arXiv subjects

Dimitrios Kelesis

Publications and source records attributed to Dimitrios Kelesis.

7 recordsLinked to original sources

arXiv2026

Improving Molecular Property Prediction in Small Language Models Using Graph-based Tools

Small language models (SLMs) have shown promise for zero-shot molecular property prediction from SMILES strings, yet they often suffer from structural blindness because sequence representations under-specify key graph-topological cues. We propose a modular Context-Augmented Prompting framework that enables agentic tool use at inference time: a trained GNN expert model provides a predictive hint with confidence, and a GNN extracts an instance-specific explanatory subgraph (e.g., a subgraph SMILES and an accompanying explanatory paragraph). We evaluate three commonly used SLMs on MUTAG and Tox21 under five prompting configurations ranging from SMILES-only to using all available tools at hand. Across two datasets, enriching prompts with graph-derived context yields substantial accuracy gains, often exceeding 25% relative improvement and up to 74% on Tox21. We further validate the functional relevance of the extracted motifs via a necessity-based edge-drop intervention. Despite the observed gains, a persistent gap remains to specialized GNN models, highlighting both the value and limits of text-conditioned reasoning for molecular structure.

cs.AI↗

arXiv2026

Enhancing Small Language Models Reasoning through Knowledge Graph Grounding

Although large language models (LLMs) have set benchmarks for zero-shot reasoning, their deployment remains cost-prohibitive and environmentally taxing. Small Language Models (SLMs) offer a sustainable alternative, but prone to errors, on tasks requiring complex, multi-hop logical grounding. We investigate a neuro-symbolic agentic framework to enhance the reasoning capabilities of SLMs, specifically Gemma 3 (1B, 4B) and Llama 3.2 (3B), using the CLUTRR kinship benchmark. Our approach transforms the SLM into a minimalist agent utilizing two specialized tool calls: extract_facts for symbolic triplet extraction and get_hint for expert reasoning via a Relational Graph Convolutional Network (RGCN). We evaluate these models across two configurations, both in an Oracle scenario with ground-truth triplets and a Realistic scenario relying on self-extracted knowledge. Our results reveal that while RGCN-derived hints provide a 1.5 - 2x performance gain over story-only baselines, the system is constrained by the extraction bottleneck and sequential deductive fragility, where early extraction errors compound over multi-hop chains. Furthermore, we identify a "distraction effect" in specific architectures where noisy, self-generated facts degrade performance despite the presence of expert hints. This work characterizes the challenges of symbolic grounding in low-resource agentic systems and provides a roadmap for iterative verification in neuro-symbolic agentic pipelines.

cs.AI↗

arXiv2025

Analyzing the Effect of Embedding Norms and Singular Values to Oversmoothing in Graph Neural Networks

In this paper, we study the factors that contribute to the effect of oversmoothing in deep Graph Neural Networks (GNNs). Specifically, our analysis is based on a new metric (Mean Average Squared Distance - $MASED$) to quantify the extent of oversmoothing. We derive layer-wise bounds on $MASED$, which aggregate to yield global upper and lower distance bounds. Based on this quantification of oversmoothing, we further analyze the importance of two different properties of the model; namely the norms of the generated node embeddings, along with the largest and smallest singular values of the weight matrices. Building on the insights drawn from the theoretical analysis, we show that oversmoothing increases as the number of trainable weight matrices and the number of adjacency matrices increases. We also use the derived layer-wise bounds on $MASED$ to form a proposal for decoupling the number of hops (i.e., adjacency depth) from the number of weight matrices. In particular, we introduce G-Reg, a regularization scheme that increases the bounds, and demonstrate through extensive experiments that by doing so node classification accuracy increases, achieving robustness at large depths. We further show that by reducing oversmoothing in deep networks, we can achieve better results in some tasks than using shallow ones. Specifically, we experiment with a ``cold start" scenario, i.e., when there is no feature information for the unlabeled nodes. Finally, we show empirically the trade-off between receptive field size (i.e., number of weight matrices) and performance, using the $MASED$ bounds. This is achieved by distributing adjacency hops across a small number of trainable layers, avoiding the extremes of under- or over-parameterization of the GNN.

