Background
Methods
Overview
Candidate generation
Position | Mention | Label | Identifier (MeSH) | |||
start | end | |||||
0 | 28 | Cardiovascular complications | Disease | D002318 | ||
45 | 56 | terbutaline | Chemical | D013726 | ||
71 | 84 | preterm labor | Disease | D007752 | ||
93 | 121 | cardiovascular complications | Disease | D002318 | ||
169 | 180 | terbutaline | Chemical | D013726 | ||
185 | 198 | preterm labor | Disease | D007752 | ||
Identifier (MeSH) | Chemical mention | Disease mention | ||||
position | mention | Position | mention | |||
start | end | start | end | |||
<D013726, D002318> | 45 | 56 | terbutaline | 0 | 28 | Cardiovascular complications |
45 | 56 | terbutaline | 93 | 121 | Cardiovascular complications | |
169 | 180 | terbutaline | 0 | 28 | Cardiovascular complications | |
169 | 180 | terbutaline | 93 | 121 | Cardiovascular complications | |
position | position | mention | ||||
start | end | Start | End | |||
<D013726, D007752> | 45 | 56 | 71 | 84 | preterm labor | |
45 | 56 | 185 | 198 | preterm labor | ||
169 | 180 | 71 | 84 | preterm labor | ||
169 | 180 | 185 | 198 | preterm labor |
Candidate classification
Input layer
Piecewise convolutional layer
RNN layer
Softmax layer
Dataset
Experimental settings
Results
Methods | Without domain knowledge (%) | With domain knowledge (%) | ||||
---|---|---|---|---|---|---|
P
|
R
|
F
|
P
|
R
|
F
| |
CNN | 50.47 | 55.61 | 52.92 | 63.70 | 74.40 | 68.64 |
CNN + piecewise | 54.48 | 53.91 | 54.20 | 63.83 | 75.16 | 69.03 |
CNN + attention | 48.40 | 58.54 | 52.99 | 62.28 | 76.58 | 68.69 |
CNN + attention+piecewise | 57.80 | 54.20 | 55.94 | 59.97 | 81.49 | 69.09 |
RPCNN | 55.17 | 63.63 | 59.10 | 65.24 | 77.21 | 70.77 |
Methods | Without domain knowledge (%) | With domain knowledge (%) | ||||
---|---|---|---|---|---|---|
P
|
R
|
F
|
P
|
R
|
F
| |
Xu et al. [8] | 59.60 | 44.00 | 50.73 | 65.80 | 68.57 | 67.16 |
Zhou et al. (LSTM) [9] | 54.91 | 51.41 | 53.10 | / | / | / |
Zhou et al. (CNN) [9] | 41.13 | 55.25 | 47.16 | / | / | / |
Gu et al. (CNN) [15] | 59.70 | 55.00 | 57.20 | / | / | / |
Patrick et al. (BRAN) [16] | 55.60 | 70.80 | 62.10 | / | / | / |
Our CNN | 57.80 | 54.20 | 55.94 | 59.97 | 81.49 | 69.09 |
Our RPCNN | 55.17 | 63.63 | 59.10 | 65.24 | 77.21 | 70.77 |