add dois

tahiri-lab · May 14, 2024 · 91ac29a · 91ac29a
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Showing 1 changed file with 160 additions and 140 deletions.
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -1,11 +1,13 @@
 @article{leveque2022quantitative,
-    title={Quantitative Structure-Activity Relationship (QSAR) modeling to predict the transfer of environmental chemicals across the placenta},
-    author={L{\'e}v{\^e}que, Laura and Tahiri, Nadia and Goldsmith, Michael-Rock and Verner, Marc-Andr{\'e}},
-    journal={Computational Toxicology},
-    volume={21},
-    pages={100211},
-    year={2022},
-    publisher={Elsevier}
+    title = {Quantitative Structure-Activity Relationship (QSAR) modeling to predict the transfer of environmental chemicals across the placenta},
+    author = {L{\'e}v{\^e}que, Laura and Tahiri, Nadia and Goldsmith, Michael-Rock and Verner, Marc-Andr{\'e}},
+    journal = {Computational Toxicology},
+    volume = {21},
+    pages = {100211},
+    year = {2022},
+    publisher = {Elsevier},
+    doi = {10.1016/j.comtox.2021.100211},
+    url = {https://doi.org/10.1016/j.comtox.2021.100211},
 }
 
 @article{tropsha2010,
@@ -16,7 +18,7 @@ @article{tropsha2010
     number = {6-7},
     pages = {476-488},
     keywords = {QSAR modeling, Model validation, Virtual screening, Drug discovery},
-    doi = {https://doi.org/10.1002/minf.201000061},
+    doi = {10.1002/minf.201000061},
     url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.201000061},
     eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/minf.201000061},
     year = {2010}
@@ -29,7 +31,7 @@ @article{anderson2016
     volume = {100},
     number = {1},
     pages = {42-52},
-    doi = {https://doi.org/10.1002/cpt.377},
+    doi = {10.1002/cpt.377},
     url = {https://ascpt.onlinelibrary.wiley.com/doi/abs/10.1002/cpt.377},
     eprint = {https://ascpt.onlinelibrary.wiley.com/doi/pdf/10.1002/cpt.377},
     year = {2016}
@@ -43,150 +45,167 @@ @article{verstegen2022
     number = {10},
     pages = {4311-4327},
     keywords = {adverse drug reactions, breastfeeding, drugs, lactation, medication},
-    doi = {https://doi.org/10.1111/bcp.14538},
+    doi = {10.1111/bcp.14538},
     url = {https://bpspubs.onlinelibrary.wiley.com/doi/abs/10.1111/bcp.14538},
     eprint = {https://bpspubs.onlinelibrary.wiley.com/doi/pdf/10.1111/bcp.14538},
     year = {2022}
 }
 
 @manual{MOE2022,
-  title = {Molecular Operating Environment (MOE)},
-  organization = {Chemical Computing Group ULC},
-  address = {910-1010 Sherbrooke St. W., Montreal, QC H3A 2R7, Canada},
-  year = {2024},
-  version = {2022.02}
+    title = {Molecular Operating Environment (MOE)},
+    organization = {Chemical Computing Group ULC},
+    address = {910-1010 Sherbrooke St. W., Montreal, QC H3A 2R7, Canada},
+    year = {2024},
+    version = {2022.02}
 }
 
 @misc{rdkit2023release,
-  title = {RDKit Software},
-  howpublished = {\url{https://zenodo.org/record/10275225}},
-  note={Accessed: 2023-12-11},
-  year={2006}
+    title = {RDKit Software},
+    howpublished = {\url{https://zenodo.org/record/10275225}},
+    note = {Accessed: 2023-12-11},
+    year = {2006}
 }
 
 @article{hoerl2000ridge,
-  title={Ridge Regression: Biased Estimation for Nonorthogonal Problems},
-  author={Hoerl, Arthur E. and Kennard, Robert W.},
-  journal={Technometrics},
-  volume={42},
-  number={1},
-  pages={80},
-  year={2000}
+    title = {Ridge Regression: Biased Estimation for Nonorthogonal Problems},
+    author = {Hoerl, Arthur E. and Kennard, Robert W.},
+    journal = {Technometrics},
+    volume = {42},
+    number = {1},
+    pages = {80},
+    year = {2000},
+    doi = {10.2307/1267351},
+    url = {https://doi.org/10.2307/1267351},
 }
 
 @article{tibshirani1996lasso,
-  title={Regression shrinkage and selection via the Lasso},
-  author={Tibshirani, Robert},
-  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
-  volume={58},
-  number={1},
-  pages={267--288},
-  year={1996}
+    title = {Regression shrinkage and selection via the Lasso},
+    author = {Tibshirani, Robert},
+    journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
+    volume = {58},
+    number = {1},
+    pages = {267--288},
+    year = {1996},
+    doi = {10.1111/j.2517-6161.1996.tb02080.x},
+    url = {http://www.jstor.org/stable/2346178},
 }
 
 @article{tay2021elasticnet,
-  title={Elastic Net Regularization Paths for All Generalized Linear Models},
-  author={Tay, J. Kenneth and Narasimhan, Balasubramanian and Hastie, Trevor},
-  journal={arXiv preprint arXiv:2103.03475},
-  year={2021}
+    title = {Elastic Net Regularization Paths for All Generalized Linear Models},
+    author = {Tay, J. Kenneth and Narasimhan, Balasubramanian and Hastie, Trevor},
+    journal = {arXiv preprint arXiv:2103.03475},
+    year = {2021},
+    doi = {10.18637/jss.v106.i01},
 }
 
 @article{chen2016xgboost,
-  title={XGBoost: A Scalable Tree Boosting System},
-  author={Chen, Tianqi and Guestrin, Carlos},
-  journal={arXiv preprint arXiv:1603.02754},
-  year={2016}
+    title = {XGBoost: A Scalable Tree Boosting System},
+    author = {Chen, Tianqi and Guestrin, Carlos},
+    journal = {arXiv preprint arXiv:1603.02754},
+    year = {2016},
+    doi = {10.1145/2939672.2939785},
 }
 
 @article{dorogush2018catboost,
-  title={CatBoost: gradient boosting with categorical features support},
-  author={Dorogush, Anna Veronika and Ershov, Vasily and Gulin, Andrey},
-  journal={arXiv preprint arXiv:1810.11363},
-  year={2018}
+    title = {CatBoost: gradient boosting with categorical features support},
+    author = {Dorogush, Anna Veronika and Ershov, Vasily and Gulin, Andrey},
+    journal = {arXiv preprint arXiv:1810.11363},
+    year = {2018},
+    doi = {10.48550/arXiv.1810.11363},
+    url = {https://doi.org/10.48550/arXiv.1810.11363},
 }
 
 @article{breiman2001randomforest,
-  author    = {Breiman, Leo},
-  title     = {Random Forests},
-  journal   = {Machine Learning},
-  volume    = {45},
-  number    = {1},
-  pages     = {5--32},
-  year      = {2001},
-  month     = {Oct},
-  doi       = {10.1023/A:1010933404324},
-  issn      = {1573-0565},
-  url       = {https://doi.org/10.1023/A:1010933404324},
+    author = {Breiman, Leo},
+    title = {Random Forests},
+    journal = {Machine Learning},
+    volume = {45},
+    number = {1},
+    pages = {5--32},
+    year = {2001},
+    month = {Oct},
+    doi = {10.1023/A:1010933404324},
+    issn = {1573-0565},
+    url = {https://doi.org/10.1023/A:1010933404324},
 }
 
 @article{hall2000correlation,
-  title={Correlation-based feature selection of discrete and numeric class machine learning},
-  author={Hall, Mark A},
-  year={2000}
+    title = {Correlation-based feature selection of discrete and numeric class machine learning},
+    author = {Hall, Mark A},
+    year = {2000},
+    doi = {}
 }
 
 @article{decao2018molgan,
-  title={MolGAN: An implicit generative model for small molecular graphs},
-  author={De Cao, Nicola and Kipf, Thomas},
-  journal={arXiv preprint arXiv:1805.11973},
-  year={2018}
+    title = {MolGAN: An implicit generative model for small molecular graphs},
+    author = {De Cao, Nicola and Kipf, Thomas},
+    journal = {arXiv preprint arXiv:1805.11973},
+    year = {2018},
+    doi = {10.48550/arXiv.1805.11973},
+    url = {https://doi.org/10.48550/arXiv.1805.11973},
 }
 
