arXiv subjects

Guojie Song

Publications and source records attributed to Guojie Song.

At least 37 records · Page 2Linked to original sources

arXiv2025

TransPlace: Transferable Circuit Global Placement via Graph Neural Network

Global placement, a critical step in designing the physical layout of computer chips, is essential to optimize chip performance. Prior global placement methods optimize each circuit design individually from scratch. Their neglect of transferable knowledge limits solution efficiency and chip performance as circuit complexity drastically increases. This study presents TransPlace, a global placement framework that learns to place millions of mixed-size cells in continuous space. TransPlace introduces i) Netlist Graph to efficiently model netlist topology, ii) Cell-flow and relative position encoding to learn SE(2)-invariant representation, iii) a tailored graph neural network architecture for informed parameterization of placement knowledge, and iv) a two-stage strategy for coarse-to-fine placement. Compared to state-of-the-art placement methods, TransPlace-trained on a few high-quality placements-can place unseen circuits with 1.2x speedup while reducing congestion by 30%, timing by 9%, and wirelength by 5%.

cs.LG↗

arXiv2025

Measuring Human and AI Values Based on Generative Psychometrics with Large Language Models

Human values and their measurement are long-standing interdisciplinary inquiry. Recent advances in AI have sparked renewed interest in this area, with large language models (LLMs) emerging as both tools and subjects of value measurement. This work introduces Generative Psychometrics for Values (GPV), an LLM-based, data-driven value measurement paradigm, theoretically grounded in text-revealed selective perceptions. The core idea is to dynamically parse unstructured texts into perceptions akin to static stimuli in traditional psychometrics, measure the value orientations they reveal, and aggregate the results. Applying GPV to human-authored blogs, we demonstrate its stability, validity, and superiority over prior psychological tools. Then, extending GPV to LLM value measurement, we advance the current art with 1) a psychometric methodology that measures LLM values based on their scalable and free-form outputs, enabling context-specific measurement; 2) a comparative analysis of measurement paradigms, indicating response biases of prior methods; and 3) an attempt to bridge LLM values and their safety, revealing the predictive power of different value systems and the impacts of various values on LLM safety. Through interdisciplinary efforts, we aim to leverage AI for next-generation psychometrics and psychometrics for value-aligned AI.

cs.CL↗

arXiv2025

DAGPrompT: Pushing the Limits of Graph Prompting with a Distribution-aware Graph Prompt Tuning Approach

The pre-train then fine-tune approach has advanced GNNs by enabling general knowledge capture without task-specific labels. However, an objective gap between pre-training and downstream tasks limits its effectiveness. Recent graph prompting methods aim to close this gap through task reformulations and learnable prompts. Despite this, they struggle with complex graphs like heterophily graphs. Freezing the GNN encoder can reduce the impact of prompting, while simple prompts fail to handle diverse hop-level distributions. This paper identifies two key challenges in adapting graph prompting methods for complex graphs: (1) adapting the model to new distributions in downstream tasks to mitigate pre-training and fine-tuning discrepancies from heterophily and (2) customizing prompts for hop-specific node requirements. To overcome these challenges, we propose Distribution-aware Graph Prompt Tuning (DAGPrompT), which integrates a GLoRA module for optimizing the GNN encoder's projection matrix and message-passing schema through low-rank adaptation. DAGPrompT also incorporates hop-specific prompts accounting for varying graph structures and distributions among hops. Evaluations on 10 datasets and 14 baselines demonstrate that DAGPrompT improves accuracy by up to 4.79 in node and graph classification tasks, setting a new state-of-the-art while preserving efficiency. Codes are available at GitHub.

cs.LG↗

arXiv2024

ReEvo: Large Language Models as Hyper-Heuristics with Reflective Evolution

The omnipresence of NP-hard combinatorial optimization problems (COPs) compels domain experts to engage in trial-and-error heuristic design. The long-standing endeavor of design automation has gained new momentum with the rise of large language models (LLMs). This paper introduces Language Hyper-Heuristics (LHHs), an emerging variant of Hyper-Heuristics that leverages LLMs for heuristic generation, featuring minimal manual intervention and open-ended heuristic spaces. To empower LHHs, we present Reflective Evolution (ReEvo), a novel integration of evolutionary search for efficiently exploring the heuristic space, and LLM reflections to provide verbal gradients within the space. Across five heterogeneous algorithmic types, six different COPs, and both white-box and black-box views of COPs, ReEvo yields state-of-the-art and competitive meta-heuristics, evolutionary algorithms, heuristics, and neural solvers, while being more sample-efficient than prior LHHs.

