Pretraining models with unsupervised graph representation learning has led to significant advancements in domains such as social network analysis, molecular design, and electronic design automation (EDA). However, prior work in EDA has mainly focused on pretraining models for digital circuits, overlooking analog and mixed-signal circuits. To bridge this gap, we introduce DICE, a Device-level Integrated Circuits Encoder, which is the first graph neural network (GNN) pretrained via self-supervised learning specifically tailored for graph-level prediction tasks in both analog and digital circuits. DICE adopts a simulation-free pretraining approach based on graph contrastive learning, leveraging two novel graph augmentation techniques. Experimental results demonstrate substantial performance improvements across three downstream tasks, highlighting the effectiveness of DICE for both analog and digital circuits. The code is available at github.com/brianlsy98/DICE.
Combinatorial optimization problems, such as scheduling and route planning, are crucial in various industries but are computationally intractable due to their NP-hard nature. Neural Combinatorial Optimization methods leverage machine learning to address these challenges but often depend on sequential decision-making, which is prone to error accumulation as small mistakes propagate throughout the process. Inspired by self-evaluation techniques in Large Language Models, we propose a novel framework that generates and evaluates subsets of assignments, moving beyond traditional stepwise approaches. Applied to the Job-Shop Scheduling Problem, our method integrates a heterogeneous graph neural network with a Transformer to build a policy model and a self-evaluation function. Experimental validation on challenging, well-known benchmarks demonstrates the effectiveness of our approach, surpassing state-of-the-art methods.
Machine learning (ML) models have become essential tools in various scenarios. Their effectiveness, however, hinges on a substantial volume of data for satisfactory performance. Model marketplaces have thus emerged as crucial platforms bridging model consumers seeking ML solutions and data owners possessing valuable data. These marketplaces leverage model trading mechanisms to properly incentive data owners to contribute their data, and return a well performing ML model to the model consumers. However, existing model trading mechanisms often assume the data owners are willing to share their data before being paid, which is not reasonable in real world. Given that, we propose a novel mechanism, named Structural Importance based Model Trading (SIMT) mechanism, that assesses the data importance and compensates data owners accordingly without disclosing the data. Specifically, SIMT procures feature and label data from data owners according to their structural importance, and then trains a graph neural network for model consumers. Theoretically, SIMT ensures incentive compatible, individual rational and budget feasible. The experiments on five popular datasets validate that SIMT consistently outperforms vanilla baselines by up to $40\%$ in both MacroF1 and MicroF1.
Recent advances in deep learning have established Transformer architectures as the predominant modeling paradigm. Central to the success of Transformers is the self-attention mechanism, which scores the similarity between query and key matrices to modulate a value matrix. This operation bears striking similarities to digraph convolution, prompting an investigation into whether digraph convolution could serve as an alternative to self-attention. In this study, we formalize this concept by introducing a synthetic unitary digraph convolution based on the digraph Fourier transform. The resulting model, which we term Converter, effectively converts a Transformer into a Directed Graph Neural Network (DGNN) form. We have tested Converter on Long-Range Arena benchmark, long document classification, and DNA sequence-based taxonomy classification. Our experimental results demonstrate that Converter achieves superior performance while maintaining computational efficiency and architectural simplicity, which establishes it as a lightweight yet powerful Transformer variant.
In recent years, Graph Neural Network (GNN) based models have shown promising results in simulating physics of complex systems. However, training dedicated graph network based physics simulators can be costly, as most models are confined to fully supervised training, which requires extensive data generated from traditional physics simulators. To date, how transfer learning could improve the model performance and training efficiency has remained unexplored. In this work, we introduce a pre-training and transfer learning paradigm for graph network simulators. We propose the scalable graph U-net (SGUNET). Incorporating an innovative depth-first search (DFS) pooling, the SGUNET is adaptable to different mesh sizes and resolutions for various simulation tasks. To enable the transfer learning between differently configured SGUNETs, we propose a set of mapping functions to align the parameters between the pre-trained model and the target model. An extra normalization term is also added into the loss to constrain the difference between the pre-trained weights and target model weights for better generalization performance. To pre-train our physics simulator we created a dataset which includes 20,000 physical simulations of randomly selected 3D shapes from the open source A Big CAD (ABC) dataset. We show that our proposed transfer learning methods allow the model to perform even better when fine-tuned with small amounts of training data than when it is trained from scratch with full extensive dataset. On the 2D Deformable Plate benchmark dataset, our pre-trained model fine-tuned on 1/16 of the training data achieved an 11.05\% improvement in position RMSE compared to the model trained from scratch.
