Vincent D. Zaballa

I work on machine learning methods in biology with a strong interest in integrating systems and structural biology with applications in drug discovery. Given the complexity of biological data, I seek to combine biological data into more robust machine learning models to reduce entropy of biological systems. A key application of this is in Bayesian optimal experimental design, which helps scientists decipher between competing biological hypotheses with maximum efficiency.

So far, the main software from my Ph.D. work is the JAX-based conditional normalizing flow library LFIAX with experimental design loss functions. I also contribute to open-source software, including an entropy-bounded sampler for discrete diffusion language models at Radical Numerics and reliable optimizer implementations in Optax.

selected publications

Scalable Diffusion SBI for Compositional Inference under Simulator Misspecification

Vincent D. Zaballa, and Elliot E. Hui

2026

UAI

Optimizing Likelihoods via Mutual Information: Bridging Simulation-Based Inference and Bayesian Optimal Experimental Design

Vincent D. Zaballa, and Elliot E. Hui

In Conference on Uncertainty in Artificial Intelligence (UAI), 2026

arXiv Bib Code

@inproceedings{zaballa2025optimizinglikelihoodsmutualinformation,
  title = {Optimizing Likelihoods via Mutual Information: Bridging Simulation-Based Inference and Bayesian Optimal Experimental Design},
  author = {Zaballa, Vincent D. and Hui, Elliot E.},
  booktitle = {Conference on Uncertainty in Artificial Intelligence (UAI)},
  year = {2026},
  eprint = {2502.08004},
  archiveprefix = {arXiv},
  primaryclass = {stat.ML},
}

MLSB @ NeurIPS

Systems-Structure-Based Drug Design

Vincent D. Zaballa, and Elliot E. Hui

In NeurIPS MLSB Workshop, 2024

arXiv Bib

@inproceedings{zaballa2024systems,
  title = {Systems-Structure-Based Drug Design},
  author = {Zaballa, Vincent D. and Hui, Elliot E.},
  booktitle = {NeurIPS MLSB Workshop},
  year = {2024},
  eprint = {2410.10108},
  archiveprefix = {arXiv},
}

ML4LMS @ ICML

Reducing Uncertainty Through Mutual Information in Structural and Systems Biology

Vincent D. Zaballa, and Elliot E. Hui

In ICML ML4LMS Workshop, 2024

arXiv Bib

@inproceedings{zaballa2024reducing,
  title = {Reducing Uncertainty Through Mutual Information in Structural and Systems Biology},
  author = {Zaballa, Vincent D. and Hui, Elliot E.},
  booktitle = {ICML ML4LMS Workshop},
  year = {2024},
  eprint = {2407.08612},
  archiveprefix = {arXiv},
}