A Joint Representation Using Continuous and Discrete Features for Cardiovascular Diseases Risk Prediction on Chest CT Scans

Cardiovascular diseases (CVD) remain a leading health concern and contribute significantly to global mortality rates. While clinical advancements have led to a decline in CVD mortality, accurately identifying individuals who could benefit from preventive interventions remains an unsolved challenge in preventive cardiology. Current CVD risk prediction models, recommended by guidelines, are based on limited traditional risk factors or use CT imaging to acquire quantitative biomarkers, and still have limitations in predictive accuracy and applicability. On the other hand, end-to-end trained CVD risk prediction methods leveraging deep learning on CT images often fail to provide transparent and explainable decision grounds for assisting physicians. In this work, we proposed a novel joint representation that integrates discrete quantitative biomarkers and continuous deep features extracted from chest CT scans. Our approach initiated with a deep CVD risk classification model by capturing comprehensive continuous deep learning features while jointly obtaining currently clinical-established quantitative biomarkers via segmentation models. In the feature joint representation stage, we use an instance-wise feature-gated mechanism to align the continuous and discrete features, followed by a soft instance-wise feature interaction mechanism fostering independent and effective feature interaction for the final CVD risk prediction. Our method substantially improves CVD risk predictive performance and offers individual contribution analysis of each biomarker, which is important in assisting physicians' decision-making processes. We validated our method on a public chest low-dose CT dataset and a private external chest standard-dose CT patient cohort of 17,207 CT volumes from 6,393 unique subjects, and demonstrated superior predictive performance, achieving AUCs of 0.875 and 0.843, respectively.

Low-Rank Continual Pyramid Vision Transformer: Incrementally Segment Whole-Body Organs in CT with Light-Weighted Adaptation

Deep segmentation networks achieve high performance when trained on specific datasets. However, in clinical practice, it is often desirable that pretrained segmentation models can be dynamically extended to enable segmenting new organs without access to previous training datasets or without training from scratch. This would ensure a much more efficient model development and deployment paradigm accounting for the patient privacy and data storage issues. This clinically preferred process can be viewed as a continual semantic segmentation (CSS) problem. Previous CSS works would either experience catastrophic forgetting or lead to unaffordable memory costs as models expand. In this work, we propose a new continual whole-body organ segmentation model with light-weighted low-rank adaptation (LoRA). We first train and freeze a pyramid vision transformer (PVT) base segmentation model on the initial task, then continually add light-weighted trainable LoRA parameters to the frozen model for each new learning task. Through a holistically exploration of the architecture modification, we identify three most important layers (i.e., patch-embedding, multi-head attention and feed forward layers) that are critical in adapting to the new segmentation tasks, while retaining the majority of the pretrained parameters fixed. Our proposed model continually segments new organs without catastrophic forgetting and meanwhile maintaining a low parameter increasing rate. Continually trained and tested on four datasets covering different body parts of a total of 121 organs, results show that our model achieves high segmentation accuracy, closely reaching the PVT and nnUNet upper bounds, and significantly outperforms other regularization-based CSS methods. When comparing to the leading architecture-based CSS method, our model has a substantial lower parameter increasing rate while achieving comparable performance.

End-to-end Multi-source Visual Prompt Tuning for Survival Analysis in Whole Slide Images

Survival analysis using pathology images poses a considerable challenge, as it requires the localization of relevant information from the multitude of tiles within whole slide images (WSIs). Current methods typically resort to a two-stage approach, where a pre-trained network extracts features from tiles, which are then used by survival models. This process, however, does not optimize the survival models in an end-to-end manner, and the pre-extracted features may not be ideally suited for survival prediction. To address this limitation, we present a novel end-to-end Visual Prompt Tuning framework for survival analysis, named VPTSurv. VPTSurv refines feature embeddings through an efficient encoder-decoder framework. The encoder remains fixed while the framework introduces tunable visual prompts and adaptors, thus permitting end-to-end training specifically for survival prediction by optimizing only the lightweight adaptors and the decoder. Moreover, the versatile VPTSurv framework accommodates multi-source information as prompts, thereby enriching the survival model. VPTSurv achieves substantial increases of 8.7% and 12.5% in the C-index on two immunohistochemical pathology image datasets. These significant improvements highlight the transformative potential of the end-to-end VPT framework over traditional two-stage methods.

