Michalis Vazirgiannis

Michail Chatzianastasis, Johannes F. Lutzeyer, George Dasoulas et al. · harvard

Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks.

Yanzhu Guo, Guokan Shang, Michalis Vazirgiannis et al.

This study investigates the consequences of training language models on synthetic data generated by their predecessors, an increasingly prevalent practice given the prominence of powerful generative models. Diverging from the usual emphasis on performance metrics, we focus on the impact of this training methodology on linguistic diversity, especially when conducted recursively over time. To assess this, we adapt and develop a set of novel metrics targeting lexical, syntactic, and semantic diversity, applying them in recursive finetuning experiments across various natural language generation tasks in English. Our findings reveal a consistent decrease in the diversity of the model outputs through successive iterations, especially remarkable for tasks demanding high levels of creativity. This trend underscores the potential risks of training language models on synthetic text, particularly concerning the preservation of linguistic richness. Our study highlights the need for careful consideration of the long-term effects of such training approaches on the linguistic capabilities of language models.

Moussa Kamal Eddine, Nadi Tomeh, Nizar Habash et al.

Like most natural language understanding and generation tasks, state-of-the-art models for summarization are transformer-based sequence-to-sequence architectures that are pretrained on large corpora. While most existing models focused on English, Arabic remained understudied. In this paper we propose AraBART, the first Arabic model in which the encoder and the decoder are pretrained end-to-end, based on BART. We show that AraBART achieves the best performance on multiple abstractive summarization datasets, outperforming strong baselines including a pretrained Arabic BERT-based model and multilingual mBART and mT5 models.

Hadi Abdine, Michail Chatzianastasis, Costas Bouyioukos et al.

In recent years, significant progress has been made in the field of protein function prediction with the development of various machine-learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e. assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein's function in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including protein sequence, structure, and textual annotation and description. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate functional descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate function prediction of existing as well as first-to-see proteins.

Guillaume Salha-Galvan, Johannes F. Lutzeyer, George Dasoulas et al. · harvard

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as powerful methods for link prediction (LP). Their performances are less impressive on community detection (CD), where they are often outperformed by simpler alternatives such as the Louvain method. It is still unclear to what extent one can improve CD with GAE and VGAE, especially in the absence of node features. It is moreover uncertain whether one could do so while simultaneously preserving good performances on LP in a multi-task setting. In this workshop paper, summarizing results from our journal publication (Salha-Galvan et al. 2022), we show that jointly addressing these two tasks with high accuracy is possible. For this purpose, we introduce a community-preserving message passing scheme, doping our GAE and VGAE encoders by considering both the initial graph and Louvain-based prior communities when computing embedding spaces. Inspired by modularity-based clustering, we further propose novel training and optimization strategies specifically designed for joint LP and CD. We demonstrate the empirical effectiveness of our approach, referred to as Modularity-Aware GAE and VGAE, on various real-world graphs.

Michail Chatzianastasis, Michalis Vazirgiannis, Zijun Zhang

The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide limited explanation for their predictions. These methods are restricted to a single biological network, which cannot capture the full complexity of tumorigenesis. Models trained on different biological networks often yield different and even opposite cancer gene predictions, hindering their trustworthy adaptation. Here, we introduce an Explainable Multilayer Graph Neural Network (EMGNN) approach to identify cancer genes by leveraging multiple genegene interaction networks and pan-cancer multi-omics data. Unlike conventional graph learning on a single biological network, EMGNN uses a multilayered graph neural network to learn from multiple biological networks for accurate cancer gene prediction. Our method consistently outperforms all existing methods, with an average 7.15% improvement in area under the precision-recall curve (AUPR) over the current state-of-the-art method. Importantly, EMGNN integrated multiple graphs to prioritize newly predicted cancer genes with conflicting predictions from single biological networks. For each prediction, EMGNN provided valuable biological insights via both model-level feature importance explanations and molecular-level gene set enrichment analysis. Overall, EMGNN offers a powerful new paradigm of graph learning through modeling the multilayered topological gene relationships and provides a valuable tool for cancer genomics research.

