harmonization
DIST-CLIP: Arbitrary Metadata and Image Guided MRI Harmonization via Disentangled Anatomy-Contrast Representations
Avci, Mehmet Yigit, Borges, Pedro, Fernandez, Virginia, Wright, Paul, Yigitsoy, Mehmet, Ourselin, Sebastien, Cardoso, Jorge
Deep learning holds immense promise for transforming medical image analysis, yet its clinical generalization remains profoundly limited. A major barrier is data heterogeneity. This is particularly true in Magnetic Resonance Imaging, where scanner hardware differences, diverse acquisition protocols, and varying sequence parameters introduce substantial domain shifts that obscure underlying biological signals. Data harmonization methods aim to reduce these instrumental and acquisition variability, but existing approaches remain insufficient. When applied to imaging data, image-based harmonization approaches are often restricted by the need for target images, while existing text-guided methods rely on simplistic labels that fail to capture complex acquisition details or are typically restricted to datasets with limited variability, failing to capture the heterogeneity of real-world clinical environments. To address these limitations, we propose DIST-CLIP (Disentangled Style Transfer with CLIP Guidance), a unified framework for MRI harmonization that flexibly uses either target images or DICOM metadata for guidance. Our framework explicitly disentangles anatomical content from image contrast, with the contrast representations being extracted using pre-trained CLIP encoders. These contrast embeddings are then integrated into the anatomical content via a novel Adaptive Style Transfer module. We trained and evaluated DIST-CLIP on diverse real-world clinical datasets, and showed significant improvements in performance when compared against state-of-the-art methods in both style translation fidelity and anatomical preservation, offering a flexible solution for style transfer and standardizing MRI data. Our code and weights will be made publicly available upon publication.
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Incorporating Structure and Chord Constraints in Symbolic Transformer-based Melodic Harmonization
Kaliakatsos-Papakostas, Maximos, Soiledis, Konstantinos, Tsamis, Theodoros, Makris, Dimos, Katsouros, Vassilis, Cambouropoulos, Emilios
Transformer architectures offer significant advantages regarding the generation of symbolic music; their capabilities for incorporating user preferences toward what they generate is being studied under many aspects. This paper studies the inclusion of predefined chord constraints in melodic harmonization, i.e., where a desired chord at a specific location is provided along with the melody as inputs and the autoregressive transformer model needs to incorporate the chord in the harmonization that it generates. The peculiarities of involving such constraints is discussed and an algorithm is proposed for tackling this task. This algorithm is called B* and it combines aspects of beam search and A* along with backtracking to force pretrained transformers to satisfy the chord constraints, at the correct onset position within the correct bar. The algorithm is brute-force and has exponential complexity in the worst case; however, this paper is a first attempt to highlight the difficulties of the problem and proposes an algorithm that offers many possibilities for improvements since it accommodates the involvement of heuristics.
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Scalable Unit Harmonization in Medical Informatics via Bayesian-Optimized Retrieval and Transformer-Based Re-ranking
Objective: To develop and evaluate a scalable methodology for harmonizing inconsistent units in large-scale clinical datasets, addressing a key barrier to data interoperability. Materials and Methods: We designed a novel unit harmonization system combining BM25, sentence embeddings, Bayesian optimization, and a bidirectional transformer based binary classifier for retrieving and matching laboratory test entries. The system was evaluated using the Optum Clinformatics Datamart dataset (7.5 billion entries). We implemented a multi-stage pipeline: filtering, identification, harmonization proposal generation, automated re-ranking, and manual validation. Performance was assessed using Mean Reciprocal Rank (MRR) and other standard information retrieval metrics. Results: Our hybrid retrieval approach combining BM25 and sentence embeddings (MRR: 0.8833) significantly outperformed both lexical-only (MRR: 0.7985) and embedding-only (MRR: 0.5277) approaches. The transformer-based reranker further improved performance (absolute MRR improvement: 0.10), bringing the final system MRR to 0.9833. The system achieved 83.39\% precision at rank 1 and 94.66\% recall at rank 5. Discussion: The hybrid architecture effectively leverages the complementary strengths of lexical and semantic approaches. The reranker addresses cases where initial retrieval components make errors due to complex semantic relationships in medical terminology. Conclusion: Our framework provides an efficient, scalable solution for unit harmonization in clinical datasets, reducing manual effort while improving accuracy. Once harmonized, data can be reused seamlessly in different analyses, ensuring consistency across healthcare systems and enabling more reliable multi-institutional studies and meta-analyses.
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Lightweight Optimal-Transport Harmonization on Edge Devices
Larchenko, Maria, Guskov, Dmitry, Lobashev, Alexander, Derevyanko, Georgy
Color harmonization adjusts the colors of an inserted object so that it perceptually matches the surrounding image, resulting in a seamless composite. The harmonization problem naturally arises in augmented reality (AR), yet harmonization algorithms are not currently integrated into AR pipelines because real-time solutions are scarce. In this work, we address color harmonization for AR by proposing a lightweight approach that supports on-device inference. For this, we leverage classical optimal transport theory by training a compact encoder to predict the Monge-Kantorovich transport map. We benchmark our MKL-Harmonizer algorithm against state-of-the-art methods and demonstrate that for real composite AR images our method achieves the best aggregated score. We release our dedicated AR dataset of composite images with pixel-accurate masks and data-gathering toolkit to support further data acquisition by researchers.
