Yanke Li

Yanke Li, Hatt Tobias, Ioana Bica et al. · oxford

Leveraging labelled data from multiple domains to enable prediction in another domain without labels is a significant, yet challenging problem. To address this problem, we introduce the framework DAPDAG (\textbf{D}omain \textbf{A}daptation via \textbf{P}erturbed \textbf{DAG} Reconstruction) and propose to learn an auto-encoder that undertakes inference on population statistics given features and reconstructing a directed acyclic graph (DAG) as an auxiliary task. The underlying DAG structure is assumed invariant among observed variables whose conditional distributions are allowed to vary across domains led by a latent environmental variable $E$. The encoder is designed to serve as an inference device on $E$ while the decoder reconstructs each observed variable conditioned on its graphical parents in the DAG and the inferred $E$. We train the encoder and decoder jointly in an end-to-end manner and conduct experiments on synthetic and real datasets with mixed variables. Empirical results demonstrate that reconstructing the DAG benefits the approximate inference. Furthermore, our approach can achieve competitive performance against other benchmarks in prediction tasks, with better adaptation ability, especially in the target domain significantly different from the source domains.

Yanke Li, Tianyu Cui, Tommaso Mansi et al.

Efficient design of genomic perturbation experiments is crucial for accelerating drug discovery and therapeutic target identification, yet exhaustive perturbation of the human genome remains infeasible due to the vast search space of potential genetic interactions and experimental constraints. Bayesian optimization (BO) has emerged as a powerful framework for selecting informative interventions, but existing approaches often fail to exploit domain-specific biological prior knowledge. We propose Biology-Informed Bayesian Optimization (BioBO), a method that integrates Bayesian optimization with multimodal gene embeddings and enrichment analysis, a widely used tool for gene prioritization in biology, to enhance surrogate modeling and acquisition strategies. BioBO combines biologically grounded priors with acquisition functions in a principled framework, which biases the search toward promising genes while maintaining the ability to explore uncertain regions. Through experiments on established public benchmarks and datasets, we demonstrate that BioBO improves labeling efficiency by 25-40%, and consistently outperforms conventional BO by identifying top-performing perturbations more effectively. Moreover, by incorporating enrichment analysis, BioBO yields pathway-level explanations for selected perturbations, offering mechanistic interpretability that links designs to biologically coherent regulatory circuits.