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@article{mccarthy1955dartmouthworkshop,
author = "McCarthy, J and Rochester, N and Shannon, C",
title = "Dartmouth workshop",
year = "1955",
}
@article{shortliffe1986medicalexpertsystems,
author = "Shortliffe, EH",
title = "Medical expert systems—knowledge tools for physicians",
year = "1986",
journal = "Unknown journal"
}
@article{vapnik1999anoverviewof,
author = "Vapnik, V.N.",
title = "An overview of statistical learning theory",
year = "1999",
journal = "IEEE transactions on neural networks",
volume = "10 5",
pages = "988-99",
month = "Sep",
doi = "10.1109/72.788640",
url = "https://doi.org/10.1109/72.788640",
publisher = "Institute of Electrical and Electronics Engineers (IEEE)",
issue = "5",
issn = "1045-9227"
}
@article{krizhevsky2012imagenetclassificationwith,
author = "Krizhevsky, A. and Sutskever, I. and Hinton, Geoffrey E.",
booktitle = "Communications of tCM",
journal = "Communications of the ACM",
pages = "84-90",
title = "ImageNet classification with deep convolutional neural networks",
volume = "60",
year = "2012",
month = "Dec",
doi = "10.1145/3065386",
url = "https://doi.org/10.1145/3065386"
}
@misc{lecun2015deeplearning,
author = "LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey",
title = "Deep learning",
year = "2015",
journal = "Nature",
volume = "521",
pages = "436-444",
month = "May",
doi = "10.1038/nature14539",
url = "https://doi.org/10.1038/nature14539",
publisher = "Springer Science and Business Media LLC",
issue = "7553",
issn = "0028-0836"
}
@inproceedings{Vaswani,
author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, \L ukasz and Polosukhin, Illia},
booktitle = {Advances in Neural Information Processing Systems},
editor = {I. Guyon and U. Von Luxburg and S. Bengio and H. Wallach and R. Fergus and S. Vishwanathan and R. Garnett},
pages = {},
publisher = {Curran Associates, Inc.},
title = {Attention is All you Need},
url = {https://proceedings.neurips.cc/paper_files/paper/2017/file/3f5ee243547dee91fbd053c1c4a845aa-Paper.pdf},
volume = {30},
year = {2017}
}
@article{rumelhart1986learning,
title={Learning representations by back-propagating errors},
author={Rumelhart, David E and Hinton, Geoffrey E and Williams, Ronald J},
journal={nature},
volume={323},
number={6088},
pages={533--536},
year={1986},
publisher={Nature Publishing Group UK London}
}
@article{hochreiter1997long,
title={Long short-term memory},
author={Hochreiter, Sepp and Schmidhuber, J{\"u}rgen},
journal={Neural computation},
volume={9},
number={8},
pages={1735--1780},
year={1997},
publisher={MIT press}
}
@article{uhler2022machinelearningapproaches,
author = "Uhler, Caroline and Shivashankar, G. V.",
title = "Machine Learning Approaches to Single-Cell Data Integration and Translation",
year = "2022",
journal = "Proceedings of the IEEE",
volume = "110",
pages = "557-576",
month = "May",
doi = "10.1109/jproc.2022.3166132",
url = "https://doi.org/10.1109/jproc.2022.3166132",
publisher = "Institute of Electrical and Electronics Engineers (IEEE)",
issue = "5",
issn = "0018-9219"
}
@article{jumper2021highly,
title={Highly accurate protein structure prediction with AlphaFold},
author={Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
journal={nature},
volume={596},
number={7873},
pages={583--589},
year={2021},
publisher={Nature Publishing Group UK London}
}
@article{weiskittel2021thetrifectaof,
