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Open problems in Image segmentation

Lack of benchmarks for real-world clinical deployment1 paper raises it · 0 address it
Current benchmarks do not reflect how clinicians actually use AI systems, limiting their predictive value for real-world performance.
- Clinician use of language models diverges from how the models are evaluatedraises
Handling gigapixel whole-slide images in segmentation1 paper raises it · 1 addresses it
Existing models operate at patch scale, but clinical supervision and labels are at the whole-slide level, creating a mismatch.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Temporal modeling of multimodal clinical trajectories1 paper raises it · 1 addresses it
Accurate risk prediction requires modeling irregular, heterogeneous clinical data over time, which current approaches often overlook.
- TRACE: Tracking Multimodal Clinical Trajectories for Inpatient Risk Predictionraises · addresses
Resistance to incidental information in clinical reasoning1 paper raises it · 0 address it
Models may misattribute or be distracted by irrelevant information in clinical documentation, leading to errors.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises
Learning from deployment experience without retraining1 paper raises it · 1 addresses it
Frozen models cannot adapt to new clinical evidence or updated guidelines without access to weights or additional training.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses

Named by an AI from these papers' abstracts.

Open problems

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Topics in this field

image segmentation · volumetric · medical image409 papers40 this week
radiology report generation · medical vision language · vision language models133 papers35 this week
clinical reasoning · question answering · language models210 papers21 this week
eeg foundation models · electroencephalography eeg · eeg foundation158 papers19 this week
patient history · clinical data · health records112 papers19 this week
electrocardiogram ecg · electrocardiogram · ecgs147 papers13 this week

