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Open problems in Image segmentation

Lack of whole-slide image generation for histopathology1 paper raises it · 1 addresses it
Current generative models only produce small patches, but clinical labels and reports operate at the whole-slide level, limiting alignment with real-world supervision.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Limited longitudinal multimodal reasoning benchmarks1 paper raises it · 1 addresses it
Most medical benchmarks assess reasoning over preselected evidence, not the ability to seek and integrate evidence across longitudinal clinical records and imaging.
- From Given to Gathered Evidence: Agentic Learning for Longitudinal Medical Reasoningraises · addresses
Frozen models cannot learn from deployment experience1 paper raises it · 1 addresses it
Deployed models in medicine do not adapt to new clinical evidence or updated guidelines without retraining, which is often impractical.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses
Benchmark misalignment with real-world clinical use1 paper raises it · 1 addresses it
Public benchmarks often do not reflect the tasks, intents, or constraints of actual clinician queries, reducing their predictive value for deployment performance.
- Clinician use of language models diverges from how the models are evaluatedraises · addresses
Sensitivity to incidental information in clinical reasoning1 paper raises it · 1 addresses it
Models may incorporate or misattribute irrelevant details (e.g., small talk, background noise) in clinical documentation or reasoning, risking contamination.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises · addresses

Named by an AI from these papers' abstracts.

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Topics in this field

image segmentation · volumetric · medical image395 papers54 this week
clinical reasoning · question answering · language models202 papers34 this week
radiology report generation · medical vision language · vision language models114 papers25 this week
patient history · clinical data · health records105 papers23 this week
eeg foundation models · electroencephalography eeg · eeg foundation150 papers19 this week
electrocardiogram ecg · electrocardiogram · ecgs141 papers13 this week

