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bug: ahref update (#4449)

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* bug: ahref update

* fix: linter

* fix: typo fix
This commit is contained in:
Damodar Panigrahi
2026-02-25 13:46:19 +00:00
committed by GitHub
parent 0417d8b9c4
commit b468809df7
2 changed files with 8 additions and 9 deletions
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notebooks/community/alphagenome/cloudai_alphagenome_finetune.ipynb
+2 -1
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@@ -50,7 +50,8 @@
"source": [
"# AlphaGenome Finetuning Tutorial using Google Cloud Platform\n",
"\n",
"This notebook demonstrates how to finetune an AlphaGenome model on custom genomic tracks.\n",
"This notebook demonstrates how to finetune an AlphaGenome model on custom genomic tracks. This notebook adds the Google Cloud Platform utilities to the Google DeepMind's \n",
"<a href=\"https://github.com/google-deepmind/alphagenome_research/blob/main/colabs/finetune.ipynb\">AlphaGenome Finetuning Tutorial</a>.\n",
"\n",
"**What you'll learn:**\n",
"\n",
notebooks/community/alphagenome/cloudai_alphagenome_vai_quickstart.ipynb
+6 -8
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@@ -37,7 +37,7 @@
" </a>\n",
" </td>\n",
" <td style=\"text-align: center\">\n",
" <a href=\"https://console.cloud.google.com/vertex-ai/colab/import/https:%2F%2Fraw.githubusercontent.com%2FGoogleCloudPlatform%2Fvertex-ai-samples%2Fmain%2Fnotebooks%2Fcommunity%2alphagenome%2Fcloudai_alphagenome_vai_quickstart.ipynb\">\n",
" <a href=\"https://console.cloud.google.com/vertex-ai/colab/import/https:%2F%2Fraw.githubusercontent.com%2FGoogleCloudPlatform%2Fvertex-ai-samples%2Fmain%2Fnotebooks%2Fcommunity%2Falphagenome%2Fcloudai_alphagenome_vai_quickstart.ipynb\">\n",
" <img width=\"32px\" src=\"https://lh3.googleusercontent.com/JmcxdQi-qOpctIvWKgPtrzZdJJK-J3sWE1RsfjZNwshCFgE_9fULcNpuXYTilIR2hjwN\" alt=\"Google Cloud Colab Enterprise logo\"><br> Open in Colab Enterprise\n",
" </a>\n",
" </td>\n",
@@ -4458,14 +4458,14 @@
"outputs": [],
"source": [
"def extract_k562(adata):\n",
" values = adata.X[:, adata.var['ontology_curie'] == 'EFO:0002067']\n",
" assert values.size == 1\n",
" return values.flatten()[0]\n",
" values = adata.X[:, adata.var[\"ontology_curie\"] == \"EFO:0002067\"]\n",
" assert values.size == 1\n",
" return values.flatten()[0]\n",
"\n",
"\n",
"ism_result = ism.ism_matrix(\n",
" [extract_k562(x[0]) for x in variant_scores],\n",
" variants=[v[0].uns['variant'] for v in variant_scores],\n",
" variants=[v[0].uns[\"variant\"] for v in variant_scores],\n",
")"
]
},
@@ -4637,9 +4637,7 @@
}
],
"source": [
"interval = Interval(\n",
" chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\"\n",
")\n",
"interval = Interval(chromosome=\"chr19\", start=2**20, end=2**20 + 2**20, strand=\".\")\n",
"\n",
"scores = dna_model.score_interval(\n",
" interval,\n",