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@Report{RegressionTransformer,
author = {Jannis Born and Matteo Manica},
date = {2022-02},
title = {Regression Transformer: Concurrent sequence regression and generation for molecular language modeling},
eprint = {2202.01338},
url = {https://github.com/IBM/regression-transformer},
archiveprefix = {arxiv},
month = feb,
year = {2022},
}
@Article{MolDreaming,
author = {Shen, Cynthia and Krenn, Mario and Eppel, Sagi and Aspuru-Guzik, Alán},
date = {2021-07},
year = {2021},
journaltitle = {Machine Learning: Science and Technology},
journal = {Machine Learning: Science and Technology},
title = {Deep molecular dreaming: inverse machine learning for de-novo molecular design and interpretability with surjective representations},
doi = {10.1088/2632-2153/ac09d6},
issn = {2632-2153},
language = {en},
number = {3},
url = {https://dx.doi.org/10.1088/2632-2153/ac09d6},
urldate = {2023-05-08},
volume = {2},
pages = {03LT02},
publisher = {IOP Publishing},
shorttitle = {Deep molecular dreaming},
}
@Report{AttnRolloutFlow,
author = {Samira Abnar and Willem Zuidema},
date = {2020-05},
title = {Quantifying Attention Flow in Transformers},
doi = {10.18653/v1/2020.acl-main.385},
journal = {Association for Computational Linguistics},
eprint = {2005.00928},
eprinttype = {arxiv},
month = {5},
year = {2020},
note = {arXiv:2005.00928},
url = {https://arxiv.org/abs/2005.00928},
}
@Article{MolGPT,
author = {Viraj Bagal and Rishal Aggarwal and P. K. Vinod and U. Deva Priyakumar},
date = {2021},
journaltitle = {Journal of Chemical Information and Modeling},
journal = {Journal of Chemical Information and Modeling},
title = {MolGPT: Molecular Generation Using a Transformer-Decoder Model},
doi = {10.1021/acs.jcim.1c00600},
issn = {1520-5142},
volume = {62},
number = {9},
pages = {2064--2076},
year = {2021},
journal = {Journal of Chemical Information and Modeling},
pmid = {34694798},
publisher = {American Chemical Society},
year = {2021},
}
@Article{CrippenLogP,
author = {Scott A. Wildman and Gordon M. Crippen},
title = {Prediction of physicochemical parameters by atomic contributions},
doi = {10.1021/ci990307l},
issn = {0095-2338},
issue = {5},
pages = {868-873},
volume = {39},
journal = {Journal of Chemical Information and Computer Sciences},
publisher = {American Chemical Society},
year = {1999},
}
@Article{ZINC15,
author = {Teague Sterling and John J. Irwin},
date = {2015-11},
journaltitle = {Journal of Chemical Information and Modeling},
journal = {Journal of Chemical Information and Modeling},
title = {ZINC 15 - Ligand Discovery for Everyone},
doi = {10.1021/acs.jcim.5b00559},
issn = {1549-960X},
issue = {11},
pages = {2324-2337},
volume = {55},
journal = {Journal of Chemical Information and Modeling},
month = {11},
pmid = {26479676},
publisher = {American Chemical Society},
year = {2015},
}
@Article{ECFP,
author = {David Rogers and Mathew Hahn},
date = {2010-05},
journaltitle = {Journal of Chemical Information and Modeling},
title = {Extended-connectivity fingerprints},
doi = {10.1021/ci100050t},
issn = {1549-960X},
issue = {5},
pages = {742-754},
volume = {50},
journal = {Journal of Chemical Information and Modeling},
month = {5},
pmid = {20426451},
publisher = {American Chemical Society},
year = {2010},
}
@Article{Bach_LRP,
author = {Sebastian Bach and Alexander Binder and Grégoire Montavon and Frederick Klauschen and Klaus Robert Müller and Wojciech Samek},
year = {2015},
date = {2015-07},
journaltitle = {PLoS ONE},
journal = {PLoS ONE},
title = {On pixel-wise explanations for non-linear classifier decisions by layer-wise relevance propagation},
doi = {10.1371/journal.pone.0130140},
issn = {1932-6203},
issue = {7},
volume = {10},
pages = {7},
journal = {Journal of Chemical Information and Computer Sciences},
month = {5},
pmid = {15154768},
year = {2004},
}
@Article{ALOGPS_VCCLab,
author = {Igor V. Tetko and Johann Gasteiger and Roberto Todeschini and Andrea Mauri and David Livingstone and Peter Ertl and Vladimir A. Palyulin and Eugene V. Radchenko and Nikolay S. Zefirov and Alexander S. Makarenko and Vsevolod Yu Tanchuk and Volodymyr V. Prokopenko},