cs.NE↗

arXiv2024

ValueBench: Towards Comprehensively Evaluating Value Orientations and Understanding of Large Language Models

Large Language Models (LLMs) are transforming diverse fields and gaining increasing influence as human proxies. This development underscores the urgent need for evaluating value orientations and understanding of LLMs to ensure their responsible integration into public-facing applications. This work introduces ValueBench, the first comprehensive psychometric benchmark for evaluating value orientations and value understanding in LLMs. ValueBench collects data from 44 established psychometric inventories, encompassing 453 multifaceted value dimensions. We propose an evaluation pipeline grounded in realistic human-AI interactions to probe value orientations, along with novel tasks for evaluating value understanding in an open-ended value space. With extensive experiments conducted on six representative LLMs, we unveil their shared and distinctive value orientations and exhibit their ability to approximate expert conclusions in value-related extraction and generation tasks. ValueBench is openly accessible at https://github.com/Value4AI/ValueBench.

cs.CL↗

arXiv2024

RoutePlacer: An End-to-End Routability-Aware Placer with Graph Neural Network

Placement is a critical and challenging step of modern chip design, with routability being an essential indicator of placement quality. Current routability-oriented placers typically apply an iterative two-stage approach, wherein the first stage generates a placement solution, and the second stage provides non-differentiable routing results to heuristically improve the solution quality. This method hinders jointly optimizing the routability aspect during placement. To address this problem, this work introduces RoutePlacer, an end-to-end routability-aware placement method. It trains RouteGNN, a customized graph neural network, to efficiently and accurately predict routability by capturing and fusing geometric and topological representations of placements. Well-trained RouteGNN then serves as a differentiable approximation of routability, enabling end-to-end gradient-based routability optimization. In addition, RouteGNN can improve two-stage placers as a plug-and-play alternative to external routers. Our experiments on DREAMPlace, an open-source AI4EDA platform, show that RoutePlacer can reduce Total Overflow by up to 16% while maintaining routed wirelength, compared to the state-of-the-art; integrating RouteGNN within two-stage placers leads to a 44% reduction in Total Overflow without compromising wirelength.

cs.LG↗

arXiv2024

AnchorGT: Efficient and Flexible Attention Architecture for Scalable Graph Transformers

Graph Transformers (GTs) have significantly advanced the field of graph representation learning by overcoming the limitations of message-passing graph neural networks (GNNs) and demonstrating promising performance and expressive power. However, the quadratic complexity of self-attention mechanism in GTs has limited their scalability, and previous approaches to address this issue often suffer from expressiveness degradation or lack of versatility. To address this issue, we propose AnchorGT, a novel attention architecture for GTs with global receptive field and almost linear complexity, which serves as a flexible building block to improve the scalability of a wide range of GT models. Inspired by anchor-based GNNs, we employ structurally important $k$-dominating node set as anchors and design an attention mechanism that focuses on the relationship between individual nodes and anchors, while retaining the global receptive field for all nodes. With its intuitive design, AnchorGT can easily replace the attention module in various GT models with different network architectures and structural encodings, resulting in reduced computational overhead without sacrificing performance. In addition, we theoretically prove that AnchorGT attention can be strictly more expressive than Weisfeiler-Lehman test, showing its superiority in representing graph structures. Our experiments on three state-of-the-art GT models demonstrate that their AnchorGT variants can achieve better results while being faster and significantly more memory efficient.

