From b34dd314653116b8dc866e1cd27efdefd02c97fa Mon Sep 17 00:00:00 2001
From: jannisborn <jab@zurich.ibm.com>
Date: Mon, 16 Oct 2023 09:21:14 +0200
Subject: [PATCH 1/2] updating README and docs [skip ci]

---
 README.md                                                  | 2 +-
 .../regression_transformer/implementation.py               | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 2a381cb0c..6cc548715 100644
--- a/README.md
+++ b/README.md
@@ -44,7 +44,7 @@ conda activate gt4sd
 pip install gt4sd
 ```
 
-**NOTE 1:** By default `gt4sd` is installed with CPU requirements. For GPU usage replace `conda env create -f conda_gpu.yml` with:
+**NOTE 1:** By default `gt4sd` is installed with CPU requirements. For GPU usage replace `conda env create -f conda.yml` with:
 ```sh
 conda env create -f conda_gpu.yml
 ```
diff --git a/src/gt4sd/training_pipelines/regression_transformer/implementation.py b/src/gt4sd/training_pipelines/regression_transformer/implementation.py
index c8df06e15..42efac702 100644
--- a/src/gt4sd/training_pipelines/regression_transformer/implementation.py
+++ b/src/gt4sd/training_pipelines/regression_transformer/implementation.py
@@ -68,9 +68,9 @@ def train(  # type: ignore
     ) -> None:
         """Generic training function for training a Regression Transformer (RT) model.
            For details see:
-            Born, J., & Manica, M. (2022). Regression Transformer: Concurrent Conditional
-            Generation and Regression by Blending Numerical and Textual Tokens.
-            `ICLR Workshop on Machine Learning for Drug Discovery`.
+            Born, J., & Manica, M. (2023). Regression Transformer enables concurrent sequence
+            regression and generation for molecular language modelling.
+            `Nature Machine Intelligence`, 5(4), 432-444.
 
         Args:
             training_args: training arguments passed to the configuration.
@@ -78,7 +78,6 @@ def train(  # type: ignore
             dataset_args: dataset arguments passed to the configuration.
         """
         try:
-
             params = {**training_args, **dataset_args, **model_args}
             # Setup logging
             logging.basicConfig(

From 866b12ef9929ad7e353c87efd519b802a0aff6cf Mon Sep 17 00:00:00 2001
From: jannisborn <jab@zurich.ibm.com>
Date: Wed, 3 Jul 2024 20:51:05 +0100
Subject: [PATCH 2/2] fix: upgrade protobuf (required for Binder)

---
 notebooks/discovery-demo.ipynb | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/notebooks/discovery-demo.ipynb b/notebooks/discovery-demo.ipynb
index 3453b832f..0677e9d3b 100644
--- a/notebooks/discovery-demo.ipynb
+++ b/notebooks/discovery-demo.ipynb
@@ -16,6 +16,16 @@
    "id": "d6a65c61",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "!pip install --upgrade protobuf"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "94cd4c8c",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from typing import List\n",
     "from rdkit import Chem\n",
@@ -2325,7 +2335,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },