Haiyan Huang

Shuni Li, Zhiyuan Ruan, Andy Shen et al.

Synthetic random heteropolymers (RHPs), consisting of a predefined set of monomers, offer an approach toward the design of protein-like materials. These RHPs, if designed appropriately, can mimic protein behavior and function. As such, there is a need for computational tools to efficiently guide RHP design. We bridge this gap by developing DeepRHP, a modified variational autoencoder (VAE) model under a semi-supervised framework. By equipping a classical VAE with an additional feature-based VAE, DeepRHP forces the latent space to capture structures of critical chemical features as well as individual RHP sequence patterns. In this sense, our method is versatile by allowing any relevant features to be incorporated in a hybrid manner. We demonstrate the effectiveness of DeepRHP by suggesting potential monomer compositions that stabilize membrane proteins (e.g. Aquaporin Z) in non-native environments and cross-validating our prediction with published results. The concordance between our model and true RHP function suggests strong potential in utilizing hybrid autoencoder architectures to guide RHP design for proteins and other biological compounds.

Yuting Ye, Christine Ho, Ci-Ren Jiang et al.

Hierarchical multi-label classification (HMC) has gained considerable attention in recent decades. A seminal line of HMC research addresses the problem in two stages: first, training individual classifiers for each class, then integrating these classifiers to provide a unified set of classification results across classes while respecting the given hierarchy. In this article, we focus on the less attended second-stage question while adhering to the given class hierarchy. This involves addressing a key challenge: how to manage the hierarchical constraint and account for statistical differences in the first-stage classifier scores across different classes to make classification decisions that are optimal under a justifiable criterion. To address this challenge, we introduce a new objective function, called CATCH, to ensure reasonable classification performance. To optimize this function, we propose a decision strategy built on a novel metric, the multidimensional Local Precision Rate (mLPR), which reflects the membership chance of an object in a class given all classifier scores and the class hierarchy. Particularly, we demonstrate that, under certain conditions, transforming the classifier scores into mLPRs and comparing mLPR values for all objects against all classes can, in theory, ensure the class hierarchy and maximize CATCH. In practice, we propose an algorithm HierRank to rank estimated mLPRs under the hierarchical constraint, leading to a ranking that maximizes an empirical version of CATCH. Our approach was evaluated on a synthetic dataset and two real datasets, exhibiting superior performance compared to several state-of-the-art methods in terms of improved decision accuracy.

Duowang Zhu, Xiaohu Huang, Haiyan Huang et al.

Change detection in remote sensing images is essential for tracking environmental changes on the Earth's surface. Despite the success of vision transformers (ViTs) as backbones in numerous computer vision applications, they remain underutilized in change detection, where convolutional neural networks (CNNs) continue to dominate due to their powerful feature extraction capabilities. In this paper, our study uncovers ViTs' unique advantage in discerning large-scale changes, a capability where CNNs fall short. Capitalizing on this insight, we introduce ChangeViT, a framework that adopts a plain ViT backbone to enhance the performance of large-scale changes. This framework is supplemented by a detail-capture module that generates detailed spatial features and a feature injector that efficiently integrates fine-grained spatial information into high-level semantic learning. The feature integration ensures that ChangeViT excels in both detecting large-scale changes and capturing fine-grained details, providing comprehensive change detection across diverse scales. Without bells and whistles, ChangeViT achieves state-of-the-art performance on three popular high-resolution datasets (i.e., LEVIR-CD, WHU-CD, and CLCD) and one low-resolution dataset (i.e., OSCD), which underscores the unleashed potential of plain ViTs for change detection. Furthermore, thorough quantitative and qualitative analyses validate the efficacy of the introduced modules, solidifying the effectiveness of our approach. The source code is available at https://github.com/zhuduowang/ChangeViT.

Christine Ho, Yuting Ye, Ci-Ren Jiang et al.

In this article we propose a novel ranking algorithm, referred to as HierLPR, for the multi-label classification problem when the candidate labels follow a known hierarchical structure. HierLPR is motivated by a new metric called eAUC that we design to assess the ranking of classification decisions. This metric, associated with the hit curve and local precision rate, emphasizes the accuracy of the first calls. We show that HierLPR optimizes eAUC under the tree constraint and some light assumptions on the dependency between the nodes in the hierarchy. We also provide a strategy to make calls for each node based on the ordering produced by HierLPR, with the intent of controlling FDR or maximizing F-score. The performance of our proposed methods is demonstrated on synthetic datasets as well as a real example of disease diagnosis using NCBI GEO datasets. In these cases, HierLPR shows a favorable result over competing methods in the early part of the precision-recall curve.