Virgile Rennard, Guokan Shang, Julie Hunter et al.

A system that could reliably identify and sum up the most important points of a conversation would be valuable in a wide variety of real-world contexts, from business meetings to medical consultations to customer service calls. Recent advances in deep learning, and especially the invention of encoder-decoder architectures, has significantly improved language generation systems, opening the door to improved forms of abstractive summarization, a form of summarization particularly well-suited for multi-party conversation. In this paper, we provide an overview of the challenges raised by the task of abstractive meeting summarization and of the data sets, models and evaluation metrics that have been used to tackle the problems.

Guokan Shang, Hadi Abdine, Yousef Khoubrane et al.

We introduce Atlas-Chat, the first-ever collection of LLMs specifically developed for dialectal Arabic. Focusing on Moroccan Arabic, also known as Darija, we construct our instruction dataset by consolidating existing Darija language resources, creating novel datasets both manually and synthetically, and translating English instructions with stringent quality control. Atlas-Chat-2B, 9B, and 27B models, fine-tuned on the dataset, exhibit superior ability in following Darija instructions and performing standard NLP tasks. Notably, our models outperform both state-of-the-art and Arabic-specialized LLMs like LLaMa, Jais, and AceGPT, e.g., our 9B model gains a 13% performance boost over a larger 13B model on DarijaMMLU, in our newly introduced evaluation suite for Darija covering both discriminative and generative tasks. Furthermore, we perform an experimental analysis of various fine-tuning strategies and base model choices to determine optimal configurations. All our resources are publicly accessible, and we believe our work offers comprehensive design methodologies of instruction-tuning for low-resource languages, which are often neglected in favor of data-rich languages by contemporary LLMs.

Yanzhu Guo, Guokan Shang, Virgile Rennard et al.

With the increasing amount of problematic peer reviews in top AI conferences, the community is urgently in need of automatic quality control measures. In this paper, we restrict our attention to substantiation -- one popular quality aspect indicating whether the claims in a review are sufficiently supported by evidence -- and provide a solution automatizing this evaluation process. To achieve this goal, we first formulate the problem as claim-evidence pair extraction in scientific peer reviews, and collect SubstanReview, the first annotated dataset for this task. SubstanReview consists of 550 reviews from NLP conferences annotated by domain experts. On the basis of this dataset, we train an argument mining system to automatically analyze the level of substantiation in peer reviews. We also perform data analysis on the SubstanReview dataset to obtain meaningful insights on peer reviewing quality in NLP conferences over recent years.

Nancy Xu, Chrysoula Kosma, Michalis Vazirgiannis

Time series forecasting lies at the core of important real-world applications in many fields of science and engineering. The abundance of large time series datasets that consist of complex patterns and long-term dependencies has led to the development of various neural network architectures. Graph neural network approaches, which jointly learn a graph structure based on the correlation of raw values of multivariate time series while forecasting, have recently seen great success. However, such solutions are often costly to train and difficult to scale. In this paper, we propose TimeGNN, a method that learns dynamic temporal graph representations that can capture the evolution of inter-series patterns along with the correlations of multiple series. TimeGNN achieves inference times 4 to 80 times faster than other state-of-the-art graph-based methods while achieving comparable forecasting performance

Yanzhu Guo, Chloé Clavel, Moussa Kamal Eddine et al.

The topic of summarization evaluation has recently attracted a surge of attention due to the rapid development of abstractive summarization systems. However, the formulation of the task is rather ambiguous, neither the linguistic nor the natural language processing community has succeeded in giving a mutually agreed-upon definition. Due to this lack of well-defined formulation, a large number of popular abstractive summarization datasets are constructed in a manner that neither guarantees validity nor meets one of the most essential criteria of summarization: factual consistency. In this paper, we address this issue by combining state-of-the-art factual consistency models to identify the problematic instances present in popular summarization datasets. We release SummFC, a filtered summarization dataset with improved factual consistency, and demonstrate that models trained on this dataset achieve improved performance in nearly all quality aspects. We argue that our dataset should become a valid benchmark for developing and evaluating summarization systems.

