Optimizing Prompt Strategies for SAM: Advancing lesion Segmentation Across Diverse Medical Imaging Modalities

Purpose: To evaluate various Segmental Anything Model (SAM) prompt strategies across four lesions datasets and to subsequently develop a reinforcement learning (RL) agent to optimize SAM prompt placement. Materials and Methods: This retrospective study included patients with four independent ovarian, lung, renal, and breast tumor datasets. Manual segmentation and SAM-assisted segmentation were performed for all lesions. A RL model was developed to predict and select SAM points to maximize segmentation performance. Statistical analysis of segmentation was conducted using pairwise t-tests. Results: Results show that increasing the number of prompt points significantly improves segmentation accuracy, with Dice coefficients rising from 0.272 for a single point to 0.806 for five or more points in ovarian tumors. The prompt location also influenced performance, with surface and union-based prompts outperforming center-based prompts, achieving mean Dice coefficients of 0.604 and 0.724 for ovarian and breast tumors, respectively. The RL agent achieved a peak Dice coefficient of 0.595 for ovarian tumors, outperforming random and alternative RL strategies. Additionally, it significantly reduced segmentation time, achieving a nearly 10-fold improvement compared to manual methods using SAM. Conclusion: While increased SAM prompts and non-centered prompts generally improved segmentation accuracy, each pathology and modality has specific optimal thresholds and placement strategies. Our RL agent achieved superior performance compared to other agents while achieving a significant reduction in segmentation time.

Optimizing prompt strategies for the Segment Anything Model are explored, focusing on prompt location, number, and reinforcement learning-based agent for prompt placement across four lesion datasets

Purpose: To evaluate various Segmental Anything Model (SAM) prompt strategies across four lesions datasets and to subsequently develop a reinforcement learning (RL) agent to optimize SAM prompt placement. Materials and Methods: This retrospective study included patients with four independent ovarian, lung, renal, and breast tumor datasets. Manual segmentation and SAM-assisted segmentation were performed for all lesions. A RL model was developed to predict and select SAM points to maximize segmentation performance. Statistical analysis of segmentation was conducted using pairwise t-tests. Results: Results show that increasing the number of prompt points significantly improves segmentation accuracy, with Dice coefficients rising from 0.272 for a single point to 0.806 for five or more points in ovarian tumors. The prompt location also influenced performance, with surface and union-based prompts outperforming center-based prompts, achieving mean Dice coefficients of 0.604 and 0.724 for ovarian and breast tumors, respectively. The RL agent achieved a peak Dice coefficient of 0.595 for ovarian tumors, outperforming random and alternative RL strategies. Additionally, it significantly reduced segmentation time, achieving a nearly 10-fold improvement compared to manual methods using SAM. Conclusion: While increased SAM prompts and non-centered prompts generally improved segmentation accuracy, each pathology and modality has specific optimal thresholds and placement strategies. Our RL agent achieved superior performance compared to other agents while achieving a significant reduction in segmentation time.

MCL: Multi-view Enhanced Contrastive Learning for Chest X-ray Report Generation

Radiology reports are crucial for planning treatment strategies and enhancing doctor-patient communication, yet manually writing these reports is burdensome for radiologists. While automatic report generation offers a solution, existing methods often rely on single-view radiographs, limiting diagnostic accuracy. To address this problem, we propose MCL, a Multi-view enhanced Contrastive Learning method for chest X-ray report generation. Specifically, we first introduce multi-view enhanced contrastive learning for visual representation by maximizing agreements between multi-view radiographs and their corresponding report. Subsequently, to fully exploit patient-specific indications (e.g., patient's symptoms) for report generation, we add a transitional ``bridge" for missing indications to reduce embedding space discrepancies caused by their presence or absence. Additionally, we construct Multi-view CXR and Two-view CXR datasets from public sources to support research on multi-view report generation. Our proposed MCL surpasses recent state-of-the-art methods across multiple datasets, achieving a 5.0% F1 RadGraph improvement on MIMIC-CXR, a 7.3% BLEU-1 improvement on MIMIC-ABN, a 3.1% BLEU-4 improvement on Multi-view CXR, and an 8.2% F1 CheXbert improvement on Two-view CXR.

