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add support for scipy distances #81

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merged 3 commits into from
Feb 21, 2025
Merged

add support for scipy distances #81

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3fa30df
fix(map): allow changing null dists caching directory
alxndrkalinin Feb 12, 2025
5d6dca9
feat(compute): add support for scipy distances
alxndrkalinin Feb 18, 2025
ac26353
chore: ruff format
alxndrkalinin Feb 18, 2025
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61 changes: 34 additions & 27 deletions examples/null_size.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,9 @@
"\n",
"## Effect of null size on mAP p-value calculation\n",
"\n",
"Let's calculate mAP significance on the given dataset using `null_size` values from $10$ to $5*10^6$ and plot results below."
"Let's calculate mAP significance on the given dataset using `null_size` values from $10$ to $5*10^6$ and plot results below.\n",
"\n",
"We'll also change the location of cached null distributions from user home to a local subdiretory."
]
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Expand All @@ -183,7 +185,7 @@
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Expand All @@ -197,7 +199,7 @@
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Expand All @@ -211,7 +213,7 @@
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Expand All @@ -225,7 +227,7 @@
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Expand All @@ -239,7 +241,7 @@
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Expand All @@ -253,7 +255,7 @@
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Expand All @@ -267,7 +269,7 @@
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Expand All @@ -281,7 +283,7 @@
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Expand All @@ -295,7 +297,7 @@
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Expand All @@ -309,7 +311,7 @@
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Expand All @@ -323,7 +325,7 @@
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Expand All @@ -337,7 +339,7 @@
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Expand All @@ -351,7 +353,7 @@
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Expand All @@ -365,7 +367,7 @@
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Expand All @@ -379,7 +381,7 @@
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Expand All @@ -393,7 +395,7 @@
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Expand All @@ -407,7 +409,7 @@
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Expand All @@ -421,7 +423,7 @@
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Expand All @@ -435,7 +437,7 @@
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Expand All @@ -449,7 +451,7 @@
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Expand All @@ -463,7 +465,7 @@
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Expand All @@ -477,7 +479,7 @@
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Expand All @@ -491,7 +493,7 @@
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Expand All @@ -505,7 +507,7 @@
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Expand All @@ -528,6 +530,9 @@
}
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"source": [
"seed = 0\n",
"null_cache_dir = \"cache\" # default is Path.home() / \".copairs\"\n",
"\n",
"activity_maps = []\n",
"for ns_pow in range(1, 7):\n",
" null_size = 10**ns_pow\n",
Expand All @@ -537,7 +542,8 @@
" [\"Metadata_broad_sample\"],\n",
" null_size=null_size,\n",
" threshold=0.05,\n",
" seed=0,\n",
" seed=seed,\n",
" cache_dir=null_cache_dir,\n",
" )\n",
" replicate_map[\"null_size\"] = null_size\n",
" activity_maps.append(replicate_map)\n",
Expand All @@ -547,7 +553,8 @@
" [\"Metadata_broad_sample\"],\n",
" null_size=5 * null_size,\n",
" threshold=0.05,\n",
" seed=0,\n",
" seed=seed,\n",
" cache_dir=null_cache_dir,\n",
" )\n",
" replicate_map[\"null_size\"] = 5 * null_size\n",
" activity_maps.append(replicate_map)\n",
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