Topics in this field

Active contributors · 90 days

Active contributors

Activity · 12 weeks

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Recent papers

All papers in Research

arXiv cs.CVSep 24
Anatomy-Aligned Surface Field Learning for Myocardial Reconstruction from Sparse Short-Axis Cine MRI
Xiaohan Yuan, Xuan Yang, Qingya Li, Yangang Wang, Lei Li
Patient-specific 4D myocardial reconstruction from cine MRI supports quantitative functional assessment, regional motion analysis, and simulation-based modeling. However, routinely acquired short-axis (SAX) cine MRI is sparsely sampled along the through-plane direction, making dense and anatomically consistent surface reconstruction challenging. In this study, we propose an anatomy-aligned surface learning framework that parameterizes the epicardial and endocardial surfaces on a shared circumferential-longitudinal UV domain. This formulation converts irregular 3D reconstruction into structured coordinate-field completion with explicit correspondence across subjects and cardiac phases. Sparse SAX contours are encoded as UV observation fields, coverage-aware sampling improves robustness to incomplete slice coverage, and topology- and distortion-aware learning preserves circumferential continuity and local surface quality. Experiments on three public cine MRI datasets showed that the proposed method consistently outperformed representative mesh-based and implicit reconstruction approaches, achieving overall Chamfer distances of $2.887$~mm on ACDC, $2.641$~mm on M\&Ms, and $2.810$~mm…
PDF arXiv
arXiv cs.AISep 24
Decoding Imagined Speech: A Strictly Subject-Independent Approach Using EEG
Frederik Møllskov Trier, Xiaopeng Mao, Sadasivan Puthusserypady
Imagined speech decoding from electroencephalography (EEG) has gained increasing attention as a potential communication pathway for individuals with severe motor impairments, yet reported performance often relies on evaluation protocols that do not clearly reflect cross-subject generalization. This study presents a transparent baseline investigation of a multi-class imagined speech EEG dataset under a strictly subject-independent evaluation framework. Two preprocessing and feature extraction pipelines were compared: a time-domain statistical feature approach and a frequency-domain spectral bandpower approach, evaluated using subject-wise cross-validation and trial-level majority voting with a random forest classifier. The spectral pipeline achieved a significantly higher mean trial-wise accuracy than the statistical pipeline (49.03 $\pm$ 4.18% vs. 37.97 $\pm$ 3.79%) for coarse-level classification across subjects. Forward feature selection further indicated that a limited subset of frequency bands captured most of the discriminative information. Overall, this work provides a strong basis for future brain-computer interface studies targeting improved cross-subject generalization…
PDF arXiv
arXiv cs.CVSep 24
Lightweight Vision Transformer-Based U-Net for Brain Tumor Segmentation from MRI
Sheekar Banerjee, Md. Srabon Chowdhury, Md. Mahbub Hasan Akash, Ishtiak Al Mamoon
Accurate brain tumor segmentation from Magnetic Resonance Imaging is essential for diagnosis, treatment planning, and surgical guidance. Although Convolutional Neural Networks, particularly UNet, have achieved significant success in medical image segmentation, they often struggle to capture the long-range spatial dependencies required to model tumors with irregular shapes and complex boundaries. This paper proposes a lightweight Vision Transformer UNet that combines the hierarchical feature extraction capability of UNet with the global context modeling of Vision Transformers. The proposed architecture incorporates a compact ViT bottleneck within a U-Net encoder-decoder framework, enabling effective learning of both local and global features while maintaining computational efficiency with only 2.6 million trainable parameters. The model was evaluated on the TCGA LGG MRI Segmentation dataset, achieving a mean Intersection over Union of 0.8100 and a Dice score of 0.8446, outperforming the baseline UNet by 3.75% and 3.15%, respectively. Extensive quantitative and qualitative analyses, including confusion matrix evaluation, precision recall curves, per-image performance distribution,…
PDF arXiv
arXiv cs.CVSep 24
Mind the Gap: Mesh-Guided Repair of Broken Vessels
Gniewosz Drwiega, Wojciech Szymanski, Marek Wodzinski
Vessel segmentation is commonly optimized as voxel-wise classification, but small local errors can strongly disrupt vascular connectivity while having little effect on overlap scores. This is particularly problematic for downstream analyses that rely on centerlines, branches, connected components, or graph structure. We propose a mesh-guided post-processing framework for repairing broken vessel segmentations produced by nnU-Net. For each predicted binary mask, a deformable template mesh is fitted to the mask surface in physical space and used as a case-specific geometric scaffold. The fitted mesh is not voxelized as the final segmentation; instead, it guides conservative reconnection of disconnected components by proposing or validating thin bridge candidates under foreground-growth constraints. We evaluated this approach in three vascular anatomies using AortaSeg24 and SEGA for the aorta, TopCoW for the Circle of Willis, and PARSE for the pulmonary arteries. Performance is measured using Dice, connected-component Dice (ccDice), and the Betti-0 number. Across these datasets, repair substantially improved connectivity while preserving overlap: Dice remained nearly unchanged,…
PDF arXiv
arXiv cs.AISep 24
AI-based detection of worsening heart failure from low-resolution telemonitoring data
Erik Aerts, Yinan Yu, Annika Rosengren, Michael Fu, Martin Lindgren +3
Objective: Heart failure (HF) presents a healthcare challenge due to its high comorbidity burden, aging patient population and frequent hospitalizations. Remote monitoring offers a promising approach to managing HF patients by early detection of health deterioration. Developing autonomous systems to detect signs of worsening in telemonitoring data is of interest to reduce the workload of healthcare personnel. Methods: We propose the TRACER model, a Transformer with Contrastive Event Representation, designed to predict timelines leading to rare hospitalization events in low-resolution and irregularly sampled telemonitoring data. TRACER incorporates time-aware embeddings for each biomarker, contrastive pre-training to enhance anomaly detection via representation learning, and independent binary classifiers for detection. We used measurement data containing remotely recorded biomarker sequences from 276 HF patients segmented into overlapping windows based on temporal rules, and labeled the windows based on the occurrence of HF relevant hospitalizations at the latter edge of the window. Results: TRACER was able to correctly predict 66.7% timelines leading up to HF hospitalizations in…
PDF arXiv
arXiv cs.CVSep 24
A Multimodal Dataset for Survival Prediction in Resected Pancreatic Ductal Adenocarcinoma
Anh-Tien Nguyen, Mawuko Tettey, Jacqueline Michelle Metsch, Teresa Zimmer, Niklas Ullrich +12
Survival research in pancreatic ductal adenocarcinoma (PDAC) is limited by the scarcity of datasets linking whole-slide histology with clinical, molecular, and long-term outcome data. We present a retrospective single-centre cohort of 302 patients who underwent PDAC resection at University Medical Center Gottingen. The dataset comprises 446 H&E whole-slide images, clinicopathological variables, targeted sequencing data for 154 patients, and overall-survival outcomes. During follow-up, 253 patients died, and the median follow-up was 76 months. To establish initial reference values, we evaluated fourteen survival-prediction configurations using identical five-repetition Monte Carlo cross-validation partitions. Ridge Cox regression using numeric clinicopathological variables achieved a mean concordance of $0.649 \pm 0.042$ and $0.652 \pm 0.046$ after adding KRAS and TP53 mutation status. The image-only attention model achieved $0.603 \pm 0.030$, while multimodal fusion achieved $0.619 \pm 0.025$, the highest concordance among the neural models. These results establish promising initial benchmarks for future research using this pancreas-specific multimodal dataset, paving the way for…
PDF arXiv