author = "Weiskittel, Taylor M. and Correia, Cristina and Yu, Grace T. and Ung, Choong Yong and Kaufmann, Scott H. and Billadeau, Daniel D. and Li, Hu",
title = "The Trifecta of Single-Cell, Systems-Biology, and Machine-Learning Approaches",
year = "2021",
journal = "Genes",
volume = "12",
pages = "1098",
month = "Jul",
doi = "10.3390/genes12071098",
url = "https://doi.org/10.3390/genes12071098",
publisher = "MDPI AG",
issue = "7",
issn = "2073-4425"
}
@article{jumper2021highlyaccurateprotein,
author = "Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and Žídek, Augustin and Potapenko, Anna and Bridgla, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis",
title = "Highly accurate protein structure prediction with AlphaFold",
year = "2021",
journal = "Nature",
volume = "596",
pages = "583-589",
month = "Jul",
doi = "10.1038/s41586-021-03819-2",
url = "https://doi.org/10.1038/s41586-021-03819-2",
publisher = "Springer Science and Business Media LLC",
issue = "7873",
issn = "0028-0836"
}
@article{nussinov2022alphafoldartificialintelligence,
author = "Nussinov, Ruth and Zhang, Mingzhen and Liu, Yonglan and Jang, Hyunbum",
title = "AlphaFold, Artificial Intelligence (AI), and Allostery",
year = "2022",
journal = "The Journal of Physical Chemistry. B",
volume = "126",
pages = "6372-6383",
month = "Aug",
doi = "10.1021/acs.jpcb.2c04346",
url = "https://doi.org/10.1021/acs.jpcb.2c04346",
publisher = "American Chemical Society (ACS)",
issue = "34",
issn = "1520-6106"
}
@article{greener2022aguideto,
author = "Greener, Joe G. and Kandathil, Shaun M. and Moffat, Lewis and Jones, David T.",
title = "A guide to machine learning for biologists",
year = "2022",
journal = "Nature Reviews Molecular Cell Biology",
volume = "23",
pages = "40-55",
month = "Sep",
doi = "10.1038/s41580-021-00407-0",
url = "https://doi.org/10.1038/s41580-021-00407-0",
publisher = "Springer Science and Business Media LLC",
issue = "1",
issn = "1471-0072"
}
@article{sealfon2021machinelearningmethods,
author = "Sealfon, Rachel S. G. and Wong, Aaron K. and Troyanskaya, Olga G.",
title = "Machine learning methods to model multicellular complexity and tissue specificity",
year = "2021",
journal = "Nature Reviews Materials",
volume = "6",
pages = "717-729",
month = "Jul",
doi = "10.1038/s41578-021-00339-3",
url = "https://doi.org/10.1038/s41578-021-00339-3",
publisher = "Springer Science and Business Media LLC",
issue = "8",
issn = "2058-8437"
}
@article{tan2021applyingmachinelearning,
author = "Tan, Xiao and Su, Andrew T. and Hajiabadi, Hamideh and Tran, Minh and Nguyen, Quan",
title = "Applying Machine Learning for Integration of Multi-Modal Genomics Data and Imaging Data to Quantify Heterogeneity in Tumour Tissues",
year = "2021",
journal = "Methods in molecular biology",
volume = "2190",
pages = "209-228",
doi = "10.1007/978-1-0716-0826-5\_10",
url = "https://doi.org/10.1007/978-1-0716-0826-5\_10",
month = "Aug",
publisher = "Springer US",
issn = "1064-3745"
}
@article{zhai2016researchonimage,
author = "Zhai, Hao",
title = "Research on Image Recognition Based on Deep Learning Technology",
year = "2016",
journal = "ArXiv",
pages = "266-270",
month = "Sep",
doi = "10.2991/amitp-16.2016.53",
url = "https://doi.org/10.2991/amitp-16.2016.53",
publisher = "Atlantis Press"
}
@article{wu2015deepimagescaling,
author = "Wu, Ren and Yan, Shengen and Shan, Yi and Dang, Qingqing and Sun, Gang",
title = "Deep Image: Scaling up Image Recognition",
year = "2015",
