HiFi-Syn: Hierarchical Granularity Discrimination for High-Fidelity Synthesis of MR Images with Structure Preservation

Synthesizing medical images while preserving their structural information is crucial in medical research. In such scenarios, the preservation of anatomical content becomes especially important. Although recent advances have been made by incorporating instance-level information to guide translation, these methods overlook the spatial coherence of structural-level representation and the anatomical invariance of content during translation. To address these issues, we introduce hierarchical granularity discrimination, which exploits various levels of semantic information present in medical images. Our strategy utilizes three levels of discrimination granularity: pixel-level discrimination using a Brain Memory Bank, structure-level discrimination on each brain structure with a re-weighting strategy to focus on hard samples, and global-level discrimination to ensure anatomical consistency during translation. The image translation performance of our strategy has been evaluated on three independent datasets (UK Biobank, IXI, and BraTS 2018), and it has outperformed state-of-the-art algorithms. Particularly, our model excels not only in synthesizing normal structures but also in handling abnormal (pathological) structures, such as brain tumors, despite the variations in contrast observed across different imaging modalities due to their pathological characteristics. The diagnostic value of synthesized MR images containing brain tumors has been evaluated by radiologists. This indicates that our model may offer an alternative solution in scenarios where specific MR modalities of patients are unavailable. Extensive experiments further demonstrate the versatility of our method, providing unique insights into medical image translation.

Extrinsic Factors Affecting the Accuracy of Biomedical NER

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can facilitate the extraction and analysis of important biomedical information, which can be used to improve downstream applications including the healthcare system. However, NER in the biomedical domain is challenging due to limited data availability, as the high expertise, time, and expenses are required to annotate its data. In this paper, by using the limited data, we explore various extrinsic factors including the corpus annotation scheme, data augmentation techniques, semi-supervised learning and Brill transformation, to improve the performance of a NER model on a clinical text dataset (i2b2 2012, \citet{sun-rumshisky-uzuner:2013}). Our experiments demonstrate that these approaches can significantly improve the model's F1 score from original 73.74 to 77.55. Our findings suggest that considering different extrinsic factors and combining these techniques is a promising approach for improving NER performance in the biomedical domain where the size of data is limited.

MouseGAN++: Unsupervised Disentanglement and Contrastive Representation for Multiple MRI Modalities Synthesis and Structural Segmentation of Mouse Brain

Segmenting the fine structure of the mouse brain on magnetic resonance (MR) images is critical for delineating morphological regions, analyzing brain function, and understanding their relationships. Compared to a single MRI modality, multimodal MRI data provide complementary tissue features that can be exploited by deep learning models, resulting in better segmentation results. However, multimodal mouse brain MRI data is often lacking, making automatic segmentation of mouse brain fine structure a very challenging task. To address this issue, it is necessary to fuse multimodal MRI data to produce distinguished contrasts in different brain structures. Hence, we propose a novel disentangled and contrastive GAN-based framework, named MouseGAN++, to synthesize multiple MR modalities from single ones in a structure-preserving manner, thus improving the segmentation performance by imputing missing modalities and multi-modality fusion. Our results demonstrate that the translation performance of our method outperforms the state-of-the-art methods. Using the subsequently learned modality-invariant information as well as the modality-translated images, MouseGAN++ can segment fine brain structures with averaged dice coefficients of 90.0% (T2w) and 87.9% (T1w), respectively, achieving around +10% performance improvement compared to the state-of-the-art algorithms. Our results demonstrate that MouseGAN++, as a simultaneous image synthesis and segmentation method, can be used to fuse cross-modality information in an unpaired manner and yield more robust performance in the absence of multimodal data. We release our method as a mouse brain structural segmentation tool for free academic usage at https://github.com/yu02019.

Denoising of 3D MR images using a voxel-wise hybrid residual MLP-CNN model to improve small lesion diagnostic confidence

Small lesions in magnetic resonance imaging (MRI) images are crucial for clinical diagnosis of many kinds of diseases. However, the MRI quality can be easily degraded by various noise, which can greatly affect the accuracy of diagnosis of small lesion. Although some methods for denoising MR images have been proposed, task-specific denoising methods for improving the diagnosis confidence of small lesions are lacking. In this work, we propose a voxel-wise hybrid residual MLP-CNN model to denoise three-dimensional (3D) MR images with small lesions. We combine basic deep learning architecture, MLP and CNN, to obtain an appropriate inherent bias for the image denoising and integrate each output layers in MLP and CNN by adding residual connections to leverage long-range information. We evaluate the proposed method on 720 T2-FLAIR brain images with small lesions at different noise levels. The results show the superiority of our method in both quantitative and visual evaluations on testing dataset compared to state-of-the-art methods. Moreover, two experienced radiologists agreed that at moderate and high noise levels, our method outperforms other methods in terms of recovery of small lesions and overall image denoising quality. The implementation of our method is available at https://github.com/laowangbobo/Residual_MLP_CNN_Mixer.