Ziqi Yin

Wenzheng Feng, Yuxiao Dong, Tinglin Huang et al.

Graph neural networks (GNNs) have been widely adopted for semi-supervised learning on graphs. A recent study shows that the graph random neural network (GRAND) model can generate state-of-the-art performance for this problem. However, it is difficult for GRAND to handle large-scale graphs since its effectiveness relies on computationally expensive data augmentation procedures. In this work, we present a scalable and high-performance GNN framework GRAND+ for semi-supervised graph learning. To address the above issue, we develop a generalized forward push (GFPush) algorithm in GRAND+ to pre-compute a general propagation matrix and employ it to perform graph data augmentation in a mini-batch manner. We show that both the low time and space complexities of GFPush enable GRAND+ to efficiently scale to large graphs. Furthermore, we introduce a confidence-aware consistency loss into the model optimization of GRAND+, facilitating GRAND+'s generalization superiority. We conduct extensive experiments on seven public datasets of different sizes. The results demonstrate that GRAND+ 1) is able to scale to large graphs and costs less running time than existing scalable GNNs, and 2) can offer consistent accuracy improvements over both full-batch and scalable GNNs across all datasets.

Wentao Zhang, Ziqi Yin, Zeang Sheng et al.

Graph neural networks (GNNs) have achieved great success in many graph-based applications. However, the enormous size and high sparsity level of graphs hinder their applications under industrial scenarios. Although some scalable GNNs are proposed for large-scale graphs, they adopt a fixed $K$-hop neighborhood for each node, thus facing the over-smoothing issue when adopting large propagation depths for nodes within sparse regions. To tackle the above issue, we propose a new GNN architecture -- Graph Attention Multi-Layer Perceptron (GAMLP), which can capture the underlying correlations between different scales of graph knowledge. We have deployed GAMLP in Tencent with the Angel platform, and we further evaluate GAMLP on both real-world datasets and large-scale industrial datasets. Extensive experiments on these 14 graph datasets demonstrate that GAMLP achieves state-of-the-art performance while enjoying high scalability and efficiency. Specifically, it outperforms GAT by 1.3\% regarding predictive accuracy on our large-scale Tencent Video dataset while achieving up to $50\times$ training speedup. Besides, it ranks top-1 on both the leaderboards of the largest homogeneous and heterogeneous graph (i.e., ogbn-papers100M and ogbn-mag) of Open Graph Benchmark.

Wentao Zhang, Zeang Sheng, Ziqi Yin et al.

Graph Neural Networks (GNNs) have achieved great success in various graph mining tasks.However, drastic performance degradation is always observed when a GNN is stacked with many layers. As a result, most GNNs only have shallow architectures, which limits their expressive power and exploitation of deep neighborhoods.Most recent studies attribute the performance degradation of deep GNNs to the \textit{over-smoothing} issue. In this paper, we disentangle the conventional graph convolution operation into two independent operations: \textit{Propagation} (\textbf{P}) and \textit{Transformation} (\textbf{T}).Following this, the depth of a GNN can be split into the propagation depth ($D_p$) and the transformation depth ($D_t$). Through extensive experiments, we find that the major cause for the performance degradation of deep GNNs is the \textit{model degradation} issue caused by large $D_t$ rather than the \textit{over-smoothing} issue mainly caused by large $D_p$. Further, we present \textit{Adaptive Initial Residual} (AIR), a plug-and-play module compatible with all kinds of GNN architectures, to alleviate the \textit{model degradation} issue and the \textit{over-smoothing} issue simultaneously. Experimental results on six real-world datasets demonstrate that GNNs equipped with AIR outperform most GNNs with shallow architectures owing to the benefits of both large $D_p$ and $D_t$, while the time costs associated with AIR can be ignored.

Ziqi Yin, Hao Wang, Kaito Horio et al.

We investigate the impact of politeness levels in prompts on the performance of large language models (LLMs). Polite language in human communications often garners more compliance and effectiveness, while rudeness can cause aversion, impacting response quality. We consider that LLMs mirror human communication traits, suggesting they align with human cultural norms. We assess the impact of politeness in prompts on LLMs across English, Chinese, and Japanese tasks. We observed that impolite prompts often result in poor performance, but overly polite language does not guarantee better outcomes. The best politeness level is different according to the language. This phenomenon suggests that LLMs not only reflect human behavior but are also influenced by language, particularly in different cultural contexts. Our findings highlight the need to factor in politeness for cross-cultural natural language processing and LLM usage.

Aritra Roy, Kevin Shen, Andrew MacBride et al.

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

Issa Sugiura, Keito Sasagawa, Keisuke Nakao et al.

Developing vision-language models (VLMs) that generalize across diverse tasks requires large-scale training datasets with diverse content. In English, such datasets are typically constructed by aggregating and curating numerous existing visual question answering (VQA) resources. However, this strategy does not readily extend to other languages, where VQA datasets remain limited in both scale and domain coverage, posing a major obstacle to building high-quality multilingual and non-English VLMs. In this work, we introduce Jagle, the largest Japanese multimodal post-training dataset to date, comprising approximately 9.2 million instances across diverse tasks. Rather than relying on existing VQA datasets, we collect heterogeneous source data, including images, image-text pairs, and PDF documents, and generate VQA pairs through multiple strategies such as VLM-based QA generation, translation, and text rendering. Experiments demonstrate that a 2.2B model trained with Jagle achieves strong performance on Japanese tasks, surpassing InternVL3.5-2B in average score across ten Japanese evaluation tasks and approaching within five points of Qwen3-VL-2B-Instruct. Furthermore, combining Jagle with FineVision does not degrade English performance; instead, it improves English performance compared to training with FineVision alone. To facilitate reproducibility and future research, we release the dataset, trained models, and code.

