fixed the issue related to the cmap-mode type

bash_files/.#train_foldseek_after-cmap-ot.sh

@@ -0,0 +1 @@
+kdevko01@minotaur.csail.mit.edu.3391666:1648490224

bash_files/topsyturvy_cmap-regression/results.log

@@ -0,0 +1,6 @@
+[2023-01-04-03:41:40] D-SCRIPT Version 0.2.2
+[2023-01-04-03:41:40] Called as: /net/scratch3.mit.edu/scratch3-3/kdevko01/conda/.conda/envs/main/bin/dscript train --train seqs-pairs/pairs/human_train.tsv --test seqs-pairs/pairs/human_test.tsv --embedding embeddings/human.h5 --topsy-turvy --glider-weight 0.2 --glider-thres 0.925 -o topsyturvy_cmap-regression/results.log --save-prefix topsyturvy_cmap-regression/ep_ --lr 0.0005 --lambda 0.05 --num-epoch 10 --weight-decay 0 --batch-size 25 --pool-width 9 --kernel-width 7 --dropout-p 0.2 --projection-dim 100 --hidden-dim 50 --kernel-width 7 --device 7
+[2023-01-04-03:41:40] Using CUDA device 7 - NVIDIA A100 80GB PCIe
+[2023-01-04-03:41:40] Loaded 843584 training pairs
+[2023-01-04-03:41:40] Loaded 52725 test pairs
+[2023-01-04-03:41:40] Loading embeddings...

bash_files/train_foldseek_after-cmap-ot.sh

@@ -4,17 +4,20 @@ TOPSY_TURVY=
 TRAIN=seqs-pairs/pairs/human_train.tsv
 TEST=seqs-pairs/pairs/human_test.tsv
 EMBEDDING=embeddings/human.h5
-OUTPUT_FOLDER=fseek_after_human_model_dscript_cmap_ot
+OUTPUT_FOLDER=dscript
+#fseek_after_human_model_dscript_cmap
 OUTPUT_PREFIX=results-
 FOLDSEEK_FASTA=../../foldseek_emb/r1_foldseekrep_seq.fa
 FOLDSEEK_VOCAB=../data/foldseek_vocab.json
-SAMPLER=../data/models/sampler/iter_9.sav
+SAMPLER="../data/models/sampler/sampler-run-Mon-26-Dec-2022-12:07:02-PM-EST/iter_999.sav"
 CMAP_TRAIN=../data/pairs/cmap_train_lt_400.tsv
 CMAP_TEST=../data/pairs/cmap_test_lt_400.tsv
 CMAP_LANG_EMB=../lynnfiles/new_cmap_embed
 CMAP_EMB=../data/embeddings/cmap_filtered_lt_400.h5
 CMAP_MODE=ot
-while getopts "d:t:T:e:vo:p:s:c:C:l:m:" args; do
+FOLDSEEK_CMD=
+CMAP_CMD=
+while getopts "d:t:T:e:vo:p:s:Xc:C:l:m:fF:M:" args; do
     case $args in
         d) DEVICE=${OPTARG}
         ;;
@@ -24,7 +27,7 @@ while getopts "d:t:T:e:vo:p:s:c:C:l:m:" args; do
         ;;
         e) EMBEDDING=${OPTARG}
         ;;
-        v) TOPSY_TURVY="--topsy-turvy --glider-weight 0.2 --glider-thres 0.925"; OUTPUT_FOLDER=fseek_after_human_model_topsyturvy_cmap_ot;
+        v) TOPSY_TURVY="--topsy-turvy --glider-weight 0.2 --glider-thres 0.925"; OUTPUT_FOLDER=topsyturvy; #fseek_after_human_model_topsyturvy_cmap;
         ;;
         o) OUTPUT_FOLDER=${OPTARG}
         ;;
@@ -32,6 +35,8 @@ while getopts "d:t:T:e:vo:p:s:c:C:l:m:" args; do
         ;;
         s) SAMPLER=${OPTARG}
         ;;
+        X) CMAP_CMD="--run-cmap"
+        ;;
         c) CMAP_TRAIN=${OPTARG}
         ;;
         C) CMAP_TEST=${OPTARG}
@@ -40,9 +45,28 @@ while getopts "d:t:T:e:vo:p:s:c:C:l:m:" args; do
         ;;
         m) CMAP_EMB=${OPTARG}
         ;;
+        M) CMAP_MODE=${OPTARG}
+        ;;
+        f) FOLDSEEK_CMD="--allow_foldseek" 
+        ;;
+        F) FOLDSEEK_FASTA=${OPTARG}
+        ;;
     esac
 done
-    
+
+# Setup the foldseek command
+if [ ! -z ${FOLDSEEK_CMD} ]; then FOLDSEEK_CMD="${FOLDSEEK_CMD} --foldseek_fasta ${FOLDSEEK_FASTA} --foldseek_vocab ${FOLDSEEK_VOCAB} --add_foldseek_after_projection"; OUTPUT_FOLDER="${OUTPUT_FOLDER}_fseek-after" ;fi
+
+
+# Setup the cmap command
+if [ ! -z ${CMAP_CMD} ] 
+then 
+    CMAP_CMD="${CMAP_CMD} --contact-map-train ${CMAP_TRAIN} --contact-map-test ${CMAP_TEST} --contact-map-mode ${CMAP_MODE} --contact-map-embedding ${CMAP_LANG_EMB} --contact-maps ${CMAP_EMB} --contact-map-lr 0.0001 --contact-map-lambda 0.1"
+    if [ ${CMAP_MODE} = "ot" ]; then CMAP_CMD="${CMAP_CMD} --contact-map-sampler ${SAMPLER} --ot-cmap-nsamples 100"; fi
+    OUTPUT_FOLDER="${OUTPUT_FOLDER}_cmap-${CMAP_MODE}"
+fi
+
+# Create the output folder
 if [ ! -d ${OUTPUT_FOLDER} ]; then mkdir -p $OUTPUT_FOLDER; fi
 
