Cleanup run scripts (#10)

* Add run scripts

* Remove wandb flag in run_scripts

* Add missing python command

* Remove SLURM

* Fix array name

* Fix wrong embeddings in clustering

README.md

@@ -86,5 +86,7 @@ For example if you used micromamba for installation:
 ```bash
 micromamba run -n klinker-conda python experiment.py movie-graph-benchmark-dataset --graph-pair "tmdb-tvdb" relational-token-blocker
 ```
-
 This would be similar to the steps described in the above usage section.
+
+In order to precisely reproduce the results from the paper we provide (adapted) run scripts from our SLURM batch scripts in the `run_scripts` folder.
+We recommend to `git checkout paper` to checkout out the tagged commit on which the experiments were run since future development does not aim to be backwards compatible with this state.

run_scripts/non_relational/run_deepblocker_autoencoder.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+small_nneighbors=500
+large_nneighbors=1000
+iebsize="512"
+hidden_dim="196"
+learning_rate="0.004542"
+
+myargs=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 deepblocker"
+)
+
+nnargs=()
+for base in "${myargs[@]}"
+do
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base --n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base --n-neighbors $large_nneighbors --block-builder-kwargs faisshnsw")
+	fi
+done
+
+sifembeddings="fasttext"
+embeddings="gtr-t5-base"
+multi_embeddings="LaBSE"
+st_other_args="--encoder autoencoder --inner-encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize --batch-size 512 --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True"
+args=()
+for base in "${nnargs[@]}"
+do
+	if [[ $base =~ .*D_Y.* ]] || [[ $base =~ .*D_W.* ]]
+	then
+		args+=("$base $st_other_args --embeddings $embeddings")
+	else
+		args+=("$base $st_other_args --embeddings $multi_embeddings")
+	fi
+done
+sif_other_args="--encoder autoencoder --inner-encoder sifembeddingtokenized --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True"
+for base in "${nnargs[@]}"
+do
+	args+=("$base $other_args --embeddings $sifembeddings")
+done
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param

run_scripts/non_relational/run_deepblocker_ctt.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+small_nneighbors=500
+large_nneighbors=1000
+iebsize="512"
+hidden_dim="384"
+learning_rate="0.0030405"
+max_perturbation="0.408395"
+pos_to_neg_ratio="1.55515"
+synth_tuples_per_tuple="5"
+
+myargs=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 deepblocker"
+)
+
+nnargs=()
+for base in "${myargs[@]}"
+do
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base --n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base --n-neighbors $large_nneighbors --block-builder-kwargs faisshnsw")
+	fi
+done
+
+embeddings="gtr-t5-base"
+multi_embeddings="LaBSE"
+st_other_args="--encoder crosstupletraining --inner-encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize --batch-size 512 --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True --max-perturbation=$max_perturbation --pos-to-neg-ratio=$pos_to_neg_ratio --synth-tuples-per-tuple=$synth_tuples_per_tuple --block-builder-kwargs faisshnsw"
+args=()
+for base in "${nnargs[@]}"
+do
+	if [[ $base =~ .*D_Y.* ]] || [[ $base =~ .*D_W.* ]]
+	then
+		args+=("$base $st_other_args --embeddings $embeddings")
+	else
+		args+=("$base $st_other_args --embeddings $multi_embeddings")
+	fi
+done
+
+sifembeddings="fasttext"
+sif_other_args="--encoder crosstupletraining --inner-encoder sifembeddingtokenized --batch-size 512 --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True --max-perturbation=$max_perturbation --pos-to-neg-ratio=$pos_to_neg_ratio --synth-tuples-per-tuple=$synth_tuples_per_tuple"
+for base in "${nnargs[@]}"
+do
+	args+=("$base $other_args --embeddings $sifembeddings")
+done
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param