From Yes-Men to Truth-Tellers: Addressing Sycophancy in Large Language Models with Pinpoint Tuning

Large Language Models (LLMs) tend to prioritize adherence to user prompts over providing veracious responses, leading to the sycophancy issue. When challenged by users, LLMs tend to admit mistakes and provide inaccurate responses even if they initially provided the correct answer. Recent works propose to employ supervised fine-tuning (SFT) to mitigate the sycophancy issue, while it typically leads to the degeneration of LLMs' general capability. To address the challenge, we propose a novel supervised pinpoint tuning (SPT), where the region-of-interest modules are tuned for a given objective. Specifically, SPT first reveals and verifies a small percentage (<5%) of the basic modules, which significantly affect a particular behavior of LLMs. i.e., sycophancy. Subsequently, SPT merely fine-tunes these identified modules while freezing the rest. To verify the effectiveness of the proposed SPT, we conduct comprehensive experiments, demonstrating that SPT significantly mitigates the sycophancy issue of LLMs (even better than SFT). Moreover, SPT introduces limited or even no side effects on the general capability of LLMs. Our results shed light on how to precisely, effectively, and efficiently explain and improve the targeted ability of LLMs.

LIDIA: Precise Liver Tumor Diagnosis on Multi-Phase Contrast-Enhanced CT via Iterative Fusion and Asymmetric Contrastive Learning

The early detection and precise diagnosis of liver tumors are tasks of critical clinical value, yet they pose significant challenges due to the high heterogeneity and variability of liver tumors. In this work, a precise LIver tumor DIAgnosis network on multi-phase contrast-enhance CT, named LIDIA, is proposed for real-world scenario. To fully utilize all available phases in contrast-enhanced CT, LIDIA first employs the iterative fusion module to aggregate variable numbers of image phases, thereby capturing the features of lesions at different phases for better tumor diagnosis. To effectively mitigate the high heterogeneity problem of liver tumors, LIDIA incorporates asymmetric contrastive learning to enhance the discriminability between different classes. To evaluate our method, we constructed a large-scale dataset comprising 1,921 patients and 8,138 lesions. LIDIA has achieved an average AUC of 93.6% across eight different types of lesions, demonstrating its effectiveness. Besides, LIDIA also demonstrated strong generalizability with an average AUC of 89.3% when tested on an external cohort of 828 patients.

Improved Esophageal Varices Assessment from Non-Contrast CT Scans

Esophageal varices (EV), a serious health concern resulting from portal hypertension, are traditionally diagnosed through invasive endoscopic procedures. Despite non-contrast computed tomography (NC-CT) imaging being a less expensive and non-invasive imaging modality, it has yet to gain full acceptance as a primary clinical diagnostic tool for EV evaluation. To overcome existing diagnostic challenges, we present the Multi-Organ-cOhesion-Network (MOON), a novel framework enhancing the analysis of critical organ features in NC-CT scans for effective assessment of EV. Drawing inspiration from the thorough assessment practices of radiologists, MOON establishes a cohesive multiorgan analysis model that unifies the imaging features of the related organs of EV, namely esophagus, liver, and spleen. This integration significantly increases the diagnostic accuracy for EV. We have compiled an extensive NC-CT dataset of 1,255 patients diagnosed with EV, spanning three grades of severity. Each case is corroborated by endoscopic diagnostic results. The efficacy of MOON has been substantiated through a validation process involving multi-fold cross-validation on 1,010 cases and an independent test on 245 cases, exhibiting superior diagnostic performance compared to methods focusing solely on the esophagus (for classifying severe grade: AUC of 0.864 versus 0.803, and for moderate to severe grades: AUC of 0.832 versus 0.793). To our knowledge, MOON is the first work to incorporate a synchronized multi-organ NC-CT analysis for EV assessment, providing a more acceptable and minimally invasive alternative for patients compared to traditional endoscopy.

Cross-Phase Mutual Learning Framework for Pulmonary Embolism Identification on Non-Contrast CT Scans

Pulmonary embolism (PE) is a life-threatening condition where rapid and accurate diagnosis is imperative yet difficult due to predominantly atypical symptomatology. Computed tomography pulmonary angiography (CTPA) is acknowledged as the gold standard imaging tool in clinics, yet it can be contraindicated for emergency department (ED) patients and represents an onerous procedure, thus necessitating PE identification through non-contrast CT (NCT) scans. In this work, we explore the feasibility of applying a deep-learning approach to NCT scans for PE identification. We propose a novel Cross-Phase Mutual learNing framework (CPMN) that fosters knowledge transfer from CTPA to NCT, while concurrently conducting embolism segmentation and abnormality classification in a multi-task manner. The proposed CPMN leverages the Inter-Feature Alignment (IFA) strategy that enhances spatial contiguity and mutual learning between the dual-pathway network, while the Intra-Feature Discrepancy (IFD) strategy can facilitate precise segmentation of PE against complex backgrounds for single-pathway networks. For a comprehensive assessment of the proposed approach, a large-scale dual-phase dataset containing 334 PE patients and 1,105 normal subjects has been established. Experimental results demonstrate that CPMN achieves the leading identification performance, which is 95.4\% and 99.6\% in patient-level sensitivity and specificity on NCT scans, indicating the potential of our approach as an economical, accessible, and precise tool for PE identification in clinical practice.

