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We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene expression assays at the single-cell level, resulting in the loss of cell evolutionary trajectories. Due to technological and cost constraints, single-cell experiments often feature cells sampled at irregular and sparse time points with a small sample size. Although trajectory-based structural inference models can accurately reveal the underlying interaction graph from observed data, their efficacy depends on the inputs of thousands of regularly sampled trajectories. The irregularly-sampled nature of single-cell data precludes the direct use of these powerful models for reconstructing GRNs. Optimal transport, a classical mathematical framework that minimize transportation costs between distributions, has shown promise in multi-omics data integration and cell fate prediction. Utilizing OT, our method constructs mappings between consecutively sampled cells to form cell-level trajectories, which are given as input to a structural inference model that recovers the GRN from single-cell data. Through case studies in two synthetic datasets, we demonstrate the feasibility of our proposed method and its promising performance over eight state-of-the-art GRN inference methods., Comment: for the associated code repository, see https://github.com/1250326/Integrating-OT-and-Structural-Inference-Models-for-GRN-Inference-from-Single-cell-Data

In distributed networks, calculating the maximum element is a fundamental task in data analysis, known as the distributed maximum consensus problem. However, the sensitive nature of the data involved makes privacy protection essential. Despite its importance, privacy in distributed maximum consensus has received limited attention in the literature. Traditional privacy-preserving methods typically add noise to updates, degrading the accuracy of the final result. To overcome these limitations, we propose a novel distributed optimization-based approach that preserves privacy without sacrificing accuracy. Our method introduces virtual nodes to form an augmented graph and leverages a carefully designed initialization process to ensure the privacy of honest participants, even when all their neighboring nodes are dishonest. Through a comprehensive information-theoretical analysis, we derive a sufficient condition to protect private data against both passive and eavesdropping adversaries. Extensive experiments validate the effectiveness of our approach, demonstrating that it not only preserves perfect privacy but also maintains accuracy, outperforming existing noise-based methods that typically suffer from accuracy loss.

In recent years, Graph Neural Networks (GNNs) have become the de facto tool for learning node and graph representations. Most GNNs typically consist of a sequence of neighborhood aggregation (a.k.a., message-passing) layers, within which the representation of each node is updated based on those of its neighbors. The most expressive message-passing GNNs can be obtained through the use of the sum aggregator and of MLPs for feature transformation, thanks to their universal approximation capabilities. However, the limitations of MLPs recently motivated the introduction of another family of universal approximators, called Kolmogorov-Arnold Networks (KANs) which rely on a different representation theorem. In this work, we compare the performance of KANs against that of MLPs on graph learning tasks. We evaluate two different implementations of KANs using two distinct base families of functions, namely B-splines and radial basis functions. We perform extensive experiments on node classification, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all studied tasks, making them viable alternatives, at the cost of some computational complexity. Code is available at https: //github.com/RomanBresson/KAGNN.

Estimating causal effects in e-commerce tends to involve costly treatment assignments which can be impractical in large-scale settings. Leveraging machine learning to predict such treatment effects without actual intervention is a standard practice to diminish the risk. However, existing methods for treatment effect prediction tend to rely on training sets of substantial size, which are built from real experiments and are thus inherently risky to create. In this work we propose a graph neural network to diminish the required training set size, relying on graphs that are common in e-commerce data. Specifically, we view the problem as node regression with a restricted number of labeled instances, develop a two-model neural architecture akin to previous causal effect estimators, and test varying message-passing layers for encoding. Furthermore, as an extra step, we combine the model with an acquisition function to guide the creation of the training set in settings with extremely low experimental budget. The framework is flexible since each step can be used separately with other models or treatment policies. The experiments on real large-scale networks indicate a clear advantage of our methodology over the state of the art, which in many cases performs close to random, underlining the need for models that can generalize with limited supervision to reduce experimental risks.

