From dff50a244255d3409e17113201426c1c9b241346 Mon Sep 17 00:00:00 2001
From: Peter Mikhael <pgmikhael@gmail.com>
Date: Thu, 15 Dec 2022 18:48:01 -0500
Subject: [PATCH 1/4] Update README.md

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 17b5f3b..84148cf 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,10 @@ python train.py
 
 See our [documentation](docs/readme.md) for a full description of Sybil's training parameters.
 
+## LDCT Orientation
+
+The model expects the input to be an Axial LDCT, where the first frame is of the abdominal region and the last frame is along the clavicles.
+
 ## Cite
 
 Coming soon.

From e23600e31046bfc4765aaab4db59a4676c9efd83 Mon Sep 17 00:00:00 2001
From: Peter Mikhael <pgmikhael@gmail.com>
Date: Thu, 15 Dec 2022 18:50:17 -0500
Subject: [PATCH 2/4] add note about input structure

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 84148cf..718425e 100644
--- a/README.md
+++ b/README.md
@@ -41,6 +41,8 @@ See our [documentation](docs/readme.md) for a full description of Sybil's traini
 
 The model expects the input to be an Axial LDCT, where the first frame is of the abdominal region and the last frame is along the clavicles.
 
+When the input is of the `dicom` type, the frames will be automatically sorted. However, for `png` inputs, the path of the PNG files must be in the right anatomical order. 
+
 ## Cite
 
 Coming soon.

From 01e74a0a5bd608f890e6b4307b55878ee1188ce6 Mon Sep 17 00:00:00 2001
From: Peter Mikhael <pgmikhael@gmail.com>
Date: Thu, 15 Dec 2022 21:20:26 -0500
Subject: [PATCH 3/4] Update requirements.txt

---
 docs/requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 6f4a608..f4db71e 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -9,7 +9,7 @@ torch==1.10.1+cu113
 torchvision==0.11.2+cu113
 pytorch_lightning==1.5.6
 # math
-sklearn==1.0.1
+sklearn==1.0.2
 # utils
 tqdm
 lifelines==0.26.4
@@ -21,4 +21,4 @@ pydicom==2.2.2
 #comet-ml
 torchio=='0.18.74'
 # downloading snapshots
-gdown==4.5.1
+gdown==4.6.0

From 92d071bd20dc3abf31f40e6b4a23e7a762c623ad Mon Sep 17 00:00:00 2001
From: Peter Mikhael <pgmikhael@gmail.com>
Date: Thu, 26 Jan 2023 15:28:48 -0500
Subject: [PATCH 4/4] add citation

---
 README.md | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 718425e..75e5784 100644
--- a/README.md
+++ b/README.md
@@ -45,5 +45,13 @@ When the input is of the `dicom` type, the frames will be automatically sorted.
 
 ## Cite
 
-Coming soon.
-
+```
+@article{mikhael2023sybil,
+  title={Sybil: a validated deep learning model to predict future lung cancer risk from a single low-dose chest computed tomography},
+  author={Mikhael, Peter G and Wohlwend, Jeremy and Yala, Adam and Karstens, Ludvig and Xiang, Justin and Takigami, Angelo K and Bourgouin, Patrick P and Chan, PuiYee and Mrah, Sofiane and Amayri, Wael and Juan, Yu-Hsiang and Yang, Cheng-Ta and Wan, Yung-Liang and Lin, Gigin and Sequist, Lecia V and Fintelmann, Florian J. and Barzilay, Regina},
+  journal={Journal of Clinical Oncology},
+  pages={JCO--22},
+  year={2023},
+  publisher={Wolters Kluwer Health}
+}
+```