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.

Giannis Nikolentzos, Michail Chatzianastasis, Michalis Vazirgiannis

In recent years, graph neural networks (GNNs) have emerged as a promising tool for solving machine learning problems on graphs. Most GNNs are members of the family of message passing neural networks (MPNNs). There is a close connection between these models and the Weisfeiler-Leman (WL) test of isomorphism, an algorithm that can successfully test isomorphism for a broad class of graphs. Recently, much research has focused on measuring the expressive power of GNNs. For instance, it has been shown that standard MPNNs are at most as powerful as WL in terms of distinguishing non-isomorphic graphs. However, these studies have largely ignored the distances between the representations of nodes/graphs which are of paramount importance for learning tasks. In this paper, we define a distance function between nodes which is based on the hierarchy produced by the WL algorithm, and propose a model that learns representations which preserve those distances between nodes. Since the emerging hierarchy corresponds to a tree, to learn these representations, we capitalize on recent advances in the field of hyperbolic neural networks. We empirically evaluate the proposed model on standard node and graph classification datasets where it achieves competitive performance with state-of-the-art models.

Konstantinos Skianis, Giannis Nikolentzos, Michalis Vazirgiannis

Large language models (LLMs) have recently achieved remarkable success in various reasoning tasks in the field of natural language processing. This success of LLMs has also motivated their use in graph-related tasks. Among others, recent work has explored whether LLMs can solve graph problems such as counting the number of connected components of a graph or computing the shortest path distance between two nodes. Although LLMs possess preliminary graph reasoning abilities, they might still struggle to solve some seemingly simple problems. In this paper, we investigate whether prompting via pseudo-code instructions can improve the performance of LLMs in solving graph problems. Our experiments demonstrate that using pseudo-code instructions generally improves the performance of all considered LLMs. The graphs, pseudo-code prompts, and evaluation code are publicly available.

Michail Chatzianastasis, Loukas Ilias, Dimitris Askounis et al.

Alzheimer's dementia (AD) affects memory, thinking, and language, deteriorating person's life. An early diagnosis is very important as it enables the person to receive medical help and ensure quality of life. Therefore, leveraging spontaneous speech in conjunction with machine learning methods for recognizing AD patients has emerged into a hot topic. Most of the previous works employ Convolutional Neural Networks (CNNs), to process the input signal. However, finding a CNN architecture is a time-consuming process and requires domain expertise. Moreover, the researchers introduce early and late fusion approaches for fusing different modalities or concatenate the representations of the different modalities during training, thus the inter-modal interactions are not captured. To tackle these limitations, first we exploit a Neural Architecture Search (NAS) method to automatically find a high performing CNN architecture. Next, we exploit several fusion methods, including Multimodal Factorized Bilinear Pooling and Tucker Decomposition, to combine both speech and text modalities. To the best of our knowledge, there is no prior work exploiting a NAS approach and these fusion methods in the task of dementia detection from spontaneous speech. We perform extensive experiments on the ADReSS Challenge dataset and show the effectiveness of our approach over state-of-the-art methods.

Chrysoula Kosma, Giannis Nikolentzos, Nancy Xu et al.

Time series forecasting is at the core of important application domains posing significant challenges to machine learning algorithms. Recently neural network architectures have been widely applied to the problem of time series forecasting. Most of these models are trained by minimizing a loss function that measures predictions' deviation from the real values. Typical loss functions include mean squared error (MSE) and mean absolute error (MAE). In the presence of noise and uncertainty, neural network models tend to replicate the last observed value of the time series, thus limiting their applicability to real-world data. In this paper, we provide a formal definition of the above problem and we also give some examples of forecasts where the problem is observed. We also propose a regularization term penalizing the replication of previously seen values. We evaluate the proposed regularization term both on synthetic and real-world datasets. Our results indicate that the regularization term mitigates to some extent the aforementioned problem and gives rise to more robust models.

