publications

2026

1. Nat Sci Rep

   DeepRetro: Retrosynthetic Pathway Discovery using Iterative LLM Reasoning

   S. V. Sathyanarayana, S. D. Hiremath, R. Shah, and 4 more authors

   Nature Scientific Reports, 2026

   Abs Bib

   DeepRetro is a novel, open-source hybrid AI framework that solves complex retrosynthesis problems by integrating the generative power of LLMs with the precision of traditional template-based engines. Achieved state-of-the-art performance with 96.3% success rate on the USPTO-190 multi-step benchmark.

   @article{deepretro2026,
     title = {DeepRetro: Retrosynthetic Pathway Discovery using Iterative LLM Reasoning},
     author = {Sathyanarayana, S. V. and Hiremath, S. D. and Shah, R. and Panda, R. and Jana, R. and Singh, R. and Ramsundar, B.},
     journal = {Nature Scientific Reports},
     year = {2026},
     category = {journal}
   }

2. RSC DD

   ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models

   R. Singh, A. A. Barsainyan, R. Irfan, and 15 more authors

   Royal Society of Chemistry’s Digital Discovery, 2026

   Bib

   @article{chemberta3_2026,
     title = {ChemBERTa-3: An Open Source Training Framework for Chemical Foundation Models},
     author = {Singh, R. and Barsainyan, A. A. and Irfan, R. and Amorin, C. J. and He, S. and Davis, T. and Thiagarajan, A. and Sankaran, S. and Chithrananda, S. and Ahmad, W. and Jones, D. and McLoughlin, K. and Kim, H. and Bhutani, A. and Sathyanarayana, S. V. and Viswanathan, V. and Allen, J. E. and Ramsundar, B.},
     journal = {Royal Society of Chemistry's Digital Discovery},
     year = {2026},
     category = {journal}
   }

2022

1. IEEE I2CT

   Speech to Equation Conversion using a PoE Tagger

   Peeta Basa Pati, and V Shreyas

   In 2022 IEEE 7th International conference for Convergence in Technology (I2CT), 2022

   Bib

   @inproceedings{PoETagger,
     author = {Basa Pati, Peeta and Shreyas, V},
     booktitle = {2022 IEEE 7th International conference for Convergence in Technology (I2CT)},
     title = {Speech to Equation Conversion using a PoE Tagger},
     year = {2022},
     pages = {1-4},
     doi = {10.1109/I2CT54291.2022.9824252},
     category = {conference},
     url = {https://ieeexplore.ieee.org/document/9824252}
   }

2025

1. ICML WS

   DeepChem-Variant: A Modular Open Source Framework for Genomic Variant Calling

   A. V. Bisoi, V Shreyas, J. Siguenza, and 1 more author

   In Championing Open-source DEvelopment in ML Workshop at ICML 2025, 2025

   Bib

   @inproceedings{deepchem_variant2025,
     title = {DeepChem-Variant: A Modular Open Source Framework for Genomic Variant Calling},
     author = {Bisoi, A. V. and Shreyas, V and Siguenza, J. and Ramsundar, B.},
     booktitle = {Championing Open-source DEvelopment in ML Workshop at ICML 2025},
     year = {2025},
     category = {workshop}
   }

2. AAAI WS

   Open-source Polymer Generative Pipeline

   D. Mohanty, V Shreyas, A. Palai, and 1 more author

   In 4th Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE), 2025

   Bib

   @inproceedings{polymer_pipeline2025,
     title = {Open-source Polymer Generative Pipeline},
     author = {Mohanty, D. and Shreyas, V and Palai, A. and Ramsundar, B.},
     booktitle = {4th Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE)},
     year = {2025},
     category = {workshop}
   }

3. NeurIPS WS

   Multi-Turn Human-LLM Interaction Through the Lens of a Two-Way Intelligibility Protocol

   H. Mestha, K. Bania, V Shreyas, and 2 more authors

   In MTI-LLM Workshop at NeurIPS 2025, 2025

   Bib

   @inproceedings{mti_llm2025,
     title = {Multi-Turn Human-LLM Interaction Through the Lens of a Two-Way Intelligibility Protocol},
     author = {Mestha, H. and Bania, K. and Shreyas, V and Liu, S. and Srinivasan, A.},
     booktitle = {MTI-LLM Workshop at NeurIPS 2025},
     year = {2025},
     category = {workshop}
   }

2024

1. NeurIPS WS

   Open Source Molecular Processing Pipeline for Generating Molecules

   V Shreyas, Jose Siguenza, Karan Bania, and 1 more author

   In Machine Learning and the Physical Sciences Workshop at NeurIPS 2024, 2024

   Also presented at MoML 2024 and Baylearn 2024

   Bib

   @inproceedings{openMolGen2024,
     title = {Open Source Molecular Processing Pipeline for Generating Molecules},
     author = {Shreyas, V and Siguenza, Jose and Bania, Karan and Ramsundar, Bharath},
     booktitle = {Machine Learning and the Physical Sciences Workshop at NeurIPS 2024},
     year = {2024},
     eprint = {2408.06261},
     archiveprefix = {arXiv},
     primaryclass = {cs.LG},
     doi = {10.48550/arXiv.2408.06261},
     category = {workshop},
     url = {https://arxiv.org/abs/2408.06261},
     note = {Also presented at MoML 2024 and Baylearn 2024}
   }

2. AAAI WS

   Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processing

   V Shreyas, and Swati Agarwal

   In 3rd Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE), 2024

   Bib

   @inproceedings{ATP-binding2024,
     title = {Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processing},
     author = {Shreyas, V and Agarwal, Swati},
     booktitle = {3rd Annual AAAI Workshop on AI to Accelerate Science and Engineering (AI2ASE)},
     year = {2024},
     eprint = {2402.01829},
     archiveprefix = {arXiv},
     primaryclass = {q-bio.BM},
     doi = {10.48550/arXiv.2402.01829},
     category = {workshop},
     url = {https://arxiv.org/abs/2402.01829}
   }

2024

1. arXiv

   CountCLIP – [Re] Teaching CLIP to Count to Ten

   Harshvardhan Mestha, Tejas Agrawal, Karan Bania, and 2 more authors

   2024

   Bib

   @misc{CountCLIP2024,
     title = {CountCLIP -- [Re] Teaching CLIP to Count to Ten},
     author = {Mestha, Harshvardhan and Agrawal, Tejas and Bania, Karan and Shreyas, V and Bhisikar, Yash},
     year = {2024},
     eprint = {2406.03586},
     archiveprefix = {arXiv},
     primaryclass = {cs.CV},
     doi = {10.48550/arXiv.2406.03586},
     category = {preprint},
     url = {https://arxiv.org/abs/2406.03586}
   }