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  booktitle = {Proceedings of the 38th International Conference on Machine Learning},
  pages = {10358--10368},
  year = {2021},
  volume = {139},
  series = {Proceedings of Machine Learning Research},
  publisher = {PMLR},
  url = {https://proceedings.mlr.press/v139/trabucco21a.html}
}

@inproceedings{designbench,
  title = {{Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization}},
  author = {Trabucco, Brandon and Geng, Xinyang and Kumar, Aviral and Levine, Sergey},
  booktitle = {Proceedings of the 39th International Conference on Machine Learning},
  pages = {21658--21676},
  year = {2022},
  volume = {162},
  series = {Proceedings of Machine Learning Research},
  publisher = {PMLR},
  url = {https://proceedings.mlr.press/v162/trabucco22a.html}
}

@article{mmseqs,
  title={MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets},
  author={Steinegger, Martin and S{\"o}ding, Johannes},
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}

@misc{mogdfm,
 title = {{Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design}},
 author = {Chen, Tong and Zhang, Yinuo and Tang, Sophia and Chatterjee, Pranam},
 year = {2025},
 eprint = {2505.07086},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2505.07086}
}

@misc{allogen,
 title = {{AlloGen: Conformation-Selective Binder Generation with Differential State Scoring}},
 author = {Cao, Hanqun and Quinn, Zachary and Pal, Aastha and Kimura, Sumi and Zhang, Jingjie and Heng, Pheng Ann and Chatterjee, Pranam},
 year = {2026},
 eprint = {2606.05474},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2606.05474}
}

@misc{peptune,
 title = {{PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion}},
 author = {Tang, Sophia and Zhang, Yinuo and Chatterjee, Pranam},
 year = {2024},
 eprint = {2412.17780},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2412.17780}
}

@misc{react,
 title = {{ReAct: Synergizing Reasoning and Acting in Language Models}},
 author = {Yao, Shunyu and Zhao, Jeffrey and Yu, Dian and Du, Nan and Shafran, Izhak and Narasimhan, Karthik and Cao, Yuan},
 year = {2022},
 eprint = {2210.03629},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2210.03629}
}

@misc{reflexion,
 title = {{Reflexion: Language Agents with Verbal Reinforcement Learning}},
 author = {Shinn, Noah and Cassano, Federico and Berman, Edward and Gopinath, Ashwin and Narasimhan, Karthik and Yao, Shunyu},
 year = {2023},
 eprint = {2303.11366},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2303.11366}
}

@misc{paperqa,
 title = {{Language agents achieve superhuman synthesis of scientific knowledge}},
 author = {Skarlinski, Michael D. and Cox, Sam and Laurent, Jon M. and Braza, James D. and Hinks, Michaela and Hammerling, Michael J. and Ponnapati, Manvitha and Rodriques, Samuel G. and White, Andrew D.},
 year = {2024},
 eprint = {2409.13740},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2409.13740}
}

@misc{conformal,
 title = {{A Gentle Introduction to Conformal Prediction and Distribution-Free Uncertainty Quantification}},
 author = {Angelopoulos, Anastasios N. and Bates, Stephen},
 year = {2021},
 eprint = {2107.07511},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2107.07511}
}

@misc{biodiscovery,
 title = {{BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments}},
 author = {Roohani, Yusuf and Lee, Andrew and Huang, Qian and Vora, Jian and Steinhart, Zachary and Huang, Kexin and Marson, Alexander and Liang, Percy and Leskovec, Jure},
 year = {2024},
 eprint = {2405.17631},
 archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2405.17631}
}

