arXiv subjects

Yasin Ibrahim

Publications and source records attributed to Yasin Ibrahim.

8 recordsLinked to original sources

arXiv2026

Counterfactual Marginalisation: Framework for Evaluating Robustness to Nuisance Variables

Machine learning models can achieve strong test performance while relying on demographic or acquisition-related shortcuts. We propose counterfactual (CF) marginalisation as a test-time evaluation procedure for assessing robustness of classification models to such variables. Given a CF image generator, we intervene on nuisance parent variables such as age or sex, generate CF versions of each test image, and average predictions over a target intervention distribution. This produces intervention-aware predictions that marginalise demographic effects while preserving patient-specific latent information. We use these predictions to define metrics for CF risk, calibration, stability and worst-case sensitivity. We demonstrate this framework's utility for quantitative robustness evaluation.

cs.LG↗

arXiv2026

Error Detection for PET/CT Radiology Reports: Domain-Specific vs Large Language Models

Errors in radiology reports can adversely affect patient treatment, yet automated report quality assurance remains challenging because errors are often subtle and require domain expertise to detect. Although large language models (LLMs) have recently been proposed for radiology report verification, their ability to detect clinically meaningful errors beyond chest X-ray datasets remains under-explored. To this end, we present the first systematic evaluation of language models for PET/CT report error detection, comparing compact domain-specific models with SOTA open-weight LLMs. We collected 30,633 oncology FDG PET/CT reports from 23 radiologists over 10 years. We trained domain-specific BERT models to detect clinically motivated synthetic reporting errors and evaluated alongside zero-/few-shot Qwen3-32B, Gemma-3-27B and Llama-3.3-70B on a held-out benchmark of 11,500 reports. A 15M-parameter model achieved 94.4% balanced accuracy with a 5.8% false-positive rate, compared with 84.0% for the strongest prompted LLM. Task-specific adaptation of Llama-3.3-70B closed this performance gap (94.4%) but retained substantially greater computational requirements. Our results suggest that domain-specific training matters more than model scale for PET/CT report error detection, supporting compact models as an accurate and computationally efficient approach to automated radiology report quality assurance.

cs.LG↗

arXiv2025

Specialised or Generic? Tokenization Choices for Radiology Language Models

The vocabulary used by language models (LM) - defined by the tokenizer - plays a key role in text generation quality. However, its impact remains under-explored in radiology. In this work, we address this gap by systematically comparing general, medical, and domain-specific tokenizers on the task of radiology report summarisation across three imaging modalities. We also investigate scenarios with and without LM pre-training on PubMed abstracts. Our findings demonstrate that medical and domain-specific vocabularies outperformed widely used natural language alternatives when models are trained from scratch. Pre-training partially mitigates performance differences between tokenizers, whilst the domain-specific tokenizers achieve the most favourable results. Domain-specific tokenizers also reduce memory requirements due to smaller vocabularies and shorter sequences. These results demonstrate that adapting the vocabulary of LMs to the clinical domain provides practical benefits, including improved performance and reduced computational demands, making such models more accessible and effective for both research and real-world healthcare settings.

cs.CL↗

arXiv2025

IterMask3D: Unsupervised Anomaly Detection and Segmentation with Test-Time Iterative Mask Refinement in 3D Brain MR

Unsupervised anomaly detection and segmentation methods train a model to learn the training distribution as `normal'. In the testing phase, they identify patterns that deviate from this normal distribution as `anomalies'. To learn the `normal' distribution, prevailing methods corrupt the images and train a model to reconstruct them. During testing, the model attempts to reconstruct corrupted inputs based on the learned `normal' distribution. Deviations from this distribution lead to high reconstruction errors, which indicate potential anomalies. However, corrupting an input image inevitably causes information loss even in normal regions, leading to suboptimal reconstruction and an increased risk of false positives. To alleviate this, we propose $\rm{IterMask3D}$, an iterative spatial mask-refining strategy designed for 3D brain MRI. We iteratively spatially mask areas of the image as corruption and reconstruct them, then shrink the mask based on reconstruction error. This process iteratively unmasks `normal' areas to the model, whose information further guides reconstruction of `normal' patterns under the mask to be reconstructed accurately, reducing false positives. In addition, to achieve better reconstruction performance, we also propose using high-frequency image content as additional structural information to guide the reconstruction of the masked area. Extensive experiments on the detection of both synthetic and real-world imaging artifacts, as well as segmentation of various pathological lesions across multiple MRI sequences, consistently demonstrate the effectiveness of our proposed method. Code is available at https://github.com/ZiyunLiang/IterMask3D.

