Large-scale foundation model on single-cell transcriptomics

M Hao, J Gong, X Zeng, C Liu, Y Guo, X Cheng… - Nature …, 2024 - nature.com
Large pretrained models have become foundation models leading to breakthroughs in
natural language processing and related fields. Developing foundation models for …

Sequential optimal experimental design of perturbation screens guided by multi-modal priors

K Huang, R Lopez, JC Hütter, T Kudo, A Rios… - … on Research in …, 2024 - Springer
Understanding a cell's expression response to genetic perturbations helps to address
important challenges in biology and medicine. This includes the inference of gene circuits …

Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization

W Zhang, Z Meng, D Wang, M Wu, K Liu… - arXiv preprint arXiv …, 2024 - arxiv.org
Recent advancements in single-cell genomics necessitate precision in gene panel selection
to interpret complex biological data effectively. Those methods aim to streamline the …

Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper

J Kim, M Ionita, M Lee, ML McKeague, A Pattekar… - bioRxiv, 2024 - biorxiv.org
High-throughput single-cell cytometry data are crucial for understanding immune system's
involvement in diseases and responses to treatment. Traditional methods for annotating …

GexMolGen: Cross-modal Generation of Hit-like Molecules via Large Language Model Encoding of Gene Expression Signatures

J Cheng, X Pan, K Yang, S Cao, B Liu, Q Yan, Y Yuan - bioRxiv, 2023 - biorxiv.org
The design of custom drugs with specific biological activity is a extremely difficult task, but it
holds the potential to generate molecules without the discovery of target genes, beyond the …

AttentionPert: Accurately Modeling Multiplexed Genetic Perturbations with Multi-scale Effects

D Bai, C Ellington, S Mo, L Song, E Xing - bioRxiv, 2024 - biorxiv.org
Genetic perturbations (ie knockouts, variants) have laid the foundation for our understanding
of many diseases, implicating pathogenic mechanisms and indicating therapeutic targets …