Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning(BioMed Central Ltd, 2023-12) Wu J; Liu B; Zhang J; Wang Z; Li JPURPOSE: Sequenced Protein-Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design of novel therapeutic interventions. Conventional methods for extracting features through experimental processes have proven to be both costly and exceedingly complex. In light of these challenges, the scientific community has turned to computational approaches, particularly those grounded in deep learning methodologies. Despite the progress achieved by current deep learning technologies, their effectiveness diminishes when applied to larger, unfamiliar datasets. RESULTS: In this study, the paper introduces a novel deep learning framework, termed DL-PPI, for predicting PPIs based on sequence data. The proposed framework comprises two key components aimed at improving the accuracy of feature extraction from individual protein sequences and capturing relationships between proteins in unfamiliar datasets. 1. Protein Node Feature Extraction Module: To enhance the accuracy of feature extraction from individual protein sequences and facilitate the understanding of relationships between proteins in unknown datasets, the paper devised a novel protein node feature extraction module utilizing the Inception method. This module efficiently captures relevant patterns and representations within protein sequences, enabling more informative feature extraction. 2. Feature-Relational Reasoning Network (FRN): In the Global Feature Extraction module of our model, the paper developed a novel FRN that leveraged Graph Neural Networks to determine interactions between pairs of input proteins. The FRN effectively captures the underlying relational information between proteins, contributing to improved PPI predictions. DL-PPI framework demonstrates state-of-the-art performance in the realm of sequence-based PPI prediction.Item Cascaded Segmented Matting Network for Human Matting(IEEE, 2021-11-04) Liu B; Jing H; Qu G; Guesgen HW; Raval MSHuman matting, high quality extraction of humans from natural images, is crucial for a wide variety of applications such as virtual reality, augmented reality, entertainment and so on. Since the matting problem is an ill-posed problem, most previous methods rely on extra user inputs such as trimap or scribbles as guidance to estimate alpha value for the pixels that are in the unknown region of the trimap. This phenomenon makes it difficult to be applied to large scale data. In order to solve these problems, we studied the unique role of semantics and details in image matting, and decomposed the matting task into two sub-tasks: trimap segmentation based on high-level semantic information and alpha regression based on low-level detailed information. Specifically, we proposed a novel Cascaded Segmented Matting Network (CSMNet), which uses a shared encoder and two separate decoders to learn these two tasks in a collaborative way to achieve the end-to-end human image matting. In addition, we established a large-scale dataset with 14,000 fine-labeled human matting images. A background dataset is also built to simulate real pictures. Comprehensive empirical studies on above datasets demonstrate that CSMNet could produce a stable and accurate alpha matte without the input of trimap and achieve an evaluation value that is comparable to the algorithm that requires trimap.