Ruiying Liu

Zihan Zhou, Ruiying Liu, Chaolong Ying et al.

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse a noising process. Diffusion on inter-atomic distances instead of conformation preserves SE(3)-equivalence and shows superior performance compared to alternative techniques, whereas related generative modelings are predominantly based upon heuristical assumptions. In response to this, we propose a novel molecular conformation generation approach driven by the observation that the disintegration of a molecule can be viewed as casting increasing force fields to its composing atoms, such that the distribution of the change of inter-atomic distance shifts from Gaussian to Maxwell-Boltzmann distribution. The corresponding generative modeling ensures a feasible inter-atomic distance geometry and exhibits time reversibility. Experimental results on molecular datasets demonstrate the advantages of the proposed shifting distribution compared to the state-of-the-art.

Dingyi Zhang, Ruiying Liu, Yun Wang

The accurate quantification of brain age from MRI has emerged as an important biomarker of brain health. However, existing approaches are often restricted to narrow age ranges and single-modality MRI data, limiting their capacity to capture the coordinated macro- and microstructural changes that unfold across the human lifespan. To address these limitations, we developed a multi-modal brain age framework to characterize the integrated evolution of brain morphology and white matter organization. Our model adopts a two-stage architecture, where modalities are processed independently and integrated via late fusion in both stages: first to classify each subject into one of six developmental stages, and then to estimate age within the predicted stage. This design enables a unified and lifespan-spanning assessment of brain maturity across diverse developmental periods.

Zihan Zhou, Ruiying Liu, Tianshu Yu

Diffusion-based generative models in SE(3)-invariant space have demonstrated promising performance in molecular conformation generation, but typically require solving stochastic differential equations (SDEs) with thousands of update steps. Till now, it remains unclear how to effectively accelerate this procedure explicitly in SE(3)-invariant space, which greatly hinders its wide application in the real world. In this paper, we systematically study the diffusion mechanism in SE(3)-invariant space via the lens of approximate errors induced by existing methods. Thereby, we develop more precise approximate in SE(3) in the context of projected differential equations. Theoretical analysis is further provided as well as empirical proof relating hyper-parameters with such errors. Altogether, we propose a novel acceleration scheme for generating molecular conformations in SE(3)-invariant space. Experimentally, our scheme can generate high-quality conformations with 50x--100x speedup compared to existing methods.

Zihan Zhou, Ruiying Liu, Jiachen Zheng et al.

Sampling viable 3D structures (e.g., molecules and point clouds) with SE(3)-invariance using diffusion-based models proved promising in a variety of real-world applications, wherein SE(3)-invariant properties can be naturally characterized by the inter-point distance manifold. However, due to the non-trivial geometry, we still lack a comprehensive understanding of the diffusion mechanism within such SE(3)-invariant space. This study addresses this gap by mathematically delineating the diffusion mechanism under SE(3)-invariance, via zooming into the interaction behavior between coordinates and the inter-point distance manifold through the lens of differential geometry. Upon this analysis, we propose accurate and projection-free diffusion SDE and ODE accordingly. Such formulations enable enhancing the performance and the speed of generation pathways; meanwhile offering valuable insights into other systems incorporating SE(3)-invariance.

Ruiying Liu, Yuanzhi Liang, Haibin Huang et al.

Group Relative Policy Optimization (GRPO) has emerged as an effective and lightweight framework for post-training visual generative models. However, its performance is fundamentally limited by the ambiguity of textual visual correspondence: a single prompt may validly describe diverse visual outputs, and a single image or video may support multiple equally correct interpretations. This many to many relationship leads reward models to generate uncertain and weakly discriminative signals, causing GRPO to underutilize reliable feedback and overfit noisy ones. We introduce Bayesian Prior-Guided Optimization (BPGO), a novel extension of GRPO that explicitly models reward uncertainty through a semantic prior anchor. BPGO adaptively modulates optimization trust at two levels: inter-group Bayesian trust allocation emphasizes updates from groups consistent with the prior while down-weighting ambiguous ones, and intra-group prior-anchored renormalization sharpens sample distinctions by expanding confident deviations and compressing uncertain scores. Across both image and video generation tasks, BPGO delivers consistently stronger semantic alignment, enhanced perceptual fidelity, and faster convergence than standard GRPO and recent variants.

Xinliu Zhong, Ruiying Liu, Emily S. Nichols et al.

Accurate placental segmentation is essential for quantitative analysis of the placenta. However, this task is particularly challenging in T2*-weighted placental imaging due to: (1) weak and inconsistent boundary contrast across individual echoes; (2) the absence of manual ground truth annotations for all echo times; and (3) motion artifacts across echoes caused by fetal and maternal movement. In this work, we propose a contrast-augmented segmentation framework that leverages complementary information across multi-echo T2*-weighted MRI to learn robust, contrast-invariant representations. Our method integrates: (i) masked autoencoding (MAE) for self-supervised pretraining on unlabeled multi-echo slices; (ii) masked pseudo-labeling (MPL) for unsupervised domain adaptation across echo times; and (iii) global-local collaboration to align fine-grained features with global anatomical context. We further introduce a semantic matching loss to encourage representation consistency across echoes of the same subject. Experiments on a clinical multi-echo placental MRI dataset demonstrate that our approach generalizes effectively across echo times and outperforms both single-echo and naive fusion baselines. To our knowledge, this is the first work to systematically exploit multi-echo T2*-weighted MRI for placental segmentation.

Hongyu Li, Zifei Liang, Chaoyi Zhang et al.

Purpose: To propose a deep learning-based reconstruction framework for ultrafast and robust diffusion tensor imaging and fiber tractography. Methods: We propose SuperDTI to learn the nonlinear relationship between diffusion-weighted images (DWIs) and the corresponding tensor-derived quantitative maps as well as the fiber tractography. Super DTI bypasses the tensor fitting procedure, which is well known to be highly susceptible to noise and motion in DWIs. The network is trained and tested using datasets from Human Connectome Project and patients with ischemic stroke. SuperDTI is compared against the state-of-the-art methods for diffusion map reconstruction and fiber tracking. Results: Using training and testing data both from the same protocol and scanner, SuperDTI is shown to generate fractional anisotropy and mean diffusivity maps, as well as fiber tractography, from as few as six raw DWIs. The method achieves a quantification error of less than 5% in all regions of interest in white matter and gray matter structures. We also demonstrate that the trained neural network is robust to noise and motion in the testing data, and the network trained using healthy volunteer data can be directly applied to stroke patient data without compromising the lesion detectability. Conclusion: This paper demonstrates the feasibility of superfast diffusion tensor imaging and fiber tractography using deep learning with as few as six DWIs directly, bypassing tensor fitting. Such a significant reduction in scan time may allow the inclusion of DTI into the clinical routine for many potential applications.