 #./train_foldseek_after-cmap-ot.sh -v -s ../data/models/sampler/sampler-run-Mon-26-Dec-2022-12\:07\:02-PM-EST/iter_999.sav -d 3
@@ -53,4 +77,14 @@ dscript train --train $TRAIN --test $TEST --embedding $EMBEDDING $TOPSY_TURVY \
               --lr 0.0005 --lambda 0.05 --num-epoch 10 \
               --weight-decay 0 --batch-size 25 --pool-width 9 \
               --kernel-width 7 --dropout-p 0.2 --projection-dim 100 \
-              --hidden-dim 50 --kernel-width 7 --device $DEVICE --run-cmap --contact-map-train ${CMAP_TRAIN} --contact-map-test ${CMAP_TEST} --contact-map-mode ot --contact-map-embedding ${CMAP_LANG_EMB} --contact-maps ${CMAP_EMB} --contact-map-sampler ${SAMPLER} --ot-cmap-nsamples 100 --contact-map-lr 0.0001 --contact-map-lambda 0.1 # --allow_foldseek --foldseek_fasta ${FOLDSEEK_FASTA} --foldseek_vocab ${FOLDSEEK_VOCAB} --add_foldseek_after_projection  ## need to add the foldseek part
+              --hidden-dim 50 --kernel-width 7 --device $DEVICE ${CMAP_COMMANDS} ${FOLDSEEK_CMD}
+
+# Training CMAP commands: Without FOLDSEEK
+## OT
+# Topsy turvy: ./train_foldseek_after-cmap-ot.sh -v -X -M ot  -d 3
+# D-SCRIPT: ./train_foldseek_after-cmap-ot.sh -v -X -M ot  -d 3
+
+## Regression
+# Topsy turvy: ./train_foldseek_after-cmap-ot.sh -v -X -M regression -d 3
+# D-SCRIPT: ./train_foldseek_after-cmap-ot.sh -v -X -M regression -d 3
+