run_scripts/non_relational/run_deepblocker_hyb.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+small_nneighbors=500
+large_nneighbors=1000
+iebsize="512"
+# hidden_dim="384"
+reduce_dim_to="192"
+reduce_sample_perc=0.3
+hidden_dim="96"
+learning_rate="0.0030405"
+max_perturbation="0.408395"
+pos_to_neg_ratio="1.55515"
+synth_tuples_per_tuple="5"
+
+myargs=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 deepblocker"
+)
+
+nnargs=()
+for base in "${myargs[@]}"
+do
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base --n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base --n-neighbors $large_nneighbors --block-builder-kwargs faisshnsw")
+	fi
+done
+
+sifembeddings="fasttext"
+embeddings="gtr-t5-base"
+multi_embeddings="LaBSE"
+other_args="--encoder hybrid --batch-size 512 --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True --max-perturbation=$max_perturbation --pos-to-neg-ratio=$pos_to_neg_ratio --synth-tuples-per-tuple=$synth_tuples_per_tuple"
+args=()
+for base in "${nnargs[@]}"
+do
+	if [[ $base =~ .*D_Y.* ]] || [[ $base =~ .*D_W.* ]]
+	then
+		args+=("$base $other_args --embeddings $embeddings --inner-encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize")
+	else
+		args+=("$base $other_args --embeddings $multi_embeddings --inner-encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize")
+	fi
+	# args+=("$base $other_args --inner-encoder sifembeddingtokenized --embeddings $sifembeddings")
+done
+for base in "${nnargs[@]}"
+do
+	args+=("$base $other_args --inner-encoder sifembeddingtokenized --embeddings $sifembeddings")
+done
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param

run_scripts/non_relational/run_only_embeddings.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+small_nneighbors=500
+large_nneighbors=1000
+myargs=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 only-embeddings-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 only-embeddings-blocker"
+)
+
+nnargs=()
+for base in "${myargs[@]}"
+do
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base --n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base --n-neighbors $large_nneighbors --block-builder-kwargs faisshnsw")
+	fi
+done
+
+sifembeddings="fasttext"
+embeddings="gtr-t5-base"
+multi_embeddings="LaBSE"
+args=()
+for base in "${nnargs[@]}"
+do
+	if [[ $base =~ .*D_Y.* ]] || [[ $base =~ .*D_W.* ]]
+	then
+		args+=("$base --embeddings $embeddings --encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize")
+	else
+		args+=("$base --embeddings $multi_embeddings --encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize")
+	fi
+done
+for base in "${nnargs[@]}"
+do
+	args+=("$base --encoder sifembeddingtokenized --embeddings $sifembeddings")
+done
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param

run_scripts/non_relational/run_token.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+args=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 token-blocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 token-blocker"
+)
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param

run_scripts/relational/run_deepblocker_autoencoder.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+small_nneighbors=250
+large_nneighbors=500
+iebsize="512"
+hidden_dim="196"
+learning_rate="0.004542"
+
+myargs=(
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 15K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 15K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 15K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 15K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_W --size 100K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair D_Y --size 100K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_DE --size 100K --version V2 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V1 relational-deepblocker"
+ "--random-seed 42 open-ea-dataset --graph-pair EN_FR --size 100K --version V2 relational-deepblocker"
+)
+
+other_args="--encoder autoencoder --batch-size 512 --hidden-dimension $hidden_dim --learning-rate $learning_rate --force True"
+args=()
+st_args="--inner-encoder sentencetransformertokenized --inner-encoder-batch-size $iebsize"
+embeddings="gtr-t5-base"
+multi_embeddings="LaBSE"
+for base in "${myargs[@]}"
+do
+	if [[ $base =~ .*D_Y.* ]] || [[ $base =~ .*D_W.* ]]
+	then
+		args+=("$base $other_args $st_other_args --embeddings $embeddings")
+	else
+		args+=("$base $other_args $st_other_args --embeddings $multi_embeddings")
+	fi
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base --n-neighbors $small_nneighbors --rel-n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base --n-neighbors $large_nneighbors --rel-n-neighbors $large_nneighbors --block-builder-kwargs faisshnsw --reduce-dim-to $reduce_dim_to --reduce-sample-perc $reduce_sample_perc")
+	fi
+done
+sif_other_args="--inner-encoder sifembeddingtokenized"
+for base in "${nnargs[@]}"
+do
+	if [[ $base =~ .*15K.* ]]
+	then
+		nnargs+=("$base $other_args $sif_other_args --embeddings fasttext --n-neighbors $small_nneighbors --rel-n-neighbors $small_nneighbors")
+	else
+		nnargs+=("$base $other_args $sif_other_args --embeddings 100wiki.en.bin --n-neighbors $small_nneighbors --rel-n-neighbors $small_nneighbors --block-builder-kwargs faisshnsw")
+	fi
+done
+
+curr_param=$(echo ${args[$1]})
+echo $curr_param
+
+micromamba run -n klinker-conda -r y python experiment.py $curr_param