-
Notifications
You must be signed in to change notification settings - Fork 0
/
score-spans-kernel.sh
executable file
·216 lines (181 loc) · 8.28 KB
/
score-spans-kernel.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
#!/bin/bash
if [[ -z $CLASSIFIERS ]]; then
echo "The variable \$CLASSIFIERS is not set"
exit 0
fi
export SAFE_CLASSIFIERS=`echo $CLASSIFIERS | tr ' ' 'x'`
if [[ -z $MAXVOTES ]]; then
echo "The variable \$MAXVOTES is not set"
exit 0
fi
## Most, if not all, of these environment variables will need to be
## customized to match your running environment.
export ENSEMBLE_DIR=/data/software/ots-ensemble-systems
export ENSEMBLE_CONDA=/data/software/anaconda3/envs/ensemble-py3.8
export ETUDE_DIR=/data/software/etude
export ETUDE_CONDA=/data/software/anaconda3/envs/etude
export CONFIG_DIR=/data/software/etude-engine-configs
export TASK=2009_i2b2_medications
export I2B2_2009_DIR=/data/i2b2_corpora/2009_i2b2_challenge_medications
## I2B2_2008_DIR
## |-- obesity_annotations_test.xml
## |-- obesity_annotations_training.xml
## |-- obesity_annotations_training2.xml
## |-- obesity_corpus_test.xml
## |-- obesity_corpus_training.xml
## |-- obesity_corpus_training2.xml
## `-- team_submissions/top_subs
## |-- prod_123_0_1_nlpoa00WJ
## |-- prod_190_0_1_nlpQF1X7H
## `-- prod_204_0_3_nlpB1l4ZH
export RESULT_DIR=/data/experiments/ots-ensemble-paper
export RESULT_FILE=${RESULT_DIR}/${TASK}/${TASK}_results.csv
## RESULT_DIR/2009_i2b2_medications
## |-- 2009_i2b2_medications_results.csv
## |-- rankedClassifiersTop.csv
## |-- etude
## | |-- voting_1_1.log
## | |-- voting_1_2.log
## | |-- voting_1_3.log
## | |-- ...
## | |-- voting_1_123.log
## | |-- ...
## | |-- voting_2_123.log
## | |-- ...
## | `-- voting_3_123.log
## `-- merged
## | |-- consolidated.xmi
## | |-- ...
## | `-- files.xmi
## `-- voting
## |-- processed.xmi
## |-- ...
## `-- files.xmi
export MERGED_OUT=${RESULT_DIR}/${TASK}/merged
export REF_DIR=${RESULT_DIR}/${TASK}/ref
export METHOD=oracle
export SYS_DIR=${RESULT_DIR}/${TASK}/${METHOD}/${SAFE_CLASSIFIERS}
mkdir -p ${SYS_DIR}
export MINVOTES=1
## Create an oracle of best possible output
${ENSEMBLE_CONDA}/bin/python3 \
${ENSEMBLE_DIR}/medspaCy/oracleEnsemble.py \
--types-dir ${ENSEMBLE_DIR}/types \
--input-dir "${MERGED_OUT}" \
--classifier-list ${CLASSIFIERS} \
--voting-unit span \
--output-dir ${SYS_DIR}
${ETUDE_CONDA}/bin/python3 ${ETUDE_DIR}/etude.py \
--reference-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--reference-input ${REF_DIR} \
--test-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--test-input ${SYS_DIR} \
--file-suffix ".xmi" \
--fuzzy-match-flags exact partial \
--metrics TP FP FN TN Recall Precision F1 \
> ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log
export EXACT_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log | cut -f 6- | head -n 1 | tr '\n' '\t'`
export PARTIAL_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log | cut -f 6- | tail -n 1 | tr '\n' '\t'`
echo "${METHOD} ${CLASSIFIERS} Exact ${EXACT_RECPRECF1}${MINVOTES} all" \
>> ${RESULT_FILE}
echo "${METHOD} ${CLASSIFIERS} Partial ${PARTIAL_RECPRECF1}${MINVOTES} all" \
>> ${RESULT_FILE}
export METHOD=decisionTemplate
export MODEL_DIR=${RESULT_DIR}/${TASK}/${METHOD}-models
export MINVOTES=1
## TODO - We don't use thresholding for decision templates yet
for MINTHRESHOLD in 0.0
do
export SYS_DIR=${RESULT_DIR}/${TASK}/${METHOD}/${MINVOTES}_${SAFE_CLASSIFIERS}
export SYS_TRAIN_DIR=${RESULT_DIR}/${TASK}/${METHOD}/${MINVOTES}_${SAFE_CLASSIFIERS}/train
export SYS_TEST_DIR=${RESULT_DIR}/${TASK}/${METHOD}/${MINVOTES}_${SAFE_CLASSIFIERS}/test
mkdir -p ${SYS_DIR}
mkdir -p ${SYS_TRAIN_DIR}
mkdir -p ${SYS_TEST_DIR}
## Train Decision Template ensemble system
${ENSEMBLE_CONDA}/bin/python3 \
