Ye Li

Se-In Jang, Tinsu Pan, Ye Li et al.

Position emission tomography (PET) is widely used in clinics and research due to its quantitative merits and high sensitivity, but suffers from low signal-to-noise ratio (SNR). Recently convolutional neural networks (CNNs) have been widely used to improve PET image quality. Though successful and efficient in local feature extraction, CNN cannot capture long-range dependencies well due to its limited receptive field. Global multi-head self-attention (MSA) is a popular approach to capture long-range information. However, the calculation of global MSA for 3D images has high computational costs. In this work, we proposed an efficient spatial and channel-wise encoder-decoder transformer, Spach Transformer, that can leverage spatial and channel information based on local and global MSAs. Experiments based on datasets of different PET tracers, i.e., $^{18}$F-FDG, $^{18}$F-ACBC, $^{18}$F-DCFPyL, and $^{68}$Ga-DOTATATE, were conducted to evaluate the proposed framework. Quantitative results show that the proposed Spach Transformer framework outperforms state-of-the-art deep learning architectures. Our codes are available at https://github.com/sijang/SpachTransformer

Ye Li, Jianan Cui, Junyu Chen et al.

In PET, the amount of relative (signal-dependent) noise present in different body regions can be significantly different and is inherently related to the number of counts present in that region. The number of counts in a region depends, in principle and among other factors, on the total administered activity, scanner sensitivity, image acquisition duration, radiopharmaceutical tracer uptake in the region, and patient local body morphometry surrounding the region. In theory, less amount of denoising operations is needed to denoise a high-count (low relative noise) image than images a low-count (high relative noise) image, and vice versa. The current deep-learning-based methods for PET image denoising are predominantly trained on image appearance only and have no special treatment for images of different noise levels. Our hypothesis is that by explicitly providing the local relative noise level of the input image to a deep convolutional neural network (DCNN), the DCNN can outperform itself trained on image appearance only. To this end, we propose a noise-level-aware framework denoising framework that allows embedding of local noise level into a DCNN. The proposed is trained and tested on 30 and 15 patient PET images acquired on a GE Discovery MI PET/CT system. Our experiments showed that the increases in both PSNR and SSIM from our backbone network with relative noise level embedding (NLE) versus the same network without NLE were statistically significant with p<0.001, and the proposed method significantly outperformed a strong baseline method by a large margin.

Shiwen Ni, Minghuan Tan, Yuelin Bai et al.

Large language models (LLMs) have demonstrated impressive performance in various natural language processing (NLP) tasks. However, there is limited understanding of how well LLMs perform in specific domains (e.g, the intellectual property (IP) domain). In this paper, we contribute a new benchmark, the first Multilingual-oriented quiZ on Intellectual Property (MoZIP), for the evaluation of LLMs in the IP domain. The MoZIP benchmark includes three challenging tasks: IP multiple-choice quiz (IPQuiz), IP question answering (IPQA), and patent matching (PatentMatch). In addition, we also develop a new IP-oriented multilingual large language model (called MoZi), which is a BLOOMZ-based model that has been supervised fine-tuned with multilingual IP-related text data. We evaluate our proposed MoZi model and four well-known LLMs (i.e., BLOOMZ, BELLE, ChatGLM and ChatGPT) on the MoZIP benchmark. Experimental results demonstrate that MoZi outperforms BLOOMZ, BELLE and ChatGLM by a noticeable margin, while it had lower scores compared with ChatGPT. Notably, the performance of current LLMs on the MoZIP benchmark has much room for improvement, and even the most powerful ChatGPT does not reach the passing level. Our source code, data, and models are available at \url{https://github.com/AI-for-Science/MoZi}.

Junyu Chen, Eric C. Frey, Yufan He et al.

In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their substantially larger receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration.