Blame for paper/source/citations.bib

@incollection{rice1976algorithm,
  title={The Algorithm Selection Problem},
  author={Rice, John R.},
  booktitle={Advances in Computers},
  volume={15},
  pages={65--118},
  year={1976},
  publisher={Elsevier},
  doi={10.1016/S0065-2458(08)60520-3}
}

@article{kerschke2019automated,
  title={Automated Algorithm Selection: Survey and Perspectives},
  author={Kerschke, Pascal and Hoos, Holger H. and Neumann, Frank and Trautmann, Heike},
  journal={Evolutionary Computation},
  volume={27},
  number={1},
  pages={3--45},
  year={2019},
  doi={10.1162/evco_a_00242}
}

@article{cohn1996active,
  title={Active Learning with Statistical Models},
  author={Cohn, David A. and Ghahramani, Zoubin and Jordan, Michael I.},
  journal={Journal of Artificial Intelligence Research},
  volume={4},
  pages={129--145},
  year={1996},
  doi={10.1613/jair.295}
}

@article{tharwat2023survey,
  title={A Survey on Active Learning: State-of-the-Art, Practical Challenges and Research Directions},
  author={Tharwat, Alaa and Schenck, Wolfram},
  journal={Mathematics},
  volume={11},
  number={4},
  pages={820},
  year={2023},
  doi={10.3390/math11040820}
}

@inproceedings{chakraborty2013active,
  title={Active Matrix Completion},
  author={Chakraborty, Shayok and Zhou, Jiayu and Balasubramanian, Vineeth and Panchanathan, Sethuraman and Davidson, Ian and Ye, Jieping},
  booktitle={2013 IEEE 13th International Conference on Data Mining},
  pages={81--90},
  year={2013},
  doi={10.1109/ICDM.2013.122}
}

@inproceedings{misir2019active,
  title={Active Matrix Completion for Algorithm Selection},
  author={M{\i}s{\i}r, Mustafa},
  booktitle={Machine Learning, Optimization, and Data Science},
  pages={321--334},
  year={2019},
  publisher={Springer},
  doi={10.1007/978-3-030-37599-7_27}
}

@article{mazumder2010spectral,
  title={Spectral Regularization Algorithms for Learning Large Incomplete Matrices},
  author={Mazumder, Rahul and Hastie, Trevor and Tibshirani, Robert},
  journal={Journal of Machine Learning Research},
  volume={11},
  pages={2287--2322},
  year={2010},
  url={https://www.jmlr.org/papers/v11/mazumder10a.html}
}

@inproceedings{qin2025active,
  title={Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations},
  author={Qin, Jason and Wessels, Hans-Hermann and Fernandez-Granda, Carlos and Hao, Yuhan},
  booktitle={Proceedings of the 42nd International Conference on Machine Learning},
  series={Proceedings of Machine Learning Research},
  volume={267},
  pages={50363--50383},
  year={2025},
  publisher={PMLR},
  url={https://proceedings.mlr.press/v267/qin25g.html}
}

@inproceedings{kirsch2019batchbald,
  title={{BatchBALD}: Efficient and Diverse Batch Acquisition for Deep Bayesian Active Learning},
  author={Kirsch, Andreas and van Amersfoort, Joost and Gal, Yarin},
  booktitle={Advances in Neural Information Processing Systems},
  volume={32},
  year={2019}
}

@inproceedings{ash2020badge,
  title={Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds},
  author={Ash, Jordan T. and Zhang, Chicheng and Krishnamurthy, Akshay and Langford, John and Agarwal, Alekh},
  booktitle={International Conference on Learning Representations},
  year={2020},
  url={https://openreview.net/forum?id=ryghZJBKPS}
}

@inproceedings{sener2018coreset,
  title={Active Learning for Convolutional Neural Networks: A Core-Set Approach},
  author={Sener, Ozan and Savarese, Silvio},
  booktitle={International Conference on Learning Representations},
  year={2018},
  url={https://openreview.net/forum?id=H1aIuk-RW}
}

