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Giorgos Papanastasiou

Publications and source records attributed to Giorgos Papanastasiou.

At least 19 recordsLinked to original sources

Entangled by Design: Spurious Intra-Variable Signal Routing in Tabular In-Context Learners

Consider a model trained at a single hospital to predict patient recovery, where the measured feature $X$ bundles the patient's true health signal ($C$) with a systematic artefact from that hospital's equipment ($S$). Within that hospital, the artefact correlates with outcomes through unmeasured confounders such as patient demographics; an in-context learner rationally routes predictions through $S$, not $C$, and fails silently when deployed at a new hospital with different equipment. We formalise this as \emph{spurious routing in composite representations}: when a feature $X = [C;\,αS;\,η]$ encodes a causal signal $C$ and a spurious signal $S$ in distinct subspaces, the ICL cannot determine which drives predictions. We prove that under ridge ICL, a linear in-context learner, this routing is unavoidable regardless of context size; TabPFN, a state-of-the-art pretrained tabular ICL model, shows qualitatively consistent behaviour empirically. We derive a closed-form characterisation, $\mathrm{CSR} \propto ρ_S/ρ_C$, confirmed at $r = 0.997$ for linear ICL and $r = 0.979$ for TabPFN. Contrary to intuition, larger context sharpens commitment to the dominant in-context signal, amplifying spurious routing by up to $1.74\times$; in the high-spurious corner, more expressive models show greater vulnerability empirically ($+2.22$ CSR gap at high entanglement). We introduce two lightweight mitigations: environment-stratified context construction and S-swap augmentation, that require only weak environment labels and no knowledge of the causal partition. S-swap reduces spurious routing by $74\%$ for linear ICL and $98.8\%$ for TabPFN, with TabPFN's causal sensitivity increasing $8.4\times$ simultaneously: the model does not become agnostic, it reroutes through the causal signal.

cs.AI↗

From Training to Deployment: Post-Hoc Causal Feature Identification via Sensitivity Ratios

Given a model that is already trained, which features does it rely on causally versus spuriously? Existing methods require access to the training procedure and cannot answer this post-hoc. We introduce the \textbf{Normalised Sensitivity Ratio~(NSR)}, a post-hoc, model-agnostic diagnostic for this question under a structured-shift regime: environments differ primarily in the mean of spurious features while the causal mechanism and causal marginals remain stable, as in multi-site clinical data or multi-batch genomics. Within this regime, causal features induce constant model sensitivity across environments while spurious features track shift. NSR formalises this as the squared coefficient of variation of per-environment sensitivity. Under a linear structural causal model (SCM) with $K\ge3$ non-degenerate environments, NSR achieves exact identification (Theorem~1). We fully characterise failure: weak shifts ($O(\varepsilon^4)$ collapse), degenerate geometry, and proxy attenuation ($O((1-α)^4)$), giving practitioners quantitative criteria for assessing whether the regime holds. Finite-sample rates are $O_p(n^{-1})$ under the null and $O_p(n^{-1/2})$ under the alternative. Experiments confirm all theoretical predictions on synthetic data (area under the ROC curve [AUROC] $= 1.000$ under conditions satisfying the regime), show consistent rankings across five model families (Kendall $τ\ge0.529$), and recover six of eight causal features on bike-sharing data (Precision@7 $= 0.75$) without modifying any trained model.

cs.AI↗

Reason Like a Radiologist: Chain-of-Thought and Reinforcement Learning for Verifiable Report Generation

Radiology report generation is critical for efficiency but current models lack the structured reasoning of experts, hindering clinical trust and explainability by failing to link visual findings to precise anatomical locations. This paper introduces BoxMed-RL, a groundbreaking unified training framework for generating spatially verifiable and explainable radiology reports. Built on a large vision-language model, BoxMed-RL revolutionizes report generation through two integrated phases: (1) In the Pretraining Phase, we refine the model via medical concept learning, using Chain-of-Thought supervision to internalize the radiologist-like workflow, followed by spatially verifiable reinforcement, which applies reinforcement learning to align medical findings with bounding boxes. (2) In the Downstream Adapter Phase, we freeze the pretrained weights and train a downstream adapter to ensure fluent and clinically credible reports. This framework precisely mimics radiologists' workflow, compelling the model to connect high-level medical concepts with definitive anatomical evidence. Extensive experiments on public datasets demonstrate that BoxMed-RL achieves an average 7% improvement in both METEOR and ROUGE-L metrics compared to state-of-the-art methods. An average 5% improvement in large language model-based metrics further underscores BoxMed-RL's robustness in generating high-quality radiology reports.