@misc{soapia,
 title = {{SOAPIA: Specificity-Guided Generation of Off-Target-Avoiding Protein Interactions with High Target Affinity}},
 author = {Vincoff, Sophia and Liu, Howard and Linardic, Corinne M. and Chatterjee, Pranam},
 year = {2026},
 note = {Supplied ICML workshop manuscript, Generative and Agentic AI for Biology}
}
@misc{td3b,
 title = {{TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation}},
 author = {Cao, Hanqun and Pal, Aastha and Tang, Sophia and Zhang, Yinuo and Zhang, Jingjie and Heng, Pheng Ann and Chatterjee, Pranam},
 year = {2026},
 note = {Supplied ICML manuscript},
 url = {https://huggingface.co/ChatterjeeLab/TD3B}
}
@misc{snooppi,
 title = {{SNOOPPI: Sequence-Normalized Database of On- and Off-Target Protein-Protein Interactions}},
 author = {{Chatterjee Lab}},
 year = {2026},
 doi = {10.57967/hf/10413},
 note = {Dataset revision a1c75633343e292db8bb25e3356d0b8cd64afa91},
 url = {https://huggingface.co/datasets/ChatterjeeLab/SNOOPPI}
}
@misc{muse,
 title = {{Muse Glimmer-30B Model Card}},
 author = {{Meta Superintelligence Lab}},
 year = {2026},
 note = {Revision a4e59da52a7bc87ae7251dd5545c0dd437c44b68. Accessed 20 September 2026},
 url = {https://huggingface.co/meta-models/Muse-Glimmer-30B}
}

@article{pepmlm,
 title = {{Target sequence-conditioned design of peptide binders using masked language modeling}},
 author = {Chen, Leo Tianlai and Quinn, Zachary and Dumas, Madeleine and Peng, Christina and Hong, Lauren and Lopez-Gonzalez, Moises and Mestre, Alexander and Watson, Rio and Vincoff, Sophia and Zhao, Lin and Wu, Jianli and Stavrand, Audrey and Schaepers-Cheu, Mayumi and Wang, Tian Zi and Srijay, Divya and Monticello, Connor and Vure, Pranay and Pulugurta, Rishab and Pertsemlidis, Sarah and Kholina, Kseniia and Goel, Shrey and DeLisa, Matthew P. and Chi, Jen-Tsan Ashley and Truant, Ray and Aguilar, Hector C. and Chatterjee, Pranam},
 year = {2025},
 journal = {Nature Biotechnology},
 doi = {10.1038/s41587-025-02761-2},
 url = {https://doi.org/10.1038/s41587-025-02761-2}
}

@misc{lapep,
 title = {{LaPep: Can Language Contribute to Property-Guided Peptide Design?}},
 author = {{Anonymous Authors}},
 year = {2026},
 note = {Supplied NeurIPS manuscript}
}

@article{duab,
 title = {Programmable protein stabilization with language model-derived peptide guides},
 author = {Hong, Lauren and Ye, Tianzheng and Wang, Tian Z. and Srijay, Divya and Liu, Howard and Zhao, Lin and Watson, Rio and Vincoff, Sophia and Chen, Tianlai and Kholina, Kseniia and Goel, Shrey and DeLisa, Matthew P. and Chatterjee, Pranam},
 journal = {Nature Communications},
 year = {2025},
 volume = {16},
 pages = {3555},
 doi = {10.1038/s41467-025-58872-6}
}

@misc{llmcompiler,
 title = {{An LLM Compiler for Parallel Function Calling}},
 author = {Kim, Sehoon and Moon, Suhong and Tabrizi, Ryan and Lee, Nicholas and Mahoney, Michael W. and Keutzer, Kurt and Gholami, Amir},
 year = {2024}, eprint = {2312.04511}, archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2312.04511}, note = {ICML 2024}
}
@misc{llmp,
 title = {{LLM+P: Empowering Large Language Models with Optimal Planning Proficiency}},
 author = {Liu, Bo and Jiang, Yuqian and Zhang, Xiaohan and Liu, Qiang and Zhang, Shiqi and Biswas, Joydeep and Stone, Peter},
 year = {2023}, eprint = {2304.11477}, archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2304.11477}
}
@misc{taubench,
 title = {{$\tau$-bench: A Benchmark for Tool-Agent-User Interaction in Real-World Domains}},
 author = {Yao, Shunyu and Shinn, Noah and Razavi, Pedram and Narasimhan, Karthik},
 year = {2024}, eprint = {2406.12045}, archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2406.12045}
}
@misc{agentbench,
 title = {{AgentBench: Evaluating LLMs as Agents}},
 author = {Liu, Xiao and Yu, Hao and Zhang, Hanchen and Xu, Yifan and Lei, Xuanyu and Lai, Hanyu and Gu, Yu and Ding, Hangliang and Men, Kaiwen and Yang, Kejuan and Zhang, Shudan and Deng, Xiang and Zeng, Aohan and Du, Zhengxiao and Zhang, Chenhui and Shen, Sheng and Zhang, Tianjun and Su, Yu and Sun, Huan and Huang, Minlie and Dong, Yuxiao and Tang, Jie},
 year = {2024}, eprint = {2308.03688}, archivePrefix = {arXiv},
 url = {https://arxiv.org/abs/2308.03688}, note = {ICLR 2024}
}