@inproceedings{bae2025uncertainty,
  title={Uncertainty Herding: One Active Learning Method for All Label Budgets},
  author={Bae, Wonho and Oliveira, Gabriel L. and Sutherland, Danica J.},
  booktitle={International Conference on Learning Representations},
  year={2025},
  url={https://openreview.net/forum?id=UgPoHhYQ2U}
}

@article{hacohen2022active,
  title={Active Learning on a Budget: Opposite Strategies Suit High and Low Budgets},
  author={Hacohen, Guy and Dekel, Avihai and Weinshall, Daphna},
  journal={arXiv preprint arXiv:2202.02794},
  year={2022},
  doi={10.48550/arXiv.2202.02794}
}

@inproceedings{parvaneh2022active,
  title={Active Learning by Feature Mixing},
  author={Parvaneh, Amin and Abbasnejad, Ehsan and Teney, Damien and Haffari, Gholamreza Reza and van den Hengel, Anton and Shi, Javen Qinfeng},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={12227--12236},
  year={2022},
  doi={10.1109/CVPR52688.2022.01192}
}

@inproceedings{astudillo2021multi,
  title={Multi-Step Budgeted Bayesian Optimization with Unknown Evaluation Costs},
  author={Astudillo, Raul and Jiang, Daniel and Balandat, Maximilian and Bakshy, Eytan and Frazier, Peter I.},
  booktitle={Advances in Neural Information Processing Systems},
  volume={34},
  pages={20197--20209},
  year={2021}
}

@inproceedings{huang2018afasmc,
  title={Active Feature Acquisition with Supervised Matrix Completion},
  author={Huang, Sheng-Jun and Xu, Miao and Xie, Ming-Kun and Sugiyama, Masashi and Niu, Gang and Chen, Songcan},
  booktitle={Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
  pages={1571--1579},
  year={2018},
  publisher={Association for Computing Machinery},
  doi={10.1145/3219819.3220084}
}

@inproceedings{gao2020cost,
  title={Cost-Accuracy Aware Adaptive Labeling for Active Learning},
  author={Gao, Ruijiang and Saar-Tsechansky, Maytal},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  volume={34},
  number={3},
  pages={2569--2576},
  year={2020},
  doi={10.1609/aaai.v34i03.5640}
}

@inproceedings{tomanek2010comparison,
  title={A Comparison of Models for Cost-Sensitive Active Learning},
  author={Tomanek, Katrin and Hahn, Udo},
  booktitle={COLING 2010: Posters},
  pages={1247--1255},
  year={2010},
  publisher={Association for Computational Linguistics},
  url={https://aclanthology.org/C10-2143/}
}

@inproceedings{haertel2015analytic,
  title={An Analytic and Empirical Evaluation of Return-on-Investment-Based Active Learning},
  author={Haertel, Robbie and Ringger, Eric and Felt, Paul and Seppi, Kevin},
  booktitle={Proceedings of the 9th Linguistic Annotation Workshop},
  pages={11--20},
  year={2015},
  publisher={Association for Computational Linguistics},
  doi={10.3115/v1/W15-1602}
}

@article{guinet2020pareto,
  title={Pareto-Efficient Acquisition Functions for Cost-Aware Bayesian Optimization},
  author={Guinet, Gauthier and Perrone, Valerio and Archambeau, C{\'e}dric},
  journal={arXiv preprint arXiv:2011.11456},
  year={2020},
  doi={10.48550/arXiv.2011.11456}
}

@inproceedings{kus2024frugal,
  title={Frugal Algorithm Selection},
  author={Ku\c{s}, Erdem and Akg\"{u}n, \"{O}zg\"{u}r and Dang, Nguyen and Miguel, Ian},
  booktitle={30th International Conference on Principles and Practice of Constraint Programming},
  series={Leibniz International Proceedings in Informatics},
  volume={307},
  pages={38:1--38:16},
  year={2024},
  publisher={Schloss Dagstuhl},
  doi={10.4230/LIPIcs.CP.2024.38}
}