journal = "Preprint",
month = "Jan",
doi = "10.48550/arxiv.1501.02876",
url = "https://doi.org/10.48550/arxiv.1501.02876",
publisher = "arXiv"
}
@misc{russakovsky2015imagenetlargescale,
author = "Russakovsky, Olga and Deng, Jia and Su, Hao and Krause, Jonathan and Satheesh, Sanjeev and Ma, Sean and Huang, Zhiheng and Karpathy, Andrej and Khosla, Aditya and Bernstein, Michael and Berg, Alexander C. and Fei-Fei, Li",
title = "ImageNet Large Scale Visual Recognition Challenge",
year = "2015",
journal = "International Journal of Computer Vision",
volume = "115",
pages = "211-252",
month = "Apr",
doi = "10.1007/s11263-015-0816-y",
url = "https://doi.org/10.1007/s11263-015-0816-y",
publisher = "Springer Science and Business Media LLC",
issue = "3",
issn = "0920-5691"
}
@article{bengio2013deeplearningof,
author = "Bengio, Yoshua",
title = "Deep Learning of Representations: Looking Forward",
year = "2013",
journal = "ArXiv",
pages = "1-37",
month = "May",
doi = "10.48550/arxiv.1305.0445",
url = "https://doi.org/10.48550/arxiv.1305.0445",
publisher = "Springer Berlin Heidelberg",
issn = "0302-9743"
}
@article{asada2021singlecellanalysisusing,
author = "Asada, Ken and Takasawa, Ken and Machino, Hidenori and Takahashi, Satoshi and Shinkai, Norio and Bolatkan, Amina and Kobayashi, Kazuma and Komatsu, Masaaki and Kaneko, Syuzo and Okamoto, Koji and Hamamoto, Ryuji",
title = "Single-Cell Analysis Using Machine Learning Techniques and Its Application to Medical Research",
year = "2021",
journal = "Biomedicines",
volume = "9",
pages = "1513",
month = "Oct",
doi = "10.3390/biomedicines9111513",
url = "https://doi.org/10.3390/biomedicines9111513",
publisher = "MDPI AG",
issue = "11",
issn = "2227-9059"
}
@misc{GoogleML, url={https://developers.google.com/machine-learning/crash-course/llm}, journal={Google}, publisher={Google}}
@article{white2021deep,
title={Deep Learning for Molecules and Materials},
journal={Living Journal of Computational Molecular Science},
author={White, Andrew D},
url={https://dmol.pub},
year={2021},
volume={3},
number={1},
pages={1499},
doi={10.33011/livecoms.3.1.1499}
}
@article{materi2007comp,
author = "Materi, Wayne and Wishart, David S.",
title = "Computational systems biology in drug discovery and development: methods and applications.",
year = "2007",
journal = "Drug discovery today",
volume = "12 7-8",
pages = "295-303",
month = "Apr",
doi = "10.1016/j.drudis.2007.02.013",
url = "https://doi.org/10.1016/j.drudis.2007.02.013",
publisher = "Elsevier BV",
issue = "7-8",
issn = "1359-6446"
}
@article{zhou2024dynamicmodelingin,
author = "Zhou, Jiayao and Yan, Shudan",
title = "Dynamic Modeling in Systems Biology: From Pathway Analysis to Whole-Cell Simulations",
year = "2024",
journal = "Computational Molecular Biology",
month = "Jan",
doi = "10.5376/cmb.2024.14.0016",
url = "https://doi.org/10.5376/cmb.2024.14.0016",
publisher = "Sophia Publishing Group, Inc.",
issn = "1927-5587"
}
@misc{schmidt2008thesimbiosnational,
author = "Schmidt, Jeanette P. and Delp, Scott L. and Sherman, Michael A. and Taylor, Charles A. and Pande, Vijay S. and Altman, Russ B.",
title = "The Simbios National Center: Systems Biology in Motion",
year = "2008",
journal = "Proceedings of the IEEE",
volume = "96",
pages = "1266-1280",
month = "Aug",
doi = "10.1109/jproc.2008.925454",
url = "https://doi.org/10.1109/jproc.2008.925454",
publisher = "Institute of Electrical and Electronics Engineers (IEEE)",
