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Xiaojie Qiu

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4 papers

2 author rows

ICML Conference 2025 Conference Paper

Geometric Generative Modeling with Noise-Conditioned Graph Networks

Peter Pao-Huang
Mitchell Black 0002
Xiaojie Qiu

Generative modeling of graphs with spatial structure is essential across many applications from computer graphics to spatial genomics. Recent flow-based generative models have achieved impressive results by gradually adding and then learning to remove noise from these graphs. Existing models, however, use graph neural network architectures that are independent of the noise level, limiting their expressiveness. To address this issue, we introduce Noise-Conditioned Graph Networks (NCGNs), a class of graph neural networks that dynamically modify their architecture according to the noise level during generation. Our theoretical and empirical analysis reveals that as noise increases, (1) graphs require information from increasingly distant neighbors and (2) graphs can be effectively represented at lower resolutions. Based on these insights, we develop Dynamic Message Passing (DMP), a specific instantiation of NCGNs that adapts both the range and resolution of message passing to the noise level. DMP consistently outperforms noise independent architectures on a variety of domains including $3$D point clouds, spatiotemporal transcriptomics, and images.

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NeurIPS Conference 2025 Conference Paper

Inferring stochastic dynamics with growth from cross-sectional data

Stephen Zhang
Suryanarayana Maddu
Xiaojie Qiu
Victor Chardès

Time-resolved single-cell omics data offers high-throughput, genome-wide measurements of cellular states, which are instrumental to reverse-engineer the processes underpinning cell fate. Such technologies are inherently destructive, allowing only cross-sectional measurements of the underlying stochastic dynamical system. Furthermore, cells may divide or die in addition to changing their molecular state. Collectively these present a major challenge to inferring realistic biophysical models. We present a novel approach, unbalanced probability flow inference, that addresses this challenge for biological processes modelled as stochastic dynamics with growth. By leveraging a Lagrangian formulation of the Fokker-Planck equation, our method accurately disentangles drift from intrinsic noise and growth. We showcase the applicability of our approach through evaluation on a range of simulated and real single-cell RNA-seq datasets. Comparing to several existing methods, we find our method achieves higher accuracy while enjoying a simple two-step training scheme.

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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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EAAI Journal 2024 Journal Article

A multi-view consistency framework with semi-supervised domain adaptation

Yuting Hong
Li Dong
Xiaojie Qiu
Hui Xiao
Baochen Yao
Siming Zheng
Chengbin Peng

Semi-Supervised Domain Adaptation (SSDA) leverages knowledge from a fully labeled source domain to classify data in a partially labeled target domain. Due to the limited number of labeled samples in the target domain, there can be intrinsic similarity of classes in the feature space, which may result in biased predictions, even when the model is trained on a balanced dataset. To overcome this limitation, we introduce a multi-view consistency framework, which includes two views for training strongly augmented data. One is a debiasing strategy for correcting class-wise prediction probabilities according to the prediction performance of the model. The other involves leveraging pseudo-negative labels derived from the model predictions. Furthermore, we introduce a cross-domain affinity learning aimed at aligning features of the same class across different domains, thereby enhancing overall performance. Experimental results demonstrate that our method outperforms the competing methods on two standard domain adaptation datasets, DomainNet and Office–Home. Combining unsupervised domain adaptation and semi-supervised learning offers indispensable contributions to the industrial sector by enhancing model adaptability, reducing annotation costs, and improving performance.

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