Update in-notebook documentation

bioinfodlsu · Nov 28, 2024 · 773a4e9 · 773a4e9
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diff --git a/experiments/3.6. Data Consolidation (ProstT5 - 3Di Tokens).ipynb b/experiments/3.6. Data Consolidation (ProstT5 - 3Di Tokens).ipynb
@@ -45,7 +45,7 @@
     "1. Feed the 3Di tokens to ProstT5 in order to generate the embeddings, following the instructions [here](https://github.com/mheinzinger/ProstT5/tree/main/scripts). \n",
     "1. Consolidate the embeddings into a single HDF5 file named `rbp_prostt5_3di_embeddings.h5`. \n",
     "1. Create a folder named `inphared` inside `data`. <br>\n",
-    "   Create a folder named `structure`, this time inside `data/inphared`, and save `rbp_prostt5_embeddings.h5` inside `data/inphared/structure`.\n",
+    "   Create a folder named `structure`, this time inside `data/inphared`, and save `rbp_prostt5_3di_embeddings.h5` inside `data/inphared/structure`.\n",
     "1. Download `consolidated.tar.gz` from this [link](https://drive.google.com/file/d/1yQSXwlb37dm2ZLXGJHdIM5vmrzwPAwvI/view?usp=sharing), and unzip it. This should result in a folder named `consolidated`. <br> Technically, this notebook only needs `consolidated/rbp.csv`.\n",
     "1. Create a folder named `inphared` inside `data`, and save the extracted `consolidated` folder inside `data/inphared`. \n",
     "   \n",
@@ -1394,7 +1394,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

diff --git a/experiments/5.12. Benchmarking - Classifier Building & Evaluation (SVM).ipynb b/experiments/5.12. Benchmarking - Classifier Building & Evaluation (SVM).ipynb
@@ -58,7 +58,7 @@
     "&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; ↳ `complete-struct-80.fasta.clstr` <br>\n",
     "&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; ↳ `complete-struct-40.fasta.clstr` <br>\n",
     "&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp; ↳ `complete-struct-60.fasta.clstr` <br>\n",
-    "↳ `5.0. Classifier Building & Evaluation (SaProt).ipynb` (this notebook) <br>"
+    "↳ `5.12. Classifier Building & Evaluation (SVM).ipynb` (this notebook) <br>"
    ]
   },
   {