De novo mutational signature discovery in tumor genomes using SparseSignatures. - Avantika Lal; Keli Liu; Robert Tibshirani; Arend Sidow; Daniele Ramazzotti (PLoS Comput. Biol., 2021)

Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models. - Masatoshi Uehara; Yulai Zhao 002; Ehsan Hajiramezanali; Gabriele Scalia; Gökcen Eraslan; Avantika Lal; Sergey Levine; Tommaso Biancalani (NeurIPS, 2024)

regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. - Avantika Lal; David Garfield; Tommaso Biancalani; Gökcen Eraslan (RECOMB, 2024)

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design. - Chenyu Wang 003; Masatoshi Uehara; Yichun He; Amy Wang; Avantika Lal; Tommi S. Jaakkola; Sergey Levine; Aviv Regev; Hanchen Wang 002; Tommaso Biancalani (ICLR, 2025)