${ENSEMBLE_DIR}/medspaCy/decisionTemplate.py \
--types-dir ${ENSEMBLE_DIR}/types \
--phase train \
--voting-unit span \
--input-dir "${MERGED_OUT}" \
--classifier-list ${CLASSIFIERS} \
--overlap-strategy rank \
--zero-strategy drop \
--decision-profiles-file "${MODEL_DIR}/${MINVOTES}_${SAFE_CLASSIFIERS}.pkl"
## Test Decision Template ensemble system
${ENSEMBLE_CONDA}/bin/python3 \
${ENSEMBLE_DIR}/medspaCy/decisionTemplate.py \
--types-dir ${ENSEMBLE_DIR}/types \
--phase test \
--voting-unit span \
--input-dir "${MERGED_OUT}" \
--classifier-list ${CLASSIFIERS} \
--overlap-strategy rank \
--zero-strategy drop \
--decision-profiles-file "${MODEL_DIR}/${MINVOTES}_${SAFE_CLASSIFIERS}.pkl" \
--output-dir ${SYS_DIR}
${ETUDE_CONDA}/bin/python3 ${ETUDE_DIR}/etude.py \
--reference-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--reference-input ${REF_DIR} \
--test-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--test-input ${SYS_TRAIN_DIR} \
--file-suffix ".xmi" \
--fuzzy-match-flags exact partial \
--metrics TP FP FN TN Recall Precision F1 \
> ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_train.log
export EXACT_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_train.log | cut -f 6- | head -n 1 | tr '\n' '\t'`
export PARTIAL_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_train.log | cut -f 6- | tail -n 1 | tr '\n' '\t'`
echo "${METHOD} ${CLASSIFIERS} Exact ${EXACT_RECPRECF1}${MINVOTES} trn" \
>> ${RESULT_FILE}
echo "${METHOD} ${CLASSIFIERS} Partial ${PARTIAL_RECPRECF1}${MINVOTES} trn" \
>> ${RESULT_FILE}
${ETUDE_CONDA}/bin/python3 ${ETUDE_DIR}/etude.py \
--reference-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--reference-input ${REF_DIR} \
--test-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--test-input ${SYS_TEST_DIR} \
--file-suffix ".xmi" \
--fuzzy-match-flags exact partial \
--metrics TP FP FN TN Recall Precision F1 \
> ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_test.log
export EXACT_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_test.log | cut -f 6- | head -n 1 | tr '\n' '\t'`
export PARTIAL_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}_test.log | cut -f 6- | tail -n 1 | tr '\n' '\t'`
echo "${METHOD} ${CLASSIFIERS} Exact ${EXACT_RECPRECF1}${MINVOTES} tst" \
>> ${RESULT_FILE}
echo "${METHOD} ${CLASSIFIERS} Partial ${PARTIAL_RECPRECF1}${MINVOTES} tst" \
>> ${RESULT_FILE}
done
export METHOD=voting
for MINVOTES in $(seq 1 ${MAXVOTES})
do
export SYS_DIR=${RESULT_DIR}/${TASK}/${METHOD}/${MINVOTES}_${SAFE_CLASSIFIERS}
mkdir -p ${SYS_DIR}
## Simple voting ensemble system
${ENSEMBLE_CONDA}/bin/python3 \
${ENSEMBLE_DIR}/medspaCy/votingEnsemble.py \
--types-dir ${ENSEMBLE_DIR}/types \
--input-dir "${MERGED_OUT}" \
--voting-unit span \
--classifier-list ${CLASSIFIERS} \
--min-votes ${MINVOTES} \
--overlap-strategy rank \
--rank-file ${RESULT_DIR}/${TASK}/rankedClassifiersTop-voting.csv \
--zero-strategy drop \
--output-dir ${SYS_DIR}
${ETUDE_CONDA}/bin/python3 ${ETUDE_DIR}/etude.py \
--reference-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--reference-input ${REF_DIR} \
--test-conf ${CONFIG_DIR}/uima/ensemble_note-nlp_xmi.conf \
--test-input ${SYS_DIR} \
--file-suffix ".xmi" \
--fuzzy-match-flags exact partial \
--metrics TP FP FN TN Recall Precision F1 \
> ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log
export EXACT_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log | cut -f 6- | head -n 1 | tr '\n' '\t'`
export PARTIAL_RECPRECF1=`grep micro ${RESULT_DIR}/${TASK}/etude/${METHOD}_${MINVOTES}_${SAFE_CLASSIFIERS}.log | cut -f 6- | tail -n 1 | tr '\n' '\t'`
echo "${METHOD} ${CLASSIFIERS} Exact ${EXACT_RECPRECF1}${MINVOTES} all" \
>> ${RESULT_FILE}
echo "${METHOD} ${CLASSIFIERS} Partial ${PARTIAL_RECPRECF1}${MINVOTES} all" \
>> ${RESULT_FILE}
done