Moussa Kamal Eddine, Guokan Shang, Michalis Vazirgiannis

The rapid development of large pretrained language models has revolutionized not only the field of Natural Language Generation (NLG) but also its evaluation. Inspired by the recent work of BARTScore: a metric leveraging the BART language model to evaluate the quality of generated text from various aspects, we introduce DATScore. DATScore uses data augmentation techniques to improve the evaluation of machine translation. Our main finding is that introducing data augmented translations of the source and reference texts is greatly helpful in evaluating the quality of the generated translation. We also propose two novel score averaging and term weighting strategies to improve the original score computing process of BARTScore. Experimental results on WMT show that DATScore correlates better with human meta-evaluations than the other recent state-of-the-art metrics, especially for low-resource languages. Ablation studies demonstrate the value added by our new scoring strategies. Moreover, we report in our extended experiments the performance of DATScore on 3 NLG tasks other than translation.

Hadi Abdine, Yanzhu Guo, Virgile Rennard et al.

With the significant increase in users on social media platforms, a new means of political campaigning has appeared. Twitter and Facebook are now notable campaigning tools during elections. Indeed, the candidates and their parties now take to the internet to interact and spread their ideas. In this paper, we aim to identify political communities formed on Twitter during the 2022 French presidential election and analyze each respective community. We create a large-scale Twitter dataset containing 1.2 million users and 62.6 million tweets that mention keywords relevant to the election. We perform community detection on a retweet graph of users and propose an in-depth analysis of the stance of each community. Finally, we attempt to detect offensive tweets and automatic bots, comparing across communities in order to gain insight into each candidate's supporter demographics and online campaign strategy.

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.

Nancy Xu, Giannis Nikolentzos, Michalis Vazirgiannis et al.

Image matching is a key component of many tasks in computer vision and its main objective is to find correspondences between features extracted from different natural images. When images are represented as graphs, image matching boils down to the problem of graph matching which has been studied intensively in the past. In recent years, graph neural networks have shown great potential in the graph matching task, and have also been applied to image matching. In this paper, we propose a graph neural network for the problem of image matching. The proposed method first generates initial soft correspondences between keypoints using localized node embeddings and then iteratively refines the initial correspondences using a series of graph neural network layers. We evaluate our method on natural image datasets with keypoint annotations and show that, in comparison to a state-of-the-art model, our method speeds up inference times without sacrificing prediction accuracy.

Giannis Nikolentzos, Michail Chatzianastasis, Michalis Vazirgiannis

In recent years, graph neural networks (GNNs) have achieved great success in the field of graph representation learning. Although prior work has shed light on the expressiveness of those models (\ie whether they can distinguish pairs of non-isomorphic graphs), it is still not clear what structural information is encoded into the node representations that are learned by those models. In this paper, we address this gap by studying the node representations learned by four standard GNN models. We find that some models produce identical representations for all nodes, while the representations learned by other models are linked to some notion of walks of specific length that start from the nodes. We establish Lipschitz bounds for these models with respect to the number of (normalized) walks. Additionally, we investigate the influence of node features on the learned representations. We find that if the initial representations of all nodes point in the same direction, the representations learned at the $k$-th layer of the models are also related to the initial features of nodes that can be reached in exactly $k$ steps. We also apply our findings to understand the phenomenon of oversquashing that occurs in GNNs. Our theoretical analysis is validated through experiments on synthetic and real-world datasets.

Hadi Abdine, Moussa Kamal Eddine, Michalis Vazirgiannis et al.

