Chi-Tung Cheng

Yu-Jen Chen, Wei-Hsiang Shen, Hao-Wei Chung et al. · pku

Medical report generation is a challenging task since it is time-consuming and requires expertise from experienced radiologists. The goal of medical report generation is to accurately capture and describe the image findings. Previous works pretrain their visual encoding neural networks with large datasets in different domains, which cannot learn general visual representation in the specific medical domain. In this work, we propose a medical report generation framework that uses a contrastive learning approach to pretrain the visual encoder and requires no additional meta information. In addition, we adopt lung segmentation as an augmentation method in the contrastive learning framework. This segmentation guides the network to focus on encoding the visual feature within the lung region. Experimental results show that the proposed framework improves the performance and the quality of the generated medical reports both quantitatively and qualitatively.

Fakai Wang, Chi-Tung Cheng, Chien-Wei Peng et al.

Liver cancer has high morbidity and mortality rates in the world. Multi-phase CT is a main medical imaging modality for detecting/identifying and diagnosing liver tumors. Automatically detecting and classifying liver lesions in CT images have the potential to improve the clinical workflow. This task remains challenging due to liver lesions' large variations in size, appearance, image contrast, and the complexities of tumor types or subtypes. In this work, we customize a multi-object labeling tool for multi-phase CT images, which is used to curate a large-scale dataset containing 1,631 patients with four-phase CT images, multi-organ masks, and multi-lesion (six major types of liver lesions confirmed by pathology) masks. We develop a two-stage liver lesion detection pipeline, where the high-sensitivity detecting algorithms in the first stage discover as many lesion proposals as possible, and the lesion-reclassification algorithms in the second stage remove as many false alarms as possible. The multi-sensitivity lesion detection algorithm maximizes the information utilization of the individual probability maps of segmentation, and the lesion-shuffle augmentation effectively explores the texture contrast between lesions and the liver. Independently tested on 331 patient cases, the proposed model achieves high sensitivity and specificity for malignancy classification in the multi-phase contrast-enhanced CT (99.2%, 97.1%, diagnosis setting) and in the noncontrast CT (97.3%, 95.7%, screening setting).

Ying-Jia Lin, Tzu-Chin Lo, Ping-Chien Li et al.

Automatic report labeling facilitates the identification of clinical findings from unstructured text and enables large-scale annotation for medical imaging research. Existing rule-based labelers struggle with the diverse descriptions in clinical reports, while fine-tuning pre-trained language models (PLMs) requires large amounts of labeled data that are often unavailable in clinical settings. In this paper, we propose PromptRad, a knowledge-enhanced multi-label \textbf{prompt}-tuning approach for \textbf{rad}iology report labeling under low-resource settings. PromptRad reformulates multi-label classification as masked language modeling and incorporates synonyms from the UMLS Metathesaurus into a multi-word verbalizer to enrich category representations. By fine-tuning the PLM without additional classification layers, PromptRad requires substantially less labeled data than conventional fine-tuning. Experiments on liver CT reports show that PromptRad outperforms dictionary-based and fine-tuning baselines with only 32 labeled training examples, and achieves competitive performance with GPT-4 despite using a much smaller model. Further analysis demonstrates that PromptRad captures complex negation patterns more effectively than existing methods, making it a promising solution for report labeling in data-scarce clinical scenarios. Our code is available at https://github.com/ila-lab/PromptRad.

Chi-Tung Cheng, Jinzheng Cai, Wei Teng et al.

