Yi Xiao

Yihua Sun, Qingsong Yao, Yuanyuan Lyu et al.

Digital chest tomosynthesis (DCT) is a technique to produce sectional 3D images of a human chest for pulmonary disease screening, with 2D X-ray projections taken within an extremely limited range of angles. However, under the limited angle scenario, DCT contains strong artifacts caused by the presence of ribs, jamming the imaging quality of the lung area. Recently, great progress has been achieved for rib suppression in a single X-ray image, to reveal a clearer lung texture. We firstly extend the rib suppression problem to the 3D case at the software level. We propose a $\textbf{T}$omosynthesis $\textbf{RI}$b Su$\textbf{P}$pression and $\textbf{L}$ung $\textbf{E}$nhancement $\textbf{Net}$work (TRIPLE-Net) to model the 3D rib component and provide a rib-free DCT. TRIPLE-Net takes the advantages from both 2D and 3D domains, which model the ribs in DCT with the exact FBP procedure and 3D depth information, respectively. The experiments on simulated datasets and clinical data have shown the effectiveness of TRIPLE-Net to preserve lung details as well as improve the imaging quality of pulmonary diseases. Finally, an expert user study confirms our findings.

Xiangxin Zhou, Mingyu Li, Yi Xiao et al.

Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative models have achieved great success in linear peptide design, several challenges prevent the development of computational methods for designing diverse types of cyclic peptides. These challenges include the scarcity of 3D structural data on target proteins and associated cyclic peptide ligands, the geometric constraints that cyclization imposes, and the involvement of non-canonical amino acids in cyclization. To address the above challenges, we introduce CpSDE, which consists of two key components: AtomSDE, a generative structure prediction model based on harmonic SDE, and ResRouter, a residue type predictor. Utilizing a routed sampling algorithm that alternates between these two models to iteratively update sequences and structures, CpSDE facilitates the generation of cyclic peptides. By employing explicit all-atom and bond modeling, CpSDE overcomes existing data limitations and is proficient in designing a wide variety of cyclic peptides. Our experimental results demonstrate that the cyclic peptides designed by our method exhibit reliable stability and affinity.