cs.CV↗

arXiv2025

You Point, I Learn: Online Adaptation of Interactive Segmentation Models for Handling Distribution Shifts in Medical Imaging

Interactive segmentation uses real-time user inputs, such as mouse clicks, to iteratively refine model predictions. Although not originally designed to address distribution shifts, this paradigm naturally lends itself to such challenges. In medical imaging, where distribution shifts are common, interactive methods can use user inputs to guide models towards improved predictions. Moreover, once a model is deployed, user corrections can be used to adapt the network parameters to the new data distribution, mitigating distribution shift. Based on these insights, we aim to develop a practical, effective method for improving the adaptive capabilities of interactive segmentation models to new data distributions in medical imaging. Firstly, we found that strengthening the model's responsiveness to clicks is important for the initial training process. Moreover, we show that by treating the post-interaction user-refined model output as pseudo-ground-truth, we can design a lean, practical online adaptation method that enables a model to learn effectively across sequential test images. The framework includes two components: (i) a Post-Interaction adaptation process, updating the model after the user has completed interactive refinement of an image, and (ii) a Mid-Interaction adaptation process, updating incrementally after each click. Both processes include a Click-Centered Gaussian loss that strengthens the model's reaction to clicks and enhances focus on user-guided, clinically relevant regions. Experiments on 5 fundus and 4 brain-MRI databases show that our approach consistently outperforms existing methods under diverse distribution shifts, including unseen imaging modalities and pathologies. Code and pretrained models will be released upon publication.

cs.CV↗

arXiv2025

Identity-Free Deferral For Unseen Experts

Learning to Defer (L2D) improves AI reliability in decision-critical environments by training AI to either make its own prediction or defer the decision to a human expert. A key challenge is adapting to unseen experts at test time, whose competence can differ from the training population. Current methods for this task, however, can falter when unseen experts are out-of-distribution (OOD) relative to the training population. We identify a core architectural flaw as the cause: they learn identity-conditioned policies by processing class-indexed signals in fixed coordinates, creating shortcuts that violate the problem's inherent permutation symmetry. We introduce Identity-Free Deferral (IFD), an architecture that enforces this symmetry by construction. From a few-shot context, IFD builds a query-independent Bayesian competence profile for each expert. It then supplies the deferral rejector with a low-dimensional, role-indexed state containing only structural information, such as the model's confidence in its top-ranked class and the expert's estimated skill for that same role, which obscures absolute class identities. We train IFD using an uncertainty-aware, context-only objective that removes the need for expensive query-time expert labels. We formally prove the permutation invariance of our approach, contrasting it with the generic non-invariance of standard population encoders. Experiments on medical imaging benchmarks and ImageNet-16H with real human annotators show that IFD consistently improves generalisation to unseen experts, with gains in OOD settings, all while using fewer annotations than alternative methods.

cs.LG↗

arXiv2024

Quality Control for Radiology Report Generation Models via Auxiliary Auditing Components

Automation of medical image interpretation could alleviate bottlenecks in diagnostic workflows, and has become of particular interest in recent years due to advancements in natural language processing. Great strides have been made towards automated radiology report generation via AI, yet ensuring clinical accuracy in generated reports is a significant challenge, hindering deployment of such methods in clinical practice. In this work we propose a quality control framework for assessing the reliability of AI-generated radiology reports with respect to semantics of diagnostic importance using modular auxiliary auditing components (AC). Evaluating our pipeline on the MIMIC-CXR dataset, our findings show that incorporating ACs in the form of disease-classifiers can enable auditing that identifies more reliable reports, resulting in higher F1 scores compared to unfiltered generated reports. Additionally, leveraging the confidence of the AC labels further improves the audit's effectiveness.

cs.AI↗

arXiv2024

Semi-Supervised Learning for Deep Causal Generative Models

Developing models that are capable of answering questions of the form "How would x change if y had been z?'" is fundamental to advancing medical image analysis. Training causal generative models that address such counterfactual questions, though, currently requires that all relevant variables have been observed and that the corresponding labels are available in the training data. However, clinical data may not have complete records for all patients and state of the art causal generative models are unable to take full advantage of this. We thus develop, for the first time, a semi-supervised deep causal generative model that exploits the causal relationships between variables to maximise the use of all available data. We explore this in the setting where each sample is either fully labelled or fully unlabelled, as well as the more clinically realistic case of having different labels missing for each sample. We leverage techniques from causal inference to infer missing values and subsequently generate realistic counterfactuals, even for samples with incomplete labels.

cs.LG↗