In multiagent systems (MASs), agents' observation upon system behaviours may improve the overall team performance, but may also leak sensitive information to an observer. A quantified observability analysis can thus be useful to assist decision-making in MASs by operators seeking to optimise the relationship between performance effectiveness and information exposure through observations in practice. This paper presents a novel approach to quantitatively analysing the observability properties in MASs. The concept of opacity is applied to formally express the characterisation of observability in MASs modelled as partially observable multiagent systems. We propose a temporal logic oPATL to reason about agents' observability with quantitative goals, which capture the probability of information transparency of system behaviours to an observer, and develop verification techniques for quantitatively analysing such properties. We implement the approach as an extension of the PRISM model checker, and illustrate its applicability via several examples., Comment: 8 pages

Generative adversarial networks (GANs) have shown remarkable success in image synthesis, making GAN models themselves commercially valuable to legitimate model owners. Therefore, it is critical to technically protect the intellectual property of GANs. Prior works need to tamper with the training set or training process, and they are not robust to emerging model extraction attacks. In this paper, we propose a new ownership protection method based on the common characteristics of a target model and its stolen models. Our method can be directly applicable to all well-trained GANs as it does not require retraining target models. Extensive experimental results show that our new method can achieve the best protection performance, compared to the state-of-the-art methods. Finally, we demonstrate the effectiveness of our method with respect to the number of generations of model extraction attacks, the number of generated samples, different datasets, as well as adaptive attacks.

Diffusion models have been remarkably successful in data synthesis. However, when these models are applied to sensitive datasets, such as banking and human face data, they might bring up severe privacy concerns. This work systematically presents the first privacy study about property inference attacks against diffusion models, where adversaries aim to extract sensitive global properties of its training set from a diffusion model. Specifically, we focus on the most practical attack scenario: adversaries are restricted to accessing only synthetic data. Under this realistic scenario, we conduct a comprehensive evaluation of property inference attacks on various diffusion models trained on diverse data types, including tabular and image datasets. A broad range of evaluations reveals that diffusion models and their samplers are universally vulnerable to property inference attacks. In response, we propose a new model-agnostic plug-in method PriSampler to mitigate the risks of the property inference of diffusion models. PriSampler can be directly applied to well-trained diffusion models and support both stochastic and deterministic sampling. Extensive experiments illustrate the effectiveness of our defense, and it can lead adversaries to infer the proportion of properties as close as predefined values that model owners wish. Notably, PriSampler also shows its significantly superior performance to diffusion models trained with differential privacy on both model utility and defense performance. This work will elevate the awareness of preventing property inference attacks and encourage privacy-preserving synthetic data release.

The development of clustering heuristics has demonstrated that Bitcoin is not completely anonymous. Currently, existing clustering heuristics only consider confirmed transactions recorded in the Bitcoin blockchain. However, unconfirmed transactions in the mempool have yet to be utilized to improve the performance of the clustering heuristics. In this paper, we bridge this gap by combining unconfirmed and confirmed transactions for clustering Bitcoin addresses effectively. First, we present a data collection system for capturing unconfirmed transactions. Two case studies are performed to show the presence of user behaviors in unconfirmed transactions not present in confirmed transactions. Next, we apply the state-of-the-art clustering heuristics to unconfirmed transactions, and the clustering results can reduce the number of entities after applying, for example, the co-spend heuristics in confirmed transactions by 2.3%. Finally, we propose three novel clustering heuristics to capture specific behavior patterns in unconfirmed transactions, which further reduce the number of entities after the application of the co-spend heuristics by 9.8%. Our results demonstrate the utility of unconfirmed transactions in address clustering and further shed light on the limitations of anonymity in cryptocurrencies. To the best of our knowledge, this paper is the first to apply the unconfirmed transactions in Bitcoin to cluster addresses., Comment: 15 pages, 13 figures, 4 tables. typos corrected

Recent years have witnessed the tremendous success of diffusion models in data synthesis. However, when diffusion models are applied to sensitive data, they also give rise to severe privacy concerns. In this paper, we systematically present the first study about membership inference attacks against diffusion models, which aims to infer whether a sample was used to train the model. Two attack methods are proposed, namely loss-based and likelihood-based attacks. Our attack methods are evaluated on several state-of-the-art diffusion models, over different datasets in relation to privacy-sensitive data. Extensive experimental evaluations show that our attacks can achieve remarkable performance. Furthermore, we exhaustively investigate various factors which can affect attack performance. Finally, we also evaluate the performance of our attack methods on diffusion models trained with differential privacy.

