update notebook readme

notebooks_tutorials/06_NTv3_generative_training.ipynb

@@ -7,9 +7,9 @@
         "id": "15bb8c23"
       },
       "source": [
-        "# 🧬 NTv3-Generative: Training Tutorial\n",
+        "# 🧬 Training a discrete diffusion model on biological sequences\n",
         "\n",
-        "This notebook demonstrates how to **fine-tune NTv3** for controllable enhancer sequence generation using **Masked Diffusion Language Modeling (MDLM)**.\n",
+        "This notebook demonstrates how to **fine-tune NTv3** for controllable enhancer sequence generation using **Masked Diffusion Language Modeling (MDLM)** ([paper](https://arxiv.org/pdf/2406.07524)).\n",
         "\n",
         "---\n",
         "\n",

notebooks_tutorials/07_enhancer_generation.ipynb

@@ -6,15 +6,15 @@
         "id": "E06SHsd4Zf82"
       },
       "source": [
-        "# 🧬 NTv3-Generative: Controllable Enhancer Sequence Generation\n",
+        "# 🧬 Controllable Enhancer Sequence Generation\n",
         "\n",
-        "This notebook demonstrates how to use **NTv3-Generative**, a diffusion-based model for generating *de novo* enhancer sequences with controllable activity levels.\n",
+        "This notebook demonstrates how to use **NTv3** as a diffusion-based model for generating *de novo* enhancer sequences with controllable activity levels.\n",
         "\n",
         "> 📝 **Note for Google Colab users:** This notebook is compatible with Colab! For faster generation, enable GPU: Runtime → Change runtime type → GPU (T4 or better recommended). \n",
         "\n",
         "## 📋 Overview\n",
         "\n",
-        "NTv3-Generative uses **Masked Diffusion Language Modeling (MDLM)** to generate enhancer sequences conditioned on:\n",
+        "NTv uses **Masked Diffusion Language Modeling (MDLM)** to generate enhancer sequences conditioned on:\n",
         "- **Promoter context** (DSCP or RpS12 backbone)\n",
         "- **Activity level** (bins 0-4, from lowest to highest)\n",
         "\n",
@@ -223,7 +223,7 @@
       },
       "outputs": [],
       "source": [
-        "# Load NTv3-Generative model from HuggingFace\n",
+        "# Load NTv3 generative model from HuggingFace\n",
         "repo_id = \"InstaDeepAI/NTv3_generative\"\n",
         "\n",
         "tokenizer = AutoTokenizer.from_pretrained(repo_id, trust_remote_code=True)\n",

tabs/home.html

@@ -88,7 +88,7 @@
         <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/03_fine_tuning_posttrained_model_biwig.ipynb" target="_blank" rel="noopener noreferrer">🎯 03 — Fine-tune a post-trained model on bigwig tracks</a></li>
         <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/04_fine_tuning_pretrained_model_annotation.ipynb" target="_blank" rel="noopener noreferrer">🏷️ 04 — Fine-tune a pre-trained model on annotations</a></li>
         <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/05_model_interpretation.ipynb" target="_blank" rel="noopener noreferrer">🔍 05 — Model interpretation</a></li>
-        <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/06_NTv3_generative_training.ipynb" target="_blank" rel="noopener noreferrer">🧪 06 — Training NTv3-generative</a></li>
+        <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/06_NTv3_generative_training.ipynb" target="_blank" rel="noopener noreferrer">🧪 06 — Fine-tuning NTv3 into a diffusion model</a></li>
         <li><a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/07_enhancer_generation.ipynb" target="_blank" rel="noopener noreferrer">🪰 07 — Generating enhancer sequences</a></li>
       </ul>
     </div>