issue = "8",
issn = "0018-9219"
}
@article{huggins2019biomolecularsimulationsfrom,
author = "Huggins, David J. and Biggin, Philip C. and Dämgen, Marc A. and Essex, Jonathan W. and Harris, Sarah A. and Henchman, Richard H. and Khalid, Syma and Kuzmanic, Antonija and Laughton, Charles A. and Michel, Julien and Mulholland, Adrian J. and Rosta, Edina and Sansom, Mark S. P. and van der Kamp, Marc W.",
title = "Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity",
year = "2019",
journal = "Wiley Interdisciplinary Reviews: Computational Molecular Science",
volume = "9",
month = "Sep",
doi = "10.1002/wcms.1393",
url = "https://doi.org/10.1002/wcms.1393",
publisher = "Wiley",
issue = "3",
issn = "1759-0876"
}
@article{metzcar2019areviewof,
author = "Metzcar, John and Wang, Yafei and Heiland, Randy W. and Macklin, P.",
title = "A Review of Cell-Based Computational Modeling in Cancer Biology",
year = "2019",
journal = "JCO Clinical Cancer Informatics",
pages = "1-13",
month = "Dec",
doi = "10.1200/cci.18.00069",
url = "https://doi.org/10.1200/cci.18.00069",
publisher = "American Society of Clinical Oncology (ASCO)",
issue = "3",
issn = "2473-4276"
}
@article{goshisht2024,
author = "Goshisht, Manoj Kumar",
title = "Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges",
year = "2024",
journal = "ACS Omega",
volume = "9",
pages = "9921-9945",
month = "Feb",
doi = "10.1021/acsomega.3c05913",
url = "https://doi.org/10.1021/acsomega.3c05913",
publisher = "American Chemical Society (ACS)",
issue = "9",
issn = "2470-1343"
}
@article{ahmed2013,
author = "Ahmed, Ashfaq and Aljahdali, K. S. and Hussain, S. and Kumari, M. and Godara, Sunila and Kinoshita, A.",
title = "Comparative Prediction Performance with Support Vector Machine and Random Forest Classification Techniques",
year = "2013",
journal = "International Journal of Computer Applications",
volume = "69",
pages = "12-16",
month = "May",
doi = "10.5120/11885-7922",
url = "https://doi.org/10.5120/11885-7922",
publisher = "Foundation of Computer Science",
issue = "11",
issn = "0975-8887"
}
@article{qi2012randomforestfor,
author = "Qi, Yanjun",
title = "Random Forest for Bioinformatics",
year = "2012",
journal = "ArXiv",
pages = "307-323",
doi = "10.1007/978-1-4419-9326-7\_11",
url = "https://doi.org/10.1007/978-1-4419-9326-7\_11",
month = "Jan",
publisher = "Springer New York"
}
@article{touw2013dataminingin,
author = "Touw, W. G. and Bayjanov, J. R. and Overmars, L. and Backus, L. and Boekhorst, J. and Wels, M. and van Hijum, S. A. F. T.",
title = "Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?",
year = "2013",
journal = "Briefings in Bioinformatics",
volume = "14",
pages = "315-326",
month = "Jul",
doi = "10.1093/bib/bbs034",
url = "https://doi.org/10.1093/bib/bbs034",
publisher = "Oxford University Press (OUP)",
issue = "3",
issn = "1467-5463"
}
@article{tarca2007machinelearningand,
author = "Tarca, Adi L and Carey, Vincent J and Chen, Xue-wen and Romero, Roberto and Drăghici, Sorin",
title = "Machine Learning and Its Applications to Biology",
year = "2007",
journal = "PLoS Computational Biology",
volume = "3",
pages = "e116",
month = "Jun",
doi = "10.1371/journal.pcbi.0030116",
url = "https://doi.org/10.1371/journal.pcbi.0030116",
publisher = "Public Library of Science (PLoS)",
issue = "6",
issn = "1553-7358"
}
@article{kumar2023,
author = "Kumar, Suresh and Guruparan, Dhanyashri and Aaron, Pavithren and Telajan, Philemon and Mahadevan, Kavinesh and Davagandhi, Dinesh and Yue, Ong Xin",
