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Jiayuan Ding

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5 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

Tabula: A Tabular Self-Supervised Foundation Model for Single-Cell Transcriptomics

Jiayuan Ding
Jianhui Lin
Shiyu Jiang
Yixin Wang
Ziyang Miao
Zhaoyu Fang
Jiliang Tang
Min Li

Foundation models (FMs) have shown great promise in single-cell genomics, yet current approaches, such as scGPT, Geneformer, and scFoundation, rely on centralized training and language modeling objectives that overlook the tabular nature of single-cell data and raise significant privacy concerns. We present TABULA, a foundation model designed for single-cell transcriptomics, which integrates a novel tabular modeling objective and federated learning framework to enable privacy-preserving pretraining across decentralized datasets. TABULA directly models the cell-by-gene expression matrix through column-wise gene reconstruction and row-wise cell contrastive learning, capturing both gene-level relationships and cell-level heterogeneity without imposing artificial gene sequence order. Extensive experiments demonstrate the effectiveness of TABULA: despite using only half the pretraining data, TABULA achieves state-of-the-art performance across key tasks, including gene imputation, perturbation prediction, cell type annotation, and multi-omics integration. It is important to note that as public single-cell datasets continue to grow, TABULA provides a scalable and privacy-aware foundation that not only validates the feasibility of federated tabular modeling but also establishes a generalizable framework for training future models under similar privacy-preserving settings.

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ICLR Conference 2024 Conference Paper

CellPLM: Pre-training of Cell Language Model Beyond Single Cells

Hongzhi Wen
Wenzhuo Tang
Xinnan Dai
Jiayuan Ding
Wei Jin 0009
Yuying Xie 0001
Jiliang Tang

The current state-of-the-art single-cell pre-trained models are greatly inspired by the success of large language models. They trained transformers by treating genes as tokens and cells as sentences. However, three fundamental differences between single-cell data and natural language data are overlooked: (1) scRNA-seq data are presented as bag-of-genes instead of sequences of RNAs; (2) Cell-cell relations are more intricate and important than inter-sentence relations; and (3) The quantity of single-cell data is considerably inferior to text data, and they are very noisy. In light of these characteristics, we propose a new pre-trained model, $\textit{CellPLM}$, which takes cells as tokens and tissues as sentences. In addition, we leverage spatially-resolved transcriptomic data in pre-training to facilitate learning cell-cell relationships and introduce a Gaussian prior distribution as an additional inductive bias to overcome data limitations. $\textit{CellPLM}$ is the first single-cell pre-trained transformer that encodes cell-cell relations and it consistently outperforms existing pre-trained and non-pre-trained models in diverse downstream tasks, with 100 times higher inference speed on generating cell embeddings than previous pre-trained models.

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TIST Journal 2024 Journal Article

Deep Learning in Single-cell Analysis

Dylan Molho
Jiayuan Ding
Wenzhuo Tang
Zhaoheng Li
Hongzhi Wen
Yixin Wang
Julian Venegas
Wei Jin

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high dimensional, sparse, and heterogeneous and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

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ICLR Conference 2023 Conference Paper

Empowering Graph Representation Learning with Test-Time Graph Transformation

Wei Jin 0009
Tong Zhao 0003
Jiayuan Ding
Yozen Liu
Jiliang Tang
Neil Shah

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by issues related to data quality, such as distribution shift, abnormal features and adversarial attacks. Recent efforts have been made on tackling these issues from a modeling perspective which requires additional cost of changing model architectures or re-training model parameters. In this work, we provide a data-centric view to tackle these issues and propose a graph transformation framework named GTrans which adapts and refines graph data at test time to achieve better performance. We provide theoretical analysis on the design of the framework and discuss why adapting graph data works better than adapting the model. Extensive experiments have demonstrated the effectiveness of GTrans on three distinct scenarios for eight benchmark datasets where suboptimal data is presented. Remarkably, GTrans performs the best in most cases with improvements up to 2.8%, 8.2% and 3.8% over the best baselines on three experimental settings.

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NeurIPS Conference 2021 Conference Paper

Graph Neural Networks with Adaptive Residual

Xiaorui Liu
Jiayuan Ding
Wei Jin
Han Xu
Yao Ma
Zitao Liu
Jiliang Tang

Graph neural networks (GNNs) have shown the power in graph representation learning for numerous tasks. In this work, we discover an interesting phenomenon that although residual connections in the message passing of GNNs help improve the performance, they immensely amplify GNNs' vulnerability against abnormal node features. This is undesirable because in real-world applications, node features in graphs could often be abnormal such as being naturally noisy or adversarially manipulated. We analyze possible reasons to understand this phenomenon and aim to design GNNs with stronger resilience to abnormal features. Our understandings motivate us to propose and derive a simple, efficient, interpretable, and adaptive message passing scheme, leading to a novel GNN with Adaptive Residual, AirGNN. Extensive experiments under various abnormal feature scenarios demonstrate the effectiveness of the proposed algorithm.

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