Pulmonary Embolism Mortality Prediction Using Multimodal Learning Based on Computed Tomography Angiography and Clinical Data

Purpose: Pulmonary embolism (PE) is a significant cause of mortality in the United States. The objective of this study is to implement deep learning (DL) models using Computed Tomography Pulmonary Angiography (CTPA), clinical data, and PE Severity Index (PESI) scores to predict PE mortality. Materials and Methods: 918 patients (median age 64 years, range 13-99 years, 52% female) with 3,978 CTPAs were identified via retrospective review across three institutions. To predict survival, an AI model was used to extract disease-related imaging features from CTPAs. Imaging features and/or clinical variables were then incorporated into DL models to predict survival outcomes. Four models were developed as follows: (1) using CTPA imaging features only; (2) using clinical variables only; (3) multimodal, integrating both CTPA and clinical variables; and (4) multimodal fused with calculated PESI score. Performance and contribution from each modality were evaluated using concordance index (c-index) and Net Reclassification Improvement, respectively. Performance was compared to PESI predictions using the Wilcoxon signed-rank test. Kaplan-Meier analysis was performed to stratify patients into high- and low-risk groups. Additional factor-risk analysis was conducted to account for right ventricular (RV) dysfunction. Results: For both data sets, the PESI-fused and multimodal models achieved higher c-indices than PESI alone. Following stratification of patients into high- and low-risk groups by multimodal and PESI-fused models, mortality outcomes differed significantly (both p<0.001). A strong correlation was found between high-risk grouping and RV dysfunction. Conclusions: Multiomic DL models incorporating CTPA features, clinical data, and PESI achieved higher c-indices than PESI alone for PE survival prediction.

MindSemantix: Deciphering Brain Visual Experiences with a Brain-Language Model

Deciphering the human visual experience through brain activities captured by fMRI represents a compelling and cutting-edge challenge in the field of neuroscience research. Compared to merely predicting the viewed image itself, decoding brain activity into meaningful captions provides a higher-level interpretation and summarization of visual information, which naturally enhances the application flexibility in real-world situations. In this work, we introduce MindSemantix, a novel multi-modal framework that enables LLMs to comprehend visually-evoked semantic content in brain activity. Our MindSemantix explores a more ideal brain captioning paradigm by weaving LLMs into brain activity analysis, crafting a seamless, end-to-end Brain-Language Model. To effectively capture semantic information from brain responses, we propose Brain-Text Transformer, utilizing a Brain Q-Former as its core architecture. It integrates a pre-trained brain encoder with a frozen LLM to achieve multi-modal alignment of brain-vision-language and establish a robust brain-language correspondence. To enhance the generalizability of neural representations, we pre-train our brain encoder on a large-scale, cross-subject fMRI dataset using self-supervised learning techniques. MindSemantix provides more feasibility to downstream brain decoding tasks such as stimulus reconstruction. Conditioned by MindSemantix captioning, our framework facilitates this process by integrating with advanced generative models like Stable Diffusion and excels in understanding brain visual perception. MindSemantix generates high-quality captions that are deeply rooted in the visual and semantic information derived from brain activity. This approach has demonstrated substantial quantitative improvements over prior art. Our code will be released.

Structural Entities Extraction and Patient Indications Incorporation for Chest X-ray Report Generation

The automated generation of imaging reports proves invaluable in alleviating the workload of radiologists. A clinically applicable reports generation algorithm should demonstrate its effectiveness in producing reports that accurately describe radiology findings and attend to patient-specific indications. In this paper, we introduce a novel method, \textbf{S}tructural \textbf{E}ntities extraction and patient indications \textbf{I}ncorporation (SEI) for chest X-ray report generation. Specifically, we employ a structural entities extraction (SEE) approach to eliminate presentation-style vocabulary in reports and improve the quality of factual entity sequences. This reduces the noise in the following cross-modal alignment module by aligning X-ray images with factual entity sequences in reports, thereby enhancing the precision of cross-modal alignment and further aiding the model in gradient-free retrieval of similar historical cases. Subsequently, we propose a cross-modal fusion network to integrate information from X-ray images, similar historical cases, and patient-specific indications. This process allows the text decoder to attend to discriminative features of X-ray images, assimilate historical diagnostic information from similar cases, and understand the examination intention of patients. This, in turn, assists in triggering the text decoder to produce high-quality reports. Experiments conducted on MIMIC-CXR validate the superiority of SEI over state-of-the-art approaches on both natural language generation and clinical efficacy metrics.

