Yuankai Luo

Yuankai Luo, Hongkang Li, Lei Shi et al.

Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE over shortest path distances in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs, including those with up to a billion nodes.

Yuankai Luo, Lei Shi, Mufan Xu et al.

Quantitatively profiling a scholar's scientific impact is important to modern research society. Current practices with bibliometric indicators (e.g., h-index), lists, and networks perform well at scholar ranking, but do not provide structured context for scholar-centric, analytical tasks such as profile reasoning and understanding. This work presents GeneticFlow (GF), a suite of novel graph-based scholar profiles that fulfill three essential requirements: structured-context, scholar-centric, and evolution-rich. We propose a framework to compute GF over large-scale academic data sources with millions of scholars. The framework encompasses a new unsupervised advisor-advisee detection algorithm, a well-engineered citation type classifier using interpretable features, and a fine-tuned graph neural network (GNN) model. Evaluations are conducted on the real-world task of scientific award inference. Experiment outcomes show that the F1 score of best GF profile significantly outperforms alternative methods of impact indicators and bibliometric networks in all the 6 computer science fields considered. Moreover, the core GF profiles, with 63.6%-66.5% nodes and 12.5%-29.9% edges of the full profile, still significantly outrun existing methods in 5 out of 6 fields studied. Visualization of GF profiling result also reveals human explainable patterns for high-impact scholars.

Yuankai Luo, Veronika Thost, Lei Shi

Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks. The main research question is how to inject the structural bias of graphs into the transformer architecture, and several proposals have been made for undirected molecular graphs and, recently, also for larger network graphs. In this paper, we study transformers over directed acyclic graphs (DAGs) and propose architecture adaptations tailored to DAGs: (1) An attention mechanism that is considerably more efficient than the regular quadratic complexity of transformers and at the same time faithfully captures the DAG structure, and (2) a positional encoding of the DAG's partial order, complementing the former. We rigorously evaluate our approach over various types of tasks, ranging from classifying source code graphs to nodes in citation networks, and show that it is effective in two important aspects: in making graph transformers generally outperform graph neural networks tailored to DAGs and in improving SOTA graph transformer performance in terms of both quality and efficiency.

Zhijun Chen, Jingzheng Li, Pengpeng Chen et al.

LLM Ensemble -- which involves the comprehensive use of multiple large language models (LLMs), each aimed at handling user queries during downstream inference, to benefit from their individual strengths -- has gained substantial attention recently. The widespread availability of LLMs, coupled with their varying strengths and out-of-the-box usability, has profoundly advanced the field of LLM Ensemble. This paper presents the first systematic review of recent developments in LLM Ensemble. First, we introduce our taxonomy of LLM Ensemble and discuss several related research problems. Then, we provide a more in-depth classification of the methods under the broad categories of "ensemble-before-inference, ensemble-during-inference, ensemble-after-inference'', and review all relevant methods. Finally, we introduce related benchmarks and applications, summarize existing studies, and suggest several future research directions. A curated list of papers on LLM Ensemble is available at https://github.com/junchenzhi/Awesome-LLM-Ensemble.

Yuankai Luo, Lei Shi, Veronika Thost

Self-supervised learning (SSL) has great potential for molecular representation learning given the complexity of molecular graphs, the large amounts of unlabelled data available, the considerable cost of obtaining labels experimentally, and the hence often only small training datasets. The importance of the topic is reflected in the variety of paradigms and architectures that have been investigated recently. Yet the differences in performance seem often minor and are barely understood to date. In this paper, we study SSL based on persistent homology (PH), a mathematical tool for modeling topological features of data that persist across multiple scales. It has several unique features which particularly suit SSL, naturally offering: different views of the data, stability in terms of distance preservation, and the opportunity to flexibly incorporate domain knowledge. We (1) investigate an autoencoder, which shows the general representational power of PH, and (2) propose a contrastive loss that complements existing approaches. We rigorously evaluate our approach for molecular property prediction and demonstrate its particular features in improving the embedding space: after SSL, the representations are better and offer considerably more predictive power than the baselines over different probing tasks; our loss increases baseline performance, sometimes largely; and we often obtain substantial improvements over very small datasets, a common scenario in practice.

Yuankai Luo, Lei Shi, Xiao-Ming Wu

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.

Yuankai Luo, Woping Chen, Tong Liang et al.

Deploying Vision-Language-Action (VLA) models in real-world robotics exposes a core multi-task learning challenge: reconciling task interference in multi-task robotic learning. When multiple tasks are jointly fine-tuned in a single stage, gradients from different tasks can conflict, causing negative transfer and reducing per-task performance. Yet maintaining a separate full checkpoint per task is often storage- and deployment-prohibitive. To address this dilemma, we present CORAL, a backbone- and embodiment-agnostic framework designed primarily to mitigate multi-task interference while remaining naturally extensible to a continuous stream of new tasks. CORAL freezes a single pre-trained VLA backbone and attaches one lightweight Low-Rank Adaptation (LoRA) expert per task; at runtime, a dynamic inference engine (the CORAL Manager) routes language instructions to the appropriate expert and swaps experts on the fly with zero inference overhead. This strict parameter isolation avoids complex gating networks and prevents parameter-level cross-task interference by construction; as an added capability, it also enables sequentially introducing new tasks without parameter overwriting caused by catastrophic forgetting. We validate CORAL on a real-world Galaxea R1 dual-arm mobile manipulator and three simulation benchmarks (LIBERO, WidowX, Google Robot), where CORAL overcomes fine-grained instructional ambiguity and substantially outperforms joint training, yielding a practical and scalable system for lifelong multi-task robot learning. Website: https://frontierrobo.github.io/CORAL

Yuankai Luo, Woping Chen, Tong Liang et al.

Vision-Language-Action (VLA) models have emerged as a promising paradigm for general-purpose robotic manipulation, leveraging large-scale pre-training to achieve strong performance. The field has rapidly evolved with additional spatial priors and diverse architectural innovations. However, these advancements are often accompanied by varying training recipes and implementation details, which can make it challenging to disentangle the precise source of empirical gains. In this work, we introduce SimVLA, a streamlined baseline designed to establish a transparent reference point for VLA research. By strictly decoupling perception from control, using a standard vision-language backbone and a lightweight action head, and standardizing critical training dynamics, we demonstrate that a minimal design can achieve state-of-the-art performance. Despite having only 0.5B parameters, SimVLA outperforms multi-billion-parameter models on standard simulation benchmarks without robot pretraining. SimVLA also reaches on-par real-robot performance compared to pi0.5. Our results establish SimVLA as a robust, reproducible baseline that enables clear attribution of empirical gains to future architectural innovations. Website: https://frontierrobo.github.io/SimVLA

Yuankai Luo, Lei Shi, Xiao-Ming Wu

Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node classification benchmarks, often significantly outperforming GNNs. In this paper, we conduct a thorough empirical analysis to reevaluate the performance of three classic GNN models (GCN, GAT, and GraphSAGE) against GTs. Our findings suggest that the previously reported superiority of GTs may have been overstated due to suboptimal hyperparameter configurations in GNNs. Remarkably, with slight hyperparameter tuning, these classic GNN models achieve state-of-the-art performance, matching or even exceeding that of recent GTs across 17 out of the 18 diverse datasets examined. Additionally, we conduct detailed ablation studies to investigate the influence of various GNN configurations, such as normalization, dropout, residual connections, and network depth, on node classification performance. Our study aims to promote a higher standard of empirical rigor in the field of graph machine learning, encouraging more accurate comparisons and evaluations of model capabilities.