Sep 2026· Zenodo (CERN European Organization for Nuclear Research)
Advanced Graph Neural Networks
Abstract
This paper introduces Epistemic Graph Neural Networks (EGNNs), a novel approach to graph neural networks that explicitly models and incorporates uncertainty into the learning process. Traditional GNNs primarily focus on learning pattern recognition from graph-structured data, often neglecting the inherent uncertainty associated with these patterns and the relationships between nodes. EGNNs address this limitation by representing the network's confidence in inferred relationships as dynamic edge weights within a graph. Nodes in the graph represent individual data points, and edges represent the strength of the inferred relationships between them. Crucially, the weight of each edge is modulated by a learned epistemic uncertainty estimate, reflecting the network's confidence in that particular connection. This allows EGNNs to not only learn patterns but also to represent and reason with uncertainty, leading to more robust and reliable predictions and decision-making. The core claim of this work is that neural networks can learn not just patterns in data, but also the *uncertainty* inherent in those patterns, represented as a dynamically evolving graph. The mechanism is a GNN where nodes represent data points and edges represent the strength of inferred relationships, with edge weights modulated by learned epistemic uncertainty estimates – representing the network's confidence in the relationship.
Agile methods continue to gain popularity. In particular, the Scrum method appears to be on the verge of becoming a de-facto standard in the industry, leading the so called Agile movement. While there are success stories and recommendations, there is little scientifically valid evidence of the challenges in the adoptio...
A. Marchenko, P. Abrahamsson· Agile Conference· 59 citations· ⚡11
A comprehensive taxonomy of the challenges faced when a medium-scale organization decided to adopt software platforms is provided, namely: business challenges, organizational challenges, technical challenges, and people challenges.
Yaser Ghanam, F. Maurer, P. Abrahamsson· Information and Software Tec...· 41 citations· ⚡3
It is shown that high article processing charges are not sufficiently justified by the publishers, which often lack transparency and may prevent authors from adopting OA.
D. Graziotin, Xiaofeng Wang, P. Abrahamsson· Scientometrics· 21 citations· ⚡1
MCGLPPI, a novel geometric representation learning framework that combines graph neural networks (GNNs) with the MARTINI molecular coarse-grained (CG) model to predict overall PPI properties accurately and efficiently, offers an effective and efficient solution for PPI overall property predictions.
Yang Yue, Shu Li, Yihua Cheng et al.· bioRxiv· 15 citations
Abstract Predicting properties from coordinate–category data—sets of vectors paired with categorical information—is fundamental to computational science, manifesting in materials science as predicting formation energies or elastic moduli from crystal structures. While large language models (LLMs) have increasingly been...
Nawaf Alampara, Santiago Miret, Kevin Maik Jablonka· Nature Computational Science· 13 citations
PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction, and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy.
Si-Long Zhai, Huifeng Zhao, Ji-Ke Wang et al.· Journal of Chemical Informat...· 13 citations· ⚡1
Related blog posts
MIT News · Artificial Intelligence· news.mit.eduOct 26, 2026
Machine-learning networks can learn without detailed instructions from a designer. Those that do may offer insight into how the brain reorganizes itself during learning.
MIT News · Artificial Intelligence· news.mit.eduJul 15, 2026
Assistant Professor Pat Pataranutaporn describes a new interface that lets everyday users glimpse inside an AI's neural network before their chatbot ever says a word.
Microsoft Research Blog· microsoft.comJul 13, 2026
Cryptographic code supports vital protections in modern computing systems. Learn how a new method helps verify code as developers write it while preserving speed and adaptability as it gets implemented and evolves. The post Verifying Rust cryptography in SymCrypt, from standards to code appeared first on Microsoft Research.
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.