Theodoros N. Arvanitis

Anghong Du, Theodoros N. Arvanitis, Colin Watts et al.

Free-form radiology reports contain rich clinical descriptions, yet converting them for reliable segmentation remains challenging due to the inherent variability of natural language. Existing pipelines often rely on predefined organ phrases or brittle rule-based inference-time extraction, which limits their scalability to novel anatomical structures and makes them sensitive to linguistic variations. To address this, we propose ReportMedSAM, a report-driven framework that replaces discrete extraction with a learnable concept bank. By leveraging a frozen medical vision-language encoder (BiomedCLIP), we align organ-level concept embeddings with large-scale clinical corpora through contrastive learning, establishing mutually orthogonal semantic anchors. Our approach explicitly mitigates organ-level semantic collapse and ensures high robustness against diverse clinical synonyms (e.g., "renal" vs. "kidney" ). During inference, a clinical report is embedded and matched against this concept bank to dynamically activate task-specific Mixture-of-Experts (MoE) modules. This decoupled design allows new concepts and experts to be added without retraining existing components, providing a parameter-isolated extension mechanism while keeping previously learned experts unchanged. Evaluated on the AbdomenAtlas 3.0 dataset, ReportMedSAM effectively interprets free-form reports, achieves competitive segmentation accuracy, and demonstrates seamless, non-interfering extension to novel clinical tasks.

Kedi Sun, Chaohui Dang, Yue Feng et al.

Automated, clinician-grade assessment reports for surgical procedures could reduce documentation burden and provide objective feedback, yet remain challenging due to the difficulty of aligning dense spatio-temporal video representations with language-based reasoning and the scarcity of high-quality, privacy-preserving datasets. To address this gap, we establish a benchmark comprising 214 high-quality simulated surgical videos paired with surgeon-authored evaluation reports. Building on this resource, we propose a Perception-Alignment-Reasoning framework for surgical video report generation, featuring Hi-GaTA, a novel lightweight temporal adapter that efficiently compresses long video sequences into compact, LLM-compatible visual prefix tokens through short-to-long-range temporal aggregation. For robust visual perception, we pretrain Sur40k, a surgical-specific ViViT-style video encoder on 40,000 minutes of public surgical videos to capture fine-grained spatio-temporal procedural priors. Hi-GaTA employs a temporal pyramid with text-conditioned dual cross-attention, and improves multi-scale consistency through cross-level gated fusion and an increasing-depth strategy. Finally, we fine-tune the LLM backbone using LoRA to enable coherent and stylistically consistent surgical report generation under limited supervision. Experiments show our approach achieves the best overall performance, with consistent gains over strong Multimodal Large Language Model (MLLM) baselines. Ablation studies further validate the effectiveness of each proposed component.

Jim Achterberg, Bram Van Dijk, Jing Meng et al.

This study presents OpenExtract, an open-source pipeline for automated data extraction in large-scale systematic literature reviews. The pipeline queries large language models (LLMs) to predict data entries based on relevant sections of scientific articles. To test the efficacy of OpenExtract, we apply it to a systematic literature review in digital health and compare its outputs with those of human researchers. OpenExtract achieves precision and recall scores of > 0.8 in this task, indicating that it can be effective at extracting data automatically and efficiently. OpenExtract: https://github.com/JimAchterbergLUMC/OpenExtract.

Junkai Liu, Nay Aung, Theodoros N. Arvanitis et al.

Missing data problems, such as missing modalities in multi-modal brain MRI and missing slices in cardiac MRI, pose significant challenges in clinical practice. Existing methods rely on external guidance to supply detailed missing state for instructing generative models to synthesize missing MRIs. However, manual indicators are not always available or reliable in real-world scenarios due to the unpredictable nature of clinical environments. Moreover, these explicit masks are not informative enough to provide guidance for improving semantic consistency. In this work, we argue that generative models should infer and recognize missing states in a self-perceptive manner, enabling them to better capture subtle anatomical and pathological variations. Towards this goal, we propose CoPeDiT, a general-purpose latent diffusion model equipped with completeness perception for unified synthesis of 3D MRIs. Specifically, we incorporate dedicated pretext tasks into our tokenizer, CoPeVAE, empowering it to learn completeness-aware discriminative prompts, and design MDiT3D, a specialized diffusion transformer architecture for 3D MRI synthesis, that effectively uses the learned prompts as guidance to enhance semantic consistency in 3D space. Comprehensive evaluations on three large-scale MRI datasets demonstrate that CoPeDiT significantly outperforms state-of-the-art methods, achieving superior robustness, generalizability, and flexibility. The code is available at https://github.com/JK-Liu7/CoPeDiT .

Junkai Liu, Nay Aung, Theodoros N. Arvanitis et al.

Magnetic resonance imaging (MRI) provides detailed soft-tissue characteristics that assist in disease diagnosis and screening. However, the accuracy of clinical practice is often hindered by missing or unusable slices due to various factors. Volumetric MRI synthesis methods have been developed to address this issue by imputing missing slices from available ones. The inherent 3D nature of volumetric MRI data, such as cardiac magnetic resonance (CMR), poses significant challenges for missing slice imputation approaches, including (1) the difficulty of modeling local inter-slice correlations and dependencies of volumetric slices, and (2) the limited exploration of crucial 3D spatial information and global context. In this study, to mitigate these issues, we present Spatial-Aware Graph Completion Network (SAGCNet) to overcome the dependency on complete volumetric data, featuring two main innovations: (1) a volumetric slice graph completion module that incorporates the inter-slice relationships into a graph structure, and (2) a volumetric spatial adapter component that enables our model to effectively capture and utilize various forms of 3D spatial context. Extensive experiments on cardiac MRI datasets demonstrate that SAGCNet is capable of synthesizing absent CMR slices, outperforming competitive state-of-the-art MRI synthesis methods both quantitatively and qualitatively. Notably, our model maintains superior performance even with limited slice data.

Omar Khan, Imran Ahmed, Joshua Cottingham et al.

The effectiveness of simple sensory cues for retraining gait have been demonstrated, yet the feasibility of humanoid avatars for entrainment have yet to be investigated. Here, we describe the development of a novel method of visually cued training, in the form of a virtual partner, and investigate its ability to provide movement guidance in the form of stepping. Real stepping movements were mapped onto an avatar using motion capture data. The trajectory of one of the avatar step cycles was then accelerated or decelerated by 15% to create a perturbation. Healthy participants were motion captured while instructed to step in time to the avatar's movements, as viewed through a virtual reality headset. Step onset times were used to measure the timing errors (asynchronies) between them. Participants completed either a visual-only condition, or auditory-visual with footstep sounds included. Participants' asynchronies exhibited slow drift in the Visual-Only condition, but became stable in the Auditory-Visual condition. Moreover, we observed a clear corrective response to the phase perturbation in both auditory-visual conditions. We conclude that an avatar's movements can be used to influence a person's own gait, but should include relevant auditory cues congruent with the movement to ensure a suitable accuracy is achieved.