Di Huang

Heming Zhang, Tim Xu, Dekang Cao et al.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Yan Chen, Di Huang, Zhichao Liao et al.

The trend of employing training-free methods for point cloud recognition is becoming increasingly popular due to its significant reduction in computational resources and time costs. However, existing approaches are limited as they typically extract either geometric or semantic features. To address this limitation, we are the first to propose a novel training-free method that integrates both geometric and semantic features. For the geometric branch, we adopt a non-parametric strategy to extract geometric features. In the semantic branch, we leverage a model aligned with text features to obtain semantic features. Additionally, we introduce the GFE module to complement the geometric information of point clouds and the MFF module to improve performance in few-shot settings. Experimental results demonstrate that our method outperforms existing state-of-the-art training-free approaches on mainstream benchmark datasets, including ModelNet and ScanObiectNN.

Zichen Tang, Hongyu Yang, Hanchen Zhang et al.

Advancements in neural implicit representations and differentiable rendering have markedly improved the ability to learn animatable 3D avatars from sparse multi-view RGB videos. However, current methods that map observation space to canonical space often face challenges in capturing pose-dependent details and generalizing to novel poses. While diffusion models have demonstrated remarkable zero-shot capabilities in 2D image generation, their potential for creating animatable 3D avatars from 2D inputs remains underexplored. In this work, we introduce 3D$^2$-Actor, a novel approach featuring a pose-conditioned 3D-aware human modeling pipeline that integrates iterative 2D denoising and 3D rectifying steps. The 2D denoiser, guided by pose cues, generates detailed multi-view images that provide the rich feature set necessary for high-fidelity 3D reconstruction and pose rendering. Complementing this, our Gaussian-based 3D rectifier renders images with enhanced 3D consistency through a two-stage projection strategy and a novel local coordinate representation. Additionally, we propose an innovative sampling strategy to ensure smooth temporal continuity across frames in video synthesis. Our method effectively addresses the limitations of traditional numerical solutions in handling ill-posed mappings, producing realistic and animatable 3D human avatars. Experimental results demonstrate that 3D$^2$-Actor excels in high-fidelity avatar modeling and robustly generalizes to novel poses. Code is available at: https://github.com/silence-tang/GaussianActor.

Heming Zhang, Wenyu Li, Di Huang et al.

Named Entity Recognition (NER) is a fundamental task in Natural Language Processing (NLP) that plays a crucial role in information extraction, question answering, and knowledge-based systems. Traditional deep learning-based NER models often struggle with domain-specific generalization and suffer from data sparsity issues. In this work, we introduce Knowledge Graph distilled for Named Entity Recognition (KoGNER), a novel approach that integrates Knowledge Graph (KG) distillation into NER models to enhance entity recognition performance. Our framework leverages structured knowledge representations from KGs to enrich contextual embeddings, thereby improving entity classification and reducing ambiguity in entity detection. KoGNER employs a two-step process: (1) Knowledge Distillation, where external knowledge sources are distilled into a lightweight representation for seamless integration with NER models, and (2) Entity-Aware Augmentation, which integrates contextual embeddings that have been enriched with knowledge graph information directly into GNN, thereby improving the model's ability to understand and represent entity relationships. Experimental results on benchmark datasets demonstrate that KoGNER achieves state-of-the-art performance, outperforming finetuned NER models and LLMs by a significant margin. These findings suggest that leveraging knowledge graphs as auxiliary information can significantly improve NER accuracy, making KoGNER a promising direction for future research in knowledge-aware NLP.

Xi Cheng, Ruiqi Lei, Di Huang et al.

Parametric point clouds are sampled from CAD shapes and are becoming increasingly common in industrial manufacturing. Most CAD-specific deep learning methods focus on geometric features, while overlooking constraints inherent in CAD shapes. This limits their ability to discern CAD shapes with similar appearances but different constraints. To tackle this challenge, we first analyze the constraint importance via simple validation experiments. Then, we introduce a deep learning-friendly constraints representation with three components, and design a constraint-aware feature learning network (CstNet), which includes two stages. Stage 1 extracts constraint representation from BRep data or point cloud based on local features. It enables better generalization ability to unseen dataset after pre-training. Stage 2 employs attention layers to adaptively adjust the weights of three constraints' components. It facilitates the effective utilization of constraints. In addition, we built the first multi-modal parametric-purpose dataset, i.e. Param20K, comprising about 20K CAD instances of 75 classes. On this dataset, CstNet achieved 3.49% (classification) and 26.17% (rotation robustness) accuracy improvements over the state-of-the-art. To the best of our knowledge, CstNet is the first constraint-aware deep learning method tailored for parametric point cloud analysis.

Heming Zhang, Di Huang, Wenyu Li et al.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.