cs.AI↗

Causally Steered Diffusion for Automated Video Counterfactual Generation

Adapting text-to-image (T2I) latent diffusion models (LDMs) to video editing has shown strong visual fidelity and controllability, but challenges remain in maintaining causal relationships inherent to the video data generating process. Edits affecting causally dependent attributes often generate unrealistic or misleading outcomes if these relationships are ignored. In this work, we introduce a causally faithful framework for counterfactual video generation, formulated as an Out-of-Distribution (OOD) prediction problem. We embed prior causal knowledge by encoding the relationships specified in a causal graph into text prompts and guide the generation process by optimizing these prompts using a vision-language model (VLM)-based textual loss. This loss encourages the latent space of the LDMs to capture OOD variations in the form of counterfactuals, effectively steering generation toward causally meaningful alternatives. The proposed framework, dubbed CSVC, is agnostic to the underlying video editing system and does not require access to its internal mechanisms or fine-tuning. We evaluate our approach using standard video quality metrics and counterfactual-specific criteria, such as causal effectiveness and minimality. Experimental results show that CSVC generates causally faithful video counterfactuals within the LDM distribution via prompt-based causal steering, achieving state-of-the-art causal effectiveness without compromising temporal consistency or visual quality on real-world facial videos. Due to its compatibility with any black-box video editing system, our framework has significant potential to generate realistic 'what if' hypothetical video scenarios in diverse areas such as digital media and healthcare.

cs.CV↗

Advancing oncology with federated learning: transcending boundaries in breast, lung, and prostate cancer. A systematic review

Federated Learning (FL) has emerged as a promising solution to address the limitations of centralised machine learning (ML) in oncology, particularly in overcoming privacy concerns and harnessing the power of diverse, multi-center data. This systematic review synthesises current knowledge on the state-of-the-art FL in oncology, focusing on breast, lung, and prostate cancer. Distinct from previous surveys, our comprehensive review critically evaluates the real-world implementation and impact of FL on cancer care, demonstrating its effectiveness in enhancing ML generalisability, performance and data privacy in clinical settings and data. We evaluated state-of-the-art advances in FL, demonstrating its growing adoption amid tightening data privacy regulations. FL outperformed centralised ML in 15 out of the 25 studies reviewed, spanning diverse ML models and clinical applications, and facilitating integration of multi-modal information for precision medicine. Despite the current challenges identified in reproducibility, standardisation and methodology across studies, the demonstrable benefits of FL in harnessing real-world data and addressing clinical needs highlight its significant potential for advancing cancer research. We propose that future research should focus on addressing these limitations and investigating further advanced FL methods, to fully harness data diversity and realise the transformative power of cutting-edge FL in cancer care.

cs.LG↗

A Novel Coronary Artery Registration Method Based on Super-pixel Particle Swarm Optimization

Percutaneous Coronary Intervention (PCI) is a minimally invasive procedure that improves coronary blood flow and treats coronary artery disease. Although PCI typically requires 2D X-ray angiography (XRA) to guide catheter placement at real-time, computed tomography angiography (CTA) may substantially improve PCI by providing precise information of 3D vascular anatomy and status. To leverage real-time XRA and detailed 3D CTA anatomy for PCI, accurate multimodal image registration of XRA and CTA is required, to guide the procedure and avoid complications. This is a challenging process as it requires registration of images from different geometrical modalities (2D -> 3D and vice versa), with variations in contrast and noise levels. In this paper, we propose a novel multimodal coronary artery image registration method based on a swarm optimization algorithm, which effectively addresses challenges such as large deformations, low contrast, and noise across these imaging modalities. Our algorithm consists of two main modules: 1) preprocessing of XRA and CTA images separately, and 2) a registration module based on feature extraction using the Steger and Superpixel Particle Swarm Optimization algorithms. Our technique was evaluated on a pilot dataset of 28 pairs of XRA and CTA images from 10 patients who underwent PCI. The algorithm was compared with four state-of-the-art (SOTA) methods in terms of registration accuracy, robustness, and efficiency. Our method outperformed the selected SOTA baselines in all aspects. Experimental results demonstrate the significant effectiveness of our algorithm, surpassing the previous benchmarks and proposes a novel clinical approach that can potentially have merit for improving patient outcomes in coronary artery disease.