Data-driven soft sensors help in process operations by providing real-time estimates of otherwise hard- to-measure process quantities, e.g., viscosities or product concentrations. Currently, soft sensors need to be developed individually per plant. Using transfer learning, machine learning-based soft sensors could be reused and fine-tuned across plants and applications. However, transferring data-driven soft sensor models is in practice often not possible, because the fixed input structure of standard soft sensor models prohibits transfer if, e.g., the sensor information is not identical in all plants. We propose a topology-aware graph neural network approach for transfer learning of soft sensor models across multiple plants. In our method, plants are modeled as graphs: Unit operations are nodes, streams are edges, and sensors are embedded as attributes. Our approach brings two advantages for transfer learning: First, we not only include sensor data but also crucial information on the plant topology. Second, the graph neural network algorithm is flexible with respect to its sensor inputs. This allows us to model data from different plants with different sensor networks. We test the transfer learning capabilities of our modeling approach on ammonia synthesis loops with different process topologies. We build a soft sensor predicting the ammonia concentration in the product. After training on data from one process, we successfully transfer our soft sensor model to a previously unseen process with a different topology. Our approach promises to extend the data-driven soft sensors to cases to leverage data from multiple plants.
This paper proposes a graph neural network (GNN) enabled power allocation scheme for non-orthogonal multiple access (NOMA) networks. In particular, a downlink scenario with one base station serving multiple users over several subchannels is considered, where the number of subchannels is less than the number of users, and thus, some users have to share a subchannel via NOMA. Our goal is to maximize the system energy efficiency subject to the rate requirement of each user and the overall budget. We propose a deep learning based approach termed NOMA net (NOMANet) to address the considered problem. Particularly, NOMANet is GNN-based, which maps channel state information to the desired power allocation scheme for all subchannels. The multi-head attention and the residual/dense connection are adopted to enhance the feature extraction. The output of NOMANet is guaranteed to be feasible via the customized activation function and the penalty method. Numerical results show that NOMANet trained unsupervised achieves performance close to that of the successive convex approximation method but with a faster inference speed by about $700$ times. Besides, NOMANet is featured by its scalability to both users and subchannels.
The pinching-antenna system is a novel flexible-antenna technology, which has the capabilities not only to combat large-scale path loss, but also to reconfigure the antenna array in a flexible manner. The key idea of pinching antennas is to apply small dielectric particles on a waveguide of arbitrary length, so that they can be positioned close to users to avoid significant large-scale path loss. This paper investigates the graph neural network (GNN) enabled transmit design for the joint optimization of antenna placement and power allocation in pinching-antenna systems. We formulate the downlink communication system equipped with pinching antennas as a bipartite graph, and propose a graph attention network (GAT) based model, termed bipartite GAT (BGAT), to solve an energy efficiency (EE) maximization problem. With the tailored readout processes, the BGAT guarantees a feasible solution, which also facilitates the unsupervised training. Numerical results demonstrate the effectiveness of pinching antennas in enhancing the system EE as well as the proposed BGAT in terms of optimality, scalability and computational efficiency.
