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Genentech

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Selected work

Representative Papers

Separate Exchangeability as Modeling Principle in Bayesian Nonparametrics

Dec 14, 2021

This paper addresses the underutilization of separate exchangeability in Bayesian nonparametric (BNP) modeling, noting that existing partially exchangeable models—such as nested Dirichlet process variants—often neglect multidimensional experimental structures (e.g., matrix-valued data, multiple treatment groups), leading to misalignment between prior specification and experimental design. To resolve this, the paper introduces the first systematic BNP framework grounded in separate exchangeability, proposing two novel models: nested random partitioning and ANOVA-type dependent Dirichlet processes (ANOVA-DDP). Both explicitly encode hierarchical experimental structure, ensuring theoretical consistency between prior construction and statistical inference. Empirical evaluation on real-world datasets demonstrates substantial improvements in regression prediction accuracy and clustering interpretability. The proposed framework establishes the first BNP paradigm that simultaneously satisfies rigorous theoretical foundations and practical applicability for complex experimental designs.

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Recent publications

Latest Papers

LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses

Aug 03, 2026

Predicting transcriptional responses to small-molecule perturbations across diverse cell lines is hindered by limited experimental coverage. This work proposes a novel retrieval-aggregation paradigm that leverages large language models (LLMs) as constrained biological priors to retrieve compounds with semantically relevant biological profiles in the target cell line and aggregates their expression profiles via averaging to predict responses to unmeasured drugs. Notably, this approach is the first to employ LLMs for prior-guided retrieval in perturbation prediction, emphasizing that high-quality retrieval outperforms complex predictors and substantially enhances zero-shot generalization. The method consistently surpasses existing baselines under unseen-drug, unseen-cell-line, and open-world settings, demonstrating particularly strong performance in cross-cell-line scenarios with higher correlation, lower error, and more accurate prediction of gene regulatory directions.

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