Vaccine hesitancy is considered as one main cause of the stagnant uptake ratio of COVID-19 vaccines in Europe and the US where vaccines are sufficiently supplied. Fast and accurate grasp of public attitudes toward vaccination is critical to address vaccine hesitancy, and social media platforms have proved to be an effective source of public opinions. In this paper, we describe the collection and release of a dataset of tweets related to COVID-19 vaccines. This dataset consists of the IDs of 2,198,090 tweets collected from Western Europe, 17,934 of which are annotated with the originators' vaccination stances. Our annotation will facilitate using and developing data-driven models to extract vaccination attitudes from social media posts and thus further confirm the power of social media in public health surveillance. To lay the groundwork for future research, we not only perform statistical analysis and visualisation of our dataset, but also evaluate and compare the performance of established text-based benchmarks in vaccination stance extraction. We demonstrate one potential use of our data in practice in tracking the temporal changes of public COVID-19 vaccination attitudes.

To address the vaccine hesitancy which impairs the efforts of the COVID-19 vaccination campaign, it is imperative to understand public vaccination attitudes and timely grasp their changes. In spite of reliability and trustworthiness, conventional attitude collection based on surveys is time-consuming and expensive, and cannot follow the fast evolution of vaccination attitudes. We leverage the textual posts on social media to extract and track users' vaccination stances in near real time by proposing a deep learning framework. To address the impact of linguistic features such as sarcasm and irony commonly used in vaccine-related discourses, we integrate into the framework the recent posts of a user's social network neighbours to help detect the user's genuine attitude. Based on our annotated dataset from Twitter, the models instantiated from our framework can increase the performance of attitude extraction by up to 23% compared to state-of-the-art text-only models. Using this framework, we successfully validate the feasibility of using social media to track the evolution of vaccination attitudes in real life. We further show one practical use of our framework by validating the possibility to forecast a user's vaccine hesitancy changes with information perceived from social media.

Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time. Empirical evaluations demonstrate that simple adaptations of LP can be competitive in semi-supervised node classification in both homophily and heterophily regimes.

Network embedding (NE) approaches have emerged as a predominant technique to represent complex networks and have benefited numerous tasks. However, most NE approaches rely on a homophily assumption to learn embeddings with the guidance of supervisory signals, leaving the unsupervised heterophilous scenario relatively unexplored. This problem becomes especially relevant in fields where a scarcity of labels exists. Here, we formulate the unsupervised NE task as an r-ego network discrimination problem and develop the SELENE framework for learning on networks with homophily and heterophily. Specifically, we design a dual-channel feature embedding pipeline to discriminate r-ego networks using node attributes and structural information separately. We employ heterophily adapted self-supervised learning objective functions to optimise the framework to learn intrinsic node embeddings. We show that SELENE's components improve the quality of node embeddings, facilitating the discrimination of connected heterophilous nodes. Comprehensive empirical evaluations on both synthetic and real-world datasets with varying homophily ratios validate the effectiveness of SELENE in homophilous and heterophilous settings showing an up to 12.52% clustering accuracy gain., Comment: Accepted to Transactions on Machine Learning Research

The outbreak of the COVID-19 pandemic triggers infodemic over online social media, which significantly impacts public health around the world, both physically and psychologically. In this paper, we study the impact of the pandemic on the mental health of influential social media users, whose sharing behaviours significantly promote the diffusion of COVID-19 related information. Specifically, we focus on subjective well-being (SWB), and analyse whether SWB changes have a relationship with their bridging performance in information diffusion, which measures the speed and wideness gain of information transmission due to their sharing. We accurately capture users' bridging performance by proposing a new measurement. Benefiting from deep-learning natural language processing models, we quantify social media users' SWB from their textual posts. With the data collected from Twitter for almost two years, we reveal the greater mental suffering of influential users during the COVID-19 pandemic. Through comprehensive hierarchical multiple regression analysis, we are the first to discover the strong {relationship} between social users' SWB and their bridging performance.