Robots are often built from standardized assemblies, (e.g. arms, legs, or fingers), but each robot must be trained from scratch to control all the actuators of all the parts together. In this paper we demonstrate a new approach that takes a single robot and its controller as input and produces a set of modular controllers for each of these assemblies such that when a new robot is built from the same parts, its control can be quickly learned by reusing the modular controllers. We achieve this with a framework called MeMo which learns (Me)aningful, (Mo)dular controllers. Specifically, we propose a novel modularity objective to learn an appropriate division of labor among the modules. We demonstrate that this objective can be optimized simultaneously with standard behavior cloning loss via noise injection. We benchmark our framework in locomotion and grasping environments on simple to complex robot morphology transfer. We also show that the modules help in task transfer. On both structure and task transfer, MeMo achieves improved training efficiency to graph neural network and Transformer baselines.
Accurate estimation of voltage drop (IR drop) in modern Application-Specific Integrated Circuits (ASICs) is highly time and resource demanding, due to the growing complexity and the transistor density in recent technology nodes. To mitigate this challenge, we investigate how Machine Learning (ML) techniques, including Extreme Gradient Boosting (XGBoost), Convolutional Neural Network (CNN), and Graph Neural Network (GNN) can aid in reducing the computational effort and implicitly the time required to estimate the IR drop in Integrated Circuits (ICs). Traditional methods, including commercial tools, require considerable time to produce accurate approximations, especially for complicated designs with numerous transistors. ML algorithms, on the other hand, are explored as an alternative solution to offer quick and precise IR drop estimation, but in considerably less time. Our approach leverages ASICs' electrical, timing, and physical to train ML models, ensuring adaptability across diverse designs with minimal adjustments. Experimental results underscore the superiority of ML models over commercial tools, greatly enhancing prediction speed. Particularly, GNNs exhibit promising performance with minimal prediction errors in voltage drop estimation. The incorporation of GNNs marks a groundbreaking advancement in accurate IR drop prediction. This study illustrates the effectiveness of ML algorithms in precisely estimating IR drop and optimizing ASIC sign-off. Utilizing ML models leads to expedited predictions, reducing calculation time and improving energy efficiency, thereby reducing environmental impact through optimized power circuits.
This study presents a hierarchical mining framework for high-dimensional imbalanced data, leveraging a depth graph model to address the inherent performance limitations of conventional approaches in handling complex, high-dimensional data distributions with imbalanced sample representations. By constructing a structured graph representation of the dataset and integrating graph neural network (GNN) embeddings, the proposed method effectively captures global interdependencies among samples. Furthermore, a hierarchical strategy is employed to enhance the characterization and extraction of minority class feature patterns, thereby facilitating precise and robust imbalanced data mining. Empirical evaluations across multiple experimental scenarios validate the efficacy of the proposed approach, demonstrating substantial improvements over traditional methods in key performance metrics, including pattern discovery count, average support, and minority class coverage. Notably, the method exhibits superior capabilities in minority-class feature extraction and pattern correlation analysis. These findings underscore the potential of depth graph models, in conjunction with hierarchical mining strategies, to significantly enhance the efficiency and accuracy of imbalanced data analysis. This research contributes a novel computational framework for high-dimensional complex data processing and lays the foundation for future extensions to dynamically evolving imbalanced data and multi-modal data applications, thereby expanding the applicability of advanced data mining methodologies to more intricate analytical domains.
With recent advancements in non-invasive techniques for measuring brain activity, such as magnetic resonance imaging (MRI), the study of structural and functional brain networks through graph signal processing (GSP) has gained notable prominence. GSP stands as a key tool in unraveling the interplay between the brain's function and structure, enabling the analysis of graphs defined by the connections between regions of interest -- referred to as connectomes in this context. Our work represents a further step in this direction by exploring supervised contrastive learning methods within the realm of graph representation learning. The main objective of this approach is to generate subject-level (i.e., graph-level) vector representations that bring together subjects sharing the same label while separating those with different labels. These connectome embeddings are derived from a graph neural network Encoder-Decoder architecture, which jointly considers structural and functional connectivity. By leveraging data augmentation techniques, the proposed framework achieves state-of-the-art performance in a gender classification task using Human Connectome Project data. More broadly, our connectome-centric methodological advances support the promising prospect of using GSP to discover more about brain function, with potential impact to understanding heterogeneity in the neurodegeneration for precision medicine and diagnosis.