date = {2005},
journaltitle = {Journal of Computer-Aided Molecular Design},
title = {Virtual computational chemistry laboratory - Design and description},
doi = {10.1007/s10822-005-8694-y},
issn = {1573-4951},
issue = {6},
pages = {453-463},
volume = {19},
journal = {Journal of Computer-Aided Molecular Design},
keywords = {Drug design,Indices calculation,Model generation and validation,On-line analysis,Physico-chemical property predictions},
pmid = {16231203},
publisher = {Springer Netherlands},
year = {2005},
}
@Article{DeepTaylorDecomp,
author = {Grégoire Montavon and Sebastian Lapuschkin and Alexander Binder and Wojciech Samek and Klaus Robert Müller},
date = {2017-05},
journaltitle = {Pattern Recognition},
journal= {Pattern Recognition},
title = {Explaining nonlinear classification decisions with deep Taylor decomposition},
doi = {10.1016/j.patcog.2016.11.008},
issn = {0031-3203},
pages = {211-222},
volume = {65},
journal = {Pattern Recognition},
keywords = {Deep neural networks,Heatmapping,Image recognition,Relevance propagation,Taylor decomposition},
month = {5},
publisher = {Elsevier Ltd},
year = {2017},
}
@Article{AlphaFold2,
author = {John Jumper and Richard Evans and Alexander Pritzel and Tim Green and Michael Figurnov and Olaf Ronneberger and Kathryn Tunyasuvunakool and Russ Bates and Augustin Žídek and Anna Potapenko and Alex Bridgland and Clemens Meyer and Simon A.A. Kohl and Andrew J. Ballard and Andrew Cowie and Bernardino Romera-Paredes and Stanislav Nikolov and Rishub Jain and Jonas Adler and Trevor Back and Stig Petersen and David Reiman and Ellen Clancy and Michal Zielinski and Martin Steinegger and Michalina Pacholska and Tamas Berghammer and Sebastian Bodenstein and David Silver and Oriol Vinyals and Andrew W. Senior and Koray Kavukcuoglu and Pushmeet Kohli and Demis Hassabis},
date = {2021-08},
journaltitle = {Nature},
journal= {Nature},
title = {Highly accurate protein structure prediction with AlphaFold},
doi = {10.1038/s41586-021-03819-2},
issn = {1476-4687},
issue = {7873},
pages = {583-589},
volume = {596},
journal = {Nature},
month = {8},
pmid = {34265844},
publisher = {Nature Research},
year = {2021},
}
'
@InProceedings{AIAYN,
author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, \Lukasz and Polosukhin, Illia},
booktitle = {Advances in Neural Information Processing Systems},
title = {Attention is All you Need},
editor = {I. Guyon and U. Von Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett},
publisher = {Curran Associates, Inc.},
url = {https://proceedings.neurips.cc/paper_files/paper/2017/file/3f5ee243547dee91fbd053c1c4a845aa-Paper.pdf},
volume = {30},
year = {2017},
}
'
@Article{Chemformer,
author = {Irwin, Ross and Dimitriadis, Spyridon and He, Jiazhen and Bjerrum, Esben Jannik},
date = {2022-01},
journaltitle = {Machine Learning: Science and Technology},
journal = {Machine Learning: Science and Technology},
title = {Chemformer: a pre-trained transformer for computational chemistry},
doi = {10.1088/2632-2153/ac3ffb},
issn = {2632-2153},
language = {en},
number = {1},
pages = {015022},
url = {https://dx.doi.org/10.1088/2632-2153/ac3ffb},
urldate = {2023-05-08},
volume = {3},
publisher = {IOP Publishing},
shorttitle = {Chemformer},
year = {2022},
}
'
@Report{MoleculeAttnTransformer,
author = {Maziarka, {\L}ukasz and Danel, Tomasz and Mucha, S{\l}awomir and Rataj, Krzysztof and Tabor, Jacek and Jastrz{\k{e}}bski, Stanis{\l}aw},
date = {2020-02},
institution = {arXiv},
title = {Molecule {Attention} {Transformer}},
doi = {10.48550/arXiv.2002.08264},
note = {arXiv:2002.08264},
url = {http://arxiv.org/abs/2002.08264},
urldate = {2023-05-08},
keywords = {Computer Science - Machine Learning, Physics - Computational Physics, Statistics - Machine Learning},
year = {2020},
}
'
@Article{SolTranNet,
author = {Francoeur, Paul G. and Koes, David R.},
date = {2021-06},
journaltitle = {Journal of Chemical Information and Modeling},
journal= {Journal of Chemical Information and Modeling},