Hepatocellular carcinoma (HCC) can be potentially discovered from abdominal computed tomography (CT) studies under varied clinical scenarios, e.g., fully dynamic contrast enhanced (DCE) studies, non-contrast (NC) plus venous phase (VP) abdominal studies, or NC-only studies. We develop a flexible three-dimensional deep algorithm, called hetero-phase volumetric detection (HPVD), that can accept any combination of contrast-phase inputs and with adjustable sensitivity depending on the clinical purpose. We trained HPVD on 771 DCE CT scans to detect HCCs and tested on external 164 positives and 206 controls, respectively. We compare performance against six clinical readers, including two radiologists, two hepato-pancreatico-biliary (HPB) surgeons, and two hepatologists. The area under curve (AUC) of the localization receiver operating characteristic (LROC) for NC-only, NC plus VP, and full DCE CT yielded 0.71, 0.81, 0.89 respectively. At a high sensitivity operating point of 80% on DCE CT, HPVD achieved 97% specificity, which is comparable to measured physician performance. We also demonstrate performance improvements over more typical and less flexible non hetero-phase detectors. Thus, we demonstrate that a single deep learning algorithm can be effectively applied to diverse HCC detection clinical scenarios.

Xinyu Zhang, Yirui Wang, Chi-Tung Cheng et al.

Object detection methods are widely adopted for computer-aided diagnosis using medical images. Anomalous findings are usually treated as objects that are described by bounding boxes. Yet, many pathological findings, e.g., bone fractures, cannot be clearly defined by bounding boxes, owing to considerable instance, shape and boundary ambiguities. This makes bounding box annotations, and their associated losses, highly ill-suited. In this work, we propose a new bone fracture detection method for X-ray images, based on a labor effective and flexible annotation scheme suitable for abnormal findings with no clear object-level spatial extents or boundaries. Our method employs a simple, intuitive, and informative point-based annotation protocol to mark localized pathology information. To address the uncertainty in the fracture scales annotated via point(s), we convert the annotations into pixel-wise supervision that uses lower and upper bounds with positive, negative, and uncertain regions. A novel Window Loss is subsequently proposed to only penalize the predictions outside of the uncertain regions. Our method has been extensively evaluated on 4410 pelvic X-ray images of unique patients. Experiments demonstrate that our method outperforms previous state-of-the-art image classification and object detection baselines by healthy margins, with an AUROC of 0.983 and FROC score of 89.6%.

Jinzheng Cai, Ke Yan, Chi-Tung Cheng et al.

Identifying, measuring and reporting lesions accurately and comprehensively from patient CT scans are important yet time-consuming procedures for physicians. Computer-aided lesion/significant-findings detection techniques are at the core of medical imaging, which remain very challenging due to the tremendously large variability of lesion appearance, location and size distributions in 3D imaging. In this work, we propose a novel deep anchor-free one-stage VULD framework that incorporates (1) P3DC operators to recycle the architectural configurations and pre-trained weights from the off-the-shelf 2D networks, especially ones with large capacities to cope with data variance, and (2) a new SPR method to effectively regress the 3D lesion spatial extents by pinpointing their representative key points on lesion surfaces. Experimental validations are first conducted on the public large-scale NIH DeepLesion dataset where our proposed method delivers new state-of-the-art quantitative performance. We also test VULD on our in-house dataset for liver tumor detection. VULD generalizes well in both large-scale and small-sized tumor datasets in CT imaging.

Haomin Chen, Yirui Wang, Kang Zheng et al.

Visual cues of enforcing bilaterally symmetric anatomies as normal findings are widely used in clinical practice to disambiguate subtle abnormalities from medical images. So far, inadequate research attention has been received on effectively emulating this practice in CAD methods. In this work, we exploit semantic anatomical symmetry or asymmetry analysis in a complex CAD scenario, i.e., anterior pelvic fracture detection in trauma PXRs, where semantically pathological (refer to as fracture) and non-pathological (e.g., pose) asymmetries both occur. Visually subtle yet pathologically critical fracture sites can be missed even by experienced clinicians, when limited diagnosis time is permitted in emergency care. We propose a novel fracture detection framework that builds upon a Siamese network enhanced with a spatial transformer layer to holistically analyze symmetric image features. Image features are spatially formatted to encode bilaterally symmetric anatomies. A new contrastive feature learning component in our Siamese network is designed to optimize the deep image features being more salient corresponding to the underlying semantic asymmetries (caused by pelvic fracture occurrences). Our proposed method have been extensively evaluated on 2,359 PXRs from unique patients (the largest study to-date), and report an area under ROC curve score of 0.9771. This is the highest among state-of-the-art fracture detection methods, with improved clinical indications.