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LLM-Assisted Emergency Triage Benchmark: Bridging Hospital-Rich and MCI-Like Field Simulation
Sebastian, Joshua, Tobden, Karma, Solaiman, KMA
Research on emergency and mass casualty incident (MCI) triage has been limited by the absence of openly usable, reproducible benchmarks. Yet these scenarios demand rapid identification of the patients most in need, where accurate deterioration prediction can guide timely interventions. While the MIMIC-IV-ED database is openly available to credentialed researchers, transforming it into a triage-focused benchmark requires extensive preprocessing, feature harmonization, and schema alignment -- barriers that restrict accessibility to only highly technical users. We address these gaps by first introducing an open, LLM-assisted emergency triage benchmark for deterioration prediction (ICU transfer, in-hospital mortality). The benchmark then defines two regimes: (i) a hospital-rich setting with vitals, labs, notes, chief complaints, and structured observations, and (ii) an MCI-like field simulation limited to vitals, observations, and notes. Large language models (LLMs) contributed directly to dataset construction by (i) harmonizing noisy fields such as AVPU and breathing devices, (ii) prioritizing clinically relevant vitals and labs, and (iii) guiding schema alignment and efficient merging of disparate tables. We further provide baseline models and SHAP-based interpretability analyses, illustrating predictive gaps between regimes and the features most critical for triage. Together, these contributions make triage prediction research more reproducible and accessible -- a step toward dataset democratization in clinical AI.
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The CRITICAL Records Integrated Standardization Pipeline (CRISP): End-to-End Processing of Large-scale Multi-institutional OMOP CDM Data
Luo, Xiaolong, Li, Michael Lingzhi
While existing critical care EHR datasets such as MIMIC and eICU have enabled significant advances in clinical AI research, the CRITICAL dataset opens new frontiers by providing extensive scale and diversity -- containing 1.95 billion records from 371,365 patients across four geographically diverse CTSA institutions. CRITICAL's unique strength lies in capturing full-spectrum patient journeys, including pre-ICU, ICU, and post-ICU encounters across both inpatient and outpatient settings. This multi-institutional, longitudinal perspective creates transformative opportunities for developing generalizable predictive models and advancing health equity research. However, the richness of this multi-site resource introduces substantial complexity in data harmonization, with heterogeneous collection practices and diverse vocabulary usage patterns requiring sophisticated preprocessing approaches. We present CRISP to unlock the full potential of this valuable resource. CRISP systematically transforms raw Observational Medical Outcomes Partnership Common Data Model data into ML-ready datasets through: (1) transparent data quality management with comprehensive audit trails, (2) cross-vocabulary mapping of heterogeneous medical terminologies to unified SNOMED-CT standards, with deduplication and unit standardization, (3) modular architecture with parallel optimization enabling complete dataset processing in $<$1 day even on standard computing hardware, and (4) comprehensive baseline model benchmarks spanning multiple clinical prediction tasks to establish reproducible performance standards. By providing processing pipeline, baseline implementations, and detailed transformation documentation, CRISP saves researchers months of preprocessing effort and democratizes access to large-scale multi-institutional critical care data, enabling them to focus on advancing clinical AI.
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MR-CLIP: Efficient Metadata-Guided Learning of MRI Contrast Representations
Avci, Mehmet Yigit, Borges, Pedro, Wright, Paul, Yigitsoy, Mehmet, Ourselin, Sebastien, Cardoso, Jorge
Accurate interpretation of Magnetic Resonance Imaging scans in clinical systems is based on a precise understanding of image contrast. This contrast is primarily governed by acquisition parameters, such as echo time and repetition time, which are stored in the DICOM metadata. To simplify contrast identification, broad labels such as T1-weighted or T2-weighted are commonly used, but these offer only a coarse approximation of the underlying acquisition settings. In many real-world datasets, such labels are entirely missing, leaving raw acquisition parameters as the only indicators of contrast. Adding to this challenge, the available metadata is often incomplete, noisy, or inconsistent. The lack of reliable and standardized metadata complicates tasks such as image interpretation, retrieval, and integration into clinical workflows. Furthermore, robust contrast-aware representations are essential to enable more advanced clinical applications, such as achieving modality-invariant representations and data harmonization. To address these challenges, we propose MR-CLIP, a multimodal contrastive learning framework that aligns MR images with their DICOM metadata to learn contrast-aware representations, without relying on manual labels. Trained on a diverse clinical dataset that spans various scanners and protocols, MR-CLIP captures contrast variations across acquisitions and within scans, enabling anatomy-invariant representations. We demonstrate its effectiveness in cross-modal retrieval and contrast classification, highlighting its scalability and potential for further clinical applications. The code and weights are publicly available at https://github.com/myigitavci/MR-CLIP.
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