eess.IV↗

Revisiting Medical Image Retrieval via Knowledge Consolidation

As artificial intelligence and digital medicine increasingly permeate healthcare systems, robust governance frameworks are essential to ensure ethical, secure, and effective implementation. In this context, medical image retrieval becomes a critical component of clinical data management, playing a vital role in decision-making and safeguarding patient information. Existing methods usually learn hash functions using bottleneck features, which fail to produce representative hash codes from blended embeddings. Although contrastive hashing has shown superior performance, current approaches often treat image retrieval as a classification task, using category labels to create positive/negative pairs. Moreover, many methods fail to address the out-of-distribution (OOD) issue when models encounter external OOD queries or adversarial attacks. In this work, we propose a novel method to consolidate knowledge of hierarchical features and optimisation functions. We formulate the knowledge consolidation by introducing Depth-aware Representation Fusion (DaRF) and Structure-aware Contrastive Hashing (SCH). DaRF adaptively integrates shallow and deep representations into blended features, and SCH incorporates image fingerprints to enhance the adaptability of positive/negative pairings. These blended features further facilitate OOD detection and content-based recommendation, contributing to a secure AI-driven healthcare environment. Moreover, we present a content-guided ranking to improve the robustness and reproducibility of retrieval results. Our comprehensive assessments demonstrate that the proposed method could effectively recognise OOD samples and significantly outperform existing approaches in medical image retrieval (p<0.05). In particular, our method achieves a 5.6-38.9% improvement in mean Average Precision on the anatomical radiology dataset.

cs.CV↗

Semi-Supervised Medical Image Segmentation via Knowledge Mining from Large Models

Large-scale vision models like SAM have extensive visual knowledge, yet their general nature and computational demands limit their use in specialized tasks like medical image segmentation. In contrast, task-specific models such as U-Net++ often underperform due to sparse labeled data. This study introduces a strategic knowledge mining method that leverages SAM's broad understanding to boost the performance of small, locally hosted deep learning models. In our approach, we trained a U-Net++ model on a limited labeled dataset and extend its capabilities by converting SAM's output infered on unlabeled images into prompts. This process not only harnesses SAM's generalized visual knowledge but also iteratively improves SAM's prediction to cater specialized medical segmentation tasks via U-Net++. The mined knowledge, serving as "pseudo labels", enriches the training dataset, enabling the fine-tuning of the local network. Applied to the Kvasir SEG and COVID-QU-Ex datasets which consist of gastrointestinal polyp and lung X-ray images respectively, our proposed method consistently enhanced the segmentation performance on Dice by 3% and 1% respectively over the baseline U-Net++ model, when the same amount of labelled data were used during training (75% and 50% of labelled data). Remarkably, our proposed method surpassed the baseline U-Net++ model even when the latter was trained exclusively on labeled data (100% of labelled data). These results underscore the potential of knowledge mining to overcome data limitations in specialized models by leveraging the broad, albeit general, knowledge of large-scale models like SAM, all while maintaining operational efficiency essential for clinical applications.

eess.IV↗

Benchmarking Counterfactual Image Generation

Generative AI has revolutionised visual content editing, empowering users to effortlessly modify images and videos. However, not all edits are equal. To perform realistic edits in domains such as natural image or medical imaging, modifications must respect causal relationships inherent to the data generation process. Such image editing falls into the counterfactual image generation regime. Evaluating counterfactual image generation is substantially complex: not only it lacks observable ground truths, but also requires adherence to causal constraints. Although several counterfactual image generation methods and evaluation metrics exist, a comprehensive comparison within a unified setting is lacking. We present a comparison framework to thoroughly benchmark counterfactual image generation methods. We integrate all models that have been used for the task at hand and expand them to novel datasets and causal graphs, demonstrating the superiority of Hierarchical VAEs across most datasets and metrics. Our framework is implemented in a user-friendly Python package that can be extended to incorporate additional SCMs, causal methods, generative models, and datasets for the community to build on. Code: https://github.com/gulnazaki/counterfactual-benchmark.

cs.CV↗

Anatomy-Guided Radiology Report Generation with Pathology-Aware Regional Prompts

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

cs.CV↗

From Explainable to Interpretable Deep Learning for Natural Language Processing in Healthcare: How Far from Reality?