Yuankai Huo, Jinzheng Cai, Chi-Tung Cheng et al.

Non-invasive radiological-based lesion characterization and identification, e.g., to differentiate cancer subtypes, has long been a major aim to enhance oncological diagnosis and treatment procedures. Here we study a specific population of human subjects, with the hope of reducing the need for invasive surgical biopsies of liver cancer patients, which can cause many harmful side-effects. To this end, we propose a fully-automated and multi-stage liver tumor characterization framework designed for dynamic contrast computed tomography (CT). Our system comprises four sequential processes of tumor proposal detection, tumor harvesting, primary tumor site selection, and deep texture-based tumor characterization. Our main contributions are that, (1) we propose a 3D non-isotropic anchor-free detection method for liver lesions; (2) we present and validate spatially adaptivedeep texture (SaDT) learning, which allows for more precise characterization of liver lesions; (3) using a semi-automatic process, we bootstrap off of 200 gold standard annotations to curate another 1001 patients. Experimental evaluations demonstrate that our new data curation strategy, combined with the SaDT deep dynamic texture analysis, can effectively improve the mean F1 scores by >8.6% compared with baselines, in differentiating four major liver lesion types. Our F1 score of (hepatocellular carcinoma versus remaining subclasses) is 0.763, which is higher than reported human observer performance using dynamic CT and comparable to an advanced magnetic resonance imagery protocol. Apart from demonstrating the benefits of our data curation approach and physician-inspired workflow, these results also indicate that analyzing texture features, instead of standard object-based analysis, is a promising strategy for lesion differentiation.

Ashwin Raju, Chi-Tung Cheng, Yunakai Huo et al.

In medical imaging, organ/pathology segmentation models trained on current publicly available and fully-annotated datasets usually do not well-represent the heterogeneous modalities, phases, pathologies, and clinical scenarios encountered in real environments. On the other hand, there are tremendous amounts of unlabelled patient imaging scans stored by many modern clinical centers. In this work, we present a novel segmentation strategy, co-heterogenous and adaptive segmentation (CHASe), which only requires a small labeled cohort of single phase imaging data to adapt to any unlabeled cohort of heterogenous multi-phase data with possibly new clinical scenarios and pathologies. To do this, we propose a versatile framework that fuses appearance based semi-supervision, mask based adversarial domain adaptation, and pseudo-labeling. We also introduce co-heterogeneous training, which is a novel integration of co-training and hetero modality learning. We have evaluated CHASe using a clinically comprehensive and challenging dataset of multi-phase computed tomography (CT) imaging studies (1147 patients and 4577 3D volumes). Compared to previous state-of-the-art baselines, CHASe can further improve pathological liver mask Dice-Sorensen coefficients by ranges of $4.2\% \sim 9.4\%$, depending on the phase combinations: e.g., from $84.6\%$ to $94.0\%$ on non-contrast CTs.

Fengze Liu, Jinzheng Cai, Yuankai Huo et al.

Multi-modal image registration is a challenging problem that is also an important clinical task for many real applications and scenarios. As a first step in analysis, deformable registration among different image modalities is often required in order to provide complementary visual information. During registration, semantic information is key to match homologous points and pixels. Nevertheless, many conventional registration methods are incapable in capturing high-level semantic anatomical dense correspondences. In this work, we propose a novel multi-task learning system, JSSR, based on an end-to-end 3D convolutional neural network that is composed of a generator, a registration and a segmentation component. The system is optimized to satisfy the implicit constraints between different tasks in an unsupervised manner. It first synthesizes the source domain images into the target domain, then an intra-modal registration is applied on the synthesized images and target images. The segmentation module are then applied on the synthesized and target images, providing additional cues based on semantic correspondences. The supervision from another fully-annotated dataset is used to regularize the segmentation. We extensively evaluate JSSR on a large-scale medical image dataset containing 1,485 patient CT imaging studies of four different contrast phases (i.e., 5,940 3D CT scans with pathological livers) on the registration, segmentation and synthesis tasks. The performance is improved after joint training on the registration and segmentation tasks by 0.9% and 1.9% respectively compared to a highly competitive and accurate deep learning baseline. The registration also consistently outperforms conventional state-of-the-art multi-modal registration methods.