Word sense induction (WSI) is a difficult problem in natural language processing that involves the unsupervised automatic detection of a word's senses (i.e. meanings). Recent work achieves significant results on the WSI task by pre-training a language model that can exclusively disambiguate word senses, whereas others employ previously pre-trained language models in conjunction with additional strategies to induce senses. In this paper, we propose a novel unsupervised method based on hierarchical clustering and invariant information clustering (IIC). The IIC is used to train a small model to optimize the mutual information between two vector representations of a target word occurring in a pair of synthetic paraphrases. This model is later used in inference mode to extract a higher quality vector representation to be used in the hierarchical clustering. We evaluate our method on two WSI tasks and in two distinct clustering configurations (fixed and dynamic number of clusters). We empirically demonstrate that, in certain cases, our approach outperforms prior WSI state-of-the-art methods, while in others, it achieves a competitive performance.

Amr Mohamed, Yang Zhang, Michalis Vazirgiannis et al.

Diffusion large language models (dLLMs) offer a promising alternative to autoregressive models, but their practical utility is severely hampered by slow, iterative sampling. We present SchED, a training-free, model-agnostic early-exit algorithm that aggregates full-span logit margins and halts decoding once a smooth, progress-dependent confidence threshold is met. We evaluated SchED on two dLLM families (Dream and LLaDA), in base and instruction-tuned variants across ten benchmarks spanning downstream tasks including multiple-choice question answering (MCQ), math, long-form QA/summarization, and translation. SchED delivers large, stable accelerations: on instruction-tuned models, it achieves $3.8$-$4.0\times$ speedups while retaining $99.8$-$100\%$ of the baseline score on average. On base models, SchED yields consistent speedup gains with $99.1$-$100\%$ performance retention, with up to $2.34\times$ under more aggressive settings. Using a conservative speed metric that heavily penalizes quality loss (QPS, $γ{=}4$), we show that SchED is robust and clearly outperforms prior confidence-based early-exit methods, which break down on long-form generation. An entropy analysis of the model's token predictions reveals that instruction tuning speeds up the decay of predictive entropy. By turning genuine confidence stabilization into computational savings, SchED makes dLLM decoding substantially more efficient.

Roman Bresson, Giannis Nikolentzos, George Panagopoulos et al.

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 implement three new KAN-based GNN layers, inspired respectively by the GCN, GAT and GIN layers. 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, link prediction, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all tasks studied in this paper. We also show that the size and training speed of RBF-based KANs is only marginally higher than for MLPs, making them viable alternatives. Code available at https://github.com/RomanBresson/KAGNN.

Johannes F. Lutzeyer, Changmin Wu, Michalis Vazirgiannis

Message-Passing Neural Networks (MPNNs), the most prominent Graph Neural Network (GNN) framework, celebrate much success in the analysis of graph-structured data. Concurrently, the sparsification of Neural Network models attracts a great amount of academic and industrial interest. In this paper we conduct a structured, empirical study of the effect of sparsification on the trainable part of MPNNs known as the Update step. To this end, we design a series of models to successively sparsify the linear transform in the Update step. Specifically, we propose the ExpanderGNN model with a tuneable sparsification rate and the Activation-Only GNN, which has no linear transform in the Update step. In agreement with a growing trend in the literature the sparsification paradigm is changed by initialising sparse neural network architectures rather than expensively sparsifying already trained architectures. Our novel benchmark models enable a better understanding of the influence of the Update step on model performance and outperform existing simplified benchmark models such as the Simple Graph Convolution. The ExpanderGNNs, and in some cases the Activation-Only models, achieve performance on par with their vanilla counterparts on several downstream tasks, while containing significantly fewer trainable parameters. Our code is publicly available at: https://github.com/ChangminWu/ExpanderGNN.

Virgile Rennard, Guokan Shang, Damien Grari et al.

Recent advances in deep learning, and especially the invention of encoder-decoder architectures, has significantly improved the performance of abstractive summarization systems. The majority of research has focused on written documents, however, neglecting the problem of multi-party dialogue summarization. In this paper, we present a dataset of French political debates for the purpose of enhancing resources for multi-lingual dialogue summarization. Our dataset consists of manually transcribed and annotated political debates, covering a range of topics and perspectives. We highlight the importance of high quality transcription and annotations for training accurate and effective dialogue summarization models, and emphasize the need for multilingual resources to support dialogue summarization in non-English languages. We also provide baseline experiments using state-of-the-art methods, and encourage further research in this area to advance the field of dialogue summarization. Our dataset will be made publicly available for use by the research community.