@article{paggi2024art,
  title={The Art and Science of Molecular Docking},
  author={Paggi, Joseph M. and Pandit, Ayush and Dror, Ron O.},
  journal={Annual Review of Biochemistry},
  volume={93},
  pages={389--410},
  year={2024},
  doi={10.1146/annurev-biochem-030222-120000}
}

@article{hu2005binding,
  title={Binding {MOAD} (Mother of All Databases)},
  author={Hu, Lihua and Benson, Mikael L. and Smith, Richard D. and Lerner, Michael G. and Carlson, Heather A.},
  journal={Proteins: Structure, Function, and Bioinformatics},
  volume={60},
  number={3},
  pages={333--340},
  year={2005},
  doi={10.1002/prot.20512}
}

@article{wang2026molecular,
  title={Molecular Embedding-Based Algorithm Selection in Protein--Ligand Docking},
  author={Wang, Jiabao Brad and Cao, Siyuan and Wu, Hongxuan and Yuan, Yiliang and M{\i}s{\i}r, Mustafa},
  journal={Journal of Cheminformatics},
  volume={18},
  number={1},
  pages={47},
  year={2026},
  publisher={Springer}
}

@article{chen2023algorithm,
  title={Algorithm Selection for Protein--Ligand Docking: Strategies and Analysis on {ACE}},
  author={Chen, Tianlai and Shu, Xiwen and Zhou, Huiyuan and Beckford, Floyd A. and M{\i}s{\i}r, Mustafa},
  journal={Scientific Reports},
  volume={13},
  number={1},
  pages={8219},
  year={2023},
  doi={10.1038/s41598-023-35163-8}
}

@inproceedings{cao2025mc,
  title={{MC-GNNAS-Dock}: Multi-Criteria {GNN}-Based Algorithm Selection for Molecular Docking},
  author={Cao, Siyuan and Wu, Hongxuan and Wang, Jiabao Brad and Yuan, Yiliang and M{\i}s{\i}r, Mustafa},
  booktitle={Pacific Rim International Conference on Artificial Intelligence},
  pages={686--696},
  year={2025},
  publisher={Springer}
}

@article{graff2021accelerating,
  title={Accelerating High-Throughput Virtual Screening through Molecular Pool-Based Active Learning},
  author={Graff, David E. and Shakhnovich, Eugene I. and Coley, Connor W.},
  journal={Chemical Science},
  volume={12},
  number={22},
  pages={7866--7881},
  year={2021},
  doi={10.1039/D0SC06805E}
}

@article{marin2024regression,
  title={Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking},
  author={Marin, Egor and Kovaleva, Margarita and Kadukova, Maria and Mustafin, Khalid and Khorn, Polina and Rogachev, Andrey and Mishin, Alexey and Guskov, Albert and Borshchevskiy, Valentin},
  journal={Journal of Chemical Information and Modeling},
  volume={64},
  number={7},
  pages={2612--2623},
  year={2024},
  doi={10.1021/acs.jcim.3c01889}
}

@article{buttenschoen2024posebusters,
  title={{PoseBusters}: AI-Based Docking Methods Fail to Generate Physically Valid Poses or Generalise to Novel Sequences},
  author={Buttenschoen, Martin and Morris, Garrett M. and Deane, Charlotte M.},
  journal={Chemical Science},
  volume={15},
  pages={3130--3139},
  year={2024},
  doi={10.1039/D3SC04185A}
}

@article{koes2013smina,
  title={Lessons Learned in Empirical Scoring with Smina from the {CSAR} 2011 Benchmarking Exercise},
  author={Koes, David Ryan and Baumgartner, Matthew P. and Camacho, Carlos J.},
  journal={Journal of Chemical Information and Modeling},
  volume={53},
  number={8},
  pages={1893--1904},
  year={2013},
  doi={10.1021/ci300604z}
}

@article{trott2010vina,
  title={{AutoDock Vina}: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading},
  author={Trott, Oleg and Olson, Arthur J.},
  journal={Journal of Computational Chemistry},
  volume={31},
  number={2},
  pages={455--461},
  year={2010},
  doi={10.1002/jcc.21334}
}

