Created using Colab

Author: wang3702

HiCFoundation.ipynb

@@ -6,7 +6,6 @@
       "private_outputs": true,
       "provenance": [],
       "gpuType": "T4",
-      "authorship_tag": "ABX9TyOMiXRcgn3vkuYcXjQWfrZD",
       "include_colab_link": true
     },
     "kernelspec": {
@@ -164,7 +163,7 @@
         "#@markdown ## Option 1: download from database <br>\n",
         "#@markdown Instead of uploading, you can also specify the link here to automatically download maps from ENCODE and other servers.\n",
         "#@markdown Example: https://www.encodeproject.org/files/ENCFF689CUX/@@download/ENCFF689CUX.hic\n",
-        "download_link = 'https://www.encodeproject.org/files/ENCFF689CUX/@@download/ENCFF689CUX.hic' #@param {type:\"string\"}\n",
+        "download_link = '' #@param {type:\"string\"}\n",
         "output_dir=\"/content/\"\n",
         "if download_link!='':\n",
         "  root_dir = os.getcwd()\n",
@@ -276,10 +275,11 @@
         "#@markdown For \"Reproducibility analysis\", \"Loop detection\", \"Resolution enhancement\",and \"Single-cell Hi-C\" task, 224$\\times$224 is suggested input size.\n",
         "#@markdown <br> For \"Epigenomic Profiling\", the suggested input size is 128$\\times$4000.\n",
         "#@markdown <br> For \"Hi-C Embedding\", please chooce the submatrix size that you are interested. Please make sure the numbers are multiplies of 16.\n",
-        "submat_height= 224 #@param {type:\"number\"}\n",
-        "submat_width= 224 #@param {type:\"number\"}\n",
+        "\n",
+        "submat_height = 128 #@param {type:\"number\"}\n",
+        "submat_width = 4000 #@param {type:\"number\"}\n",
         "#@markdown Configure scanning stride for the input Hi-C matrix. The default should applies to most settings.\n",
-        "stride = 20 #@param {type:\"number\"}\n",
+        "stride = 32 #@param {type:\"number\"}\n",
         "#@markdown Configure scanning boundary for the input Hi-C matrix. Default 0 indicates scanning across the diagonal, should work for most tasks. You can adjust based on your need.\n",
         "scan_boundary = 0 #@param {type:\"number\"}\n",
         "#@markdown Configure the batch size for HiCFoundation inference.\n",
@@ -313,8 +313,8 @@
         "  file.write(\"%s\"%command_line)"
       ],
       "metadata": {
-        "cellView": "form",
-        "id": "ul4yLfwbQzpp"
+        "id": "ul4yLfwbQzpp",
+        "cellView": "form"
       },
       "execution_count": null,
       "outputs": []