arXiv subjects

Xiaojie Qiu

Publications and source records attributed to Xiaojie Qiu.

8 recordsLinked to original sources

arXiv2026

Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning

Pre-trained foundation models (FMs) have begun transforming single-cell genomics, but scaling them raises privacy concerns. Moreover, unlike text data, single-cell data is unordered and exhibits a unique tabular structure that current single-cell FMs overlook. We introduce Tabula, a privacy-preserving FM designed with federated learning (FL) that explicitly models the tabular structure of single-cell data. To deploy Tabula, we further developed Chiron, a decentralized AI agent-enabled platform for collaborative training across institutions without sharing raw data. Beyond strong performance across downstream benchmarks, Tabula reveals combinatorial regulatory logic across diverse biological systems, including hematopoiesis, pancreatic endogenesis, neurogenesis, and cardiogenesis. Using a new scRNA-seq dataset of paired young and aged human fibroblasts, Tabula nominates rejuvenation factors through age- and identity score-guided in silico prioritization, outperforming conventional approaches. Thus, Tabula represents an important advance in single-cell foundation modeling by integrating tabular learning with FL, paving the way toward privacy-preserving virtual cells for human health.

cs.LG↗

arXiv2026

Generative Modeling with Flux Matching

We introduce Flux Matching, a new paradigm for generative modeling that generalizes existing score-based models to a broader family of vector fields that need not be conservative. Rather than requiring the model to equal the data score, the Flux Matching objective imposes a weaker condition that admits infinitely many vector fields whose stationary distribution is the data. This flexibility enables a class of generative models that cannot be learned under score matching, in which inductive biases, structural priors, and properties of the dynamics can be directly imposed or optimized. We show that Flux Matching performs strongly on high-dimensional image datasets and, more importantly, that our added freedom unlocks a range of applications including faster sampling, interpretable and mechanistic models, and dynamics that encode directed dependencies between variables. More broadly, Flux Matching opens a new dimension in generative modeling by turning the vector field itself into a design choice rather than a fixed target. Code is available at https://github.com/peterpaohuang/flux_matching.

cs.LG↗

arXiv2026

Inferring stochastic dynamics with growth from cross-sectional data

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.

cs.LG↗

arXiv2026

A Multi-View Consistency Framework with Semi-Supervised Domain Adaptation

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.

cs.CV↗

arXiv2026

Exploiting Minority Pseudo-Labels for Semi-Supervised Fine-grained Road Scene Understanding

In fine-grained road scene understanding, semantic segmentation plays a crucial role in enabling vehicles to perceive and comprehend their surroundings. By assigning a specific class label to each pixel in an image, it allows for precise identification and localization of detailed road features, which is vital for high-quality scene understanding and downstream perception tasks. A key challenge in this domain lies in improving the recognition performance of minority classes while mitigating the dominance of majority classes, which is essential for achieving balanced and robust overall performance. However, traditional semi-supervised learning methods often train models overlooking the imbalance between classes. To address this issue, firstly, we propose a general training module that learns from all the pseudo-labels without a conventional filtering strategy. Secondly, we propose a professional training module to learn specifically from reliable minority-class pseudo-labels identified by a novel mismatch score metric. The two modules are crossly supervised by each other so that it reduces model coupling which is essential for semi-supervised learning. During contrastive learning, to avoid the dominance of the majority classes in the feature space, we propose a strategy to assign evenly distributed anchors for different classes in the feature space. Experimental results on multiple public benchmarks show that our method surpasses traditional approaches in recognizing tail classes.

cs.CV↗

arXiv2025

Evolution without an Oracle: Driving Effective Evolution with LLM Judges

The integration of Large Language Models (LLMs) with Evolutionary Computation (EC) has unlocked new frontiers in scientific discovery but remains shackled by a fundamental constraint: the reliance on an Oracle--an objective, machine-computable fitness function. This paper breaks this barrier by asking: Can evolution thrive in a purely subjective landscape governed solely by LLM judges? We introduce MADE (Multi-Agent Decomposed Evolution), a framework that tames the inherent noise of subjective evaluation through "Problem Specification." By decomposing vague instructions into specific, verifiable sub-requirements, MADE transforms high-variance LLM feedback into stable, precise selection pressure. The results are transformative: across complex benchmarks like DevAI and InfoBench, MADE outperforms strong baselines by over 50% in software requirement satisfaction (39.9% to 61.9%) and achieves a 95% perfect pass rate on complex instruction following. This work validates a fundamental paradigm shift: moving from optimizing "computable metrics" to "describable qualities," thereby unlocking evolutionary optimization for the vast open-ended domains where no ground truth exists.

cs.SE↗

arXiv2025

Geometric Generative Modeling with Noise-Conditioned Graph Networks

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 \textit{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. Code is available at https://github.com/peterpaohuang/ncgn.

cs.LG↗

arXiv2023

Semi-Supervised Learning with Pseudo-Negative Labels for Image Classification

Semi-supervised learning frameworks usually adopt mutual learning approaches with multiple submodels to learn from different perspectives. To avoid transferring erroneous pseudo labels between these submodels, a high threshold is usually used to filter out a large number of low-confidence predictions for unlabeled data. However, such filtering can not fully exploit unlabeled data with low prediction confidence. To overcome this problem, in this work, we propose a mutual learning framework based on pseudo-negative labels. Negative labels are those that a corresponding data item does not belong. In each iteration, one submodel generates pseudo-negative labels for each data item, and the other submodel learns from these labels. The role of the two submodels exchanges after each iteration until convergence. By reducing the prediction probability on pseudo-negative labels, the dual model can improve its prediction ability. We also propose a mechanism to select a few pseudo-negative labels to feed into submodels. In the experiments, our framework achieves state-of-the-art results on several main benchmarks. Specifically, with our framework, the error rates of the 13-layer CNN model are 9.35% and 7.94% for CIFAR-10 with 1000 and 4000 labels, respectively. In addition, for the non-augmented MNIST with only 20 labels, the error rate is 0.81% by our framework, which is much smaller than that of other approaches. Our approach also demonstrates a significant performance improvement in domain adaptation.

cs.CV↗