Examples
========

Presentations about Colmena, examples of using Colmena in the scientific literature, and in other open-source codes.

Presentations
--------------

Presentations focused on Colmena's design or how to use it

- SIAM PP 2024's symposium on the Exascale Computing Project [`YouTube <https://youtu.be/L1nhpaDerCM>`_]
- Exascale Computing Project's 2023 Annual Meeting [`YouTube <https://youtu.be/XiU0SI1SyRU>`_]

Publications
------------

Improvements to Colmena
+++++++++++++++++++++++

Papers about improving the performance or utility of Colmena

- Ward et al. "Employing artificial intelligence to steer exascale workflows with colmena"
  *The International Journal of High Performance Computing Applications*
  [`paper <https://doi.org/10.1177/10943420241288242>`](https://doi.org/10.1177/10943420241288242)
- Ward et al. "Colmena: Scalable Machine-Learning-Based Steering of Ensemble Simulations for High Performance Computing".
  *2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments (MLHPC)*
  [`paper <https://doi.org/10.1109/MLHPC54614.2021.00007>`_]
  [`ArXiv <https://arxiv.org/abs/2110.02827>`_]
  [`slides <https://www.researchgate.net/publication/357777568>`_]
  [`YouTube <https://youtu.be/-3KnbJcm-tQ>`_]
- Ward et al. "Cloud Services Enable Efficient AI-Guided Simulation Workflows across Heterogeneous Resources".
  *Heterogenous Computing Workshop at IPDPS 2023*
  [`ArXiv <https://arxiv.org/abs/2303.08803>`_]
  [`slides <https://www.researchgate.net/publication/371753699>`_]
  [`YouTube <https://youtu.be/KO7anZs4G48>`_]

Applications of Colmena
+++++++++++++++++++++++

Papers where Colmena was used

- Guo et al. "Composition-transferable machine learning potential for LiCl-KCl molten salts validated by high-energy x-ray diffraction"
  *Physical Review B*
  [`paper <https://doi.org/10.1103/PhysRevB.106.014209>`_]
  [`ChemRxiv <https://doi.org/10.26434/chemrxiv-2022-8w9ft>`_]
- Zvyagin et al. "GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics."
  [`bioRxiv <https://doi.org/10.1101/2022.10.10.511571>`_]
- Dharuman et al. "Protein Generation via Genome-scale Language Models with Bio-physical Scoring"
  [`SC-W '23 <https://dl.acm.org/doi/abs/10.1145/3624062.3626087>`_]

Open-Source Software
--------------------

Other codes which use Colmena

- `ExaMol <https://github.com/exalearn/ExaMol>`_: Performs molecule design on HPC by combining AI and quantum chemistry (same devs as Colmena)