A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction

Table 3

The comparison with other kernel based methods on PPI task. Random sdpCNN model: sdpCNN model with randomly initialized word embedding. Pretrained sdpCNN model: sdpCNN model built on pretrained word embedding.

Method	BioInfer			Aimed
	Random sdpCNN model (baseline)	69.6	77.8	73.4	54.5	75.2	62.7
Pretrained sdpCNN model	73.4	77.0	75.2	64.8	67.8	66.0
sdp based methods
Walk-weighted subsequence kernel	61.8	54.2	57.6	61.4	53.3	56.6
Graph kernel	—	—	—	52.9	61.8	56.4
SDP-CPT	—	—	62.4	—	—	58.1
Tree kernel	—	—	62.8	—	—	51.4
Edit-distance kernel	—	—	—	58.4	61.2	59.6
Hybrid kernel based methods
Hybrid kernel	65.7	71.1	68.1	55.0	68.8	60.8
Multiple features and parser	—	—	67.6	—	—	64.2
Multiple kernel	57.0	77.3	65.8	57.7	71.1	64.4