The Signed Two-Space Proximity Model for Learning Representations in Protein-Protein Interaction Networks

Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally expensive. Thus, attention has been recently drawn to machine learning approaches. Furthermore, insufficient effort has been made toward analyzing signed PPI networks, which capture both activating (positive) and inhibitory (negative) interactions. To accurately represent biological relationships, we present the Signed Two-Space Proximity Model (S2-SPM) for signed PPI networks, which explicitly incorporates both types of interactions, reflecting the complex regulatory mechanisms within biological systems. This is achieved by leveraging two independent latent spaces to differentiate between positive and negative interactions while representing protein similarity through proximity in these spaces. Our approach also enables the identification of archetypes representing extreme protein profiles. S2-SPM's superior performance in predicting the presence and sign of interactions in SPPI networks is demonstrated in link prediction tasks against relevant baseline methods. Additionally, the biological prevalence of the identified archetypes is confirmed by an enrichment analysis of Gene Ontology (GO) terms, which reveals that distinct biological tasks are associated with archetypal groups formed by both interactions. This study is also validated regarding statistical significance and sensitivity analysis, providing insights into the functional roles of different interaction types. Finally, the robustness and consistency of the extracted archetype structures are confirmed using the Bayesian Normalized Mutual Information (BNMI) metric, proving the model's reliability in capturing meaningful SPPI patterns.

KAN KAN Buff Signed Graph Neural Networks?

Graph Representation Learning aims to create embeddings for nodes and edges, capturing their features and interconnections. Graph Neural Networks (GNNs) have excelled in this task, leveraging neural networks to model complex graph relationships. Recently, the Kolmogorov-Arnold Neural Network (KAN) emerged as an alternative to Multi-Layer Perceptron (MLP), showing improved accuracy and interpretability with fewer parameters. While KANs have been integrated into unsigned GNNs, their application in signed GNNs remains unexplored. This paper integrates KAN into Signed Graph Convolutional Networks (SGCNs) to evaluate its performance on signed graphs where edges have positive or negative signs. We empirically assess KAN-enhanced SGCNs (KASGCN) on downstream tasks such as signed community detection and link sign prediction to enhance the embedding quality in signed networks. Considering the variability in the results indicated by the relatively large standard deviation, KASGCN demonstrates competitive performance with, or similar to, the vanilla SGCN in the evaluated downstream tasks, and its effectiveness is context-dependent (signed graph and parameters...etc.).

Effective and Lightweight Representation Learning for Link Sign Prediction in Signed Bipartite Graphs

How can we effectively and efficiently learn node representations in signed bipartite graphs? A signed bipartite graph is a graph consisting of two nodes sets where nodes of different types are positively or negative connected, and it has been extensively used to model various real-world relationships such as e-commerce, etc. To analyze such a graph, previous studies have focused on designing methods for learning node representations using graph neural networks. In particular, these methods insert edges between nodes of the same type based on balance theory, enabling them to leverage augmented structures in their learning. However, the existing methods rely on a naive message passing design, which is prone to over-smoothing and susceptible to noisy interactions in real-world graphs. Furthermore, they suffer from computational inefficiency due to their heavy design and the significant increase in the number of added edges. In this paper, we propose ELISE, an effective and lightweight GNN-based approach for learning signed bipartite graphs. We first extend personalized propagation to a signed bipartite graph, incorporating signed edges during message passing. This extension adheres to balance theory without introducing additional edges, mitigating the over-smoothing issue and enhancing representation power. We then jointly learn node embeddings on a low-rank approximation of the signed bipartite graph, which reduces potential noise and emphasizes its global structure, further improving expressiveness without significant loss of efficiency. We encapsulate these ideas into ELISE, designing it to be lightweight, unlike the previous methods that add too many edges and cause inefficiency. Through extensive experiments on real-world signed bipartite graphs, we demonstrate that ELISE outperforms its competitors for predicting link signs while providing faster training and inference time.

