Sachini Weerasekara

Sachini Weerasekara, Natasha Darras, Sagar Kamarthi et al.

Single-cell representation learning (SCRL) from gene expression data offers a way to uncover the complex regulatory logic underlying cellular function. Inspired by large language models in natural language modeling, several single-cell pretrained models have recently been proposed that treat genes as tokens and cells as sentences. However, these models are fundamentally limited by the long-tailed nature of cell-type distributions and struggle to generalize under covariate shifts in gene expression data. While fine-tuning is often used to mitigate these issues, we observe that performance remains bounded. To address this challenge, we introduce CellRefine, a post-pretraining method that operates between the pretraining and fine-tuning stages of a single-cell foundation model. CellRefine uses a multi-faceted objective that incorporates marker-gene sets as structural priors to guide post-pretraining and refine the latent embedding manifold of cells. Across multiple computational biology tasks, empirical results show that CellRefine consistently improves downstream performance, yielding gains up to 15%.

Sachini Weerasekara, Sagar Kamarthi, Jacqueline Isaacs

Predicting medical events in advance within critical care settings is paramount for patient outcomes and resource management. Utilizing predictive models, healthcare providers can anticipate issues such as cardiac arrest, sepsis, or respiratory failure before they manifest. Recently, there has been a surge in research focusing on forecasting adverse medical event onsets prior to clinical manifestation using machine learning. However, while these models provide temporal prognostic predictions for the occurrence of a specific adverse event of interest within defined time intervals, their interpretability often remains a challenge. In this work, we explore the applicability of neural temporal point processes in the context of adverse event onset prediction, with the aim of explaining clinical pathways and providing interpretable insights. Our experiments span six state-of-the-art neural point processes and six critical care datasets, each focusing on the onset of distinct adverse events. This work represents a novel application class of neural temporal point processes in event prediction.