Topics in this field

Active contributors · 90 days

Active contributors

Activity · 12 weeks

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All papers in Research

arXiv cs.AIOct 5
Signature-Based Feature Learning for Human Activity Recognition: A Reproducible Machine Learning Study of Representation, Depth, and Model Choice
Kamal Jarrar, Jacky Cresson, Christian Paroissin
Human activity recognition (HAR) relies on transforming sensor signals into informative representations for classification. Although deep learning and handcrafted features are widely used, the role of representation itself is often not systematically isolated. Signature transforms provide a mathematically grounded way to encode temporal order and cross-channel interactions, but their value for HAR under a fully reproducible and leakage-aware framework remains unclear. To evaluate whether signature-based feature learning improves HAR performance compared with raw-signal baselines, and to assess the effects of embedding strategy, truncation depth, model choice, and sensor configuration. Experiments were conducted on the UCI HAR dataset using a fully reproducible pipeline with the original train--test split preserved and subject-disjoint validation to prevent leakage. Three representations were compared: raw flattened signals, time-augmented paths, and lead--lag transformed paths. Signature features were computed at multiple truncation depths and evaluated using multilayer perceptron (MLP) and Random Forest (RF) classifiers under identical preprocessing and validation procedures. A…
PDF arXiv
arXiv cs.AIOct 5
Proof-Grounded Patient-Specific Clinical Explanations from Knowledge-Graph Reasoning
Surajit Das
Clinical decision-support outputs can lack an au- ditable link between patient observations, encoded knowledge, conclusions, and recommendations. We present the CKG Clinical Explanation Engine, a downstream layer for a frozen, training-free clinical knowledge-graph reasoner that converts patient inference states and disease knowledge into typed facts, explicit rule-application traces, provenance-linked conclusions, and policy-licensed recommendations. The design separates measurement availability, representation completeness, and disease-specific activation; consequently, observed zero-activation evience is not treated as missing and partial representation is distinct from unobserved evidence. Optional language generation is restricted to symbolically licensed content. Across five usable workbooks (6,720 patients; 20,160 patient-disease traces; 1,021,440 feature-evidence rows), IG-range validity and knowledge provenance were 100%, numerical cross-sheet fidelity was 100% (120,960/120,960), and exported logical/report trace completeness was 100% (20,160/20,160). Availability representation consistency was 99.7028% (1,018,404/1,021,440); all 3,036 disagreements were confined to…
PDF arXiv
arXiv cs.LGOct 5
Conditional Flow Matching for Single-Neuron Electrophysiology: Capturing Multimodal Responses Across Stimuli
Cameron Schofield, Luca Ghafourpour, Philip H. Wong, Costas A. Anastassiou, Richard E. Turner
Neurons of the brain exhibit a rich repertoire of electrophysiology dynamics with the same repeated stimulus eliciting very different voltage responses from the same cell. One common approach in biophysically detailed models is to capture this variability through ensembles of deterministic parametrizations, at a cost of hundreds of thousands of CPU hours. Existing machine learning surrogates inherit the same limitation, where a stimulus is mapped to a single voltage response. We address this challenge by learning a conditional generative model for single-neuron electrophysiology, using flow matching with a velocity field conditioned on the input current. On biophysically detailed models of two human cortical interneuron types, the generated responses closely reproduce the electrophysiological feature distributions, spike-time structure, and excitability profiles, even matching the experimental recordings from the corresponding human cortical neurons. Near the firing threshold, firing and non-firing responses coexist at the same stimulus amplitude, and at high amplitudes, ensembles may split into low- and high-firing modes near depolarization block. We show that our model recovers…
PDF arXiv
arXiv cs.CVOct 5
NeuroCBIR: A Fast and Accurate Image Retrieval System for Whole-Brain and Region-Specific MRI
Felix Nieto-del-Amor, Jingru Fu, J. -Sebastian Muehlboeck, Eric Westman, Daniel Ferreira +1
Content-based image retrieval (CBIR) in neuroimaging enables the identification of structurally similar brain scans, supporting diagnosis, prognosis, and treatment planning; however, existing methods are often limited to small datasets, single brain regions, or coarse class labels, thereby restricting their clinical utility and generalizability. Here, we present NeuroCBIR, a framework for fast and flexible retrieval of both whole-brain and region-specific 3D T1w MRI scans. A total of 103 cortical and subcortical regions are extracted to enable both whole-brain and region-level queries. NeuroCBIR leverages latent representations learned by a variational autoencoder (VAE) combined with contrastive learning, producing scan-specific embeddings that capture anatomical patterns. These embeddings were evaluated for subject re-identification, zero-shot age prediction, and zero-shot multi-class pathology stratification. Re-identification performance was high across both whole-brain and brain-region levels (mean average precision across the top-5 retrieved images (mAP@5) >= 98.4%), with robust generalization across datasets and acquisition conditions. While NeuroCBIR is not trained for age…
PDF arXiv
arXiv cs.CVOct 5
Topology-Informed Prompt-Conditioned Universal Segmentation of Uterine Structures from Ultrasound and MRI
Yongheng Sun, Yuexi Gu, Jingwen Sun, Maureen Kohi, Mingxia Liu
Multi-structure segmentation of the uterus is important for computer-assisted screening, diagnosis, and treatment planning of uterine diseases, where ultrasound and MRI provide complementary clinical information. However, developing a unified model across these modalities is challenging due to their substantially different image appearances, anatomical contexts, spatial resolutions, and label spaces. Moreover, existing datasets often define different segmentation targets, making joint learning challenging and potentially leading to negative transfer across heterogeneous tasks. To this end, we propose a Topology-informed Prompt-conditioned Universal Segmentation (TPUS) framework for segmenting multiple uterine structures across ultrasound and MRI. TPUS introduces a graph-based multi-dataset backbone comprising modality-specific stems and a modality-shared graph-based encoder-decoder to support modality-sensitive input adaptation, structural feature reasoning, and joint representation learning across heterogeneous uterine segmentation tasks. In addition, TPUS uses task-aware class prompts to condition the segmentation process for different datasets and label spaces, a dynamic…
PDF arXiv
arXiv cs.LGOct 5
EMG-FM-Bench: A Comprehensive Benchmark for Foundation Model Transfer and Adaptation on Electromyography
Tianhao Wu, Jiawei Yu, Xiangdong Hu, Xu Wu, Hongyu Wu +6
Foundation models (FMs) are increasingly being developed for general time series and physiological signals, yet their transferability to downstream physiological tasks remains poorly understood. This question is particularly challenging for electromyography (EMG), where signal distributions vary substantially across users, sensing configurations, acquisition hardware, and downstream tasks. We introduce EMG-FM-Bench, a systematic benchmark for studying foundation-model transfer and adaptation on EMG. EMG-FM-Bench unifies 20 public datasets with over 1 million EMG segments and evaluates nine pretrained foundation models across four questions: how pretrained models perform when frozen or fully fine-tuned, how much pretraining helps compared with training the same model from scratch, how well models generalize to new users with limited labeled data, and how performance changes across different EMG tasks. Across the benchmark, linear probing provides useful information about pretrained representations, but full fine-tuning can substantially change downstream EMG performance. Comparing each pretrained model with the same model trained from scratch shows that the benefit of pretraining…
PDF arXiv