@inproceedings{corso2023diffdock,
  title={{DiffDock}: Diffusion Steps, Twists, and Turns for Molecular Docking},
  author={Corso, Gabriele and St\"{a}rk, Hannes and Jing, Bowen and Barzilay, Regina and Jaakkola, Tommi},
  booktitle={International Conference on Learning Representations},
  year={2023},
  url={https://openreview.net/forum?id=kKF8_K-mBbS}
}

@article{corso2024diffdockl,
  title={Deep Confident Steps to New Pockets: Strategies for Docking Generalization},
  author={Corso, Gabriele and Deng, Arthur and Fry, Bowen and Polizzi, Nicholas and Barzilay, Regina and Jaakkola, Tommi},
  journal={arXiv preprint arXiv:2402.18396},
  year={2024},
  doi={10.48550/arXiv.2402.18396}
}

@article{cao2025surfdock,
  title={{SurfDock} Is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein--Ligand Complex Prediction},
  author={Cao, Dong and others},
  journal={Nature Methods},
  volume={22},
  number={2},
  pages={310--322},
  year={2025}
}

@article{mcnutt2021gnina,
  title={{GNINA} 1.0: Molecular Docking with Deep Learning},
  author={McNutt, Andrew T. and Francoeur, Paul and Aggarwal, Rishal and Masuda, Tairan and Meli, Rocco and Ragoza, Matthew and Sunseri, Jocelyn and Koes, David Ryan},
  journal={Journal of Cheminformatics},
  volume={13},
  number={1},
  pages={43},
  year={2021},
  doi={10.1186/s13321-021-00522-2}
}

@inproceedings{zhou2023unimol,
  title={{Uni-Mol}: A Universal 3D Molecular Representation Learning Framework},
  author={Zhou, Gengmo and Gao, Zhifeng and Ding, Qiankun and Zheng, Hang and Xu, Hongteng and Wei, Zhewei and Zhang, Linfeng and Ke, Guolin},
  booktitle={International Conference on Learning Representations},
  year={2023},
  url={https://openreview.net/forum?id=6K2RM6wVqKu}
}

@inproceedings{alcaide2025unimol,
  title={{Uni-Mol Docking V2}: Towards Realistic and Accurate Binding Pose Prediction},
  author={Alcaide, Eric and Gao, Zhi and Ke, Guolin and others},
  booktitle={International Conference on Artificial Neural Networks},
  pages={34--41},
  year={2025},
  publisher={Springer}
}

@article{ahmad2022chemberta2,
  title={{ChemBERTa-2}: Towards Chemical Foundation Models},
  author={Ahmad, Walid and Simon, Etienne and Chithrananda, Seyone and Grand, Gabriel and Ramsundar, Bharath},
  journal={arXiv preprint arXiv:2209.01712},
  year={2022},
  doi={10.48550/arXiv.2209.01712}
}

@misc{esm2024cambrian,
  title={{ESM Cambrian}: Revealing the Mysteries of Proteins with Unsupervised Learning},
  author={{ESM Team}},
  year={2024},
  url={https://www.evolutionaryscale.ai/blog/esm-cambrian}
}

@article{kus2026frugal,
  title={Frugal Algorithm Selection for Combinatorial Search},
  author={Kus, Erdem and Akg{\"u}n, {\"O}zg{\"u}r and Dang, Nguyen and Miguel, Ian and Kotthoff, Lars},
  journal={Journal of Artificial Intelligence Research},
  volume={86},
  year={2026}
}


@article{volpato2019active,
  title   = {Active Learning to Optimise Time-Expensive Algorithm Selection},
  author  = {Volpato, Riccardo and Song, Guangyan},
  journal = {arXiv preprint arXiv:1909.03261},
  year    = {2019}
}

@inproceedings{huseljic2026refine,
  title     = {Cleaning the Pool: Progressive Filtering of Unlabeled Pools in Deep Active Learning},
  author    = {Huseljic, Denis and Herde, Marek and Rauch, Lukas and Hahn, Paul and Sick, Bernhard},
  booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages     = {22238--22247},
  month     = jun,
  year      = {2026}
}