Yi Xiong

Mingchen Li, Liqi Kang, Yi Xiong et al.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Chaoyu Chen, Xin Yang, Ruobing Huang et al.

Regression learning is classic and fundamental for medical image analysis. It provides the continuous mapping for many critical applications, like the attribute estimation, object detection, segmentation and non-rigid registration. However, previous studies mainly took the case-wise criteria, like the mean square errors, as the optimization objectives. They ignored the very important population-wise correlation criterion, which is exactly the final evaluation metric in many tasks. In this work, we propose to revisit the classic regression tasks with novel investigations on directly optimizing the fine-grained correlation losses. We mainly explore two complementary correlation indexes as learnable losses: Pearson linear correlation (PLC) and Spearman rank correlation (SRC). The contributions of this paper are two folds. First, for the PLC on global level, we propose a strategy to make it robust against the outliers and regularize the key distribution factors. These efforts significantly stabilize the learning and magnify the efficacy of PLC. Second, for the SRC on local level, we propose a coarse-to-fine scheme to ease the learning of the exact ranking order among samples. Specifically, we convert the learning for the ranking of samples into the learning of similarity relationships among samples. We extensively validate our method on two typical ultrasound image regression tasks, including the image quality assessment and bio-metric measurement. Experiments prove that, with the fine-grained guidance in directly optimizing the correlation, the regression performances are significantly improved. Our proposed correlation losses are general and can be extended to more important applications.

Jiamin Liang, Xin Yang, Yuhao Huang et al.

Ultrasound (US) is widely used for its advantages of real-time imaging, radiation-free and portability. In clinical practice, analysis and diagnosis often rely on US sequences rather than a single image to obtain dynamic anatomical information. This is challenging for novices to learn because practicing with adequate videos from patients is clinically unpractical. In this paper, we propose a novel framework to synthesize high-fidelity US videos. Specifically, the synthesis videos are generated by animating source content images based on the motion of given driving videos. Our highlights are three-fold. First, leveraging the advantages of self- and fully-supervised learning, our proposed system is trained in weakly-supervised manner for keypoint detection. These keypoints then provide vital information for handling complex high dynamic motions in US videos. Second, we decouple content and texture learning using the dual decoders to effectively reduce the model learning difficulty. Last, we adopt the adversarial training strategy with GAN losses for further improving the sharpness of the generated videos, narrowing the gap between real and synthesis videos. We validate our method on a large in-house pelvic dataset with high dynamic motion. Extensive evaluation metrics and user study prove the effectiveness of our proposed method.

Xin Yang, Yuhao Huang, Ruobing Huang et al.

3D ultrasound (US) has become prevalent due to its rich spatial and diagnostic information not contained in 2D US. Moreover, 3D US can contain multiple standard planes (SPs) in one shot. Thus, automatically localizing SPs in 3D US has the potential to improve user-independence and scanning-efficiency. However, manual SP localization in 3D US is challenging because of the low image quality, huge search space and large anatomical variability. In this work, we propose a novel multi-agent reinforcement learning (MARL) framework to simultaneously localize multiple SPs in 3D US. Our contribution is four-fold. First, our proposed method is general and it can accurately localize multiple SPs in different challenging US datasets. Second, we equip the MARL system with a recurrent neural network (RNN) based collaborative module, which can strengthen the communication among agents and learn the spatial relationship among planes effectively. Third, we explore to adopt the neural architecture search (NAS) to automatically design the network architecture of both the agents and the collaborative module. Last, we believe we are the first to realize automatic SP localization in pelvic US volumes, and note that our approach can handle both normal and abnormal uterus cases. Extensively validated on two challenging datasets of the uterus and fetal brain, our proposed method achieves the average localization accuracy of 7.03 degrees/1.59mm and 9.75 degrees/1.19mm. Experimental results show that our light-weight MARL model has higher accuracy than state-of-the-art methods.