Graph Spring Neural ODEs for Link Sign Prediction

Signed graphs allow for encoding positive and negative relations between nodes and are used to model various online activities. Node representation learning for signed graphs is a well-studied task with important applications such as sign prediction. While the size of datasets is ever-increasing, recent methods often sacrifice scalability for accuracy. We propose a novel message-passing layer architecture called Graph Spring Network (GSN) modeled after spring forces. We combine it with a Graph Neural Ordinary Differential Equations (ODEs) formalism to optimize the system dynamics in embedding space to solve a downstream prediction task. Once the dynamics is learned, embedding generation for novel datasets is done by solving the ODEs in time using a numerical integration scheme. Our GSN layer leverages the fast-to-compute edge vector directions and learnable scalar functions that only depend on nodes' distances in latent space to compute the nodes' positions. Conversely, Graph Convolution and Graph Attention Network layers rely on learnable vector functions that require the full positions of input nodes in latent space. We propose a specific implementation called Spring-Neural-Network (SPR-NN) using a set of small neural networks mimicking attracting and repulsing spring forces that we train for link sign prediction. Experiments show that our method achieves accuracy close to the state-of-the-art methods with node generation time speedup factors of up to 28,000 on large graphs.

DropEdge not Foolproof: Effective Augmentation Method for Signed Graph Neural Networks

The paper discusses signed graphs, which model friendly or antagonistic relationships using edges marked with positive or negative signs, focusing on the task of link sign prediction. While Signed Graph Neural Networks (SGNNs) have advanced, they face challenges like graph sparsity and unbalanced triangles. The authors propose using data augmentation (DA) techniques to address these issues, although many existing methods are not suitable for signed graphs due to a lack of side information. They highlight that the random DropEdge method, a rare DA approach applicable to signed graphs, does not enhance link sign prediction performance. In response, they introduce the Signed Graph Augmentation (SGA) framework, which includes a structure augmentation module to identify candidate edges and a strategy for selecting beneficial candidates, ultimately improving SGNN training. Experimental results show that SGA significantly boosts the performance of SGNN models, with a notable 32.3% improvement in F1-micro for SGCN on the Slashdot dataset.

CSGDN: Contrastive Signed Graph Diffusion Network for Predicting Crop Gene-Trait Associations

Positive and negative association preidiction between gene and trait help studies for crops to perform complex physiological functions. The transcription and regulation activity of specific genes will be adjusted accordingly in different cell types, developmental stages, and physiological states to meet the needs of organisms. Determing gene-trait associations can resolve the mechanism of trait formation and benefit the improvement of crop yield and quality. There are the following two problems in obtaining the positive/negative associations between gene and trait: 1) High-throughput DNA/RNA sequencing and trait data collection are expensive and time-consuming due to the need to process large sample sizes; 2) experiments introduce both random and systematic errors, and, at the same time, calculations or predictions using software or models may produce noise. To address these two issues, we propose a Contrastive Signed Graph Diffusion Network, CSGDN, to learn robust node representations with fewer training samples to achieve higher link prediction accuracy. CSGDN employs a signed graph diffusion method to uncover the underlying regulatory associations between genes and traits. Then, stochastic perterbation strategies are used to create two views for both original and diffusive graphs. At last, a multi-view contrastive learning paradigm loss is designed to unify the node presentations learned from the two views to resist interference and reduce noise. We conduct experiments to validate the performance of CSGDN on three crop datasets: Gossypium hirsutum, Brassica napus, and Triticum turgidum. The results demonstrate that the proposed model outperforms state-of-the-art methods by up to 9.28% AUC for link sign prediction in G. hirsutum dataset.

CardioLab: Laboratory Values Estimation and Monitoring from Electrocardiogram Signals -- A Multimodal Deep Learning Approach

Background: Laboratory values are fundamental to medical diagnosis and management, but acquiring these values can be costly, invasive, and time-consuming. While electrocardiogram (ECG) patterns have been linked to certain laboratory abnormalities, the comprehensive modeling of these relationships remains underexplored. Methods: We utilize MIMIC-IV dataset to develop multimodal deep-learning models to demonstrate the feasibility of estimating (real-time) and monitoring (predict at future intervals) laboratory value abnormalities from ECG waveforms, demographics, biometrics, and vital signs. Results: The models exhibit a strong predictive performance with AUROC scores above 0.70 in a statistically significant manner for 23 laboratory values in the estimation setting and up to 26 values in the monitoring setting. Most notably, the accurately predictable values encompassing abnormalities across diverse physiological categories such as cardiac, renal, hematological, metabolic, immunological and coagulation. To name examples, for estimation NTproBNP (>353 pg/mL) with 0.882, whereas for monitoring at 30 minutes Urea nitrogen (<6 mg/dL) with 0.851, at 60 minutes creatinine (<0.5 mg/dL) with 0.85, and at 120 minutes hemoglobin (>17.5 g/dL) with 0.821. Conclusions: This study provides first evidence for the feasibility of using ECG data alongside clinical routine data for the real-time estimation and monitoring of laboratory value abnormalities, which could provide a non-invasive, cost-effective supplement to traditional laboratory testing, with strong implications for enhanced patient monitoring and early intervention. Further validation could facilitate their integration into routine clinical practice.