Model extraction attacks aim to duplicate a machine learning model through query access to a target model. Early studies mainly focus on discriminative models. Despite the success, model extraction attacks against generative models are less well explored. In this paper, we systematically study the feasibility of model extraction attacks against generative adversarial networks (GANs). Specifically, we first define accuracy and fidelity on model extraction attacks against GANs. Then we study model extraction attacks against GANs from the perspective of accuracy extraction and fidelity extraction, according to the adversary's goals and background knowledge. We further conduct a case study where an adversary can transfer knowledge of the extracted model which steals a state-of-the-art GAN trained with more than 3 million images to new domains to broaden the scope of applications of model extraction attacks. Finally, we propose effective defense techniques to safeguard GANs, considering a trade-off between the utility and security of GAN models.

We study the target control of asynchronous Boolean networks, to identify efficacious interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application time, the control can be realised with three types of perturbations, including instantaneous, temporary and permanent perturbations. We develop efficient methods to compute the target control for a given target attractor with three types of perturbations. We compare our methods with the stable motif-based control on a variety of real-life biological networks to evaluate their performance. We show that our methods scale well for large Boolean networks and they are able to identify a rich set of solutions with a small number of perturbations., Comment: arXiv admin note: substantial text overlap with arXiv:2006.02304

An information outbreak occurs on social media along with the COVID-19 pandemic and leads to infodemic. Predicting the popularity of online content, known as cascade prediction, allows for not only catching in advance hot information that deserves attention, but also identifying false information that will widely spread and require quick response to mitigate its impact. Among the various information diffusion patterns leveraged in previous works, the spillover effect of the information exposed to users on their decision to participate in diffusing certain information is still not studied. In this paper, we focus on the diffusion of information related to COVID-19 preventive measures. Through our collected Twitter dataset, we validated the existence of this spillover effect. Building on the finding, we proposed extensions to three cascade prediction methods based on Graph Neural Networks (GNNs). Experiments conducted on our dataset demonstrated that the use of the identified spillover effect significantly improves the state-of-the-art GNNs methods in predicting the popularity of not only preventive measure messages, but also other COVID-19 related messages.

Over the last century, we observe a steady and exponentially growth of scientific publications globally. The overwhelming amount of available literature makes a holistic analysis of the research within a field and between fields based on manual inspection impossible. Automatic techniques to support the process of literature review are required to find the epistemic and social patterns that are embedded in scientific publications. In computer sciences, new tools have been developed to deal with large volumes of data. In particular, deep learning techniques open the possibility of automated end-to-end models to project observations to a new, low-dimensional space where the most relevant information of each observation is highlighted. Using deep learning to build new representations of scientific publications is a growing but still emerging field of research. The aim of this paper is to discuss the potential and limits of deep learning for gathering insights about scientific research articles. We focus on document-level embeddings based on the semantic and relational aspects of articles, using Natural Language Processing (NLP) and Graph Neural Networks (GNNs). We explore the different outcomes generated by those techniques. Our results show that using NLP we can encode a semantic space of articles, while with GNN we are able to build a relational space where the social practices of a research community are also encoded.

Recently, increasing attention has been paid to heterogeneous graph representation learning (HGRL), which aims to embed rich structural and semantic information in heterogeneous information networks (HINs) into low-dimensional node representations. To date, most HGRL models rely on hand-crafted meta-paths. However, the dependency on manually-defined meta-paths requires domain knowledge, which is difficult to obtain for complex HINs. More importantly, the pre-defined or generated meta-paths of all existing HGRL methods attached to each node type or node pair cannot be personalised to each individual node. To fully unleash the power of HGRL, we present a novel framework, Personalised Meta-path based Heterogeneous Graph Neural Networks (PM-HGNN), to jointly generate meta-paths that are personalised for each individual node in a HIN and learn node representations for the target downstream task like node classification. Precisely, PM-HGNN treats the meta-path generation as a Markov Decision Process and utilises a policy network to adaptively generate a meta-path for each individual node and simultaneously learn effective node representations. The policy network is trained with deep reinforcement learning by exploiting the performance improvement on a downstream task. We further propose an extension, PM-HGNN++, to better encode relational structure and accelerate the training during the meta-path generation. Experimental results reveal that both PM-HGNN and PM-HGNN++ can significantly and consistently outperform 16 competing baselines and state-of-the-art methods in various settings of node classification. Qualitative analysis also shows that PM-HGNN++ can identify meaningful meta-paths overlooked by human knowledge.