Haokai Zhao

Fang Wu, Haokai Zhao, Da Xing et al.

Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In this work, we challenge this assumption and introduce NoiseRater, a meta-learning framework for instance-level noise valuation in diffusion model training. We propose a parametric noise rater that assigns importance scores to individual noise realizations conditioned on data and timestep, enabling adaptive reweighting of the training objective. The rater is trained via bilevel optimization to improve downstream validation performance after inner-loop diffusion updates. To enable efficient deployment, we further design a decoupled two-stage pipeline that transitions from soft weighting during meta-training to hard noise selection during standard training. Extensive experiments on FFHQ and ImageNet demonstrate that not all noise samples contribute equally, and that prioritizing informative noise improves both training efficiency and generation quality. Our results establish noise valuation as a complementary and previously underexplored axis for improving diffusion model training. Our code is available at: https://anonymous.4open.science/r/NoiseRater-DEB116.

Haokai Zhao, Haowei Lou, Lina Yao et al.

Computational neuroimaging involves analyzing brain images or signals to provide mechanistic insights and predictive tools for human cognition and behavior. While diffusion models have shown stability and high-quality generation in natural images, there is increasing interest in adapting them to analyze brain data for various neurological tasks such as data enhancement, disease diagnosis and brain decoding. This survey provides an overview of recent efforts to integrate diffusion models into computational neuroimaging. We begin by introducing the common neuroimaging data modalities, follow with the diffusion formulations and conditioning mechanisms. Then we discuss how the variations of the denoising starting point, condition input and generation target of diffusion models are developed and enhance specific neuroimaging tasks. For a comprehensive overview of the ongoing research, we provide a publicly available repository at https://github.com/JoeZhao527/dm4neuro.

Haokai Zhao, Haowei Lou, Lina Yao et al.

Functional magnetic resonance imaging (fMRI) is an emerging neuroimaging modality that is commonly modeled as networks of Regions of Interest (ROIs) and their connections, named functional connectivity, for understanding the brain functions and mental disorders. However, due to the high cost of fMRI data acquisition and labeling, the amount of fMRI data is usually small, which largely limits the performance of recognition models. With the rise of generative models, especially diffusion models, the ability to generate realistic samples close to the real data distribution has been widely used for data augmentations. In this work, we present a transformer-based latent diffusion model for functional connectivity generation and demonstrate the effectiveness of the diffusion model as an augmentation tool for fMRI functional connectivity. Furthermore, extended experiments are conducted to provide detailed analysis of the generation quality and interpretations for the learned feature pattern. Our code will be made public upon acceptance.

Fang Wu, Weihao Xuan, Heli Qi et al.

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

Jiyu Cui, Fang Wu, Haokai Zhao et al.

Large language models have demonstrated remarkable reasoning capabilities across diverse natural language tasks. However, comparable breakthroughs in scientific discovery are more limited, because understanding complex physical phenomena demands multifaceted representations far beyond language alone. A compelling example is the design of functional materials such as MOFs-critical for a range of impactful applications like carbon capture and hydrogen storage. Navigating their vast and intricate design space in language-based representations interpretable by LLMs is challenging due to the numerous possible three-dimensional atomic arrangements and strict reticular rules of coordination geometry and topology. Despite promising early results in LLM-assisted discovery for simpler materials systems, MOF design remains heavily reliant on tacit human expertise rarely codified in textual information alone. To overcome this barrier, we introduce L2M3OF, the first multimodal LLM for MOFs. L2M3OF integrates crystal representation learning with language understanding to process structural, textual, and knowledge modalities jointly. L2M3OF employs a pre-trained crystal encoder with a lightweight projection layer to compress structural information into a token space, enabling efficient alignment with language instructions. To facilitate training and evaluation, we curate a structure-property-knowledge database of crystalline materials and benchmark L2M3OF against state-of-the-art closed-source LLMs such as GPT-5, Gemini-2.5-Pro and DeepSeek-R1. Experiments show that L2M3OF outperforms leading text-based closed-source LLMs in property prediction and knowledge generation tasks, despite using far fewer parameters. These results highlight the importance of multimodal approaches for porous material understanding and establish L2M3OF as a foundation for next-generation AI systems in materials discovery.