title = "Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlook",
year = "2023",
journal = "ArXiv",
volume = "abs/2310.03086",
month = "Oct",
doi = "10.48550/arxiv.2310.03086",
url = "https://doi.org/10.48550/arxiv.2310.03086",
publisher = "arXiv"
}
@article{hein2025aiandmachine,
author = "Hein, Zaw Myo and Guruparan, Dhanyashri and Okunsai, Blaire and Nassir, Che Mohd Nasril Che Mohd and Ramli, Muhammad Danial Che and Kumar, Suresh",
title = "AI and Machine Learning in Biology: From Genes to Proteins",
year = "2025",
journal = "Biology",
volume = "14",
pages = "1453",
month = "Oct",
doi = "10.3390/biology14101453",
url = "https://doi.org/10.3390/biology14101453",
publisher = "MDPI AG",
issue = "10",
issn = "2079-7737"
}
@article{li2024progress,
author = "Li, Qing and Hu, Zhihang and Wang, Yixuan and Li, Lei and Fan, Yimin and King, Irwin and Song, Le and Li, Yu",
title = "Progress and opportunities of foundation models in bioinformatics",
year = "2024",
journal = "Briefings in Bioinformatics",
volume = "25",
month = "Feb",
doi = "10.48550/arxiv.2402.04286",
url = "https://doi.org/10.48550/arxiv.2402.04286",
publisher = "arXiv"
}
@article{guo2025foundationmodelsin,
author = "Guo, Fei and Guan, Renchu and Li, Yaohang and Liu, Qi and Wang, Xiaowo and Yang, Can and Wang, Jianxin",
title = "Foundation models in bioinformatics",
year = "2025",
journal = "National Science Review",
volume = "12",
month = "Jan",
doi = "10.1093/nsr/nwaf028",
url = "https://doi.org/10.1093/nsr/nwaf028",
publisher = "Oxford University Press (OUP)",
issn = "2095-5138"
}
@article{lin2022languagemodelsof,
author = "Lin, Z and Akin, H and Rao, R and Hie, B and Zhu, Z and Lu, W",
title = "Language models of protein sequences at the scale of evolution enable accurate structure prediction",
year = "2022",
journal = "MedRxiv",
doi = "10.1101/2022.07.20.500902v1",
url = "https://doi.org/10.1101/2022.07.20.500902v1"
}
@misc{lin2023evolutionaryscalepredictionof,
author = "Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and Smetanin, Nikita and Verkuil, Robert and Kabeli, Ori and Shmueli, Yaniv and dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Salvatore and Rives, Alexander",
title = "Evolutionary-scale prediction of atomic-level protein structure with a language model",
year = "2023",
journal = "Science",
volume = "379",
pages = "1123-1130",
month = "Mar",
doi = "10.1126/science.ade2574",
url = "https://doi.org/10.1126/science.ade2574",
publisher = "American Association for the Advancement of Science (AAAS)",
issue = "6637",
issn = "0036-8075"
}
@article{farea2025using,
author = "Farea, Amer and Yli-Harja, Olli and Emmert-Streib, Frank",
title = "Using Physics-Informed Neural Networks for Modeling Biological and Epidemiological Dynamical Systems",
year = "2025",
journal = "Mathematics",
volume = "13",
pages = "1664",
month = "May",
doi = "10.3390/math13101664",
url = "https://doi.org/10.3390/math13101664",
publisher = "MDPI AG",
issue = "10",
issn = "2227-7390"
}
@article{alquraishi2021,
author = "AlQuraishi, Mohammed and Sorger, Peter K.",
title = "Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms",
year = "2021",
journal = "Nature Methods",
volume = "18",
pages = "1169-1180",
month = "Oct",
doi = "10.1038/s41592-021-01283-4",
url = "https://doi.org/10.1038/s41592-021-01283-4",
publisher = "Springer Science and Business Media LLC",