cs.LG↗

arXiv2023

Continual Learning on Dynamic Graphs via Parameter Isolation

Many real-world graph learning tasks require handling dynamic graphs where new nodes and edges emerge. Dynamic graph learning methods commonly suffer from the catastrophic forgetting problem, where knowledge learned for previous graphs is overwritten by updates for new graphs. To alleviate the problem, continual graph learning methods are proposed. However, existing continual graph learning methods aim to learn new patterns and maintain old ones with the same set of parameters of fixed size, and thus face a fundamental tradeoff between both goals. In this paper, we propose Parameter Isolation GNN (PI-GNN) for continual learning on dynamic graphs that circumvents the tradeoff via parameter isolation and expansion. Our motivation lies in that different parameters contribute to learning different graph patterns. Based on the idea, we expand model parameters to continually learn emerging graph patterns. Meanwhile, to effectively preserve knowledge for unaffected patterns, we find parameters that correspond to them via optimization and freeze them to prevent them from being rewritten. Experiments on eight real-world datasets corroborate the effectiveness of PI-GNN compared to state-of-the-art baselines.

cs.LG↗

arXiv2023

On Structural Expressive Power of Graph Transformers

Graph Transformer has recently received wide attention in the research community with its outstanding performance, yet its structural expressive power has not been well analyzed. Inspired by the connections between Weisfeiler-Lehman (WL) graph isomorphism test and graph neural network (GNN), we introduce \textbf{SEG-WL test} (\textbf{S}tructural \textbf{E}ncoding enhanced \textbf{G}lobal \textbf{W}eisfeiler-\textbf{L}ehman test), a generalized graph isomorphism test algorithm as a powerful theoretical tool for exploring the structural discriminative power of graph Transformers. We theoretically prove that the SEG-WL test is an expressivity upper bound on a wide range of graph Transformers, and the representational power of SEG-WL test can be approximated by a simple Transformer network arbitrarily under certain conditions. With the SEG-WL test, we show how graph Transformers' expressive power is determined by the design of structural encodings, and present conditions that make the expressivity of graph Transformers beyond WL test and GNNs. Moreover, motivated by the popular shortest path distance encoding, we follow the theory-oriented principles and develop a provably stronger structural encoding method, Shortest Path Induced Subgraph (\textit{SPIS}) encoding. Our theoretical findings provide a novel and practical paradigm for investigating the expressive power of graph Transformers, and extensive synthetic and real-world experiments empirically verify the strengths of our proposed methods.

cs.LG↗

arXiv2023

Dual Intent Enhanced Graph Neural Network for Session-based New Item Recommendation

Recommender systems are essential to various fields, e.g., e-commerce, e-learning, and streaming media. At present, graph neural networks (GNNs) for session-based recommendations normally can only recommend items existing in users' historical sessions. As a result, these GNNs have difficulty recommending items that users have never interacted with (new items), which leads to a phenomenon of information cocoon. Therefore, it is necessary to recommend new items to users. As there is no interaction between new items and users, we cannot include new items when building session graphs for GNN session-based recommender systems. Thus, it is challenging to recommend new items for users when using GNN-based methods. We regard this challenge as '\textbf{G}NN \textbf{S}ession-based \textbf{N}ew \textbf{I}tem \textbf{R}ecommendation (GSNIR)'. To solve this problem, we propose a dual-intent enhanced graph neural network for it. Due to the fact that new items are not tied to historical sessions, the users' intent is difficult to predict. We design a dual-intent network to learn user intent from an attention mechanism and the distribution of historical data respectively, which can simulate users' decision-making process in interacting with a new item. To solve the challenge that new items cannot be learned by GNNs, inspired by zero-shot learning (ZSL), we infer the new item representation in GNN space by using their attributes. By outputting new item probabilities, which contain recommendation scores of the corresponding items, the new items with higher scores are recommended to users. Experiments on two representative real-world datasets show the superiority of our proposed method. The case study from the real-world verifies interpretability benefits brought by the dual-intent module and the new item reasoning module. The code is available at Github: https://github.com/Ee1s/NirGNN

cs.IR↗

arXiv2023

Hierarchical Transformer for Scalable Graph Learning

Graph Transformer is gaining increasing attention in the field of machine learning and has demonstrated state-of-the-art performance on benchmarks for graph representation learning. However, as current implementations of Graph Transformer primarily focus on learning representations of small-scale graphs, the quadratic complexity of the global self-attention mechanism presents a challenge for full-batch training when applied to larger graphs. Additionally, conventional sampling-based methods fail to capture necessary high-level contextual information, resulting in a significant loss of performance. In this paper, we introduce the Hierarchical Scalable Graph Transformer (HSGT) as a solution to these challenges. HSGT successfully scales the Transformer architecture to node representation learning tasks on large-scale graphs, while maintaining high performance. By utilizing graph hierarchies constructed through coarsening techniques, HSGT efficiently updates and stores multi-scale information in node embeddings at different levels. Together with sampling-based training methods, HSGT effectively captures and aggregates multi-level information on the hierarchical graph using only Transformer blocks. Empirical evaluations demonstrate that HSGT achieves state-of-the-art performance on large-scale benchmarks with graphs containing millions of nodes with high efficiency.

