Related papers: Deep Reinforcement Learning for Modelling Protein …

Classical force fields (FF) based on machine learning (ML) methods show great potential for large scale simulations of materials. MLFFs have hitherto largely been designed and fitted for specific systems and are not usually transferable to…

Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

Various Graph Neural Networks (GNNs) have been successful in analyzing data in non-Euclidean spaces, however, they have limitations such as oversmoothing, i.e., information becomes excessively averaged as the number of hidden layers…

The Graph Convolutional Network (GCN) has been successfully applied to many graph-based applications. Training a large-scale GCN model, however, is still challenging: Due to the node dependency and layer dependency of the GCN architecture,…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and…

Recent studies reveal that Convolutional Neural Networks (CNNs) are typically vulnerable to adversarial attacks, which pose a threat to security-sensitive applications. Many adversarial defense methods improve robustness at the cost of…

Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…

The pursuit of a universal AI-generated image (AIGI) detector often relies on aggregating data from numerous generators to improve generalization. However, this paper identifies a paradoxical phenomenon we term the Benefit then Conflict…

Estimation of Distribution Algorithms (EDAs) require flexible probability models that can be efficiently learned and sampled. Generative Adversarial Networks (GAN) are generative neural networks which can be trained to implicitly model the…

Deep graph neural networks (GNNs) have achieved excellent results on various tasks on increasingly large graph datasets with millions of nodes and edges. However, memory complexity has become a major obstacle when training deep GNNs for…

We define a novel type of ensemble Graph Convolutional Network (GCN) model. Using optimized linear projection operators to map between spatial scales of graph, this ensemble model learns to aggregate information from each scale for its…

In recent years, the rapid development of generative artificial intelligence technology has significantly lowered the barrier to creating high-quality fake images, posing a serious challenge to information authenticity and credibility.…

Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…

Unsupervised graph representation learning aims to learn low-dimensional node embeddings without supervision while preserving graph topological structures and node attributive features. Previous graph neural networks (GNN) require a large…

Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…

Link prediction in structured-data is an important problem for many applications, especially for recommendation systems. Existing methods focus on how to learn the node representation based on graph-based structure. High-dimensional sparse…

Generative adversarial networks (GANs) provide a way to learn deep representations without extensively annotated training data. They achieve this through deriving backpropagation signals through a competitive process involving a pair of…

Deep learning-based approaches, such as AlphaFold2 (AF2), have significantly advanced protein tertiary structure prediction, achieving results comparable to real biological experimental methods. While AF2 has shown limitations in predicting…

The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…