Related papers: SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Ne…
Graph neural networks (GNNs) have been widely investigated in the field of semi-supervised graph machine learning. Most methods fail to exploit adequate graph information when labeled data is limited, leading to the problem of…
Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has…
Graph neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
Property prediction on molecular graphs is an important application of Graph Neural Networks. Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the…
Obtaining high-quality labels is costly, whereas unlabeled covariates are often abundant, motivating semi-supervised inference methods with reliable uncertainty quantification. Prediction-powered inference (PPI) leverages a machine-learning…
There is a growing interest in designing Graph Neural Networks (GNNs) for seeded graph matching, which aims to match two unlabeled graphs using only topological information and a small set of seed nodes. However, most previous GNNs for this…
The pre-training on the graph neural network model can learn the general features of large-scale networks or networks of the same type by self-supervised methods, which allows the model to work even when node labels are missing. However,…
Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…
Graph Neural Networks (GNNs) are the first choice methods for graph machine learning problems thanks to their ability to learn state-of-the-art level representations from graph-structured data. However, centralizing a massive amount of…
Graph Neural Networks have shown excellent performance on semi-supervised classification tasks. However, they assume access to a graph that may not be often available in practice. In the absence of any graph, constructing k-Nearest Neighbor…
Graph neural networks (GNNs) are among the most powerful tools in deep learning. They routinely solve complex problems on unstructured networks, such as node classification, graph classification, or link prediction, with high accuracy.…
Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that…
Graph Neural Networks (GNNs) have become a central tool for learning on graph-structured data, yet their applicability to real-world systems remains limited by key challenges such as scalability, temporality, directionality, data…
Graph Neural Networks (GNNs) have achieved promising results for semi-supervised learning tasks on graphs such as node classification. Despite the great success of GNNs, many real-world graphs are often sparsely and noisily labeled, which…
Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
We developed an explainable deep learning framework integrating protein-protein interaction (PPI) network centrality metrics with node embeddings for cancer therapeutic target prioritization. A high-confidence PPI network was constructed…
In recent years, graph neural networks (GNNs) have facilitated the development of graph data mining. However, training GNNs requires sufficient labeled task-specific data, which is expensive and sometimes unavailable. To be less dependent…
Sequential recommendation effectively addresses information overload by modeling users' temporal and sequential interaction patterns. To overcome the limitations of supervision signals, recent approaches have adopted self-supervised…