cs.LG↗

arXiv2022

LEReg: Empower Graph Neural Networks with Local Energy Regularization

Researches on analyzing graphs with Graph Neural Networks (GNNs) have been receiving more and more attention because of the great expressive power of graphs. GNNs map the adjacency matrix and node features to node representations by message passing through edges on each convolution layer. However, the message passed through GNNs is not always beneficial for all parts in a graph. Specifically, as the data distribution is different over the graph, the receptive field (the farthest nodes that a node can obtain information from) needed to gather information is also different. Existing GNNs treat all parts of the graph uniformly, which makes it difficult to adaptively pass the most informative message for each unique part. To solve this problem, we propose two regularization terms that consider message passing locally: (1) Intra-Energy Reg and (2) Inter-Energy Reg. Through experiments and theoretical discussion, we first show that the speed of smoothing of different parts varies enormously and the topology of each part affects the way of smoothing. With Intra-Energy Reg, we strengthen the message passing within each part, which is beneficial for getting more useful information. With Inter-Energy Reg, we improve the ability of GNNs to distinguish different nodes. With the proposed two regularization terms, GNNs are able to filter the most useful information adaptively, learn more robustly and gain higher expressiveness. Moreover, the proposed LEReg can be easily applied to other GNN models with plug-and-play characteristics. Extensive experiments on several benchmarks verify that GNNs with LEReg outperform or match the state-of-the-art methods. The effectiveness and efficiency are also empirically visualized with elaborate experiments.

cs.LG↗

arXiv2022

Meta-Weight Graph Neural Network: Push the Limits Beyond Global Homophily

Graph Neural Networks (GNNs) show strong expressive power on graph data mining, by aggregating information from neighbors and using the integrated representation in the downstream tasks. The same aggregation methods and parameters for each node in a graph are used to enable the GNNs to utilize the homophily relational data. However, not all graphs are homophilic, even in the same graph, the distributions may vary significantly. Using the same convolution over all nodes may lead to the ignorance of various graph patterns. Furthermore, many existing GNNs integrate node features and structure identically, which ignores the distributions of nodes and further limits the expressive power of GNNs. To solve these problems, we propose Meta Weight Graph Neural Network (MWGNN) to adaptively construct graph convolution layers for different nodes. First, we model the Node Local Distribution (NLD) from node feature, topological structure and positional identity aspects with the Meta-Weight. Then, based on the Meta-Weight, we generate the adaptive graph convolutions to perform a node-specific weighted aggregation and boost the node representations. Finally, we design extensive experiments on real-world and synthetic benchmarks to evaluate the effectiveness of MWGNN. These experiments show the excellent expressive power of MWGNN in dealing with graph data with various distributions.

cs.LG↗

arXiv2022

Equivalent Distance Geometry Error for Molecular Conformation Comparison

Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug design. However, existing loss functions in these models either cost overmuch time or fail to guarantee the equivalence during optimization, which means treating different items unfairly, resulting in poor local geometry in generated conformation. So, we propose Equivalent Distance Geometry Error (EDGE) to calculate the differential discrepancy between conformations where the essential factors of three kinds in conformation geometry (i.e. bond lengths, bond angles and dihedral angles) are equivalently optimized with certain weights. And in the improved version of our method, the optimization features minimizing linear transformations of atom-pair distances within 3-hop. Extensive experiments show that, compared with existing loss functions, EDGE performs effectively and efficiently in two tasks under the same backbones.