 @article{akiba2019optuna,
-  title={Optuna: A Next-generation Hyperparameter Optimization Framework},
-  author={Akiba, Takuya and Sano, Shotaro and Yanase, Toshihiko and Ohta, Takeru and Koyama, Masanori},
-  journal={arXiv:1907.10902 [cs.LG]},
-  year={2019}
+    title = {Optuna: A Next-generation Hyperparameter Optimization Framework},
+    author = {Akiba, Takuya and Sano, Shotaro and Yanase, Toshihiko and Ohta, Takeru and Koyama, Masanori},
+    journal = {arXiv:1907.10902 [cs.LG]},
+    year = {2019},
+    doi = {10.48550/arXiv.1907.10902},
 }
 
 @article{goodfellow2014generative,
-  title={Generative Adversarial Nets},
-  author={Goodfellow, Ian J. and Pouget-Abadie, Jean and Mirza, Mehdi and Xu, Bing and Warde-Farley, David and Ozair, Sherjil and Courville, Aaron and Bengio, Yoshua},
-  journal={arXiv preprint arXiv:1406.2661},
-  year={2014}
+    title = {Generative Adversarial Nets},
+    author = {Goodfellow, Ian J. and Pouget-Abadie, Jean and Mirza, Mehdi and Xu, Bing and Warde-Farley, David and Ozair, Sherjil and Courville, Aaron and Bengio, Yoshua},
+    journal = {arXiv preprint arXiv:1406.2661},
+    year = {2014},
+    doi = {10.48550/arXiv.1406.2661},
 }
 
 @article{allen2005benefits,
-  title={Benefits of breastfeeding},
-  author={Allen, Jane and Hector, Debra},
-  journal={New South Wales public health bulletin},
-  volume={16},
-  number={4},
-  pages={42--46},
-  year={2005},
+    title = {Benefits of breastfeeding},
+    author = {Allen, Jane and Hector, Debra},
+    journal = {New South Wales public health bulletin},
+    volume = {16},
+    number = {4},
+    pages = {42--46},
+    year = {2005},
+    doi = {10.1071/nb05011},
 }
 
 @article{ito2003drug,
-  title={Drug excretion into breast milk—overview},
-  author={Ito, Shinya and Lee, Amy},
-  journal={Advanced drug delivery reviews},
-  volume={55},
-  number={5},
-  pages={617--627},
-  year={2003},
-  publisher={Elsevier}
+    title = {Drug excretion into breast milk—overview},
+    author = {Ito, Shinya and Lee, Amy},
+    journal = {Advanced drug delivery reviews},
+    volume = {55},
+    number = {5},
+    pages = {617--627},
+    year = {2003},
+    publisher = {Elsevier},
+    doi = {10.1016/s0169-409x(03)00034-6},
 }
 
 @article{lawrence2000breastfeeding,
-  title={Breastfeeding: benefits, risks and alternatives},
-  author={Lawrence, Ruth A},
-  journal={Current Opinion in Obstetrics and Gynecology},
-  volume={12},
-  number={6},
-  pages={519--524},
-  year={2000},
-  publisher={LWW}
+    title = {Breastfeeding: benefits, risks and alternatives},
+    author = {Lawrence, Ruth A},
+    journal = {Current Opinion in Obstetrics and Gynecology},
+    volume = {12},
+    number = {6},
+    pages = {519--524},
+    year = {2000},
+    publisher = {LWW},
+    doi = {10.1097/00001703-200012000-00011},
 }
 
 @article{binns2016long,
-  title={The long-term public health benefits of breastfeeding},
-  author={Binns, Colin and Lee, MiKyung and Low, Wah Yun},
-  journal={Asia Pacific Journal of Public Health},
-  volume={28},
-  number={1},
-  pages={7--14},
-  year={2016},
-  publisher={Sage Publications Sage CA: Los Angeles, CA}
+    title = {The long-term public health benefits of breastfeeding},
+    author = {Binns, Colin and Lee, MiKyung and Low, Wah Yun},
+    journal = {Asia Pacific Journal of Public Health},
+    volume = {28},
+    number = {1},
+    pages = {7--14},
+    year = {2016},
+    publisher = {Sage Publications Sage CA: Los Angeles, CA},
+    doi = {10.1177/1010539515624964},
 }
 