Papers

Topics in this field

image segmentation · volumetric · medical image395 papers54 this week
clinical reasoning · question answering · language models202 papers34 this week
radiology report generation · medical vision language · vision language models114 papers25 this week
patient history · clinical data · health records105 papers23 this week
eeg foundation models · electroencephalography eeg · eeg foundation150 papers19 this week
electrocardiogram ecg · electrocardiogram · ecgs141 papers13 this week

Active contributors · 90 days

Recent papers

All papers in Research

arXiv cs.AIOct 5
Signature-Based Feature Learning for Human Activity Recognition: A Reproducible Machine Learning Study of Representation, Depth, and Model Choice
Kamal Jarrar, Jacky Cresson, Christian Paroissin
Human activity recognition (HAR) relies on transforming sensor signals into informative representations for classification. Although deep learning and handcrafted features are widely used, the role of representation itself is often not systematically isolated. Signature transforms provide a mathematically grounded way to encode temporal order and cross-channel interactions, but their value for HAR under a fully reproducible and leakage-aware framework remains unclear. To evaluate whether signature-based feature learning improves HAR performance compared with raw-signal baselines, and to assess the effects of embedding strategy, truncation depth, model choice, and sensor configuration. Experiments were conducted on the UCI HAR dataset using a fully reproducible pipeline with the original train--test split preserved and subject-disjoint validation to prevent leakage. Three representations were compared: raw flattened signals, time-augmented paths, and lead--lag transformed paths. Signature features were computed at multiple truncation depths and evaluated using multilayer perceptron (MLP) and Random Forest (RF) classifiers under identical preprocessing and validation procedures. A…
PDF arXiv
arXiv cs.AIOct 5
Proof-Grounded Patient-Specific Clinical Explanations from Knowledge-Graph Reasoning
Surajit Das
Clinical decision-support outputs can lack an au- ditable link between patient observations, encoded knowledge, conclusions, and recommendations. We present the CKG Clinical Explanation Engine, a downstream layer for a frozen, training-free clinical knowledge-graph reasoner that converts patient inference states and disease knowledge into typed facts, explicit rule-application traces, provenance-linked conclusions, and policy-licensed recommendations. The design separates measurement availability, representation completeness, and disease-specific activation; consequently, observed zero-activation evience is not treated as missing and partial representation is distinct from unobserved evidence. Optional language generation is restricted to symbolically licensed content. Across five usable workbooks (6,720 patients; 20,160 patient-disease traces; 1,021,440 feature-evidence rows), IG-range validity and knowledge provenance were 100%, numerical cross-sheet fidelity was 100% (120,960/120,960), and exported logical/report trace completeness was 100% (20,160/20,160). Availability representation consistency was 99.7028% (1,018,404/1,021,440); all 3,036 disagreements were confined to…
PDF arXiv
arXiv cs.LGOct 5
Conditional Flow Matching for Single-Neuron Electrophysiology: Capturing Multimodal Responses Across Stimuli
Cameron Schofield, Luca Ghafourpour, Philip H. Wong, Costas A. Anastassiou, Richard E. Turner
Neurons of the brain exhibit a rich repertoire of electrophysiology dynamics with the same repeated stimulus eliciting very different voltage responses from the same cell. One common approach in biophysically detailed models is to capture this variability through ensembles of deterministic parametrizations, at a cost of hundreds of thousands of CPU hours. Existing machine learning surrogates inherit the same limitation, where a stimulus is mapped to a single voltage response. We address this challenge by learning a conditional generative model for single-neuron electrophysiology, using flow matching with a velocity field conditioned on the input current. On biophysically detailed models of two human cortical interneuron types, the generated responses closely reproduce the electrophysiological feature distributions, spike-time structure, and excitability profiles, even matching the experimental recordings from the corresponding human cortical neurons. Near the firing threshold, firing and non-firing responses coexist at the same stimulus amplitude, and at high amplitudes, ensembles may split into low- and high-firing modes near depolarization block. We show that our model recovers…
PDF arXiv
arXiv cs.CVOct 5
NeuroCBIR: A Fast and Accurate Image Retrieval System for Whole-Brain and Region-Specific MRI
Felix Nieto-del-Amor, Jingru Fu, J. -Sebastian Muehlboeck, Eric Westman, Daniel Ferreira +1
Content-based image retrieval (CBIR) in neuroimaging enables the identification of structurally similar brain scans, supporting diagnosis, prognosis, and treatment planning; however, existing methods are often limited to small datasets, single brain regions, or coarse class labels, thereby restricting their clinical utility and generalizability. Here, we present NeuroCBIR, a framework for fast and flexible retrieval of both whole-brain and region-specific 3D T1w MRI scans. A total of 103 cortical and subcortical regions are extracted to enable both whole-brain and region-level queries. NeuroCBIR leverages latent representations learned by a variational autoencoder (VAE) combined with contrastive learning, producing scan-specific embeddings that capture anatomical patterns. These embeddings were evaluated for subject re-identification, zero-shot age prediction, and zero-shot multi-class pathology stratification. Re-identification performance was high across both whole-brain and brain-region levels (mean average precision across the top-5 retrieved images (mAP@5) >= 98.4%), with robust generalization across datasets and acquisition conditions. While NeuroCBIR is not trained for age…
PDF arXiv
arXiv cs.CVOct 5
Topology-Informed Prompt-Conditioned Universal Segmentation of Uterine Structures from Ultrasound and MRI
Yongheng Sun, Yuexi Gu, Jingwen Sun, Maureen Kohi, Mingxia Liu
Multi-structure segmentation of the uterus is important for computer-assisted screening, diagnosis, and treatment planning of uterine diseases, where ultrasound and MRI provide complementary clinical information. However, developing a unified model across these modalities is challenging due to their substantially different image appearances, anatomical contexts, spatial resolutions, and label spaces. Moreover, existing datasets often define different segmentation targets, making joint learning challenging and potentially leading to negative transfer across heterogeneous tasks. To this end, we propose a Topology-informed Prompt-conditioned Universal Segmentation (TPUS) framework for segmenting multiple uterine structures across ultrasound and MRI. TPUS introduces a graph-based multi-dataset backbone comprising modality-specific stems and a modality-shared graph-based encoder-decoder to support modality-sensitive input adaptation, structural feature reasoning, and joint representation learning across heterogeneous uterine segmentation tasks. In addition, TPUS uses task-aware class prompts to condition the segmentation process for different datasets and label spaces, a dynamic…
PDF arXiv
arXiv cs.LGOct 5
EMG-FM-Bench: A Comprehensive Benchmark for Foundation Model Transfer and Adaptation on Electromyography
Tianhao Wu, Jiawei Yu, Xiangdong Hu, Xu Wu, Hongyu Wu +6
Foundation models (FMs) are increasingly being developed for general time series and physiological signals, yet their transferability to downstream physiological tasks remains poorly understood. This question is particularly challenging for electromyography (EMG), where signal distributions vary substantially across users, sensing configurations, acquisition hardware, and downstream tasks. We introduce EMG-FM-Bench, a systematic benchmark for studying foundation-model transfer and adaptation on EMG. EMG-FM-Bench unifies 20 public datasets with over 1 million EMG segments and evaluates nine pretrained foundation models across four questions: how pretrained models perform when frozen or fully fine-tuned, how much pretraining helps compared with training the same model from scratch, how well models generalize to new users with limited labeled data, and how performance changes across different EMG tasks. Across the benchmark, linear probing provides useful information about pretrained representations, but full fine-tuning can substantially change downstream EMG performance. Comparing each pretrained model with the same model trained from scratch shows that the benefit of pretraining…
PDF arXiv