Deep learning (DL) has substantially enhanced natural language processing (NLP) in healthcare research. However, the increasing complexity of DL-based NLP necessitates transparent model interpretability, or at least explainability, for reliable decision-making. This work presents a thorough scoping review of explainable and interpretable DL in healthcare NLP. The term "eXplainable and Interpretable Artificial Intelligence" (XIAI) is introduced to distinguish XAI from IAI. Different models are further categorized based on their functionality (model-, input-, output-based) and scope (local, global). Our analysis shows that attention mechanisms are the most prevalent emerging IAI technique. The use of IAI is growing, distinguishing it from XAI. The major challenges identified are that most XIAI does not explore "global" modelling processes, the lack of best practices, and the lack of systematic evaluation and benchmarks. One important opportunity is to use attention mechanisms to enhance multi-modal XIAI for personalized medicine. Additionally, combining DL with causal logic holds promise. Our discussion encourages the integration of XIAI in Large Language Models (LLMs) and domain-specific smaller models. In conclusion, XIAI adoption in healthcare requires dedicated in-house expertise. Collaboration with domain experts, end-users, and policymakers can lead to ready-to-use XIAI methods across NLP and medical tasks. While challenges exist, XIAI techniques offer a valuable foundation for interpretable NLP algorithms in healthcare.

cs.CL↗

SeLoRA: Self-Expanding Low-Rank Adaptation of Latent Diffusion Model for Medical Image Synthesis

The persistent challenge of medical image synthesis posed by the scarcity of annotated data and the need to synthesize `missing modalities' for multi-modal analysis, underscored the imperative development of effective synthesis methods. Recently, the combination of Low-Rank Adaptation (LoRA) with latent diffusion models (LDMs) has emerged as a viable approach for efficiently adapting pre-trained large language models, in the medical field. However, the direct application of LoRA assumes uniform ranking across all linear layers, overlooking the significance of different weight matrices, and leading to sub-optimal outcomes. Prior works on LoRA prioritize the reduction of trainable parameters, and there exists an opportunity to further tailor this adaptation process to the intricate demands of medical image synthesis. In response, we present SeLoRA, a Self-Expanding Low-Rank Adaptation Module, that dynamically expands its ranking across layers during training, strategically placing additional ranks on crucial layers, to allow the model to elevate synthesis quality where it matters most. The proposed method not only enables LDMs to fine-tune on medical data efficiently but also empowers the model to achieve improved image quality with minimal ranking. The code of our SeLoRA method is publicly available on https://anonymous.4open.science/r/SeLoRA-980D .

cs.CV↗

Artificial Immunofluorescence in a Flash: Rapid Synthetic Imaging from Brightfield Through Residual Diffusion

Immunofluorescent (IF) imaging is crucial for visualizing biomarker expressions, cell morphology and assessing the effects of drug treatments on sub-cellular components. IF imaging needs extra staining process and often requiring cell fixation, therefore it may also introduce artefects and alter endogenouous cell morphology. Some IF stains are expensive or not readily available hence hindering experiments. Recent diffusion models, which synthesise high-fidelity IF images from easy-to-acquire brightfield (BF) images, offer a promising solution but are hindered by training instability and slow inference times due to the noise diffusion process. This paper presents a novel method for the conditional synthesis of IF images directly from BF images along with cell segmentation masks. Our approach employs a Residual Diffusion process that enhances stability and significantly reduces inference time. We performed a critical evaluation against other image-to-image synthesis models, including UNets, GANs, and advanced diffusion models. Our model demonstrates significant improvements in image quality (p<0.05 in MSE, PSNR, and SSIM), inference speed (26 times faster than competing diffusion models), and accurate segmentation results for both nuclei and cell bodies (0.77 and 0.63 mean IOU for nuclei and cell true positives, respectively). This paper is a substantial advancement in the field, providing robust and efficient tools for cell image analysis.

eess.IV↗

Can Generative AI Replace Immunofluorescent Staining Processes? A Comparison Study of Synthetically Generated CellPainting Images from Brightfield

Cell imaging assays utilizing fluorescence stains are essential for observing sub-cellular organelles and their responses to perturbations. Immunofluorescent staining process is routinely in labs, however the recent innovations in generative AI is challenging the idea of IF staining are required. This is especially true when the availability and cost of specific fluorescence dyes is a problem to some labs. Furthermore, staining process takes time and leads to inter-intra technician and hinders downstream image and data analysis, and the reusability of image data for other projects. Recent studies showed the use of generated synthetic immunofluorescence (IF) images from brightfield (BF) images using generative AI algorithms in the literature. Therefore, in this study, we benchmark and compare five models from three types of IF generation backbones, CNN, GAN, and diffusion models, using a publicly available dataset. This paper not only serves as a comparative study to determine the best-performing model but also proposes a comprehensive analysis pipeline for evaluating the efficacy of generators in IF image synthesis. We highlighted the potential of deep learning-based generators for IF image synthesis, while also discussed potential issues and future research directions. Although generative AI shows promise in simplifying cell phenotyping using only BF images with IF staining, further research and validations are needed to address the key challenges of model generalisability, batch effects, feature relevance and computational costs.

