Terrace: A Hierarchical Graph Container for Skewed Dynamic Graphs

Abstract Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this paper, we propose an accurate predictor, GraphBind, for identifying nucleic-acid-binding residues on proteins based on an end-to-end graph neural network. Considering that binding sites often behave in highly conservative patterns on local tertiary structures, we first construct graphs based on the structural contexts of target residues and their spatial neighborhood. Then, hierarchical graph neural networks (HGNNs) are used to embed the latent local patterns of structural and bio-physicochemical characteristics for binding residue recognition. We comprehensively evaluate GraphBind on DNA/RNA benchmark datasets. The results demonstrate the superior performance of GraphBind than state-of-the-art methods. Moreover, GraphBind is extended to other ligand-binding residue prediction to verify its generalization capability. Web server of GraphBind is freely available at http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/.

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Approximate Mining of Frequent -Subgraph Patterns in Evolving Graphs

ACM Transactions on Knowledge Discovery from Data ◽

10.1145/3442590 ◽

2021 ◽

Vol 15 (3) ◽

pp. 1-35

Author(s):

Muhammad Anis Uddin Nasir ◽

Cigdem Aslay ◽

Gianmarco De Francisci Morales ◽

Matteo Riondato

Keyword(s):

Sample Size ◽

State Of The Art ◽

Empirical Evaluation ◽

Connected Subgraph ◽

Dynamic Graphs ◽

High Quality ◽

Complexity Bounds ◽

Approximation Quality ◽

Uniform Sample ◽

Waiting For Godot

“Perhaps he could dance first and think afterwards, if it isn’t too much to ask him.” S. Beckett, Waiting for Godot Given a labeled graph, the collection of -vertex induced connected subgraph patterns that appear in the graph more frequently than a user-specified minimum threshold provides a compact summary of the characteristics of the graph, and finds applications ranging from biology to network science. However, finding these patterns is challenging, even more so for dynamic graphs that evolve over time, due to the streaming nature of the input and the exponential time complexity of the problem. We study this task in both incremental and fully-dynamic streaming settings, where arbitrary edges can be added or removed from the graph. We present TipTap , a suite of algorithms to compute high-quality approximations of the frequent -vertex subgraphs w.r.t. a given threshold, at any time (i.e., point of the stream), with high probability. In contrast to existing state-of-the-art solutions that require iterating over the entire set of subgraphs in the vicinity of the updated edge, TipTap operates by efficiently maintaining a uniform sample of connected -vertex subgraphs, thanks to an optimized neighborhood-exploration procedure. We provide a theoretical analysis of the proposed algorithms in terms of their unbiasedness and of the sample size needed to obtain a desired approximation quality. Our analysis relies on sample-complexity bounds that use Vapnik–Chervonenkis dimension, a key concept from statistical learning theory, which allows us to derive a sufficient sample size that is independent from the size of the graph. The results of our empirical evaluation demonstrates that TipTap returns high-quality results more efficiently and accurately than existing baselines.

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