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Repository has been restructured with new reproducibility folder.
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@paulfogeladvestis
paulfogeladvestis committed Aug 2, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -10,7 +10,7 @@ ILSM is Integrated Latent Multi Source Model.

# Reference

https://www.preprints.org/manuscript/202402.1001/v3
https://doi.org/10.36922/aih.3427

# Usage

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19 changes: 12 additions & 7 deletions examples/abis_all.ipynb → examples/reproducibily/abis_all.ipynb
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"cells": [
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.13\n"
]
}
],
"source": [
"from adnmtf import NMF, NTF\n",
"# from sklearn.decomposition import NMF\n",
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"# from umap import umap_\n",
"from scipy.spatial import distance_matrix\n",
"import hoggorm as ho\n",
"import tensorly as tl\n",
"from tensorly.decomposition import non_negative_parafac_hals\n",
"\n",
"from sklearn.metrics.cluster import adjusted_rand_score\n",
"from sklearn.metrics.cluster import normalized_mutual_info_score\n",
"from sklearn.preprocessing import StandardScaler\n",
Expand All @@ -48,8 +53,8 @@
"\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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6 changes: 3 additions & 3 deletions examples/abis_gfa.ipynb → examples/reproducibily/abis_gfa.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"from gfa import gfa_experiments\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'\n"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'\n"
]
},
{
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6 changes: 3 additions & 3 deletions examples/abis_gfa_screeplot.ipynb → ...es/reproducibily/abis_gfa_screeplot.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"\n",
"from gfa import gfa_experiments\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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6 changes: 3 additions & 3 deletions examples/abis_ism.ipynb → examples/reproducibily/abis_ism.ipynb
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Expand Up @@ -31,7 +31,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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6 changes: 3 additions & 3 deletions examples/abis_mofa.ipynb → examples/reproducibily/abis_mofa.ipynb
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Expand Up @@ -18,7 +18,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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6 changes: 3 additions & 3 deletions examples/abis_mofa_screeplot.ipynb → ...s/reproducibily/abis_mofa_screeplot.ipynb
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"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"from scipy.stats import trim_mean\n",
"\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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8 changes: 4 additions & 4 deletions examples/abis_mvmds_screeplot.ipynb → .../reproducibily/abis_mvmds_screeplot.ipynb
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Expand Up @@ -2,14 +2,14 @@
"cells": [
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"from sklearn.preprocessing import StandardScaler\n",
"from sklearn.metrics.cluster import rand_score\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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0 examples/getting_started_mofa.ipynb → .../reproducibily/getting_started_mofa.ipynb
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0 examples/gfa.py → examples/reproducibily/gfa.py
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0 examples/ism_utils.py → examples/reproducibily/ism_utils.py
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0 examples/mofa_template_script_matrix.py → ...roducibily/mofa_template_script_matrix.py
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10 changes: 5 additions & 5 deletions examples/mowgli_ilsm.ipynb → examples/reproducibily/mowgli_ilsm.ipynb
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Expand Up @@ -263,14 +263,14 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
},
{
Expand All @@ -279,7 +279,7 @@
"True"
]
},
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
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"from mofapy2.run.entry_point import entry_point\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'\n",
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'\n",
"\n",
"torch.cuda.is_available()"
]
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6 changes: 3 additions & 3 deletions examples/prokaryotic_ilsm.ipynb → ...ples/reproducibily/prokaryotic_ilsm.ipynb
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Expand Up @@ -59,7 +59,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
},
{
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"from mofapy2.run.entry_point import entry_point\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'\n",
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'\n",
"\n",
"torch.cuda.is_available()"
]
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6 changes: 3 additions & 3 deletions examples/reuters_ilsm.ipynb → examples/reproducibily/reuters_ilsm.ipynb
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Expand Up @@ -49,7 +49,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
},
{
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"from mofapy2.run.entry_point import entry_point\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'\n",
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'\n",
"\n",
"torch.cuda.is_available()"
]
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6 changes: 3 additions & 3 deletions examples/uci_digits_all.ipynb → examples/reproducibily/uci_digits_all.ipynb
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Expand Up @@ -9,7 +9,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.11\n"
"adilsm version=0.0.13\n"
]
}
],
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"\n",
"from gfa import gfa_experiments\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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8 changes: 4 additions & 4 deletions examples/uci_digits_gfa.ipynb → examples/reproducibily/uci_digits_gfa.ipynb
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Expand Up @@ -2,14 +2,14 @@
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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"from gfa import gfa_experiments\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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2 changes: 1 addition & 1 deletion examples/uci_digits_gfa_screeplot.ipynb → ...roducibily/uci_digits_gfa_screeplot.ipynb
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Expand Up @@ -9,7 +9,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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16 changes: 12 additions & 4 deletions examples/uci_digits_ism.ipynb → examples/reproducibily/uci_digits_ism.ipynb
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Expand Up @@ -25,9 +25,17 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 1,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.13\n"
]
}
],
"source": [
"import pandas as pd\n",
"import numpy as np\n",
Expand All @@ -51,8 +59,8 @@
"import adilsm.adilsm as ilsm\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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6 changes: 3 additions & 3 deletions examples/uci_digits_mofa.ipynb → examples/reproducibily/uci_digits_mofa.ipynb
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Expand Up @@ -9,7 +9,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
Expand Down Expand Up @@ -53,8 +53,8 @@
"\n",
"from ism_utils import specificity_score, specificity_plot\n",
"\n",
"RESULTS_PATH = './results/'\n",
"DATA_PATH = './data/'"
"RESULTS_PATH = '../results/'\n",
"DATA_PATH = '../data/'"
]
},
{
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2 changes: 1 addition & 1 deletion examples/uci_digits_mofa_screeplot.ipynb → ...oducibily/uci_digits_mofa_screeplot.ipynb
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Expand Up @@ -9,7 +9,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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2 changes: 1 addition & 1 deletion examples/uci_digits_mvmds_screeplot.ipynb → ...ducibily/uci_digits_mvmds_screeplot.ipynb
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Expand Up @@ -9,7 +9,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"adilsm version=0.0.12\n"
"adilsm version=0.0.13\n"
]
}
],
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