q-bio.BM↗

arXiv2021

Stepping Back to SMILES Transformers for Fast Molecular Representation Inference

In the intersection of molecular science and deep learning, tasks like virtual screening have driven the need for a high-throughput molecular representation generator on large chemical databases. However, as SMILES strings are the most common storage format for molecules, using deep graph models to extract molecular feature from raw SMILES data requires an SMILES-to-graph conversion, which significantly decelerates the whole process. Directly deriving molecular representations from SMILES is feasible, yet there exists a performance gap between the existing unpretrained SMILES-based models and graph-based models at large-scale benchmark results, while pretrain models are resource-demanding at training. To address this issue, we propose ST-KD, an end-to-end \textbf{S}MILES \textbf{T}ransformer for molecular representation learning boosted by \textbf{K}nowledge \textbf{D}istillation. In order to conduct knowledge transfer from graph Transformers to ST-KD, we have redesigned the attention layers and introduced a pre-transformation step to tokenize the SMILES strings and inject structure-based positional embeddings. Without expensive pretraining, ST-KD shows competitive results on latest standard molecular datasets PCQM4M-LSC and QM9, with $3\text{-}14\times$ inference speed compared with existing graph models.

cs.CE↗

arXiv2021

Deep Molecular Representation Learning via Fusing Physical and Chemical Information

Molecular representation learning is the first yet vital step in combining deep learning and molecular science. To push the boundaries of molecular representation learning, we present PhysChem, a novel neural architecture that learns molecular representations via fusing physical and chemical information of molecules. PhysChem is composed of a physicist network (PhysNet) and a chemist network (ChemNet). PhysNet is a neural physical engine that learns molecular conformations through simulating molecular dynamics with parameterized forces; ChemNet implements geometry-aware deep message-passing to learn chemical / biomedical properties of molecules. Two networks specialize in their own tasks and cooperate by providing expertise to each other. By fusing physical and chemical information, PhysChem achieved state-of-the-art performances on MoleculeNet, a standard molecular machine learning benchmark. The effectiveness of PhysChem was further corroborated on cutting-edge datasets of SARS-CoV-2.

q-bio.QM↗

arXiv2021

Spatial-Temporal Graph ODE Networks for Traffic Flow Forecasting

Spatial-temporal forecasting has attracted tremendous attention in a wide range of applications, and traffic flow prediction is a canonical and typical example. The complex and long-range spatial-temporal correlations of traffic flow bring it to a most intractable challenge. Existing works typically utilize shallow graph convolution networks (GNNs) and temporal extracting modules to model spatial and temporal dependencies respectively. However, the representation ability of such models is limited due to: (1) shallow GNNs are incapable to capture long-range spatial correlations, (2) only spatial connections are considered and a mass of semantic connections are ignored, which are of great importance for a comprehensive understanding of traffic networks. To this end, we propose Spatial-Temporal Graph Ordinary Differential Equation Networks (STGODE). Specifically, we capture spatial-temporal dynamics through a tensor-based ordinary differential equation (ODE), as a result, deeper networks can be constructed and spatial-temporal features are utilized synchronously. To understand the network more comprehensively, semantical adjacency matrix is considered in our model, and a well-design temporal dialated convolution structure is used to capture long term temporal dependencies. We evaluate our model on multiple real-world traffic datasets and superior performance is achieved over state-of-the-art baselines.

cs.LG↗

arXiv2021

HamNet: Conformation-Guided Molecular Representation with Hamiltonian Neural Networks

Well-designed molecular representations (fingerprints) are vital to combine medical chemistry and deep learning. Whereas incorporating 3D geometry of molecules (i.e. conformations) in their representations seems beneficial, current 3D algorithms are still in infancy. In this paper, we propose a novel molecular representation algorithm which preserves 3D conformations of molecules with a Molecular Hamiltonian Network (HamNet). In HamNet, implicit positions and momentums of atoms in a molecule interact in the Hamiltonian Engine following the discretized Hamiltonian equations. These implicit coordinations are supervised with real conformations with translation- & rotation-invariant losses, and further used as inputs to the Fingerprint Generator, a message-passing neural network. Experiments show that the Hamiltonian Engine can well preserve molecular conformations, and that the fingerprints generated by HamNet achieve state-of-the-art performances on MoleculeNet, a standard molecular machine learning benchmark.

cs.LG↗