issue = "10",
issn = "1548-7091"
}
@article{devlin2019bertpretrainingof,
author = "Devlin, Jacob and Chang, Ming-Wei and Lee, Kenton and Toutanova, Kristina",
title = "BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding",
year = "2019",
journal = "ArXiv",
pages = "4171-4186",
doi = "10.48550/arxiv.1810.04805",
url = "https://doi.org/10.48550/arxiv.1810.04805"
}
@article{gu2021domain,
author = "Gu, Yu and Tinn, Robert and Cheng, Hao and Lucas, Michael and Usuyama, Naoto and Liu, Xiaodong and Naumann, Tristan and Gao, Jianfeng and Poon, Hoifung",
title = "Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing",
year = "2021",
journal = "ACM Transactions on Computing for Healthcare",
volume = "3",
pages = "1-23",
month = "Oct",
doi = "10.1145/3458754",
url = "https://doi.org/10.1145/3458754",
publisher = "Association for Computing Machinery (ACM)",
issue = "1",
issn = "2691-1957"
}
@article{luo2022biogpt,
author = "Luo, Renqian and Sun, Liai and Xia, Yingce and Qin, Tao and Zhang, Sheng and Poon, Hoifung and Liu, Tie-Yan",
title = "BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining",
year = "2022",
journal = "Briefings in bioinformatics",
month = "Sep",
doi = "10.48550/arxiv.2210.10341",
url = "https://doi.org/10.48550/arxiv.2210.10341",
volume = "23",
publisher = "Oxford University Press (OUP)",
issue = "6",
issn = "1467-5463"
}
@article{brandes2022proteinbertauniversal,
author = "Brandes, Nadav and Ofer, Dan and Peleg, Yam and Rappoport, Nadav and Linial, Michal",
title = "ProteinBERT: a universal deep-learning model of protein sequence and function",
year = "2022",
journal = "Bioinformatics",
volume = "38",
pages = "2102-2110",
month = "Feb",
doi = "10.1093/bioinformatics/btac020",
url = "https://doi.org/10.1093/bioinformatics/btac020",
publisher = "Oxford University Press (OUP)",
issue = "8",
issn = "1367-4803"
}
@article{ouyang2022traininglanguagemodels,
author = "Ouyang, Long and Wu, Jeff and Jiang, Xu and Almeida, Diogo and Wainwright, Carroll L. and Mishkin, Pamela and Zhang, Chong and Agarwal, Sandhini and Slama, Katarina and Ray, Alex and Schulman, John and Hilton, Jacob and Kelton, Fraser and Miller, Luke and Simens, Maddie and Askell, Amanda and Welinder, Peter and Christiano, Paul and Leike, Jan and Lowe, Ryan",
title = "Training language models to follow instructions with human feedback",
year = "2022",
journal = "Preprint",
month = "Jan",
doi = "10.48550/arxiv.2203.02155",
url = "https://doi.org/10.48550/arxiv.2203.02155",
publisher = "arXiv"
}
@misc{chaudhari2025rlhfdeciphereda,
author = "Chaudhari, Shreyas and Aggarwal, Pranjal and Murahari, Vishvak and Rajpurohit, Tanmay and Kalyan, Ashwin and Narasimhan, Karthik and Deshpande, Ameet and da Silva, Bruno Castro",
title = "RLHF Deciphered: A Critical Analysis of Reinforcement Learning from Human Feedback for LLMs",
year = "2025",
journal = "ACM Computing Surveys",
month = "Jun",
doi = "10.1145/3743127",
url = "https://doi.org/10.1145/3743127",
publisher = "Association for Computing Machinery (ACM)",
issn = "0360-0300"
}
@article{ouyang2022training,
title={Training language models to follow instructions with human feedback},
author={Ouyang, Long and Wu, Jeffrey and Jiang, Xu and Almeida, Diogo and Wainwright, Carroll and Mishkin, Pamela and Zhang, Chong and Agarwal, Sandhini and Slama, Katarina and Ray, Alex and others},
journal={Advances in neural information processing systems},
