Genomic studies, including CRISPR-based PerturbSeq analyses, face a vast hypothesis space, while gene perturbations remain costly and time-consuming. Gene expression models based on graph neural networks are trained to predict the outcomes of gene perturbations to facilitate such experiments. Active learning methods are often employed to train these models due to the cost of the genomic experiments required to build the training set. However, poor model initialization in active learning can result in suboptimal early selections, wasting time and valuable resources. While typical active learning mitigates this issue over many iterations, the limited number of experimental cycles in genomic studies exacerbates the risk. To this end, we propose graph-based one-shot data selection methods for training gene expression models. Unlike active learning, one-shot data selection predefines the gene perturbations before training, hence removing the initialization bias. The data selection is motivated by theoretical studies of graph neural network generalization. The criteria are defined over the input graph and are optimized with submodular maximization. We compare them empirically to baselines and active learning methods that are state-of-the-art on this problem. The results demonstrate that graph-based one-shot data selection achieves comparable accuracy while alleviating the aforementioned risks.

Federated Learning (FL) enables collaborative learning without directly sharing individual's raw data. FL can be implemented in either a centralized (server-based) or decentralized (peer-to-peer) manner. In this survey, we present a novel perspective: the fundamental difference between centralized FL (CFL) and decentralized FL (DFL) is not merely the network topology, but the underlying training protocol: separate aggregation vs. joint optimization. We argue that this distinction in protocol leads to significant differences in model utility, privacy preservation, and robustness to attacks. We systematically review and categorize existing works in both CFL and DFL according to the type of protocol they employ. This taxonomy provides deeper insights into prior research and clarifies how various approaches relate or differ. Through our analysis, we identify key gaps in the literature. In particular, we observe a surprising lack of exploration of DFL approaches based on distributed optimization methods, despite their potential advantages. We highlight this under-explored direction and call for more research on leveraging distributed optimization for federated learning. Overall, this work offers a comprehensive overview from centralized to decentralized FL, sheds new light on the core distinctions between approaches, and outlines open challenges and future directions for the field.

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 each of these layers, the representation of each node is updated from an aggregation and transformation of its neighbours representations at the previous layer. The upper bound for the expressive power of message passing GNNs was reached through the use of MLPs as a transformation, due to their universal approximation capabilities. However, MLPs suffer from well-known limitations, which recently motivated the introduction of Kolmogorov-Arnold Networks (KANs). KANs rely on the Kolmogorov-Arnold representation theorem, rendering them a promising alternative to MLPs. In this work, we compare the performance of KANs against that of MLPs in graph learning tasks. We perform extensive experiments on node classification, graph classification and graph regression datasets. Our preliminary results indicate that while KANs are on-par with MLPs in classification tasks, they seem to have a clear advantage in the graph regression tasks. 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.

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. Such successes have also driven diffusion models to apply to sensitive data, such as human face data, but this might bring about severe privacy concerns. In this work, we systematically present the first privacy study about property inference attacks against diffusion models, in which adversaries aim to extract sensitive global properties of the training set from a diffusion model, such as the proportion of the training data for certain sensitive properties. Specifically, we consider the most practical attack scenario: adversaries are only allowed to obtain synthetic data. Under this realistic scenario, we evaluate the property inference attacks on different types of samplers and diffusion models. A broad range of evaluations shows that various diffusion models and their samplers are all vulnerable to property inference attacks. Furthermore, one case study on off-the-shelf pre-trained diffusion models also demonstrates the effectiveness of the attack in practice. Finally, we propose a new model-agnostic plug-in method PriSampler to mitigate 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 makes adversaries infer the proportion of properties as close as random guesses. PriSampler also shows its significantly superior performance to diffusion models trained with differential privacy on both model utility and defense performance.

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.

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.

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.