Merge remote-tracking branch 'origin/master'

CITATION.cff

@@ -2,48 +2,65 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: >-
-  Simple Behavioral Analysis (SimBA): an open source toolkit
-  for computer classification of complex social behaviors in
-  experimental animals
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file
-type: software
+message: "If you use this research or software, please cite the following publication."
+title: "Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience"
 authors:
-  - given-names: Simon
-    family-names: Nilsson
-    email: [email protected]
-  - given-names: Nastacia
-    family-names: Goodwin
-  - given-names: Jia Jie
-    family-names: Choong
-  - given-names: Sophia
-    family-names: Hwang
-  - given-names: Hayden
-    family-names: Wright
-  - given-names: Zane
-    family-names: Norville
-  - given-names: Xiaoyu
-    family-names: Tong
-  - given-names: Dayu
-    family-names: Lin
-  - given-names: Brandon
-    family-names: Bentzley
-  - given-names: Neir
-    family-names: Eshel
-  - given-names: Ryan
-    family-names: McLaughlin
-  - given-names: Sam
-    family-names: Golden
+  - family-names: "Goodwin"
+    given-names: "Nastacia L."
+  - family-names: "Choong"
+    given-names: "Jia J."
+  - family-names: "Hwang"
+    given-names: "Sophia"
+  - family-names: "Pitts"
+    given-names: "Kayla"
+  - family-names: "Bloom"
+    given-names: "Liana"
+  - family-names: "Islam"
+    given-names: "Aasiya"
+  - family-names: "Zhang"
+    given-names: "Yizhe Y."
+  - family-names: "Szelenyi"
+    given-names: "Eric R."
+  - family-names: "Tong"
+    given-names: "Xiaoyu"
+  - family-names: "Newman"
+    given-names: "Emily L."
+  - family-names: "Miczek"
+    given-names: "Klaus"
+  - family-names: "Wright"
+    given-names: "Hayden R."
+  - family-names: "McLaughlin"
+    given-names: "Ryan J."
+  - family-nnames: "Norville"
+    given-names: "Zane C."
+  - family-names: "Eshel"
+    given-names: "Neir"
+  - family-names: "Heshmati"
+    given-names: "Mitra"
+  - family-names: "Nilsson"
+    given-names: "Simon R. O."
+  - family-names: "Golden"
+    given-names: "Sam A."
+contact:
+  - family-names: "Golden"
+    given-names: "Sam A."
+    email: "[email protected]"
+  - family-names: "Nilsson"
+    given-names: "Simon R. O."
+    email: "[email protected]"
+date-released: "2024-05-22"
+url: "https://simba-uw-tf-dev.readthedocs.io/"
+repository-code: "https://github.com/sgoldenlab/simba"
+repository: "https://osf.io/tmu6y/"
 identifiers:
   - type: doi
-    value: 10.1101/2020.04.19.049452
-    description: bioRxiv preprint
-repository-code: 'https://github.com/sgoldenlab/simba'
-url: 'https://simba-uw-tf-dev.readthedocs.io/'
-repository: 'https://osf.io/tmu6y/'
+    value: "10.1038/s41593-024-01649-9"
+    description: "DOI for the published article"
 abstract: >-
-  Toolkit for classification of behaviors in experimental
-  animals
+  The study of complex behaviors is often challenging when using manual annotation due to the absence of quantifiable behavioral definitions and the subjective nature of behavioral annotation. Integration of supervised machine learning approaches mitigates some of these issues through accessible and explainable model interpretation. To decrease barriers to access, we developed Simple Behavioral Analysis (SimBA) for behavioral neuroscientists. SimBA introduces machine learning interpretability tools, including SHapley Additive exPlanation (SHAP) scores, for explainable classifiers, enabling comparisons across species and providing a sharable framework.
 license: GPL-3.0
+keywords:
+  - behavioral neuroscience
+  - machine learning
+  - animal behavior analysis
+  - explainable AI

README.md

@@ -239,18 +239,19 @@ This project is licensed under the GPLv3. Note that the software is provided 'as
 
 If you find **any** part of the code or data useful for your own work, please cite us. You can view and download the citation file by clicking the <kbd>Cite this repository</kbd> button at the top right of this page. Thank you 🙏!
 
-    @article{Nilsson2020.04.19.049452,
-      author = {Nilsson, Simon RO and Goodwin, Nastacia L. and Choong, Jia Jie and Hwang, Sophia and Wright, Hayden R and Norville, Zane C and Tong, Xiaoyu and Lin, Dayu and Bentzley, Brandon S. and Eshel, Neir and McLaughlin, Ryan J and Golden, Sam A.},
-      title = {Simple Behavioral Analysis (SimBA) {\textendash} an open source toolkit for computer classification of complex social behaviors in experimental animals},
-      elocation-id = {2020.04.19.049452},
-      year = {2020},
-      doi = {10.1101/2020.04.19.049452},
-      publisher = {Cold Spring Harbor Laboratory},
-      URL = {https://www.biorxiv.org/content/early/2020/04/21/2020.04.19.049452},
-      eprint = {https://www.biorxiv.org/content/early/2020/04/21/2020.04.19.049452.full.pdf},
-      journal = {bioRxiv}
-    }
-
+	@article{Goodwin2024,
+  		author = {Goodwin, Nastacia L. and Choong, Jia J. and Hwang, Sophia and Pitts, Kayla and Bloom, Liana and Islam, Aasiya and Zhang, Yizhe Y. and Szelenyi, Eric R. and Tong, Xiaoyu and Newman, Emily L. and Miczek, Klaus and Wright, 	Hayden R. and McLaughlin, Ryan J. and Norville, Zane C. and Eshel, Neir and Heshmati, Mitra and Nilsson, Simon R. O. and Golden, Sam A.},
+  		title = {Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience},
+  		journal = {Nature Neuroscience},
+  		volume = {27},
+  		pages = {1411--1424},
+  		year = {2024},
+  		doi = {10.1038/s41593-024-01649-9},
+  		publisher = {Nature Publishing Group},
+  		URL = {https://simba-uw-tf-dev.readthedocs.io/},
+  		repository = {https://github.com/sgoldenlab/simba},
+    		license = {GPL-3.0}
+			}
 ## References 📜
 
 [![Foo](https://github.com/sgoldenlab/simba/blob/master/images/cos_center_logo_small.original.png)](https://osf.io/d69jt/)