The widespread use of social media has accelerated the dissemination of information, but it has also facilitated the spread of harmful rumours, which can disrupt economies, influence political outcomes, and exacerbate public health crises, such as the COVID-19 pandemic. While Graph Neural Network (GNN)-based approaches have shown significant promise in automated rumour detection, they often lack transparency, making their predictions difficult to interpret. Existing graph explainability techniques fall short in addressing the unique challenges posed by the dependencies among feature dimensions in high-dimensional text embeddings used in GNN-based models. In this paper, we introduce Contrastive Token Layerwise Relevance Propagation (CT-LRP), a novel framework designed to enhance the explainability of GNN-based rumour detection. CT-LRP extends current graph explainability methods by providing token-level explanations that offer greater granularity and interpretability. We evaluate the effectiveness of CT-LRP across multiple GNN models trained on three publicly available rumour detection datasets, demonstrating that it consistently produces high-fidelity, meaningful explanations, paving the way for more robust and trustworthy rumour detection systems.
Fitness landscapes in test-based program synthesis are known to be extremely rugged, with even minimal modifications of programs often leading to fundamental changes in their behavior and, consequently, fitness values. Relying on fitness as the only guidance in iterative search algorithms like genetic programming is thus unnecessarily limiting, especially when combined with purely syntactic search operators that are agnostic about their impact on program behavior. In this study, we propose a semantics-aware search operator that steers the search towards candidate programs that are valuable not only actually (high fitness) but also only potentially, i.e. are likely to be turned into high-quality solutions even if their current fitness is low. The key component of the method is a graph neural network that learns to model the interactions between program instructions and processed data, and produces a saliency map over graph nodes that represents possible search decisions. When applied to a suite of symbolic regression benchmarks, the proposed method outperforms conventional tree-based genetic programming and the ablated variant of the method.
This paper investigates the graph neural network (GNN)-enabled beamforming design for interference channels. We propose a model termed interference channel GNN (ICGNN) to solve a quality-of-service constrained energy efficiency maximization problem. The ICGNN is two-stage, where the direction and power parts of beamforming vectors are learned separately but trained jointly via unsupervised learning. By formulating the dimensionality of features independent of the transceiver pairs, the ICGNN is scalable with the number of transceiver pairs. Besides, to improve the performance of the ICGNN, the hybrid maximum ratio transmission and zero-forcing scheme reduces the output ports, the feature enhancement module unifies the two types of links into one type, the subgraph representation enhances the message passing efficiency, and the multi-head attention and residual connection facilitate the feature extracting. Furthermore, we present the over-the-air distributed implementation of the ICGNN. Ablation studies validate the effectiveness of key components in the ICGNN. Numerical results also demonstrate the capability of ICGNN in achieving near-optimal performance with an average inference time less than 0.1 ms. The scalability of ICGNN for unseen problem sizes is evaluated and enhanced by transfer learning with limited fine-tuning cost. The results of the centralized and distributed implementations of ICGNN are illustrated.
This paper investigates the deep learning based approaches for simultaneous wireless information and power transfer (SWIPT). The quality-of-service (QoS) constrained sum-rate maximization problems are, respectively, formulated for power-splitting (PS) receivers and time-switching (TS) receivers and solved by a unified graph neural network (GNN) based model termed SWIPT net (SWIPTNet). To improve the performance of SWIPTNet, we first propose a single-type output method to reduce the learning complexity and facilitate the satisfaction of QoS constraints, and then, utilize the Laplace transform to enhance input features with the structural information. Besides, we adopt the multi-head attention and layer connection to enhance feature extracting. Furthermore, we present the implementation of transfer learning to the SWIPTNet between PS and TS receivers. Ablation studies show the effectiveness of key components in the SWIPTNet. Numerical results also demonstrate the capability of SWIPTNet in achieving near-optimal performance with millisecond-level inference speed which is much faster than the traditional optimization algorithms. We also show the effectiveness of transfer learning via fast convergence and expressive capability improvement.