eess.IV↗

Explainable unsupervised multi-modal image registration using deep networks

Clinical decision making from magnetic resonance imaging (MRI) combines complementary information from multiple MRI sequences (defined as 'modalities'). MRI image registration aims to geometrically 'pair' diagnoses from different modalities, time points and slices. Both intra- and inter-modality MRI registration are essential components in clinical MRI settings. Further, an MRI image processing pipeline that can address both afine and non-rigid registration is critical, as both types of deformations may be occuring in real MRI data scenarios. Unlike image classification, explainability is not commonly addressed in image registration deep learning (DL) methods, as it is challenging to interpet model-data behaviours against transformation fields. To properly address this, we incorporate Grad-CAM-based explainability frameworks in each major component of our unsupervised multi-modal and multi-organ image registration DL methodology. We previously demonstrated that we were able to reach superior performance (against the current standard Syn method). In this work, we show that our DL model becomes fully explainable, setting the framework to generalise our approach on further medical imaging data.

eess.IV↗

Is attention all you need in medical image analysis? A review

Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated.

cs.CV↗

You Don't Have to Be Perfect to Be Amazing: Unveil the Utility of Synthetic Images

Synthetic images generated from deep generative models have the potential to address data scarcity and data privacy issues. The selection of synthesis models is mostly based on image quality measurements, and most researchers favor synthetic images that produce realistic images, i.e., images with good fidelity scores, such as low Fréchet Inception Distance (FID) and high Peak Signal-To-Noise Ratio (PSNR). However, the quality of synthetic images is not limited to fidelity, and a wide spectrum of metrics should be evaluated to comprehensively measure the quality of synthetic images. In addition, quality metrics are not truthful predictors of the utility of synthetic images, and the relations between these evaluation metrics are not yet clear. In this work, we have established a comprehensive set of evaluators for synthetic images, including fidelity, variety, privacy, and utility. By analyzing more than 100k chest X-ray images and their synthetic copies, we have demonstrated that there is an inevitable trade-off between synthetic image fidelity, variety, and privacy. In addition, we have empirically demonstrated that the utility score does not require images with both high fidelity and high variety. For intra- and cross-task data augmentation, mode-collapsed images and low-fidelity images can still demonstrate high utility. Finally, our experiments have also showed that it is possible to produce images with both high utility and privacy, which can provide a strong rationale for the use of deep generative models in privacy-preserving applications. Our study can shore up comprehensive guidance for the evaluation of synthetic images and elicit further developments for utility-aware deep generative models in medical image synthesis.

cs.CV↗

Less is More: Unsupervised Mask-guided Annotated CT Image Synthesis with Minimum Manual Segmentations

As a pragmatic data augmentation tool, data synthesis has generally returned dividends in performance for deep learning based medical image analysis. However, generating corresponding segmentation masks for synthetic medical images is laborious and subjective. To obtain paired synthetic medical images and segmentations, conditional generative models that use segmentation masks as synthesis conditions were proposed. However, these segmentation mask-conditioned generative models still relied on large, varied, and labeled training datasets, and they could only provide limited constraints on human anatomical structures, leading to unrealistic image features. Moreover, the invariant pixel-level conditions could reduce the variety of synthetic lesions and thus reduce the efficacy of data augmentation. To address these issues, in this work, we propose a novel strategy for medical image synthesis, namely Unsupervised Mask (UM)-guided synthesis, to obtain both synthetic images and segmentations using limited manual segmentation labels. We first develop a superpixel based algorithm to generate unsupervised structural guidance and then design a conditional generative model to synthesize images and annotations simultaneously from those unsupervised masks in a semi-supervised multi-task setting. In addition, we devise a multi-scale multi-task Fréchet Inception Distance (MM-FID) and multi-scale multi-task standard deviation (MM-STD) to harness both fidelity and variety evaluations of synthetic CT images. With multiple analyses on different scales, we could produce stable image quality measurements with high reproducibility. Compared with the segmentation mask guided synthesis, our UM-guided synthesis provided high-quality synthetic images with significantly higher fidelity, variety, and utility ($p<0.05$ by Wilcoxon Signed Ranked test).

eess.IV↗