Weijian Li, Yuhang Lu, Kang Zheng et al.

Image landmark detection aims to automatically identify the locations of predefined fiducial points. Despite recent success in this field, higher-ordered structural modeling to capture implicit or explicit relationships among anatomical landmarks has not been adequately exploited. In this work, we present a new topology-adapting deep graph learning approach for accurate anatomical facial and medical (e.g., hand, pelvis) landmark detection. The proposed method constructs graph signals leveraging both local image features and global shape features. The adaptive graph topology naturally explores and lands on task-specific structures which are learned end-to-end with two Graph Convolutional Networks (GCNs). Extensive experiments are conducted on three public facial image datasets (WFLW, 300W, and COFW-68) as well as three real-world X-ray medical datasets (Cephalometric (public), Hand and Pelvis). Quantitative results comparing with the previous state-of-the-art approaches across all studied datasets indicating the superior performance in both robustness and accuracy. Qualitative visualizations of the learned graph topologies demonstrate a physically plausible connectivity laying behind the landmarks.

Bo Zhou, Adam P. Harrison, Jiawen Yao et al.

As the demand for more descriptive machine learning models grows within medical imaging, bottlenecks due to data paucity will exacerbate. Thus, collecting enough large-scale data will require automated tools to harvest data/label pairs from messy and real-world datasets, such as hospital PACS. This is the focus of our work, where we present a principled data curation tool to extract multi-phase CT liver studies and identify each scan's phase from a real-world and heterogenous hospital PACS dataset. Emulating a typical deployment scenario, we first obtain a set of noisy labels from our institutional partners that are text mined using simple rules from DICOM tags. We train a deep learning system, using a customized and streamlined 3D SE architecture, to identify non-contrast, arterial, venous, and delay phase dynamic CT liver scans, filtering out anything else, including other types of liver contrast studies. To exploit as much training data as possible, we also introduce an aggregated cross entropy loss that can learn from scans only identified as "contrast". Extensive experiments on a dataset of 43K scans of 7680 patient imaging studies demonstrate that our 3DSE architecture, armed with our aggregated loss, can achieve a mean F1 of 0.977 and can correctly harvest up to 92.7% of studies, which significantly outperforms the text-mined and standard-loss approach, and also outperforms other, and more complex, model architectures.

Yirui Wang, Le Lu, Chi-Tung Cheng et al.

Hip and pelvic fractures are serious injuries with life-threatening complications. However, diagnostic errors of fractures in pelvic X-rays (PXRs) are very common, driving the demand for computer-aided diagnosis (CAD) solutions. A major challenge lies in the fact that fractures are localized patterns that require localized analyses. Unfortunately, the PXRs residing in hospital picture archiving and communication system do not typically specify region of interests. In this paper, we propose a two-stage hip and pelvic fracture detection method that executes localized fracture classification using weakly supervised ROI mining. The first stage uses a large capacity fully-convolutional network, i.e., deep with high levels of abstraction, in a multiple instance learning setting to automatically mine probable true positive and definite hard negative ROIs from the whole PXR in the training data. The second stage trains a smaller capacity model, i.e., shallower and more generalizable, with the mined ROIs to perform localized analyses to classify fractures. During inference, our method detects hip and pelvic fractures in one pass by chaining the probability outputs of the two stages together. We evaluate our method on 4 410 PXRs, reporting an area under the ROC curve value of 0.975, the highest among state-of-the-art fracture detection methods. Moreover, we show that our two-stage approach can perform comparably to human physicians (even outperforming emergency physicians and surgeons), in a preliminary reader study of 23 readers.