An emerging fluid antenna system (FAS) brings a new dimension, i.e., the antenna positions, to deal with the deep fading, but simultaneously introduces challenges related to the transmit design. This paper proposes an ``unsupervised learning to optimize" paradigm to optimize the FAS. Particularly, we formulate the sum-rate and energy efficiency (EE) maximization problems for a multiple-user multiple-input single-output (MU-MISO) FAS and solved by a two-stage graph neural network (GNN) where the first stage and the second stage are for the inference of antenna positions and beamforming vectors, respectively. The outputs of the two stages are jointly input into a unsupervised loss function to train the two-stage GNN. The numerical results demonstrates that the advantages of the FAS for performance improvement and the two-stage GNN for real-time and scalable optimization. Besides, the two stages can function separately.
Functional MRI (fMRI) and single-cell transcriptomics are pivotal in Alzheimer's disease (AD) research, each providing unique insights into neural function and molecular mechanisms. However, integrating these complementary modalities remains largely unexplored. Here, we introduce scBIT, a novel method for enhancing AD prediction by combining fMRI with single-nucleus RNA (snRNA). scBIT leverages snRNA as an auxiliary modality, significantly improving fMRI-based prediction models and providing comprehensive interpretability. It employs a sampling strategy to segment snRNA data into cell-type-specific gene networks and utilizes a self-explainable graph neural network to extract critical subgraphs. Additionally, we use demographic and genetic similarities to pair snRNA and fMRI data across individuals, enabling robust cross-modal learning. Extensive experiments validate scBIT's effectiveness in revealing intricate brain region-gene associations and enhancing diagnostic prediction accuracy. By advancing brain imaging transcriptomics to the single-cell level, scBIT sheds new light on biomarker discovery in AD research. Experimental results show that incorporating snRNA data into the scBIT model significantly boosts accuracy, improving binary classification by 3.39% and five-class classification by 26.59%. The codes were implemented in Python and have been released on GitHub (https://github.com/77YQ77/scBIT) and Zenodo (https://zenodo.org/records/11599030) with detailed instructions.
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however, lack spatial context and rely on incomplete datasets of ligand-receptor interactions (LRIs), limiting accurate cell type annotation and cell-cell communication (CCC) inference. This study addresses these challenges using a novel graph neural network (GNN) model that enhances cell type prediction and cell interaction analysis. Our study utilized a dataset consisting of 49,020 cells from 19 patients across three cancer types: Leukemia, Breast Invasive Carcinoma, and Colorectal Cancer. The proposed scGSL model demonstrated robust performance, achieving an average accuracy of 84.83%, precision of 86.23%, recall of 81.51%, and an F1 score of 80.92% across all datasets. These metrics represent a significant enhancement over existing methods, which typically exhibit lower performance metrics. Additionally, by reviewing existing literature on gene interactions within the TME, the scGSL model proves to robustly identify biologically meaningful gene interactions in an unsupervised manner, validated by significant expression differences in key gene pairs across various cancers. The source code and data used in this paper can be found in https://github.com/LiYuechao1998/scGSL.
Reinforcement Learning (RL) methods used for solving real-world optimization problems often involve dynamic state-action spaces, larger scale, and sparse rewards, leading to significant challenges in convergence, scalability, and efficient exploration of the solution space. This study introduces GNN-DT, a novel Decision Transformer (DT) architecture that integrates Graph Neural Network (GNN) embedders with a novel residual connection between input and output tokens crucial for handling dynamic environments. By learning from previously collected trajectories, GNN-DT tackles the sparse rewards limitations of online RL algorithms and delivers high-quality solutions in real-time. We evaluate GNN-DT on the complex electric vehicle (EV) charging optimization problem and prove that its performance is superior and requires significantly fewer training trajectories, thus improving sample efficiency compared to existing DT and offline RL baselines. Furthermore, GNN-DT exhibits robust generalization to unseen environments and larger action spaces, addressing a critical gap in prior offline and online RL approaches.