notesum.ai

Published at November 3

Customized Subgraph Selection and Encoding for Drug-drug Interaction Prediction

cs.LG

cs.AI

q-bio.BM

Released Date: November 3, 2024

Authors: Haotong Du¹, Quanming Yao², Juzheng Zhang², Yang Liu¹, Zhen Wang¹

Aff.: ¹Northwestern Polytechnical University; ²Tsinghua University

Arxiv: http://arxiv.org/abs/2411.01535v1

Model Type	Dataset	Dataset 1: DrugBank			Dataset 2: TWOSIDES
	Task Type	Multi-class			Multi-label
	Methods	F1 Score	Accuracy	Cohen’s $\kappa$	ROC-AUC	PR-AUC	AP@50
GNN- based	Decagon	57.35 $\pm$ 0.26	87.19 $\pm$ 0.28	86.07 $\pm$ 0.08	91.72 $\pm$ 0.04	90.60 $\pm$ 0.12	82.06 $\pm$ 0.45
	GAT	33.49 $\pm$ 0.36	77.18 $\pm$ 0.15	74.20 $\pm$ 0.23	91.18 $\pm$ 0.14	89.86 $\pm$ 0.05	82.80 $\pm$ 0.17
	SkipGNN	59.66 $\pm$ 0.26	85.83 $\pm$ 0.18	84.20 $\pm$ 0.16	92.04 $\pm$ 0.08	90.90 $\pm$ 0.10	84.25 $\pm$ 0.25
	CompGCN	71.20 $\pm$ 0.70	88.30 $\pm$ 0.29	86.15 $\pm$ 0.35	93.00 $\pm$ 0.07	91.26 $\pm$ 0.07	86.18 $\pm$ 0.10
	ACDGNN	86.24 $\pm$ 0.93	90.53 $\pm$ 0.38	87.81 $\pm$ 0.33	93.69 $\pm$ 0.47	92.12 $\pm$ 0.21	87.45 $\pm$ 0.24
	TransFOL	89.97 $\pm$ 1.64	91.92 $\pm$ 0.89	90.92 $\pm$ 0.72	94.16 $\pm$ 0.62	93.52 $\pm$ 0.53	88.13 $\pm$ 0.39
Subgraph- based	SEAL	48.82 $\pm$ 0.98	76.61 $\pm$ 0.26	71.91 $\pm$ 0.59	90.74 $\pm$ 0.22	90.11 $\pm$ 0.17	84.13 $\pm$ 0.13
	GraIL	73.20 $\pm$ 0.69	85.40 $\pm$ 0.39	82.70 $\pm$ 0.47	92.93 $\pm$ 0.10	91.69 $\pm$ 0.14	87.43 $\pm$ 0.09
	SumGNN	78.35 $\pm$ 0.51	89.05 $\pm$ 0.36	87.28 $\pm$ 0.08	92.62 $\pm$ 0.04	90.80 $\pm$ 0.40	85.75 $\pm$ 0.10
	SNRI	85.57 $\pm$ 0.32	90.15 $\pm$ 0.21	88.94 $\pm$ 0.36	93.12 $\pm$ 0.18	92.64 $\pm$ 0.12	87.53 $\pm$ 0.11
	KnowDDI	90.06 $\pm$ 0.27	93.15 $\pm$ 0.19	91.87 $\pm$ 0.21	95.05 $\pm$ 0.06	93.75 $\pm$ 0.05	89.24 $\pm$ 0.06
	LaGAT	81.63 $\pm$ 0.56	86.21 $\pm$ 0.18	85.38 $\pm$ 0.23	89.78 $\pm$ 0.21	86.33 $\pm$ 0.15	83.75 $\pm$ 0.36
NAS- based	MR-GNAS	74.24 $\pm$ 0.45	88.17 $\pm$ 0.24	87.31 $\pm$ 0.11	93.85 $\pm$ 0.07	91.80 $\pm$ 0.03	87.16 $\pm$ 0.05
	AutoGEL	76.87 $\pm$ 0.63	89.35 $\pm$ 0.59	86.14 $\pm$ 0.41	94.11 $\pm$ 0.32	92.35 $\pm$ 0.29	88.13 $\pm$ 0.41
	CSSE-DDI-FS	86.31 $\pm$ 0.36	91.08 $\pm$ 0.21	89.17 $\pm$ 0.27	94.35 $\pm$ 0.07	93.01 $\pm$ 0.06	89.08 $\pm$ 0.04
	CSSE-DDI-FF	80.96 $\pm$ 0.65	90.27 $\pm$ 0.23	88.69 $\pm$ 0.31	94.26 $\pm$ 0.08	92.74 $\pm$ 0.06	88.91 $\pm$ 0.09
	CSSE-DDI	92.08 $\pm$ 0.22	95.56 $\pm$ 0.15	94.72 $\pm$ 0.26	95.47 $\pm$ 0.02	94.21 $\pm$ 0.05	89.76 $\pm$ 0.05