volume={35},
pages={27730--27744},
year={2022}
}
@article{duchettoUnknownyearaligninglargelanguage,
author = "Duchetto, F Del",
title = "Aligning Large Language Models: A Study on Reinforcement Learning from Human Feedback",
year = "Unknown year",
journal = "Unknown journal"
}
@article{mars2022fromwordembeddings,
author = "Mars, Mourad",
title = "From Word Embeddings to Pre-Trained Language Models: A State-of-the-Art Walkthrough",
year = "2022",
journal = "Applied Sciences",
volume = "12",
pages = "8805",
month = "Sep",
doi = "10.3390/app12178805",
url = "https://doi.org/10.3390/app12178805",
publisher = "MDPI AG",
issue = "17",
issn = "2076-3417"
}
@article{hallee2023proteinproteininteractionprediction,
author = "Hallee, Logan and Gleghorn, Jason P.",
title = "Protein-Protein Interaction Prediction is Achievable with Large Language Models",
year = "2023",
journal = "bioRxiv",
month = "Jun",
doi = "10.1101/2023.06.07.544109",
url = "https://doi.org/10.1101/2023.06.07.544109",
publisher = "Cold Spring Harbor Laboratory"
}
@misc{lewis2021,
title={Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks},
author={Patrick Lewis and Ethan Perez and Aleksandra Piktus and Fabio Petroni and Vladimir Karpukhin and Naman Goyal and Heinrich Küttler and Mike Lewis and Wen-tau Yih and Tim Rocktäschel and Sebastian Riedel and Douwe Kiela},
year={2021},
eprint={2005.11401},
archivePrefix={arXiv},
primaryClass={cs.CL},
url={https://arxiv.org/abs/2005.11401},
}
@article{ruffolo2024designing,
title={Designing proteins with language models},
author={Ruffolo, Jeffrey A and Madani, Ali},
journal={Nature Biotechnology},
volume={42},
number={2},
pages={200--202},
year={2024},
publisher={Nature Publishing Group US New York}
}
@article{ovchinnikov2017protein,
title={Protein structure determination using metagenome sequence data},
author={Ovchinnikov, Sergey and Park, Hahnbeom and Varghese, Neha and Huang, Po-Ssu and Pavlopoulos, Georgios A and Kim, David E and Kamisetty, Hetunandan and Kyrpides, Nikos C and Baker, David},
journal={Science},
volume={355},
number={6322},
pages={294--298},
year={2017},
publisher={American Association for the Advancement of Science}
}
@article{bialek2005physical,
title={Physical limits to biochemical signaling},
author={Bialek, William and Setayeshgar, Sima},
journal={Proceedings of the National Academy of Sciences},
volume={102},
number={29},
pages={10040--10045},
year={2005},
publisher={National Academy of Sciences}
}
@article{ten2016fundamental,
title={Fundamental limits to cellular sensing},
author={ten Wolde, Pieter Rein and Becker, Nils B and Ouldridge, Thomas E and Mugler, Andrew},
journal={Journal of Statistical Physics},
volume={162},
number={5},
pages={1395--1424},
year={2016},
publisher={Springer}
}
@article{ji2021dnabert,
title={DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome},
author={Ji, Yanrong and Zhou, Zhihan and Liu, Han and Davuluri, Ramana V},
journal={Bioinformatics},
volume={37},
number={15},
pages={2112--2120},
year={2021},
publisher={Oxford University Press}
}
@inproceedings{zhou2024dnabert,
title={DNABERT-2: Efficient foundation model and benchmark for multi-species genomes},
author={Zhou, Zhihan and Ji, Yanrong and Li, Weijian and Dutta, Pratik and Davuluri, Ramana and Liu, Han},
booktitle={International Conference on Learning Representations},
volume={2024},
pages={41642--41665},
year={2024}
}
@article{avsec2021effective,