title = {{SolTranNet}-{A} {Machine} {Learning} {Tool} for {Fast} {Aqueous} {Solubility} {Prediction}},
doi = {10.1021/acs.jcim.1c00331},
issn = {1549-960X},
language = {eng},
number = {6},
pages = {2530--2536},
volume = {61},
keywords = {Machine Learning, Software, Solubility, Water},
pmcid = {PMC8900744},
pmid = {34038123},
year = {2021},
}
'
@Article{SaliencyMaps,
author = {Gevrey, Muriel and Dimopoulos, Ioannis and Lek, Sovan},
date = {2003-02},
journaltitle = {Ecological Modelling},
journal= {Ecological Modelling},
title = {Review and comparison of methods to study the contribution of variables in artificial neural network models},
doi = {10.1016/S0304-3800(02)00257-0},
issn = {0304-3800},
language = {en},
number = {3},
pages = {249--264},
series = {Modelling the structure of acquatic communities: concepts, methods and problems.},
url = {https://www.sciencedirect.com/science/article/pii/S0304380002002570},
urldate = {2023-05-08},
volume = {160},
keywords = {Artificial neural networks, Backpropagation, Non-linear relationships, Variables contribution, Sensitivity analysis, Perturbation, Partial derivatives, Trout, Habitat modelling},
year = {2003},
}
'
@Report{GradCAM,
author = {Ramprasaath R Selvaraju and Michael Cogswell and Abhishek Das and Ramakrishna Vedantam and Devi Parikh and Dhruv Batra},
date = {2017-10},
title = {Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization},
doi = {10.1109/iccv.2017.74},
note = {ISSN: 2380-7504},
pages = {618--626},
url = {http://gradcam.cloudcv.org},
booktitle = {2017 {IEEE} {International} {Conference} on {Computer} {Vision} ({ICCV})},
issn = {2380-7504},
keywords = {Visualization, Cats, Dogs, Computer architecture, Knowledge discovery},
shorttitle = {Grad-{CAM}},
year = {2017},
}
'
@InProceedings{DeepLIFT_LRP,
author = {Shrikumar, Avanti and Greenside, Peyton and Kundaje, Anshul},
booktitle = {Proceedings of the 34th {International} {Conference} on {Machine} {Learning} - {Volume} 70},
date = {2017-08},
title = {Learning important features through propagating activation differences},
location = {Sydney, NSW, Australia},
pages = {3145--3153},
publisher = {JMLR.org},
series = {{ICML}'17},
urldate = {2023-05-08},
year = {2017},
}
'
@Report{MolBERT,
author = {Fabian, Benedek and Edlich, Thomas and Gaspar, Héléna and Segler, Marwin and Meyers, Joshua and Fiscato, Marco and Ahmed, Mohamed},
date = {2020-11},
institution = {arXiv},
title = {Molecular representation learning with language models and domain-relevant auxiliary tasks},
doi = {10.48550/arXiv.2011.13230},
note = {arXiv:2011.13230},
url = {http://arxiv.org/abs/2011.13230},
urldate = {2023-05-25},
keywords = {Computer Science - Machine Learning, Computer Science - Artificial Intelligence},
year = {2020},
}
'
@Report{BART,
author = {Lewis, Mike and Liu, Yinhan and Goyal, Naman and Ghazvininejad, Marjan and Mohamed, Abdelrahman and Levy, Omer and Stoyanov, Ves and Zettlemoyer, Luke},
date = {2019-10},
institution = {arXiv},
title = {{BART}: {Denoising} {Sequence}-to-{Sequence} {Pre}-training for {Natural} {Language} {Generation}, {Translation}, and {Comprehension}},
doi = {10.48550/arXiv.1910.13461},
note = {arXiv:1910.13461},
url = {http://arxiv.org/abs/1910.13461},
urldate = {2023-08-10},
keywords = {Computer Science - Computation and Language, Computer Science - Machine Learning, Statistics - Machine Learning},
readstatus = {read},
shorttitle = {{BART}},
year = {2019},
}
'
@Article{Perspective_MolViz,
author = {Wellawatte, Geemi P. and Gandhi, Heta A. and Seshadri, Aditi and White, Andrew D.},
date = {2023-04},
journaltitle = {Journal of Chemical Theory and Computation},
journal= {Journal of Chemical Theory and Computation},
title = {A {Perspective} on {Explanations} of {Molecular} {Prediction} {Models}},
doi = {10.1021/acs.jctc.2c01235},
issn = {1549-9618},
number = {8},
pages = {2149--2160},
url = {https://doi.org/10.1021/acs.jctc.2c01235},
urldate = {2023-08-18},
volume = {19},
publisher = {American Chemical Society},
year = {2023},
}
'
@Report{unreliablesaliency,