Ziqi Yin, Gao Cong, Kai Zeng et al.

Although Approximate Nearest Neighbor (ANN) search has been extensively studied, large-k ANN queries that aim to retrieve a large number of nearest neighbors remain underexplored, despite their numerous real-world applications. Existing ANN methods face significant performance degradation for such queries. In this work, we first investigate the reasons for the performance degradation of quantization-based ANN indexes: (1) the inefficiency of existing top-k collectors, which incurs significant overhead in candidate maintenance, and (2) the reduced pruning effectiveness of quantization methods, which leads to a costly re-ranking process. To address this, we propose a novel bucket-based result collector (BBC) to enhance the efficiency of existing quantization-based ANN indexes for large-k ANN queries. BBC introduces two key components: (1) a bucket-based result buffer that organizes candidates into buckets by their distances to the query. This design reduces ranking costs and improves cache efficiency, enabling high performance maintenance of a candidate superset and a lightweight final selection of top-k results. (2) two re-ranking algorithms tailored for different types of quantization methods, which accelerate their re-ranking process by reducing either the number of candidate objects to be re-ranked or cache misses. Extensive experiments on real-world datasets demonstrate that BBC accelerates existing quantization-based ANN methods by up to 3.8x at recall@k = 0.95 for large-k ANN queries.

Zhiqiu Zou, Ziqi Yin, Rong-Hua Li et al.

Range-filtered approximate nearest neighbor (RFANN) search is a fundamental operation in modern data systems. Given a set of objects, each with a vector and a numerical attribute, an RFANN query retrieves the nearest neighbors to a query vector among those objects whose numerical attributes fall within the range specified by the query. Existing state-of-the-art methods for RFANN search often require constructing multiple range-specific graph indexes to achieve high query performance, which incurs significant indexing overhead. To address this, we first establish a novel graph indexing theory, the range-aware relative neighborhood graph (RRNG), which jointly considers spatial and attribute proximity. We prove that the RRNG satisfies two crucial properties: (1) monotonic search-ability, which ensures correct nearest neighbor retrieval via beam search; and (2) structural heredity, which guarantees that any range-induced subgraph remains a valid RRNG, thus enabling efficient search with a single graph index. Based on this theoretical foundation, we propose a new graph index called RNSG as a practical solution that efficiently approximates RRNG. We develop fast algorithms for both constructing the RNSG index and processing RFANN queries with it. Extensive experiments on five real-world datasets show that RNSG achieves significantly higher query performance with a more compact index and lower construction cost than existing state-of-the-art methods.

Mingxin Zhang, Xiaofeng Dai, Yu Yao et al.

In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that preserves per-bin alignment and supports replication-aware representations. Hi-C information is injected through a transformer-based encoder and cross-attention, enforcing a physically interpretable one-way constraint from Hi-C to structure. The model is trained using a flow-matching objective for stable optimization. On held-out ensembles, generated structures reproduce the input Hi-C distance-decay and structural correlation metrics while maintaining substantial conformational diversity, demonstrating the effectiveness of diffusion-based generative modeling for ensemble-level 3D genome reconstruction.

Hao Wang, Eiki Murata, Lingfang Zhang et al.

Recent advances in multimodal large language models (MLLMs) have significantly enhanced video understanding capabilities, opening new possibilities for practical applications. Yet current video benchmarks focus largely on indoor scenes or short-range outdoor activities, leaving the challenges associated with long-distance travel largely unexplored. Mastering extended geospatial-temporal trajectories is critical for next-generation MLLMs, underpinning real-world tasks such as embodied-AI planning and navigation. To bridge this gap, we present VIR-Bench, a novel benchmark consisting of 200 travel videos that frames itinerary reconstruction as a challenging task designed to evaluate and push forward MLLMs' geospatial-temporal intelligence. Experimental results reveal that state-of-the-art MLLMs, including proprietary ones, struggle to achieve high scores, underscoring the difficulty of handling videos that span extended spatial and temporal scales. Moreover, we conduct an in-depth case study in which we develop a prototype travel-planning agent that leverages the insights gained from VIR-Bench. The agent's markedly improved itinerary recommendations verify that our evaluation protocol not only benchmarks models effectively but also translates into concrete performance gains in user-facing applications.

Wentao Zhang, Ziqi Yin, Zeang Sheng et al.

Graph neural networks (GNNs) have recently achieved state-of-the-art performance in many graph-based applications. Despite the high expressive power, they typically need to perform an expensive recursive neighborhood expansion in multiple training epochs and face a scalability issue. Moreover, most of them are inflexible since they are restricted to fixed-hop neighborhoods and insensitive to actual receptive field demands for different nodes. We circumvent these limitations by introducing a scalable and flexible Graph Attention Multilayer Perceptron (GAMLP). With the separation of the non-linear transformation and feature propagation, GAMLP significantly improves the scalability and efficiency by performing the propagation procedure in a pre-compute manner. With three principled receptive field attention, each node in GAMLP is flexible and adaptive in leveraging the propagated features over the different sizes of reception field. We conduct extensive evaluations on the three large open graph benchmarks (e.g., ogbn-papers100M, ogbn-products and ogbn-mag), demonstrating that GAMLP not only achieves the state-of-art performance, but also additionally provide high scalability and efficiency.