@article{hongreview,
  title = {{AI-Designed Peptides as Tools for Biochemistry}},
  author = {Hong, Lauren and Vincoff, Sophia and Chatterjee, Pranam},
  year = {2026},
  journal = {Biochemistry},
  volume = {65},
  number = {8},
  pages = {1071--1083},
  doi = {10.1021/acs.biochem.6c00138},
  url = {https://doi.org/10.1021/acs.biochem.6c00138}
}

@article{therapeutic2022,
  title = {{Therapeutic peptides: current applications and future directions}},
  author = {Wang, Lei and Wang, Nanxi and Zhang, Wenping and Cheng, Xurui and Yan, Zhibin and Shao, Gang and Wang, Xi and Wang, Rui and Fu, Caiyun},
  year = {2022},
  journal = {Signal Transduction and Targeted Therapy},
  volume = {7},
  number = {1},
  pages = {48},
  doi = {10.1038/s41392-022-00904-4},
  url = {https://doi.org/10.1038/s41392-022-00904-4}
}

@article{membranemacrocycles,
  title = {{Accurate de novo design of membrane-traversing macrocycles}},
  author = {Bhardwaj, Gaurav and O’Connor, Jacob and Rettie, Stephen and Huang, Yen-Hua and Ramelot, Theresa A. and Mulligan, Vikram Khipple and Alpkilic, Gizem Gokce and Palmer, Jonathan and Bera, Asim K. and Bick, Matthew J. and Di Piazza, Maddalena and Li, Xinting and Hosseinzadeh, Parisa and Craven, Timothy W. and Tejero, Roberto and Lauko, Anna and Choi, Ryan and Glynn, Calina and Dong, Linlin and Griffin, Robert and van Voorhis, Wesley C. and Rodriguez, Jose and Stewart, Lance and Montelione, Gaetano T. and Craik, David and Baker, David},
  year = {2022},
  journal = {Cell},
  volume = {185},
  number = {19},
  pages = {3520--3532.e26},
  doi = {10.1016/j.cell.2022.07.019},
  url = {https://doi.org/10.1016/j.cell.2022.07.019}
}

@article{rfpeptides,
  title = {{Accurate de novo design of high-affinity protein-binding macrocycles using deep learning}},
  author = {Rettie, Stephen A. and Juergens, David and Adebomi, Victor and Bueso, Yensi Flores and Zhao, Qinqin and Leveille, Alexandria N. and Liu, Andi and Bera, Asim K. and Wilms, Joana A. and Üffing, Alina and Kang, Alex and Brackenbrough, Evans and Lamb, Mila and Gerben, Stacey R. and Murray, Analisa and Levine, Paul M. and Schneider, Maika and Vasireddy, Vibha and Ovchinnikov, Sergey and Weiergräber, Oliver H. and Willbold, Dieter and Kritzer, Joshua A. and Mougous, Joseph D. and Baker, David and DiMaio, Frank and Bhardwaj, Gaurav},
  year = {2025},
  journal = {Nature Chemical Biology},
  volume = {21},
  number = {12},
  pages = {1948--1956},
  doi = {10.1038/s41589-025-01929-w},
  url = {https://doi.org/10.1038/s41589-025-01929-w}
}

@article{afcycdesign,
  title = {{Cyclic peptide structure prediction and design using AlphaFold2}},
  author = {Rettie, Stephen A. and Campbell, Katelyn V. and Bera, Asim K. and Kang, Alex and Kozlov, Simon and Bueso, Yensi Flores and De La Cruz, Joshmyn and Ahlrichs, Maggie and Cheng, Suna and Gerben, Stacey R. and Lamb, Mila and Murray, Analisa and Adebomi, Victor and Zhou, Guangfeng and DiMaio, Frank and Ovchinnikov, Sergey and Bhardwaj, Gaurav},
  year = {2025},
  journal = {Nature Communications},
  volume = {16},
  number = {1},
  pages = {4730},
  doi = {10.1038/s41467-025-59940-7},
  url = {https://doi.org/10.1038/s41467-025-59940-7}
}

