Graph Neural Network refers to a type of neural network designed to process and analyze graph-structured data. GNNs are particularly effective for tasks involving node classification, link prediction, and graph-level prediction.

Posts

Impeller: A Path-based Heterogeneous Graph Learning Method for Spatial Transcriptomic Data Imputation

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Recent advances in spatial transcriptomics allow spatially resolved gene expression measurements with cellular or even sub-cellular resolution, directly characterizing the complex spatiotemporal gene expression landscape and cell-to-cell interactions in their native microenvironments. Due to technology limitations, most spatial transcriptomic technologies still yield incomplete expression measurements with excessive missing values. Therefore, gene imputation is critical to filling in missing data, enhancing resolution, and improving overall interpretability. However, existing methods either require additional matched single-cell RNA-seq data, which is rarely available, or ignore spatial proximity or expression similarity information

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A Deep Generative Model for Molecule Optimization via One Fragment Modification

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Molecule optimization is a critical step in drug development to improve the desired properties of drug candidates through chemical modification. We have developed a novel deep generative model, Modof, over molecular graphs for molecule optimization. Modof modifies a given molecule through the prediction of a single site of disconnection at the molecule and the removal and/or addition of fragments at that site. A pipeline of multiple, identical Modof models is implemented into Modof-pipe to modify an input molecule at multiple disconnection sites. Here we show that Modof-pipe is able to retain major molecular scaffolds, allow controls over intermediate optimization steps and better constrain molecule similarities. Modof-pipe outperforms the state-of-the-art methods on benchmark datasets. Without molecular similarity constraints, Modof-pipe achieves 81.2% improvement in the octanol–water partition coefficient, penalized by synthetic accessibility and ring size, and 51.2%, 25.6% and 9.2% improvement if the optimized molecules are at least 0.2, 0.4 and 0.6 similar to those before optimization, respectively. Modof-pipe is further enhanced into Modof-pipem to allow modification of one molecule to multiple optimized ones. Modof-pipem achieves additional performance improvement, at least 17.8% better than Modof-pipe.

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Structural Temporal Graph Neural Networks for Anomaly Detection in Dynamic Graphs

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Detecting anomalies in dynamic graphs is a vital task, with numerous practical applications in areas such as security, finance, and social media. Existing network embedding based methods have mostly focused on learning good node representations, whereas largely ignoring the subgraph structural changes related to the target nodes in a given time window. In this paper, we propose StrGNN, an end-to-end structural temporal Graph Neural Network model for detecting anomalous edges in dynamic graphs. In particular, we first extract the h-hop enclosing subgraph centered on the target edge and propose a node labeling function to identify the role of each node in the subgraph. Then, we leverage the graph convolution operation and Sortpooling layer to extract the fixed-size feature from each snapshot/timestamp. Based on the extracted features, we utilize the Gated Recurrent Units to capture the temporal information for anomaly detection. We fully implement StrGNN and deploy it into a real enterprise security system, and it greatly helps detect advanced threats and optimize the incident response. Extensive experiments on six benchmark datasets also demonstrate the effectiveness of StrGNN.

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Attentional Heterogeneous Graph Neural Network: Application to Program Reidentification

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Program or process is an integral part of almost every IT/OT system. Can we trust the identity/ID (e.g., executable name) of the program? To avoid detection, malware may disguise itself using the ID of a legitimate program, and a system tool (e.g., PowerShell) used by the attackers may have the fake ID of another common software, which is less sensitive. However, existing intrusion detection techniques often overlook this critical program reidentification problem (i.e., checking the program’s identity). In this paper, we propose an attentional heterogeneous graph neural network model (DeepHGNN) to verify the program’s identity based on its system behaviors. The key idea is to leverage the representation learning of the heterogeneous program behavior graph to guide the reidentification process. We formulate the program reidentification as a graph classification problem and develop an effective attentional heterogeneous graph embedding algorithm to solve it. Extensive experiments — using real-world enterprise monitoring data and real attacks — demonstrate the effectiveness of DeepHGNN across multiple popular metrics and the robustness to the normal dynamic changes like program version upgrades.

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