 @article{Comesana2022,
@@ -196,56 +215,57 @@ @article{Comesana2022
     pages = {123836},
     year = {2022},
     issn = {0016-2361},
-    doi = {https://doi.org/10.1016/j.fuel.2022.123836},
+    doi = {10.1016/j.fuel.2022.123836},
     url = {https://www.sciencedirect.com/science/article/pii/S0016236122006950},
     author = {Ana E. Comesana and Tyler T. Huntington and Corinne D. Scown and Kyle E. Niemeyer and Vi H. Rapp},
     keywords = {Chemical descriptors, Machine learning, Biofuel, TPOT},
 }
 
 @article{prematunga2012correlational,
-  title={Correlational analysis},
-  author={Prematunga, Roshani K},
-  journal={Australian Critical Care},
-  volume={25},
-  number={3},
-  pages={195--199},
-  year={2012},
-  publisher={Elsevier}
+    title = {Correlational analysis},
+    author = {Prematunga, Roshani K},
+    journal = {Australian Critical Care},
+    volume = {25},
+    number = {3},
+    pages = {195--199},
+    year = {2012},
+    publisher = {Elsevier},
+    doi = {10.1016/j.aucc.2012.02.003},
 }
 
 @article{remeseiro2019review,
-  title={A review of feature selection methods in medical applications},
-  author={Remeseiro, Beatriz and Bolon-Canedo, Veronica},
-  journal={Computers in biology and medicine},
-  volume={112},
-  pages={103375},
-  year={2019},
-  publisher={Elsevier}
+    title = {A review of feature selection methods in medical applications},
+    author = {Remeseiro, Beatriz and Bolon-Canedo, Veronica},
+    journal = {Computers in biology and medicine},
+    volume = {112},
+    pages = {103375},
+    year = {2019},
+    publisher = {Elsevier},
+    doi = {10.1016/j.compbiomed.2019.103375},
 }
 
 @article{guyon2002gene,
-  title={Gene selection for cancer classification using support vector machines},
-  author={Guyon, Isabelle and Weston, Jason and Barnhill, Stephen and Vapnik, Vladimir},
-  journal={Machine learning},
-  volume={46},
-  pages={389--422},
-  year={2002},
-  publisher={Springer}
+    title = {Gene selection for cancer classification using support vector machines},
+    author = {Guyon, Isabelle and Weston, Jason and Barnhill, Stephen and Vapnik, Vladimir},
+    journal = {Machine learning},
+    volume = {46},
+    pages = {389--422},
+    year = {2002},
+    publisher = {Springer},
+    doi = {10.1023/a:1012487302797},
 }
 
 @inproceedings{li2022,
-  title     = {Transformer-based Objective-reinforced Generative Adversarial Network to Generate Desired Molecules},
-  author    = {Li, Chen and Yamanaka, Chikashige and Kaitoh, Kazuma and Yamanishi, Yoshihiro},
-  booktitle = {Proceedings of the Thirty-First International Joint Conference on
-               Artificial Intelligence, {IJCAI-22}},
-  publisher = {International Joint Conferences on Artificial Intelligence Organization},
-  editor    = {Lud De Raedt},
-  pages     = {3884--3890},
-  year      = {2022},
-  month     = {7},
-  note      = {Main Track},
-  doi       = {10.24963/ijcai.2022/539},
-  url       = {https://doi.org/10.24963/ijcai.2022/539},
-}
-
-# TODO: Add DOIS
+    title = {Transformer-based Objective-reinforced Generative Adversarial Network to Generate Desired Molecules},
+    author = {Li, Chen and Yamanaka, Chikashige and Kaitoh, Kazuma and Yamanishi, Yoshihiro},
+    booktitle = {Proceedings of the Thirty-First International Joint Conference on
+ Artificial Intelligence, {IJCAI-22}},
+    publisher = {International Joint Conferences on Artificial Intelligence Organization},
+    editor = {Lud De Raedt},
+    pages = {3884--3890},
+    year = {2022},
+    month = {7},
+    note = {Main Track},
+    doi = {10.24963/ijcai.2022/539},
+    url = {https://doi.org/10.24963/ijcai.2022/539},
+}