@article{pepinvent,
  title = {{PepINVENT: generative peptide design beyond natural amino acids}},
  author = {Geylan, Gökçe and Janet, Jon Paul and Tibo, Alessandro and He, Jiazhen and Patronov, Atanas and Kabeshov, Mikhail and Czechtizky, Werngard and David, Florian and Engkvist, Ola and De Maria, Leonardo},
  year = {2025},
  journal = {Chemical Science},
  volume = {16},
  number = {20},
  pages = {8682--8696},
  doi = {10.1039/d4sc07642g},
  url = {https://doi.org/10.1039/d4sc07642g}
}

@article{helmgpt,
  title = {{HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer}},
  author = {Xu, Xiaopeng and Xu, Chencheng and He, Wenjia and Wei, Lesong and Li, Haoyang and Zhou, Juexiao and Zhang, Ruochi and Wang, Yu and Xiong, Yuanpeng and Gao, Xin},
  year = {2024},
  journal = {Bioinformatics},
  volume = {40},
  number = {6},
  pages = {btae364},
  doi = {10.1093/bioinformatics/btae364},
  url = {https://doi.org/10.1093/bioinformatics/btae364}
}

@article{boltzgen,
  title = {{BoltzGen: Toward Universal Binder Design}},
  author = {Stark, Hannes and Faltings, Felix and Choi, MinGyu and Xie, Yuxin and Hur, Eunsu and O’Donnell, Timothy and Bushuiev, Anton and Uçar, Talip and Passaro, Saro and Mao, Weian and Reveiz, Mateo and Bushuiev, Roman and Portnoi, Tally and Pluskal, Tomáš and Sivic, Josef and Kreis, Karsten and Vahdat, Arash and Ray, Shamayeeta and Goldstein, Jonathan T. and Savinov, Andrew and Hambalek, Jacob A. and Gupta, Anshika and Taquiri-Diaz, Diego A. and Zhang, Yaotian and Snyder, Samuel J. and Hatstat, A. Katherine and Arada, Angelika and Kim, Nam Hyeong and Fan, Haoyu and Tackie-Yarboi, Ethel and Boselli, Dylan and Schnaider, Lee and Liu, Chang C. and Li, Gene-Wei and Hnisz, Denes and Sabatini, David M. and DeGrado, William F. and Wohlwend, Jeremy and Corso, Gabriele and Barzilay, Regina and Jaakkola, Tommi},
  year = {2025},
  journal = {bioRxiv},
  doi = {10.1101/2025.11.20.689494},
  url = {https://doi.org/10.1101/2025.11.20.689494},
  note = {Preprint}
}

@article{erkdarpins,
  title = {{Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries}},
  author = {Kummer, Lutz and Parizek, Petra and Rube, Peter and Millgramm, Bastian and Prinz, Anke and Mittl, Peer R. E. and Kaufholz, Melanie and Zimmermann, Bastian and Herberg, Friedrich W. and Plückthun, Andreas},
  year = {2012},
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  number = {34},
  doi = {10.1073/pnas.1205399109},
  url = {https://doi.org/10.1073/pnas.1205399109}
}

@misc{peptiversespace,
  author = {{ChatterjeeLab}},
  title = {{PeptiVerse Hugging Face Space}},
  year = {2026},
  url = {https://huggingface.co/spaces/ChatterjeeLab/PeptiVerse},
  note = {Accessed 20 September 2026}
}

@misc{astramodel,
  author = {{OpenAI}},
  title = {{GPT-6 Astra model documentation}},
  year = {2026},
  url = {https://developers.openai.com/api/docs/models/gpt-6-astra},
  note = {Accessed 20 September 2026}
}

@misc{claudeeffort,
  author = {{Anthropic}},
  title = {{Effort controls for Claude models}},
  year = {2026},
  url = {https://platform.claude.com/docs/en/build-with-claude/effort},
  note = {Accessed 20 September 2026}
}