Virgile Rennard, Guokan Shang, Michalis Vazirgiannis et al.

We introduce an extractive summarization system for meetings that leverages discourse structure to better identify salient information from complex multi-party discussions. Using discourse graphs to represent semantic relations between the contents of utterances in a meeting, we train a GNN-based node classification model to select the most important utterances, which are then combined to create an extractive summary. Experimental results on AMI and ICSI demonstrate that our approach surpasses existing text-based and graph-based extractive summarization systems, as measured by both classification and summarization metrics. Additionally, we conduct ablation studies on discourse structure and relation type to provide insights for future NLP applications leveraging discourse analysis theory.

Guokan Shang, Hadi Abdine, Ahmad Chamma et al.

We introduce Nile-Chat-4B, 3x4B-A6B, and 12B, a collection of LLMs for Egyptian dialect, uniquely designed to understand and generate texts written in both Arabic and Latin scripts. Specifically, with Nile-Chat-3x4B-A6B, we introduce a novel language adaptation approach by leveraging the Branch-Train-MiX strategy to merge script-specialized experts, into a single MoE model. Our Nile-Chat models significantly outperform leading multilingual and Arabic LLMs, such as LLaMa, Jais, and ALLaM, on our newly introduced Egyptian evaluation benchmarks, which span both understanding and generative tasks. Notably, our 12B model yields a 14.4% performance gain over Qwen2.5-14B-Instruct on Latin-script benchmarks. All our resources are publicly available. We believe this work presents a comprehensive methodology for adapting LLMs to dual-script languages, addressing an often overlooked aspect in modern LLM development.

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.

Yassine Abbahaddou, Sofiane Ennadir, Johannes F. Lutzeyer et al.

Graph Neural Networks (GNNs), which are nowadays the benchmark approach in graph representation learning, have been shown to be vulnerable to adversarial attacks, raising concerns about their real-world applicability. While existing defense techniques primarily concentrate on the training phase of GNNs, involving adjustments to message passing architectures or pre-processing methods, there is a noticeable gap in methods focusing on increasing robustness during inference. In this context, this study introduces RobustCRF, a post-hoc approach aiming to enhance the robustness of GNNs at the inference stage. Our proposed method, founded on statistical relational learning using a Conditional Random Field, is model-agnostic and does not require prior knowledge about the underlying model architecture. We validate the efficacy of this approach across various models, leveraging benchmark node classification datasets.

Michail Chatzianastasis, Yang Zhang, George Dasoulas et al.

Protein representation learning aims to learn informative protein embeddings capable of addressing crucial biological questions, such as protein function prediction. Although sequence-based transformer models have shown promising results by leveraging the vast amount of protein sequence data in a self-supervised way, there is still a gap in exploiting the available 3D protein structures. In this work, we propose a pre-training scheme going beyond trivial masking methods leveraging 3D and hierarchical structures of proteins. We propose a novel self-supervised method to pretrain 3D graph neural networks on 3D protein structures, by predicting the distances between local geometric centroids of protein subgraphs and the global geometric centroid of the protein. By considering subgraphs and their relationships to the global protein structure, our model can better learn the geometric properties of the protein structure. We experimentally show that our proposed pertaining strategy leads to significant improvements up to 6\%, in the performance of 3D GNNs in various protein classification tasks. Our work opens new possibilities in unsupervised learning for protein graph models while eliminating the need for multiple views, augmentations, or masking strategies which are currently used so far.

Guillaume Salha-Galvan, Johannes F. Lutzeyer, George Dasoulas et al.

