Multimodal Language Modeling for High-Accuracy Single Cell
  Transcriptomics Analysis and Generation
Authors: name: Yaorui Shi; name: Jiaqi Yang; name: Sihang Li; name: Junfeng Fang; name: Xiang Wang; name: Zhiyuan Liu; name: Yang Zhang
Published: 2025-03-12 14:26:16

Abstract: Pre-trained language models (PLMs) have revolutionized scientific research,
yet their application to single-cell analysis remains limited. Text PLMs cannot
process single-cell RNA sequencing data, while cell PLMs lack the ability to
handle free text, restricting their use in multimodal tasks. Existing efforts
to bridge these modalities often suffer from information loss or inadequate
single-modal pre-training, leading to suboptimal performances. To address these
challenges, we propose Single-Cell MultiModal Generative Pre-trained
Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT
effectively integrates the state-of-the-art cell and text PLMs, facilitating
cross-modal knowledge sharing for improved performance. To bridge the text-cell
modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes
extensive pre-training on 27 million cells -- the largest dataset for
multimodal cell-text PLMs to date. This large-scale pre-training enables
scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative
improvement of textual discrepancy for cell description generation, 20.5\%
higher accuracy for cell type annotation, and 4\% improvement in k-NN
accuracy for text-conditioned pseudo-cell generation, outperforming baselines.