Iakovos Evdaimon

Iakovos Evdaimon, Hadi Abdine, Christos Xypolopoulos et al.

The era of transfer learning has revolutionized the fields of Computer Vision and Natural Language Processing, bringing powerful pretrained models with exceptional performance across a variety of tasks. Specifically, Natural Language Processing tasks have been dominated by transformer-based language models. In Natural Language Inference and Natural Language Generation tasks, the BERT model and its variants, as well as the GPT model and its successors, demonstrated exemplary performance. However, the majority of these models are pretrained and assessed primarily for the English language or on a multilingual corpus. In this paper, we introduce GreekBART, the first Seq2Seq model based on BART-base architecture and pretrained on a large-scale Greek corpus. We evaluate and compare GreekBART against BART-random, Greek-BERT, and XLM-R on a variety of discriminative tasks. In addition, we examine its performance on two NLG tasks from GreekSUM, a newly introduced summarization dataset for the Greek language. The model, the code, and the new summarization dataset will be publicly available.

Nikolaos Nakis, Chrysoula Kosma, Giannis Nikolentzos et al.

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.

Roman Bresson, Konstantinos Divriotis, Johannes F. Lutzeyer et al.

We introduce GraViti, a transformer-based graph-level variational autoencoder that maps entire graphs to compact latent vectors. This design produces a true graph-level latent space that supports smooth interpolation, property-guided search, and other downstream tasks beyond the constraints of node-level embeddings. On molecular benchmarks, GraViti learns to decode valid samples that follow the chemical constraints present in the training data, showing that the model recovers domain rules directly from graph-level representations. We also show that, in domains where a reliable canonical node ordering exists such as molecules or bayesian networks, enforcing permutation invariance can prove detrimental for consistent reconstruction. GraViti achieves state-of-the-art reconstruction accuracy on large datasets, and provides solid generative performance. Its single-step decoding offers a lightweight alternative to more complex generation pipelines while maintaining practical sample quality.

Iakovos Evdaimon, Giannis Nikolentzos, Christos Xypolopoulos et al.

Graph generation has emerged as a crucial task in machine learning, with significant challenges in generating graphs that accurately reflect specific properties. Existing methods often fall short in efficiently addressing this need as they struggle with the high-dimensional complexity and varied nature of graph properties. In this paper, we introduce the Neural Graph Generator (NGG), a novel approach which utilizes conditioned latent diffusion models for graph generation. NGG demonstrates a remarkable capacity to model complex graph patterns, offering control over the graph generation process. NGG employs a variational graph autoencoder for graph compression and a diffusion process in the latent vector space, guided by vectors summarizing graph statistics. We demonstrate NGG's versatility across various graph generation tasks, showing its capability to capture desired graph properties and generalize to unseen graphs. We also compare our generator to the graph generation capabilities of different LLMs. This work signifies a shift in graph generation methodologies, offering a more practical and efficient solution for generating diverse graphs with specific characteristics.

Christos Xypolopoulos, Guokan Shang, Xiao Fei et al.

Large language models have evolved to process multiple modalities beyond text, such as images and audio, which motivates us to explore how to effectively leverage them for graph reasoning tasks. The key question, therefore, is how to transform graphs into linear sequences of tokens, a process we term "graph linearization", so that LLMs can handle graphs naturally. We consider that graphs should be linearized meaningfully to reflect certain properties of natural language text, such as local dependency and global alignment, in order to ease contemporary LLMs, trained on trillions of textual tokens, better understand graphs. To achieve this, we developed several graph linearization methods based on graph centrality and degeneracy. These methods are further enhanced using node relabeling techniques. The experimental results demonstrate the effectiveness of our methods compared to the random linearization baseline. Our work introduces novel graph representations suitable for LLMs, contributing to the potential integration of graph machine learning with the trend of multimodal processing using a unified transformer model.

Nikolaos Nakis, Chrysoula Kosma, Anastasia Brativnyk et al.

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.