Papers

Topics in this field

image segmentation · volumetric · medical image409 papers40 this week
radiology report generation · medical vision language · vision language models133 papers35 this week
clinical reasoning · question answering · language models210 papers21 this week
eeg foundation models · electroencephalography eeg · eeg foundation158 papers19 this week
patient history · clinical data · health records112 papers19 this week
electrocardiogram ecg · electrocardiogram · ecgs147 papers13 this week

Active contributors · 90 days

Recent papers

All papers in Research

arXiv cs.CVSep 24
Anatomy-Aligned Surface Field Learning for Myocardial Reconstruction from Sparse Short-Axis Cine MRI
Xiaohan Yuan, Xuan Yang, Qingya Li, Yangang Wang, Lei Li
Patient-specific 4D myocardial reconstruction from cine MRI supports quantitative functional assessment, regional motion analysis, and simulation-based modeling. However, routinely acquired short-axis (SAX) cine MRI is sparsely sampled along the through-plane direction, making dense and anatomically consistent surface reconstruction challenging. In this study, we propose an anatomy-aligned surface learning framework that parameterizes the epicardial and endocardial surfaces on a shared circumferential-longitudinal UV domain. This formulation converts irregular 3D reconstruction into structured coordinate-field completion with explicit correspondence across subjects and cardiac phases. Sparse SAX contours are encoded as UV observation fields, coverage-aware sampling improves robustness to incomplete slice coverage, and topology- and distortion-aware learning preserves circumferential continuity and local surface quality. Experiments on three public cine MRI datasets showed that the proposed method consistently outperformed representative mesh-based and implicit reconstruction approaches, achieving overall Chamfer distances of $2.887$~mm on ACDC, $2.641$~mm on M\&Ms, and $2.810$~mm…
PDF arXiv
arXiv cs.AISep 24
Decoding Imagined Speech: A Strictly Subject-Independent Approach Using EEG
Frederik Møllskov Trier, Xiaopeng Mao, Sadasivan Puthusserypady
Imagined speech decoding from electroencephalography (EEG) has gained increasing attention as a potential communication pathway for individuals with severe motor impairments, yet reported performance often relies on evaluation protocols that do not clearly reflect cross-subject generalization. This study presents a transparent baseline investigation of a multi-class imagined speech EEG dataset under a strictly subject-independent evaluation framework. Two preprocessing and feature extraction pipelines were compared: a time-domain statistical feature approach and a frequency-domain spectral bandpower approach, evaluated using subject-wise cross-validation and trial-level majority voting with a random forest classifier. The spectral pipeline achieved a significantly higher mean trial-wise accuracy than the statistical pipeline (49.03 $\pm$ 4.18% vs. 37.97 $\pm$ 3.79%) for coarse-level classification across subjects. Forward feature selection further indicated that a limited subset of frequency bands captured most of the discriminative information. Overall, this work provides a strong basis for future brain-computer interface studies targeting improved cross-subject generalization…
PDF arXiv
arXiv cs.CVSep 24
Lightweight Vision Transformer-Based U-Net for Brain Tumor Segmentation from MRI
Sheekar Banerjee, Md. Srabon Chowdhury, Md. Mahbub Hasan Akash, Ishtiak Al Mamoon
Accurate brain tumor segmentation from Magnetic Resonance Imaging is essential for diagnosis, treatment planning, and surgical guidance. Although Convolutional Neural Networks, particularly UNet, have achieved significant success in medical image segmentation, they often struggle to capture the long-range spatial dependencies required to model tumors with irregular shapes and complex boundaries. This paper proposes a lightweight Vision Transformer UNet that combines the hierarchical feature extraction capability of UNet with the global context modeling of Vision Transformers. The proposed architecture incorporates a compact ViT bottleneck within a U-Net encoder-decoder framework, enabling effective learning of both local and global features while maintaining computational efficiency with only 2.6 million trainable parameters. The model was evaluated on the TCGA LGG MRI Segmentation dataset, achieving a mean Intersection over Union of 0.8100 and a Dice score of 0.8446, outperforming the baseline UNet by 3.75% and 3.15%, respectively. Extensive quantitative and qualitative analyses, including confusion matrix evaluation, precision recall curves, per-image performance distribution,…
PDF arXiv
arXiv cs.CVSep 24
Mind the Gap: Mesh-Guided Repair of Broken Vessels
Gniewosz Drwiega, Wojciech Szymanski, Marek Wodzinski
Vessel segmentation is commonly optimized as voxel-wise classification, but small local errors can strongly disrupt vascular connectivity while having little effect on overlap scores. This is particularly problematic for downstream analyses that rely on centerlines, branches, connected components, or graph structure. We propose a mesh-guided post-processing framework for repairing broken vessel segmentations produced by nnU-Net. For each predicted binary mask, a deformable template mesh is fitted to the mask surface in physical space and used as a case-specific geometric scaffold. The fitted mesh is not voxelized as the final segmentation; instead, it guides conservative reconnection of disconnected components by proposing or validating thin bridge candidates under foreground-growth constraints. We evaluated this approach in three vascular anatomies using AortaSeg24 and SEGA for the aorta, TopCoW for the Circle of Willis, and PARSE for the pulmonary arteries. Performance is measured using Dice, connected-component Dice (ccDice), and the Betti-0 number. Across these datasets, repair substantially improved connectivity while preserving overlap: Dice remained nearly unchanged,…
PDF arXiv
arXiv cs.AISep 24
AI-based detection of worsening heart failure from low-resolution telemonitoring data
Erik Aerts, Yinan Yu, Annika Rosengren, Michael Fu, Martin Lindgren +3
Objective: Heart failure (HF) presents a healthcare challenge due to its high comorbidity burden, aging patient population and frequent hospitalizations. Remote monitoring offers a promising approach to managing HF patients by early detection of health deterioration. Developing autonomous systems to detect signs of worsening in telemonitoring data is of interest to reduce the workload of healthcare personnel. Methods: We propose the TRACER model, a Transformer with Contrastive Event Representation, designed to predict timelines leading to rare hospitalization events in low-resolution and irregularly sampled telemonitoring data. TRACER incorporates time-aware embeddings for each biomarker, contrastive pre-training to enhance anomaly detection via representation learning, and independent binary classifiers for detection. We used measurement data containing remotely recorded biomarker sequences from 276 HF patients segmented into overlapping windows based on temporal rules, and labeled the windows based on the occurrence of HF relevant hospitalizations at the latter edge of the window. Results: TRACER was able to correctly predict 66.7% timelines leading up to HF hospitalizations in…
PDF arXiv
arXiv cs.CVSep 24
A Multimodal Dataset for Survival Prediction in Resected Pancreatic Ductal Adenocarcinoma
Anh-Tien Nguyen, Mawuko Tettey, Jacqueline Michelle Metsch, Teresa Zimmer, Niklas Ullrich +12
Survival research in pancreatic ductal adenocarcinoma (PDAC) is limited by the scarcity of datasets linking whole-slide histology with clinical, molecular, and long-term outcome data. We present a retrospective single-centre cohort of 302 patients who underwent PDAC resection at University Medical Center Gottingen. The dataset comprises 446 H&E whole-slide images, clinicopathological variables, targeted sequencing data for 154 patients, and overall-survival outcomes. During follow-up, 253 patients died, and the median follow-up was 76 months. To establish initial reference values, we evaluated fourteen survival-prediction configurations using identical five-repetition Monte Carlo cross-validation partitions. Ridge Cox regression using numeric clinicopathological variables achieved a mean concordance of $0.649 \pm 0.042$ and $0.652 \pm 0.046$ after adding KRAS and TP53 mutation status. The image-only attention model achieved $0.603 \pm 0.030$, while multimodal fusion achieved $0.619 \pm 0.025$, the highest concordance among the neural models. These results establish promising initial benchmarks for future research using this pancreas-specific multimodal dataset, paving the way for…
PDF arXiv