cs.LG↗

arXiv2024

Reducing Oversmoothing through Informed Weight Initialization in Graph Neural Networks

In this work, we generalize the ideas of Kaiming initialization to Graph Neural Networks (GNNs) and propose a new scheme (G-Init) that reduces oversmoothing, leading to very good results in node and graph classification tasks. GNNs are commonly initialized using methods designed for other types of Neural Networks, overlooking the underlying graph topology. We analyze theoretically the variance of signals flowing forward and gradients flowing backward in the class of convolutional GNNs. We then simplify our analysis to the case of the GCN and propose a new initialization method. Our results indicate that the new method (G-Init) reduces oversmoothing in deep GNNs, facilitating their effective use. Experimental validation supports our theoretical findings, demonstrating the advantages of deep networks in scenarios with no feature information for unlabeled nodes (i.e., ``cold start'' scenario).

cs.LG↗

arXiv2024

Partially Trained Graph Convolutional Networks Resist Oversmoothing

In this work we investigate an observation made by Kipf \& Welling, who suggested that untrained GCNs can generate meaningful node embeddings. In particular, we investigate the effect of training only a single layer of a GCN, while keeping the rest of the layers frozen. We propose a basis on which the effect of the untrained layers and their contribution to the generation of embeddings can be predicted. Moreover, we show that network width influences the dissimilarity of node embeddings produced after the initial node features pass through the untrained part of the model. Additionally, we establish a connection between partially trained GCNs and oversmoothing, showing that they are capable of reducing it. We verify our theoretical results experimentally and show the benefits of using deep networks that resist oversmoothing, in a ``cold start'' scenario, where there is a lack of feature information for unlabeled nodes.

cs.LG↗

arXiv2022

Detecting and analysing the topology of the cosmic web with spatial clustering algorithms I: Methods

In this paper we explore the use of spatial clustering algorithms as a new computational approach for modeling the cosmic web. We demonstrate that such algorithms are efficient in terms of computing time needed. We explore three distinct spatial methods which we suitably adjust for (i) detecting the topology of the cosmic web and (ii) categorizing various cosmic structures as voids, walls, clusters and superclusters based on a variety of topological and physical criteria such as the physical distance between objects, their masses and local densities. The methods explored are (1) a new spatial method called Gravity Lattice ; (2) a modified version of another spatial clustering algorithm, the ABACUS; and (3) the well known spatial clustering algorithm HDBSCAN. We utilize HDBSCAN in order to detect cosmic structures and categorize them using their overdensity. We demonstrate that the ABACUS method can be combined with the classic DTFE method to obtain similar results in terms of the achieved accuracy with about an order of magnitude less computation time. To further solidify our claims, we draw insights from the computer science domain and compare the quality of the results with and without the application of our method. Finally, we further extend our experiments and verify their effectiveness by showing their ability to scale well with different cosmic web structures that formed at different redshifts.

astro-ph.IM↗

arXiv2021

Tree-based Focused Web Crawling with Reinforcement Learning

A focused crawler aims at discovering as many web pages and web sites relevant to a target topic as possible, while avoiding irrelevant ones. Reinforcement Learning (RL) has been a promising direction for optimizing focused crawling, because RL can naturally optimize the long-term profit of discovering relevant web locations within the context of a reward. In this paper, we propose TRES, a novel RL-empowered framework for focused crawling that aims at maximizing both the number of relevant web pages (aka \textit{harvest rate}) and the number of relevant web sites (\textit{domains}). We model the focused crawling problem as a novel Markov Decision Process (MDP), which the RL agent aims to solve by determining an optimal crawling strategy. To overcome the computational infeasibility of exhaustively searching for the best action at each time step, we propose Tree-Frontier, a provably efficient tree-based sampling algorithm that adaptively discretizes the large state and action spaces and evaluates only a few representative actions. Experimentally, utilizing online real-world data, we show that TRES significantly outperforms and Pareto-dominates state-of-the-art methods in terms of harvest rate and the number of retrieved relevant domains, while it provably reduces by orders of magnitude the number of URLs needed to be evaluated at each crawling step.

cs.IR↗