Mufan Qiu

Gengwei Zhang, Jie Peng, Zhen Tan et al.

The recent success of reinforcement learning (RL) in large reasoning models has inspired the growing adoption of RL for post-training Multimodal Large Language Models (MLLMs) to enhance their visual reasoning capabilities. Although many studies have reported improved performance, it remains unclear whether RL training truly enables models to learn from visual information. In this work, we propose the Hallucination-as-Cue Framework, an analytical framework designed to investigate the effects of RL-based post-training on multimodal reasoning models from the perspective of model hallucination. Specifically, we introduce hallucination-inductive, modality-specific corruptions that remove or replace essential information required to derive correct answers, thereby forcing the model to reason by hallucination. By applying these corruptions during both training and evaluation, our framework provides a unique perspective for diagnosing RL training dynamics and understanding the intrinsic properties of datasets. Through extensive experiments and analyses across multiple multimodal reasoning benchmarks, we reveal that the role of model hallucination for RL-training is more significant than previously recognized. For instance, we find that RL post-training under purely hallucination-inductive settings can still significantly improve models' reasoning performance, and in some cases even outperform standard training. These findings challenge prevailing assumptions about MLLM reasoning training and motivate the development of more modality-aware RL-based training designs.

Mufan Qiu, Genhui Zheng, Yinuo Xu et al.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

Zhenglun Kong, Mufan Qiu, John Boesen et al.

Understanding how cellular morphology, gene expression, and spatial organization jointly shape tissue function is a central challenge in biology. Image-based spatial transcriptomics technologies now provide high-resolution measurements of cell images and gene expression profiles, but machine learning methods typically analyze these modalities in isolation or at limited resolution. We address the problem of learning unified, spatially aware representations that integrate cell morphology, gene expression, and spatial context across biological scales. This requires models that can operate at single-cell resolution, reason across spatial neighborhoods, and generalize to whole-slide tissue organization. Here, we introduce SPATIA, a multi-scale generative and predictive model for spatial transcriptomics. SPATIA learns cell-level embeddings by fusing image-derived morphological tokens and transcriptomic vector tokens using cross-attention and then aggregates them at niche and tissue levels using transformer modules to capture spatial dependencies. SPATIA incorporates token merging in its generative diffusion decoder to synthesize high-resolution cell images conditioned on gene expression. We assembled a multi-scale dataset consisting of 17 million cell-gene pairs, 1 million niche-gene pairs, and 10,000 tissue-gene pairs across 49 donors, 17 tissue types, and 12 disease states. We benchmark SPATIA against 13 existing models across 12 individual tasks, which span several categories including cell annotation, cell clustering, gene imputation, cross-modal prediction, and image generation. SPATIA achieves improved performance over all baselines and generates realistic cell morphologies that reflect transcriptomic perturbations.