Rapid and Accurate Diagnosis of Acute Aortic Syndrome using Non-contrast CT: A Large-scale, Retrospective, Multi-center and AI-based Study

Chest pain symptoms are highly prevalent in emergency departments (EDs), where acute aortic syndrome (AAS) is a catastrophic cardiovascular emergency with a high fatality rate, especially when timely and accurate treatment is not administered. However, current triage practices in the ED can cause up to approximately half of patients with AAS to have an initially missed diagnosis or be misdiagnosed as having other acute chest pain conditions. Subsequently, these AAS patients will undergo clinically inaccurate or suboptimal differential diagnosis. Fortunately, even under these suboptimal protocols, nearly all these patients underwent non-contrast CT covering the aorta anatomy at the early stage of differential diagnosis. In this study, we developed an artificial intelligence model (DeepAAS) using non-contrast CT, which is highly accurate for identifying AAS and provides interpretable results to assist in clinical decision-making. Performance was assessed in two major phases: a multi-center retrospective study (n = 20,750) and an exploration in real-world emergency scenarios (n = 137,525). In the multi-center cohort, DeepAAS achieved a mean area under the receiver operating characteristic curve of 0.958 (95% CI 0.950-0.967). In the real-world cohort, DeepAAS detected 109 AAS patients with misguided initial suspicion, achieving 92.6% (95% CI 76.2%-97.5%) in mean sensitivity and 99.2% (95% CI 99.1%-99.3%) in mean specificity. Our AI model performed well on non-contrast CT at all applicable early stages of differential diagnosis workflows, effectively reduced the overall missed diagnosis and misdiagnosis rate from 48.8% to 4.8% and shortened the diagnosis time for patients with misguided initial suspicion from an average of 681.8 (74-11,820) mins to 68.5 (23-195) mins. DeepAAS could effectively fill the gap in the current clinical workflow without requiring additional tests.

Boosting Medical Image-based Cancer Detection via Text-guided Supervision from Reports

The absence of adequately sufficient expert-level tumor annotations hinders the effectiveness of supervised learning based opportunistic cancer screening on medical imaging. Clinical reports (that are rich in descriptive textual details) can offer a "free lunch'' supervision information and provide tumor location as a type of weak label to cope with screening tasks, thus saving human labeling workloads, if properly leveraged. However, predicting cancer only using such weak labels can be very changeling since tumors are usually presented in small anatomical regions compared to the whole 3D medical scans. Weakly semi-supervised learning (WSSL) utilizes a limited set of voxel-level tumor annotations and incorporates alongside a substantial number of medical images that have only off-the-shelf clinical reports, which may strike a good balance between minimizing expert annotation workload and optimizing screening efficacy. In this paper, we propose a novel text-guided learning method to achieve highly accurate cancer detection results. Through integrating diagnostic and tumor location text prompts into the text encoder of a vision-language model (VLM), optimization of weakly supervised learning can be effectively performed in the latent space of VLM, thereby enhancing the stability of training. Our approach can leverage clinical knowledge by large-scale pre-trained VLM to enhance generalization ability, and produce reliable pseudo tumor masks to improve cancer detection. Our extensive quantitative experimental results on a large-scale cancer dataset, including 1,651 unique patients, validate that our approach can reduce human annotation efforts by at least 70% while maintaining comparable cancer detection accuracy to competing fully supervised methods (AUC value 0.961 versus 0.966).

CT-GLIP: 3D Grounded Language-Image Pretraining with CT Scans and Radiology Reports for Full-Body Scenarios

Medical Vision-Language Pretraining (Med-VLP) establishes a connection between visual content from medical images and the relevant textual descriptions. Existing Med-VLP methods primarily focus on 2D images depicting a single body part, notably chest X-rays. In this paper, we extend the scope of Med-VLP to encompass 3D images, specifically targeting full-body scenarios, by using a multimodal dataset of CT images and reports. Compared with the 2D counterpart, 3D VLP is required to effectively capture essential semantics from significantly sparser representation in 3D imaging. In this paper, we introduce CT-GLIP (Grounded Language-Image Pretraining with CT scans), a novel method that constructs organ-level image-text pairs to enhance multimodal contrastive learning, aligning grounded visual features with precise diagnostic text. Additionally, we developed an abnormality dictionary to augment contrastive learning with diverse contrastive pairs. Our method, trained on a multimodal CT dataset comprising 44,011 organ-level vision-text pairs from 17,702 patients across 104 organs, demonstrates it can identify organs and abnormalities in a zero-shot manner using natural languages. The performance of CT-GLIP is validated on a separate test set of 1,130 patients, focusing on the 16 most frequent abnormalities across 7 organs. The experimental results show our model's superior performance over the standard CLIP framework across zero-shot and fine-tuning scenarios, using both CNN and ViT architectures.