author = {Kindermans, Pieter-Jan and Hooker, Sara and Adebayo, Julius and Alber, Maximilian and Schütt, Kristof T. and Dähne, Sven and Erhan, Dumitru and Kim, Been},
date = {2017-11},
institution = {arXiv},
title = {The ({Un})reliability of saliency methods},
doi = {10.48550/arXiv.1711.00867},
note = {arXiv:1711.00867},
url = {http://arxiv.org/abs/1711.00867},
urldate = {2023-08-21},
keywords = {Statistics - Machine Learning, Computer Science - Machine Learning},
year = {2017},
}
'
@Report{ChemBERTa,
author = {Chithrananda, Seyone and Grand, Gabriel and Ramsundar, Bharath},
date = {2020-10},
institution = {arXiv},
title = {{ChemBERTa}: {Large}-{Scale} {Self}-{Supervised} {Pretraining} for {Molecular} {Property} {Prediction}},
doi = {10.48550/arXiv.2010.09885},
note = {arXiv:2010.09885},
url = {http://arxiv.org/abs/2010.09885},
urldate = {2023-08-28},
annotation = {Comment: Submitted to NeurIPS 2020 ML for Molecules Workshop},
keywords = {Computer Science - Machine Learning, Computer Science - Computation and Language, Physics - Chemical Physics, Quantitative Biology - Biomolecules, I.2.7, I.2.1, J.2, J.3},
shorttitle = {{ChemBERTa}},
year = {2020},
}
@InProceedings{BERT,
author = {Devlin, Jacob and Chang, Ming-Wei and Lee, Kenton and Toutanova, Kristina},
booktitle = {Proceedings of the 2019 {Conference} of the {North} {American} {Chapter} of the {Association} for {Computational} {Linguistics}: {Human} {Language} {Technologies}, {Volume} 1 ({Long} and {Short} {Papers})},
date = {2019-06},
title = {{BERT}: {Pre}-training of {Deep} {Bidirectional} {Transformers} for {Language} {Understanding}},
doi = {10.18653/v1/N19-1423},
location = {Minneapolis, Minnesota},
pages = {4171--4186},
publisher = {Association for Computational Linguistics},
url = {https://aclanthology.org/N19-1423},
urldate = {2023-09-06},
shorttitle = {{BERT}},
year = {2019},
}
@Report{chinchilla,
author = {Hoffmann, Jordan and Borgeaud, Sebastian and Mensch, Arthur and Buchatskaya, Elena and Cai, Trevor and Rutherford, Eliza and Casas, Diego de Las and Hendricks, Lisa Anne and Welbl, Johannes and Clark, Aidan and Hennigan, Tom and Noland, Eric and Millican, Katie and Driessche, George van den and Damoc, Bogdan and Guy, Aurelia and Osindero, Simon and Simonyan, Karen and Elsen, Erich and Rae, Jack W. and Vinyals, Oriol and Sifre, Laurent},
date = {2022-03},
institution = {arXiv},
title = {Training {Compute}-{Optimal} {Large} {Language} {Models}},
doi = {10.48550/arXiv.2203.15556},
note = {arXiv:2203.15556},
url = {http://arxiv.org/abs/2203.15556},
urldate = {2023-09-11},
keywords = {Computer Science - Computation and Language, Computer Science - Machine Learning},
publisher = {arxiv},
year = {2022},
}
@Report{toy_models_superpos,
author = {Elhage, Nelson and Hume, Tristan and Olsson, Catherine and Schiefer, Nicholas and Henighan, Tom and Kravec, Shauna and Hatfield-Dodds, Zac and Lasenby, Robert and Drain, Dawn and Chen, Carol and Grosse, Roger and McCandlish, Sam and Kaplan, Jared and Amodei, Dario and Wattenberg, Martin and Olah, Christopher},
date = {2022-09},
institution = {arXiv},
title = {Toy {Models} of {Superposition}},
doi = {10.48550/arXiv.2209.10652},
note = {arXiv:2209.10652},
url = {http://arxiv.org/abs/2209.10652},
urldate = {2023-10-11},
annotation = {Comment: Also available at https://transformer-circuits.pub/2022/toy\_model/index.html},
keywords = {Computer Science - Machine Learning},
year = {2022},
}
@Report{monosemantic,
author = {Bricken, Trenton and Templeton, Adly and Batson, Joshua and Chen, Brian and Jermyn, Adam and Conerly, Tom and Turner, Nick and Anil, Cem and Denison, Carson and Askell, Amanda and Lasenby, Robert and Wu, Yifan and Kravec, Shauna and Schiefer, Nicholas and Maxwell, Tim and Joseph, Nicholas and Hatfield-Dodds, Zac and Tamkin, Alex and Nguyen, Karina and McLean, Brayden and Burke, Josiah E and Hume, Tristan and Carter, Shan and Henighan, Tom and Olah, Christopher},
date = {2023},
institution = {arXiv},
title = {Towards Monosemanticity: Decomposing Language Models With Dictionary Learning},
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