Activity · 12 weeks

Fields · AI · updated 38m ago

Image segmentation

Found by the topic model: image segmentation, clinical reasoning, eeg foundation models.

147papers this week−29.7% vs last week

All papers · 1.2k With code · 4

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952 papers this month

Open problems in Image segmentation

Lack of benchmarks for real-world clinical deployment1 paper raises it · 0 address it
Current benchmarks do not reflect how clinicians actually use AI systems, limiting their predictive value for real-world performance.
- Clinician use of language models diverges from how the models are evaluatedraises
Handling gigapixel whole-slide images in segmentation1 paper raises it · 1 addresses it
Existing models operate at patch scale, but clinical supervision and labels are at the whole-slide level, creating a mismatch.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Temporal modeling of multimodal clinical trajectories1 paper raises it · 1 addresses it
Accurate risk prediction requires modeling irregular, heterogeneous clinical data over time, which current approaches often overlook.
- TRACE: Tracking Multimodal Clinical Trajectories for Inpatient Risk Predictionraises · addresses
Resistance to incidental information in clinical reasoning1 paper raises it · 0 address it
Models may misattribute or be distracted by irrelevant information in clinical documentation, leading to errors.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises
Learning from deployment experience without retraining1 paper raises it · 1 addresses it
Frozen models cannot adapt to new clinical evidence or updated guidelines without access to weights or additional training.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses

Named by an AI from these papers' abstracts.