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as powerful methods for link prediction. Their performances are less impressive on community detection problems where, according to recent and concurring experimental evaluations, they are often outperformed by simpler alternatives such as the Louvain method. It is currently still unclear to which extent one can improve community detection with GAE and VGAE, especially in the absence of node features. It is moreover uncertain whether one could do so while simultaneously preserving good performances on link prediction. In this paper, we show that jointly addressing these two tasks with high accuracy is possible. For this purpose, we introduce and theoretically study a community-preserving message passing scheme, doping our GAE and VGAE encoders by considering both the initial graph structure and modularity-based prior communities when computing embedding spaces. We also propose novel training and optimization strategies, including the introduction of a modularity-inspired regularizer complementing the existing reconstruction losses for joint link prediction and community detection. We demonstrate the empirical effectiveness of our approach, referred to as Modularity-Aware GAE and VGAE, through in-depth experimental validation on various real-world graphs.

Giannis Nikolentzos, George Dasoulas, Michalis Vazirgiannis

Graph neural networks (GNNs) have recently emerged as a dominant paradigm for machine learning with graphs. Research on GNNs has mainly focused on the family of message passing neural networks (MPNNs). Similar to the Weisfeiler-Leman (WL) test of isomorphism, these models follow an iterative neighborhood aggregation procedure to update vertex representations, and they next compute graph representations by aggregating the representations of the vertices. Although very successful, MPNNs have been studied intensively in the past few years. Thus, there is a need for novel architectures which will allow research in the field to break away from MPNNs. In this paper, we propose a new graph neural network model, so-called $π$-GNN which learns a "soft" permutation (i.e., doubly stochastic) matrix for each graph, and thus projects all graphs into a common vector space. The learned matrices impose a "soft" ordering on the vertices of the input graphs, and based on this ordering, the adjacency matrices are mapped into vectors. These vectors can be fed into fully-connected or convolutional layers to deal with supervised learning tasks. In case of large graphs, to make the model more efficient in terms of running time and memory, we further relax the doubly stochastic matrices to row stochastic matrices. We empirically evaluate the model on graph classification and graph regression datasets and show that it achieves performance competitive with state-of-the-art models.

Antoine J. -P. Tixier, Maria-Evgenia G. Rossi, Fragkiskos D. Malliaros et al.

Some of the most effective influential spreader detection algorithms are unstable to small perturbations of the network structure. Inspired by bagging in Machine Learning, we propose the first Perturb and Combine (P&C) procedure for networks. It (1) creates many perturbed versions of a given graph, (2) applies a node scoring function separately to each graph, and (3) combines the results. Experiments conducted on real-world networks of various sizes with the k-core, generalized k-core, and PageRank algorithms reveal that P&C brings substantial improvements. Moreover, this performance boost can be obtained at almost no extra cost through parallelization. Finally, a bias-variance analysis suggests that P&C works mainly by reducing bias, and that therefore, it should be capable of improving the performance of all vertex scoring functions, including stable ones.

Stamatina Thomaidou, Michalis Vazirgiannis, Kyriakos Liakopoulos

Creating and monitoring competitive and cost-effective pay-per-click advertisement campaigns through the web-search channel is a resource demanding task in terms of expertise and effort. Assisting or even automating the work of an advertising specialist will have an unrivaled commercial value. In this paper we propose a methodology, an architecture, and a fully functional framework for semi- and fully- automated creation, monitoring, and optimization of cost-efficient pay-per-click campaigns with budget constraints. The campaign creation module generates automatically keywords based on the content of the web page to be advertised extended with corresponding ad-texts. These keywords are used to create automatically the campaigns fully equipped with the appropriate values set. The campaigns are uploaded to the auctioneer platform and start running. The optimization module focuses on the learning process from existing campaign statistics and also from applied strategies of previous periods in order to invest optimally in the next period. The objective is to maximize the performance (i.e. clicks, actions) under the current budget constraint. The fully functional prototype is experimentally evaluated on real world Google AdWords campaigns and presents a promising behavior with regards to campaign performance statistics as it outperforms systematically the competing manually maintained campaigns.