| @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} |
| } |