title={Effective gene expression prediction from sequence by integrating long-range interactions},
author={Avsec, {\v{Z}}iga and Agarwal, Vikram and Visentin, Daniel and Ledsam, Joseph R and Grabska-Barwinska, Agnieszka and Taylor, Kyle R and Assael, Yannis and Jumper, John and Kohli, Pushmeet and Kelley, David R},
journal={Nature methods},
volume={18},
number={10},
pages={1196--1203},
year={2021},
publisher={Nature Publishing Group US New York}
}
@article{nguyen2023hyenadna,
title={Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution},
author={Nguyen, Eric and Poli, Michael and Faizi, Marjan and Thomas, Armin and Wornow, Michael and Birch-Sykes, Callum and Massaroli, Stefano and Patel, Aman and Rabideau, Clayton and Bengio, Yoshua and others},
journal={Advances in neural information processing systems},
volume={36},
pages={43177--43201},
year={2023}
}
@article{cui2024scgpt,
title={scGPT: toward building a foundation model for single-cell multi-omics using generative AI},
author={Cui, Haotian and Wang, Chloe and Maan, Hassaan and Pang, Kuan and Luo, Fengning and Duan, Nan and Wang, Bo},
journal={Nature methods},
volume={21},
number={8},
pages={1470--1480},
year={2024},
publisher={Nature Publishing Group US New York}
}
@article{theodoris2023transfer,
title={Transfer learning enables predictions in network biology},
author={Theodoris, Christina V and Xiao, Ling and Chopra, Anant and Chaffin, Mark D and Al Sayed, Zeina R and Hill, Matthew C and Mantineo, Helene and Brydon, Elizabeth M and Zeng, Zexian and Liu, X Shirley and others},
journal={Nature},
volume={618},
number={7965},
pages={616--624},
year={2023},
publisher={Nature Publishing Group UK London}
}
@article{ferruz2022protgpt2,
title={ProtGPT2 is a deep unsupervised language model for protein design},
author={Ferruz, Noelia and Schmidt, Steffen and H{\"o}cker, Birte},
journal={Nature communications},
volume={13},
number={1},
pages={4348},
year={2022},
publisher={Nature Publishing Group UK London}
}
@article{madani2023large,
title={Large language models generate functional protein sequences across diverse families},
author={Madani, Ali and Krause, Ben and Greene, Eric R and Subramanian, Subu and Mohr, Benjamin P and Holton, James M and Olmos Jr, Jose Luis and Xiong, Caiming and Sun, Zachary Z and Socher, Richard and others},
journal={Nature biotechnology},
volume={41},
number={8},
pages={1099--1106},
year={2023},
publisher={Nature Publishing Group US New York}
}
@article{brandes2022proteinbert,
title={ProteinBERT: a universal deep-learning model of protein sequence and function},
author={Brandes, Nadav and Ofer, Dan and Peleg, Yam and Rappoport, Nadav and Linial, Michal},
journal={Bioinformatics},
volume={38},
number={8},
pages={2102--2110},
year={2022},
publisher={Oxford University Press}
}
@article{hendrycks2020measuring,
title={Measuring massive multitask language understanding},
author={Hendrycks, Dan and Burns, Collin and Basart, Steven and Zou, Andy and Mazeika, Mantas and Song, Dawn and Steinhardt, Jacob},
journal={arXiv preprint arXiv:2009.03300},
year={2020}
}
@article{laurent2024lab,
title={Lab-bench: Measuring capabilities of language models for biology research},
author={Laurent, Jon M and Janizek, Joseph D and Ruzo, Michael and Hinks, Michaela M and Hammerling, Michael J and Narayanan, Siddharth and Ponnapati, Manvitha and White, Andrew D and Rodriques, Samuel G},
journal={arXiv preprint arXiv:2407.10362},
year={2024}
}