Signed Graph Autoencoder for Explainable and Polarization-Aware Network Embeddings

Autoencoders based on Graph Neural Networks (GNNs) have garnered significant attention in recent years for their ability to extract informative latent representations, characterizing the structure of complex topologies, such as graphs. Despite the prevalence of Graph Autoencoders, there has been limited focus on developing and evaluating explainable neural-based graph generative models specifically designed for signed networks. To address this gap, we propose the Signed Graph Archetypal Autoencoder (SGAAE) framework. SGAAE extracts node-level representations that express node memberships over distinct extreme profiles, referred to as archetypes, within the network. This is achieved by projecting the graph onto a learned polytope, which governs its polarization. The framework employs a recently proposed likelihood for analyzing signed networks based on the Skellam distribution, combined with relational archetypal analysis and GNNs. Our experimental evaluation demonstrates the SGAAEs' capability to successfully infer node memberships over the different underlying latent structures while extracting competing communities formed through the participation of the opposing views in the network. Additionally, we introduce the 2-level network polarization problem and show how SGAAE is able to characterize such a setting. The proposed model achieves high performance in different tasks of signed link prediction across four real-world datasets, outperforming several baseline models.

SE-SGformer: A Self-Explainable Signed Graph Transformer for Link Sign Prediction

Signed Graph Neural Networks (SGNNs) have been shown to be effective in analyzing complex patterns in real-world situations where positive and negative links coexist. However, SGNN models suffer from poor explainability, which limit their adoptions in critical scenarios that require understanding the rationale behind predictions. To the best of our knowledge, there is currently no research work on the explainability of the SGNN models. Our goal is to address the explainability of decision-making for the downstream task of link sign prediction specific to signed graph neural networks. Since post-hoc explanations are not derived directly from the models, they may be biased and misrepresent the true explanations. Therefore, in this paper we introduce a Self-Explainable Signed Graph transformer (SE-SGformer) framework, which can not only outputs explainable information while ensuring high prediction accuracy. Specifically, We propose a new Transformer architecture for signed graphs and theoretically demonstrate that using positional encoding based on signed random walks has greater expressive power than current SGNN methods and other positional encoding graph Transformer-based approaches. We constructs a novel explainable decision process by discovering the $K$-nearest (farthest) positive (negative) neighbors of a node to replace the neural network-based decoder for predicting edge signs. These $K$ positive (negative) neighbors represent crucial information about the formation of positive (negative) edges between nodes and thus can serve as important explanatory information in the decision-making process. We conducted experiments on several real-world datasets to validate the effectiveness of SE-SGformer, which outperforms the state-of-the-art methods by improving 2.2\% prediction accuracy and 73.1\% explainablity accuracy in the best-case scenario.

A Survey on Signed Graph Embedding: Methods and Applications

A signed graph (SG) is a graph where edges carry sign information attached to it. The sign of a network can be positive, negative, or neutral. A signed network is ubiquitous in a real-world network like social networks, citation networks, and various technical networks. There are many network embedding models have been proposed and developed for signed networks for both homogeneous and heterogeneous types. SG embedding learns low-dimensional vector representations for nodes of a network, which helps to do many network analysis tasks such as link prediction, node classification, and community detection. In this survey, we perform a comprehensive study of SG embedding methods and applications. We introduce here the basic theories and methods of SGs and survey the current state of the art of signed graph embedding methods. In addition, we explore the applications of different types of SG embedding methods in real-world scenarios. As an application, we have explored the citation network to analyze authorship networks. We also provide source code and datasets to give future direction. Lastly, we explore the challenges of SG embedding and forecast various future research directions in this field.