Multi-modality Regional Alignment Network for Covid X-Ray Survival Prediction and Report Generation

In response to the worldwide COVID-19 pandemic, advanced automated technologies have emerged as valuable tools to aid healthcare professionals in managing an increased workload by improving radiology report generation and prognostic analysis. This study proposes Multi-modality Regional Alignment Network (MRANet), an explainable model for radiology report generation and survival prediction that focuses on high-risk regions. By learning spatial correlation in the detector, MRANet visually grounds region-specific descriptions, providing robust anatomical regions with a completion strategy. The visual features of each region are embedded using a novel survival attention mechanism, offering spatially and risk-aware features for sentence encoding while maintaining global coherence across tasks. A cross LLMs alignment is employed to enhance the image-to-text transfer process, resulting in sentences rich with clinical detail and improved explainability for radiologist. Multi-center experiments validate both MRANet's overall performance and each module's composition within the model, encouraging further advancements in radiology report generation research emphasizing clinical interpretation and trustworthiness in AI models applied to medical studies. The code is available at https://github.com/zzs95/MRANet.

Factual Serialization Enhancement: A Key Innovation for Chest X-ray Report Generation

The automation of writing imaging reports is a valuable tool for alleviating the workload of radiologists. Crucial steps in this process involve the cross-modal alignment between medical images and reports, as well as the retrieval of similar historical cases. However, the presence of presentation-style vocabulary (e.g., sentence structure and grammar) in reports poses challenges for cross-modal alignment. Additionally, existing methods for similar historical cases retrieval face suboptimal performance owing to the modal gap issue. In response, this paper introduces a novel method, named Factual Serialization Enhancement (FSE), for chest X-ray report generation. FSE begins with the structural entities approach to eliminate presentation-style vocabulary in reports, providing specific input for our model. Then, uni-modal features are learned through cross-modal alignment between images and factual serialization in reports. Subsequently, we present a novel approach to retrieve similar historical cases from the training set, leveraging aligned image features. These features implicitly preserve semantic similarity with their corresponding reference reports, enabling us to calculate similarity solely among aligned features. This effectively eliminates the modal gap issue for knowledge retrieval without the requirement for disease labels. Finally, the cross-modal fusion network is employed to query valuable information from these cases, enriching image features and aiding the text decoder in generating high-quality reports. Experiments on MIMIC-CXR and IU X-ray datasets from both specific and general scenarios demonstrate the superiority of FSE over state-of-the-art approaches in both natural language generation and clinical efficacy metrics.

Region-specific Risk Quantification for Interpretable Prognosis of COVID-19

The COVID-19 pandemic has strained global public health, necessitating accurate diagnosis and intervention to control disease spread and reduce mortality rates. This paper introduces an interpretable deep survival prediction model designed specifically for improved understanding and trust in COVID-19 prognosis using chest X-ray (CXR) images. By integrating a large-scale pretrained image encoder, Risk-specific Grad-CAM, and anatomical region detection techniques, our approach produces regional interpretable outcomes that effectively capture essential disease features while focusing on rare but critical abnormal regions. Our model's predictive results provide enhanced clarity and transparency through risk area localization, enabling clinicians to make informed decisions regarding COVID-19 diagnosis with better understanding of prognostic insights. We evaluate the proposed method on a multi-center survival dataset and demonstrate its effectiveness via quantitative and qualitative assessments, achieving superior C-indexes (0.764 and 0.727) and time-dependent AUCs (0.799 and 0.691). These results suggest that our explainable deep survival prediction model surpasses traditional survival analysis methods in risk prediction, improving interpretability for clinical decision making and enhancing AI system trustworthiness.

SMC-UDA: Structure-Modal Constraint for Unsupervised Cross-Domain Renal Segmentation

Medical image segmentation based on deep learning often fails when deployed on images from a different domain. The domain adaptation methods aim to solve domain-shift challenges, but still face some problems. The transfer learning methods require annotation on the target domain, and the generative unsupervised domain adaptation (UDA) models ignore domain-specific representations, whose generated quality highly restricts segmentation performance. In this study, we propose a novel Structure-Modal Constrained (SMC) UDA framework based on a discriminative paradigm and introduce edge structure as a bridge between domains. The proposed multi-modal learning backbone distills structure information from image texture to distinguish domain-invariant edge structure. With the structure-constrained self-learning and progressive ROI, our methods segment the kidney by locating the 3D spatial structure of the edge. We evaluated SMC-UDA on public renal segmentation datasets, adapting from the labeled source domain (CT) to the unlabeled target domain (CT/MRI). The experiments show that our proposed SMC-UDA has a strong generalization and outperforms generative UDA methods.