Activity · 12 weeks

Fields · AI · updated 30m ago

Image segmentation

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

168papers this week−20.4% vs last week

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1k papers this month

Open problems in Image segmentation

Lack of whole-slide image generation for histopathology1 paper raises it · 1 addresses it
Current generative models only produce small patches, but clinical labels and reports operate at the whole-slide level, limiting alignment with real-world supervision.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Limited longitudinal multimodal reasoning benchmarks1 paper raises it · 1 addresses it
Most medical benchmarks assess reasoning over preselected evidence, not the ability to seek and integrate evidence across longitudinal clinical records and imaging.
- From Given to Gathered Evidence: Agentic Learning for Longitudinal Medical Reasoningraises · addresses
Frozen models cannot learn from deployment experience1 paper raises it · 1 addresses it
Deployed models in medicine do not adapt to new clinical evidence or updated guidelines without retraining, which is often impractical.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses
Benchmark misalignment with real-world clinical use1 paper raises it · 1 addresses it
Public benchmarks often do not reflect the tasks, intents, or constraints of actual clinician queries, reducing their predictive value for deployment performance.
- Clinician use of language models diverges from how the models are evaluatedraises · addresses
Sensitivity to incidental information in clinical reasoning1 paper raises it · 1 addresses it
Models may incorporate or misattribute irrelevant details (e.g., small talk, background noise) in clinical documentation or reasoning, risking contamination.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises · addresses

Named by an AI from these papers' abstracts.