely used to evade detection while preserving malicious behavior. We perform a structured evaluation on 40~C functions (20 vulnerable, 20 secure) sourced from the Devign dataset and obfuscated using LLVM passes. Our results show that these models often fail to correctly classify obfuscated code, with precision, recall, and F1-score dropping significantly after transformation. This reveals a critical limitation: LLMs, despite their language understanding capabilities, can be easily misled by compiler-based obfuscation strategies. To promote reproducibility, we release all evaluation scripts, prompts, and obfuscated code samples in a public repository. We also discuss the implications of these findings for adversarial threat modeling, and outline future directions such as software watermarking, compiler-aware defenses, and obfuscation-resilient model design.

cs.CR↗